gebhart/patrepeval huggingface dataset:
Protein Trans -Splicing as a Means for Viral Vector-Mediated In Vivo Gene Therapy (2008)

Inteins catalyze protein splicing in a fashion similar to how self-splicing introns catalyze RNA splicing. Splitinteins catalyze precise ligation of two separate polypeptides through trans-splicing in a highly specific manner. Here we report a method of using protein trans-splicing to circumvent the packaging size limit of gene therapy vectors. To demonstrate this method, we chose a large dystrophin gene and an adeno-associated viral (AAV) vector, which has a small packaging size. A highly functional 6.3-kb Becker-form dystrophin cDNA was broken into two pieces and modified by adding appropriate split-intein coding sequences, resulting in splitgenes sufficiently small for packaging in AAV vectors. The two split-genes, after codelivery into target cells, produced two polypeptides that spontaneously trans-spliced to form the expected Becker-form dystrophin protein in cell culture in vitro. Delivering the split-genes by AAV1 vectors into the muscle of a mouse model of Duchenne muscular dystrophy rendered therapeutic gene expression and benefits.
Ovarian Follicle Development Requires Smad3 (2004)

Smad3 is an important mediator of the TGF beta signaling pathway. Interestingly, Smad3-deficient (Smad3-/-) mice have reduced fertility compared with wild-type (WT) mice. To better understand the molecular mechanisms underlying the reduced fertility in Smad3-/- animals, this work tested the hypothesis that Smad3 deficiency interferes with three critical aspects of folliculogenesis: growth, atresia, and differentiation. Growth was assessed by comparing the size of follicles, expression of proliferating cell nuclear antigen, and expression of cell cycle genes in Smad3-/- and WT mice. Atresia was assessed by comparing the incidence of atresia and expression of bcl-2 genes involved in cell death and cell survival in Smad3-/- and WT mice. Differentiation was assessed by comparing the expression of FSH receptor (FSHR), estrogen receptor (ER) alpha, ER beta, and inhibin alpha-, beta(A)-, and beta(B)-subunits in Smad3-/- and WT mice. Because growth, atresia, and differentiation are regulated by hormones, estradiol, FSH, and LH levels were compared in Smad3-/- and WT mice. Moreover, because alterations in folliculogenesis can affect the ability of mice to ovulate, the number of corpora lutea and ovulated eggs in response to gonadotropin treatments were compared in Smad3-/- and WT animals. The results indicate that Smad3 deficiency slows follicle growth, which is characterized by small follicle diameters, low levels of proliferating cell nuclear antigen, and low expression of cell cycle genes (cyclin-dependent kinase 4 and cyclin D2). Smad3 deficiency also causes atretic follicles, degenerated oocytes, and low expression of bcl-2. Furthermore, Smad3 deficiency affects follicular differentiation as evidenced by decreased expression of ER beta, increased expression of ER alpha, and decreased expression of inhibin alpha-subunits. Smad3 deficiency causes low estradiol and high FSH levels. Finally, Smad3-/- ovaries have no corpora lutea, and they do not ovulate after ovulatory induction with exogenous gonadotropins. Collectively, these data provide the first evidence that reduced fertility in Smad3-/- mice is due to impaired folliculogenesis, associated with altered expression of genes that control cell cycle progression, cell survival, and cell differentiation. The findings that Smad3-/- follicles have impaired growth, increased atresia, and altered differentiation in the presence of high FSH levels, normal expression of FSHR, and lower expression of cyclin D2, suggest a possible interaction between Smad3 and FSH signaling downstream of FSHR in the mouse ovary.
Interleukin-12-deficient mice are at greater risk of UV radiation–induced skin tumors and malignant transformation of papillomas to carcinomas (2006)

