gebhart/patrepeval huggingface dataset:
Convergent transcription confers a bistable switch in Enterococcus faecalis conjugation (2011)

Convergent gene pairs with head-to-head configurations are widespread in both eukaryotic and prokaryotic genomes and are speculated to be involved in gene regulation. Here we present a unique mechanism of gene regulation due to convergent transcription from the antagonistic prgX/prgQ operon in Enterococcus faecalis controlling conjugative transfer of the antibiotic resistance plasmid pCF10 from donor cells to recipient cells. Using mathematical modeling and experimentation, we demonstrate that convergent transcription in the prgX/prgQ operon endows the system with the properties of a robust genetic switch through premature termination of elongating transcripts due to collisions between RNA polymerases (RNAPs) transcribing from opposite directions and antisense regulation between complementary counter-transcripts. Evidence is provided for the presence of truncated RNAs resulting from convergent transcription from both the promoters that are capable of sense-antisense interactions. A mathematical model predicts that both RNAP collision and antisense regulation are essential for a robust bistable switch behavior in the control of conjugation initiation by prgX/prgQ operons. Moreover, given that convergent transcription is conserved across species, the mechanism of coupling RNAP collision and antisense interaction is likely to have a significant regulatory role in gene expression.
Optimization and transformation of Arundo donax L. using particle bombardment (2010)

An optimized particle bombardment protocol to introduce DNA into Arundo donax L. (giant reed) embryogenic callus cells was developed. The physical and biological parameters tested for optimal transient expression of s-glucuronidase (GUS) and green fluorescent protein (GFP) genes were: helium pressure, distance from stopping screen to target tissue and vacuum pressure together with other factors such as gold microparticle size, DNA concentration and the number of bombardments. The highest transient GUS and GFP expression was obtained when cells were bombarded twice at 1100 psi, with 9 cm target distance, 24 mm Hg vacuum pressure, 1 mm gold particle size, 1.5 mg DNA per bombardment, three days pre-culture prior to bombardment and six days post bombardment culture. This is the first report of optimization of particle bombardment parameters for high-efficiency DNA delivery combined with minimum damage to target giant reed tissues. Key words : Arundo donax, particle bombardment, s-glucuronidase (GUS), green fluorescent protein (GFP), transient gene expression, genetic transformation.
An additional homolog of the fission yeast cdc25+ gene occurs in humans and is highly expressed in some cancer cells. (1991)

The gene cdc25+ is a mitotic inducer controlling transition from the G2 to the M phase of the cell cycle in the fission yeast, Schizosaccharomyces pombe. Using phenotypic complementation of a mutant of S. pombe, we have cloned a human homolog (CDC25Hu2) of the cdc25+ gene that differs markedly in structure from CDC25 (referred to here as CDC25Hu1), the first such homolog to be isolated. The carboxyl-terminal region of p63CDC25Hu2 shares significant sequence similarity with cdc25 protein homologs from other eukaryotes and possesses full complementation activity. CDC25Hu2 is expressed in human cell lines 10 to 100 times more than CDC25Hu1, and its expression is particularly high in some cancers, including SV40-transformed fibroblasts. Whereas CDC25Hu1 is predominantly expressed in G2, CDC25Hu2 is expressed throughout the cell cycle with a moderate increase in G2. Thus, at least two homologs of the cdc25 gene exist and are both expressed in human cells. The implications of CDC25Hu2 overexpression in some cancer cells are discussed.
Liposome-Anchored Vascular Endothelial Growth Factor Aptamers (1998)

Nuclease-resistant aptamers identified from randomized nucleic acid libraries represent a novel class of drug candidates. Aptamers are synthesized chemically and therefore can be readily modified with functional groups that modulate their properties. We report here on the preparation, initial characterization, and functional properties of a nuclease-resistant vascular endothelial growth factor (VEGF) aptamer anchored in liposome bilayers through a lipid group on the aptamer. While the high-affinity binding to VEGF is maintained, the plasma residence time of the liposome-anchored aptamer is considerably improved compared with that of the free aptamer. The lipid group attachment and/or liposome anchoring leads to a dramatic improvement in inhibitory activity of the aptamer toward VEGF-induced endothelial cell proliferation in vitro and vascular permeability increase and angiogenesis in vivo.
Expanding the CITE-seq tool-kit: Detection of proteins, transcriptomes, clonotypes and CRISPR perturbations with multiplexing, in a single assay (2018)