Solar UV radiation-induced immunosuppression is a risk factor for nonmelanoma skin cancer. Interleukin (IL)-12 has been shown to possess antitumor activity and inhibit the immunosuppressive effects of UV radiation in mice. In this study, we generated IL-12 knockout (KO) mice on a C3H/HeN background to characterize the role of IL-12 in photocarcinogenesis. After exposure of the mice to UVB (180 mJ/cm2) radiation thrice a week for 35 weeks, the development of UV-induced tumors was more rapid and the tumor multiplicity and tumor size were significantly higher in IL-12 KO mice than their wild-type (WT) counterparts (P < 0.05-0.001). Moreover, the malignant transformation of UVB-induced papillomas to carcinomas was higher in IL-12 KO mice in terms of carcinoma incidence (55%, P < 0.001), carcinoma multiplicity (77%, P < 0.001), and carcinoma size (81%, P < 0.001). As IL-12 has the ability to repair UV-induced DNA damage, we determined this effect in our in vivo IL-12 KO mouse model. We found that UVB-induced DNA damage in the form of cyclobutane pyrimidine dimers was removed or repaired more rapidly in WT mice than IL-12 KO mice. Similarly, the UVB-induced sunburn cell formation is primarily a consequence of DNA damage. It was observed that UVB-induced sunburn cells were repaired rapidly in WT mice compared with IL-12 KO mice. The rapid removal or repair of UV-induced cyclobutane pyrimidine dimers or sunburn cells will result in reduced risk of photocarcinogenesis. Taken together, our data show that IL-12 deficiency is associated with the greater risk of photocarcinogenesis in mice, and this may be due to reduction in damaged DNA repair ability.
Statistical averaging and PARTAN-some alternatives to LMS and RLS (1992)

Statistical averaging and PARTAN (parallel tangent) are shown as potential alternatives to the conventional least mean square (LMS) and recursive least squares (RLS) for adaptive filtering and signal processing. These new algorithms exhibit the RLS-like fast adaptation, and yet relate well to the popular LMS in conceptual simplicity and in implementation. Compared with the RLS, these new algorithms seem to be more robust in guarding against the signal bursting phenomenon. The computational complexity of these algorithms, in their direct forms, is less than that of the standard RLS but higher than the fast RLS and LMS.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pentraxin 3 Inhibits Fibroblast Growth Factor 2–Dependent Activation of Smooth Muscle Cells In Vitro and Neointima Formation In Vivo (2005)

PTX3 is a potent inhibitor of the autocrine and paracrine stimulation exerted by FGF2 on SMCs. Local PTX3 upregulation may modulate SMC activation after arterial injury.
Methods of X-ray and Neutron Scattering in Polymer Science (2000)

This book presents the basic theories underlying x-ray and neutron scattering, as well as the various techniques that have been developed for their application to the study of polymers. The two scattering methods are discussed together from the beginning, so as to allow readers to gain a unified view of the scattering phenomena. The book is introductory and may be used as a textbook in polumer science class or for self-study by polymer scientists new in scattering techniques.
Insulin-like growth factor II mRNA binding protein 3 (IMP3) is overexpressed in prostate cancer and correlates with higher Gleason scores (2010)

Although IMP3 is overexpressed in a significant proportion of prostate cancer cases, which might be of importance for novel therapeutic approaches, it does not appear to possess any immediate diagnostic or prognostic value, limiting its potential as a tissue biomarker for prostate cancer. These results might be corroborated by the fact, that two independent tumor cohorts were separately reviewed.
Tagged and untagged TRAIL show different activity against tumor cells (2012)

The tumor necrosis factor-related apoptosis-inducing ligand (TRAIL/Apo2L) is a novel cytotoxic ligand belonging to the TNF superfamily which is currently being developed as a cancer therapeutic drug. Here, we observed the different functions of recombinant TRAIL protein with a foreign protein label and non-labeled TRAIL. We used a prokaryotic expression system to prepare two different versions of the extracellular TRAIL 114-281aa protein: TRAIL-HS, a protein modified with 6xHis-Tag and S-Tag; and TRAIL-FT, which had no foreign protein. The proteins were purified using Ni-NTA chromatography (TRAIL-HS) and cation ion-exchange column chromatography (TRAIL-FT) and identified by SDS-PAGE and western blot analysis. We compared the abilities of the proteins to bind to death receptor 5 (DR5) by ELISA and to induce apoptosis in a normal liver cell line (Chang liver) and a human T-lymphocyte leukemia cell line (Jurkat) by MTT assay, GR staining and FACS. The results indicate that the biological functions of TRAIL-FT were superior to those of TRAIL-HS in binding and the induction of apoptosis, and may be useful to further the development and applications of TRAIL.
Stable isotope dilution analysis of 4-hydroxybutyric acid: An accurate method for quantification in physiological fluids and the prenatal diagnosis of 4-hydroxybutyric aciduria (1990)