ABSTRACT Rapid technological progress in the recent years has allowed the high-throughput interrogation of different types of biomolecules from single cells. Combining several of these readouts into integrated multi-omic assays is essential to comprehensively understand and model cellular processes. Here, we report the development of E xpanded C RISPR-compatible C ellular I ndexing of T ranscriptomes and E pitopes by seq uencing (ECCITE-seq) for the high-throughput characterization of at least five modalities of information from each single cell: transcriptome, immune receptor clonotypes, surface markers, sample identity and sgRNAs. We demonstrate the use of ECCITE-seq to directly and efficiently capture sgRNA molecules and measure their effects on gene expression and protein levels, opening the possibility of performing high throughput single cell CRISPR screens with multimodal readout using existing libraries and commonly used vectors. Finally, by utilizing the combined phenotyping of clonotype and cell surface markers in immune cells, we apply ECCITE to study a lymphoma sample to discriminate cells and define molecular signatures of malignant cells within a heterogeneous population.
Enhanced Antiproliferative Activity of Transferrin-Conjugated Paclitaxel-Loaded Nanoparticles Is Mediated via Sustained Intracellular Drug Retention (2005)

We studied the molecular mechanism of greater efficacy of paclitaxel-loaded nanoparticles (Tx-NPs) following conjugation to transferrin (Tf) ligand in breast cancer cell line. NPs were formulated using biodegradable polymer, poly(lactic-co-glycolide) (PLGA), with encapsulated Tx and conjugated to Tf ligand via an epoxy linker. Tf-conjugated NPs demonstrated greater and sustained antiproliferative activity of the drug in dose- and time-dependent studies compared to that with drug in solution or unconjugated NPs in MCF-7 and MCF-7/Adr cells. The mechanism of greater antiproliferative activity of the drug with conjugated NPs was determined to be due to their greater cellular uptake and reduced exocytosis compared to that of unconjugated NPs, thus leading to higher and sustained intracellular drug levels. The increase in antiproliferative activity of the drug with incubation time in MCF-7/Adr cells with Tf-conjugated NPs suggests that the drug resistance can be overcome by sustaining intracellular drug retention. The intracellular disposition characteristics of Tf-conjugated NPs following their cellular uptake via Tf receptors could have been different from that of unconjugated NPs via nonspecific endocytic pathway, thus influencing the NP uptake, their intracellular retention, and hence the therapeutic efficacy of the encapsulated drug.
Comparison of the electrophysiologically based optimization methods with different pacing parameters in patient undergoing resynchronization treatment (2008)

Many studies conducted on patients suffering from congestive heart failure have shown the efficacy of cardiac resynchronization therapy (CRT). The presented research investigates an off-line optimization algorithm based on different electrode positioning and timing delays. A computer model of the heart was used to simulate left bundle branch block (LBBB), myocardial infarction (MI) and reduction of intraventricular conduction velocity in order to customize the patient symptom. The optimization method evaluates the error between the healthy heart and pathology with/without pacing in terms of activation time and QRS length. Additionally, a torso model of the patient is extracted to compute the body surface potential map (BSPM) and to simulate the ECG with Wilson leads to validate the results obtained by the electrophysiological heart model optimization.
Investigating three methods for improving the performance of the SIM algorithm (2002)

A sparse iterative method for solving electromagnetic problems has been implemented in an object-oriented version of NEC. The SIM is based on the generation of a sparse matrix which is factored and subsequently used in an iterative solution of a matrix equation. The paper investigates three methods of filling the sparse matrix. The three methods are compared by investigating the effect they have on the density of the sparse matrix and the number of iterations required to converge to a solution. It also reports on the use of an extrapolation technique in order to reduce the iteration count in the solution of the matrix equation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
New molecular insights into osteosarcoma targeted therapy (2013)

These translational studies in osteosarcoma have identified new molecular targets for osteosarcoma.
Chromoendoscopy (1998)

Tissue staining during endoscopy (chromoendoscopy) is a technique used to study the fine details of the mucosa throughout the gastrointestinal tract. Unfortunately, its applications and results are not known by many gastrointestinal or surgical endoscopists. Each stain has a few specific clinical applications. The mechanism of action of the stains should be fully understood before their use. Ideally, the clinician should use chromoendoscopy and the variety of stains either to confirm a clinical suspicion or to provide new information that could aid management in a specific setting. Endoscopic tattooing is a different technique where a specific site in the gastrointestinal tract is labeled by an intramural injection of a carbon ink suspension solution for future surgical or endoscopic identification.
Modelling nitrite in wastewater treatment systems: a discussion of different modelling concepts (2008)

Originally presented at the 1st IWA/WEF Wastewater Treatment Modelling Seminar (WWTmod 2008), this contribution has been updated to also include the valuable feedback that was received during the Modelling Seminar. This paper addresses a number of basic issues concerning the modelling of nitrite in key processes involved in biological wastewater water treatment. To this end, we review different model concepts (together with model structures and corresponding parameter sets) proposed for processes such as two-step nitrification/denitrification, anaerobic ammonium oxidation and phosphorus uptake processes. After critically discussing these models with respect to their assumptions and parameter sets, common points of agreement as well as disagreement were elucidated. From this discussion a general picture of the state-of-the-art in the modelling of nitrite is provided. Taking this into account, a number of recommendations are provided to focus further research and development on nitrite modelling in biological wastewater treatment.
ClpE, a novel member of the HSP100 family, is involved in cell division and virulence of Listeria monocytogenes (1999)

We identified, in the facultative intracellular pathogen Listeria monocytogenes, a previously unknown Clp ATPase, unique among the HSP100 proteins because of the presence of a short N-terminal region with a potential zinc finger motif. This protein of 726 amino acids is highly homologous to ClpE of Bacillus subtilis, and is a member of a new subfamily of HSP100/Clp ATPases. The clpE gene is transcribed as a monocistronic mRNA from a typical consensus sigma A promoter. clpE is not stimulated by various stresses, but is upregulated in a clpC mutant. This is the first example of cross-regulation between Clp ATPases. By constructing a clpE mutant of L. monocytogenes, we found that ClpE is required for prolonged survival at 42 degrees C and is involved in the virulence of this pathogen. A double mutant deficient in both ClpE and ClpC was avirulent in a mouse model and completely eliminated in the liver. Electron microscopy studies did not show any morphological alterations in clpE or clpC mutants. In the clpE-clpC double mutant, however, cell division was affected, indicating that ClpE acts synergistically with ClpC in cell septation. These results show that the Clp chaperones play a crucial role in both cell division and virulence of L. monocytogenes.
Pharmacological specificity of novel, synthetic, cyclic peptides as antagonists at tachykinin receptors (1991)

1. The interaction at tachykinin receptors of a series of novel cyclic hexapeptides has been examined by use of radioligand binding assays (NK1 and NK3 sites in rat cortex, NK2 sites in hamster urinary bladder) and functional pharmacological assays (guinea-pig ileum, rat vas deferens and rat portal vein for NK1, NK2 and NK3 receptors, respectively). 2. The compounds cyclo(GlnTrpPhe(R)Gly[ANC-2]LeuMet) (L-659,837) and cyclo(GlnTrpPheGly-LeuMet) (L-659,877) were powerful and selective displacers of NK2 binding (pIC50 6.9 and 8.0, respectively), and were competitive antagonists of responses to stimulation of NK2 receptors in rat vas deferens (pKB for antagonism of responses to eledoisin 6.7 and 8.1, respectively). Responses in the NK1 and NK3 pharmacological assays were blocked only weakly, if at all. 3. In the longitudinal muscle of the small intestine of the rat, responses to stimulation of the putative NK2 receptor by eledoisin, neurokinin A or neurokinin B were antagonized by both cyclo(GlnTrpPhe(R)-Gly[ANC-2]LeuMet) and cyclo (GlnTrpPheGlyLeuMet) in a manner consistent with the presence in this tissue of a uniform population of receptors, indistinguishable from the NK2 receptor of the rat vas deferens. 4. The compounds cyclo(GlnTrpPheGlyLeuMet) and the lactam-containing analogue are among the most selective antagonists for the NK2 receptor that have been described; their availability should be of value in the characterization of the receptors mediating responses to tachykinins, and in elucidating the physiological functions of the tachykinin receptors.
Fatty acids antagonize bupivacaine - induced INablockade (2011)