A quantitative assay for 4-hydroxybutyric acid was developed using D6-4-hydroxybutyric acid as an internal standard. 4-Hydroxybutyric acid was isolated by liquid chromatography and the amount quantified by selected ion monitoring, ammonia chemical ionization gas chromatography/mass spectrometry of the trimethylsilyl derivatives. The concentrations of 4-hydroxybutyric in control physiological fluids were: 2.64 +/- 3.46 mmol mol-1 creatinine in urine, 1.09 +/- 2.87 mumol l-1 in plasma, 0.98 +/- 1.17 mumol l-1 in cerebrospinal fluid and 1.28 +/- 0.47 mumol l-1 in amniotic fluid. The concentration of 4-hydroxybutyric acid in the amniotic fluid from a pregnancy at risk for 4-hydroxybutyric aciduria was 2.30 mumol l-1, indicating an unaffected fetus. The stable isotope dilution assay of 4-hydroxybutyric acid in physiological fluid samples is a rapid, sensitive and accurate method for quantification, as well as a valuable technique for the prenatal diagnosis of 4-hydroxybutyric aciduria.
Myostatin Is a Skeletal Muscle Target of Growth Hormone Anabolic Action (2003)

Myostatin is a cytokine that has recently been shown to selectively and potently inhibit myogenesis. To investigate the mechanisms of anabolic actions of GH on skeletal muscle growth, we examined the in vitro and in vivo effects of GH on myostatin regulation. Twelve GH-deficient hypopituitary adult subjects were treated with recombinant GH (5 micro g/kg.d) in a double-blind, placebo-controlled fashion. Body composition and physical function were assessed and skeletal muscle biopsies from the vastus lateralis performed at 6-monthly intervals during 18 months of treatment. Myostatin mRNA expression was significantly inhibited to 31 +/- 9% (P < 0.001) of control by GH but not by placebo administration (79 +/- 11%) as determined by quantitative real-time PCR normalized for the housekeeping glyceraldehyde-3-phosphate dehydrogenase gene. The inhibitory effect of GH on myostatin was sustained after 12 and 18 months of GH treatment. These effects were associated with increases in lean body mass and translated into enhanced aerobic performance as determined by maximal oxygen uptake and ventilation threshold. Parallel in vitro studies of skeletal muscle cells demonstrated significant reduction of myostatin expression by myotubes in response to GH, compared with vehicle treatment. Conversely, GH receptor antagonism resulted in up-regulation of myostatin in myoblasts. Given the potent catabolic actions of myostatin, our data suggest that myostatin represents a potential key target for GH-induced anabolism.
Mouse model of intrahepatic cholangiocarcinoma validates FIG–ROS as a potent fusion oncogene and therapeutic target (2013)

Cholangiocarcinoma is the second most common primary liver cancer and responds poorly to existing therapies. Intrahepatic cholangiocarcinoma (ICC) likely originates from the biliary tree and develops within the hepatic parenchyma. We have generated a flexible orthotopic allograft mouse model of ICC that incorporates common genetic alterations identified in human ICC and histologically resembles the human disease. We examined the utility of this model to validate driver alterations in ICC and tested their suitability as therapeutic targets. Specifically, we showed that the fused-in-glioblastoma-c-ros-oncogene1 (FIG-ROS1(S); FIG-ROS) fusion gene dramatically accelerates ICC development and that its inactivation in established tumors has a potent antitumor effect. Our studies establish a versatile model of ICC that will be a useful preclinical tool and validate ROS1 fusions as potent oncoproteins and therapeutic targets in ICC and potentially other tumor types.
Signaling Messages and AVPs for 3P-AAA Framework (2011)

This papers looks at the details of signaling required for the implementation of the novel Third-Party Authentication, Authorization and Accounting (3P-AAA) framework. The motivation and functionality of the main 3P-AAA interfaces is discussed. As a result of this discussion, new and modified messages based on the Diameter protocol have been outlined.
Generalized recovery algorithm for 3D super-resolution microscopy using rotating point spread functions (2016)

Super-resolution microscopy with phase masks is a promising technique for 3D imaging and tracking. Due to the complexity of the resultant point spread functions, generalized recovery algorithms are still missing. We introduce a 3D super-resolution recovery algorithm that works for a variety of phase masks generating 3D point spread functions. A fast deconvolution process generates initial guesses, which are further refined by least squares fitting. Overfitting is suppressed using a machine learning determined threshold. Preliminary results on experimental data show that our algorithm can be used to super-localize 3D adsorption events within a porous polymer film and is useful for evaluating potential phase masks. Finally, we demonstrate that parallel computation on graphics processing units can reduce the processing time required for 3D recovery. Simulations reveal that, through desktop parallelization, the ultimate limit of real-time processing is possible. Our program is the first open source recovery program for generalized 3D recovery using rotating point spread functions.
Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: role of DNA mismatch repair. (1988)

To investigate the mechanisms of spontaneous mutation in the Escherichia coli mutD5 mutator strain, 502 mutations generated in this strain in the N-terminal part of the lacI gene were sequenced (i-d mutations). Since the mutator strength of this strain depends on the medium in which it grows, mutations were analyzed in both minimal medium (moderate mutator activity) and rich medium (high mutator activity). In either case, 95% of all mutations were base substitutions and 5% were single-base deletions. However, the nature and site distribution of the base substitutions differed dramatically for the two conditions. In minimal medium (mutation frequency, 480-fold above background), a majority (62%) were transversions, notably A.T----T.A at three 5'-GTGG-3' sequences. Most (64%) of the transitions under this condition occurred at specific sequences that are suggestive of a "dislocation" type of mutagenesis. In rich medium (mutation frequency, 37,000-fold above background), 90% of the base substitutions were transitions. These observations suggest that different modes of mutagenesis operate under the two conditions. mutD5 cells have been reported to be defective in exonucleolytic proofreading during DNA replication. The present data suggest that mutD cells in rich medium also suffer a defect in mutHLS-encoded mismatch correction. This hypothesis was confirmed by the direct measurement of mismatch repair in mutD5 cells by transfection of M13mp2 heteroduplex DNA.
A component and communication model for push systems (1999)

We present a communication and component model for push systems. Surprisingly, despite the widespread use of many push services on the Internet, no such models exist. Our communication model contrasts push systems with client-server and event-based systems. Our component model provides a basis for comparison and evaluation of different push systems and their design alternatives. We compare several prominent push systems using our component model. The component model consists of producers and consumers, broadcasters and channels, and a transport system. We detail the concerns of each of these components. Finally, we discuss a number of open issues that challenge the widespread deployment of push or any other system on an Internet-wide scale. Payment models are the most important among these and are not adequately addressed by any existing system. We briefly present the payment approach in our Minstrel project.
Modulation of RNA Tertiary Folding by Incorporation of Caged Nucleotides (2005)

Knock it off: Individual RNA nucleotides with a caged nucleobase were incorporated, through their phosphoramidites, into a 160-mer RNA molecule that adopts a specific tertiary structure (see picture). Position-dependent local and global effects on RNA structure were observed, and photocleavage of the caging group was seen to restore the native folding. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z502928_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.
Complete amino acid sequence of staphylococcal enterotoxin A. (1987)

The amino acid sequence of staphylococcal enterotoxin A is presented. Staphylococcal enterotoxin A is a single-chain polypeptide which consists of 233 amino acid residues with a molecular weight of 27,078 and has the amino acid composition Cys2, Asp17, Asn19, Thr16, Ser13, Glu15, Gln12, Pro4, Gly15, Ala7, Val13, Met2, Ile10, Leu23, Tyr18, Phe8, His6, Lys24, Arg7, Trp2, with serine as both amino- and carboxyl-terminal amino acids. Automated sequence analysis of intact enterotoxin A, as well as characterization of the peptides obtained from cyanogen bromide treatment and trypsin and chymotrypsin digestion, led to the elucidation of the complete primary structure of this protein. Less structural homology is observed among staphylococcal enterotoxins A, B (Huang, I-Y., and Bergdoll, M. S. (1970) J. Biol. Chem. 245, 3518-3525), and C1 (Schmidt, J. J., and Spero, L. (1983) J. Biol. Chem. 258, 6300-6306) than that seen between enterotoxins B and C1.
Importance of the lipophilic group in carbamates having histamine H3-receptor antagonist activity. (2000)

In order to evaluate changes in the lipophilic part of designed carbamates concerning their potential histamine H3-receptor antagonist properties a new series of O-[3-(1H-imidazol-4-yl)propanol]carbamates was derived containing N-mono- or di-alkenyl, alkynyl, cycloalkyl, or double-branched alkyl substituents. The compounds were tested in vitro for their H3-receptor antagonist activity on synaptosomes of rat cerebral cortex and shared moderate to high antagonist activity in vitro. In this series 3-(1H-imidazol-4-yl)propyl N-(4-pentenyl)carbamate (4) was the most potent compound in vitro (Ki = 6.3 nM). H3-receptor antagonist activity in the central nervous system (CNS) was detected for most compounds in the in vivo H3-receptor assay based upon measurement of brain N tau-methylhistamine levels after p.o. administration to mice. The most effective carbamate in vivo, 3-(1H-imidazol-4-yl)propyl N-(allyl)carbamate (3), showed higher CNS potency (ED50 = 0.48 mg/kg p.o.) than the reference antagonist thioperamide. For some novel carbamates their histamine H1- and H2-receptor activities were determined on isolated organs of guinea-pig thereby demonstrating their high H3-receptor selectivity.
Direct immunoassay for detecting Escherichia coli colonies that contain polypeptides encoded by cloned DNA segments. (1981)

We describe a simple in situ immunoassay for screening Escherichia coli colonies, to detect those that express polypeptide antigens encoded by cloned DNA segments. In the colony immunoassay that we have developed, only one antibody molecule need bind to the polypeptide molecule. Hence short fragments of coding sequences should be detectable, and problems imposed by the conformation of polypeptides "fused" to protein fragments encoded by the vector should be minimized. The method should allow the use of monoclonal antibodies, which bind to only one determinant. Colonies grown on nitrocellulose filters were lysed in situ and proteins from the lysates were blotted onto CNBr-activated filter papers. Antigens covalently bound to the CNBr paper were detected by reaction with antiserum, followed by 125I-labeled protein A from Staphylococcus aureus and autoradiography. We have used the colony immunoassay to determine what proportion of ptrpED5-1 clones containing mouse mu chain cDNA segments express mu polypeptides. Surprisingly, about 50% of the clones were positive. Because only one in six clones would be expected to contain the insert in the correct orientation and reading frame to encode a fused polypeptide, it is likely that polypeptides that initiate within the insert can be detected. A similarly high proportion of pBR322 clones containing mu cDNA were positive, and about 25% of pBR322 clones containing mouse gamma 2a chain cDNA were positive to anti-gamma 2a serum. EAch of the positive mu clones reacted with affinity-purified anti-mu antibodies but not with normal serum, and clones containing irrelevant sequences were negative. The mu cDNA segment was inserted in the correct orientation in all six clones studied, and discrete mu polypeptides corresponding in size both to fused polypeptides and internally initiated polypeptides were detected by electrophoresis of protein extracts.
Sok antisense RNA from plasmid R1 is functionally inactivated by RNase E and polyadenylated by poly(A) polymerase I (1997)

The hok/sok system of plasmid R1, which mediates plasmid stabilization by the killing of plasmid-free cells, codes for two RNA species, Sok antisense RNA and hok mRNA. Sok RNA, which is unstable, inhibits translation of the stable hok mRNA. The 64nt Sok RNA folds into a single stem-loop domain with an 11 nt unstructured 5' domain. The initial recognition reaction between Sok RNA and hok mRNA takes place between the 5' domain and the complementary region in hok mRNA. In this communication we examine the metabolism of Sok antisense RNA. We find that RNase E cleaves the RNA 6nt from its 5' end and that this cleavage initiates Sok RNA decay. The RNase E cleavage occurs in the part of Sok RNA that is responsible for the initial recognition of the target loop in hok mRNA and thus leads to functional inactivation of the antisense. The major RNase E cleavage product (denoted pSok-6) is rapidly degraded by polynucleotide phosphorylase (PNPase). Thus, the RNase E cleavage tags pSok-6 for further rapid degradation by PNPase from its 3' end. We also show that Sok RNA is polyadenylated by poly(A) polymerase I (PAP I), and that the poly(A)-tailing is prerequisite for the rapid 3'-exonucleolytic degradation by PNPase.
Sequential Virtual Screening Approach to the Identification of Small Organic Molecules as Potential BACE‐1 Inhibitors (2011)

In this letter, we report on the sequential application of two different in silico screening approaches combined with bioassays aimed at the identification of small organic molecules as potential BACE-1 inhibitors. Two hits endowed of micromolar inhibitory potency were selected, and the binding mode of the most potent compound was further characterized through docking simulations.