Theories regarding the mechanism of intravenous fat emulsion for bupivacaine cardiotoxicity include creation of an intravascular lipid sink into which the cardiotoxic drug is sequestered, an improvement of impaired cardiac metabolism, and restoration of cardiomyocyte function by increasing intracellular calcium. However, work in this area is inconclusive and a more mechanistic explanation is desirable. We used a heterologous expression system (HEK-293 cells) and voltage clamp techniques to study the electrophysiologic effects of bupivacaine, polyunsaturated, and saturated fatty acids on sodium current (I(Na)) in stable cell lines expressing human cardiac sodium channels. Linolenic (polyunsaturated) and stearic (saturated) fatty acids were selected for study as they are components of commonly used lipid infusions. Bupivacaine-induced significant tonic and use dependent I(Na) block, as expected. Linolenic and stearic fatty acids directly modulated I(Na), inducing primarily tonic block. Greater block was seen with linolenic acid as compared with stearic acid. Simultaneous exposure to bupivacaine and fatty acids reduced both the tonic and use dependent block compared with bupivacaine alone. Reduction of bupivacaine-induced I(Na) block was greatest in cells treated with linolenic acid. These results suggest that the salutary effects of intravenous fat emulsion may be, in part, due to a direct modulatory effect of fatty acids on cardiac sodium channels.
Will the real Cowden syndrome please stand up (again)? Expanding mutational and clinical spectra of the PTEN hamartoma tumour syndrome: Table 1 (2004)

PTEN hamartoma tumour syndrome

Since consensus operational diagnostic criteria for Cowden syndrome (MIM 158350) were first established in 1995, our understanding of this complex disease—and the spectrum of disorders related to it by virtue of also having germline mutations in the PTEN tumour suppressor gene—has continued to evolve. This was reflected in a commentary1 in this journal in 2000 in which it was proposed that endometrial cancer and renal cell carcinoma be added to the operational diagnostic criteria for Cowden syndrome (table 1). This updated commentary is intended to provide a review of significant changes in our understanding of the growing group of disorders, which are known to be caused by germline mutations in PTEN on 10q23.3, and which have been termed the PTEN hamartoma tumour syndrome.

View this table:

 Table 1 
International Cowden Consortium operational criteria for the diagnosis of Cowden syndrome. Ver 2000 



Cowden syndrome is a complex disorder with malignant and benign (hamartomatous) lesions affecting derivatives of all three germ cell layers. Major organs involved include the breast, thyroid, uterus, brain, and mucocutaneous tissues.2 It has been estimated to affect about 1 in 200 000 individuals,3,4 although this is probably an underestimate given the difficulty in diagnosis presented by this highly variable disease and the fact that many component features in and of themselves can occur in the general population. Penetrance is related to age, with most patients presenting by their late twenties with at least the mucocutaneous lesions of this disorder, which are reportedly seen in 99% of affected individuals. The lifetime risk for breast cancer in Cowden syndrome is estimated to be 25–50%, with an average age of diagnosis between 38 and 46 years old.2,5 The risk for thyroid cancer (typically follicular, but occasionally papillary) is approximately 10%, while the risk for endometrial cancer, …
“Chemical Ligation”: A Versatile Method for Nucleoside Modification with Boron Clusters (2008)

A general approach to the synthesis of nucleoside conjugates containing carborane and metallocarborane complexes, based on Huisgen 1,3-dipolar cycloaddition ("chemical ligation"), is described. Boron-cluster-donors bearing terminal azide or ethynyl groups were prepared in the ring-opening reaction of dioxane-boron-cluster adducts and an azide anion or suitable alkynol-derived alcoholate nucleophile. Analogous derivatives bearing terminal sulfhydryl groups were also prepared. Nucleosides with various spacers containing terminal azide or ethynyl groups, located within nucleobases or sugar residues, were used as boron-cluster acceptors. The proposed methodology provides a convenient way to synthesize libraries of boron-cluster-modified nucleosides for various applications.
Purification of mouse L cell interferon. Essentially pure preparations with associated cell growth inhibitory activity. (1978)

Mouse L cell interferon induced by Newcastle disease virus was purified by a combination of salt precipitation, ion exchange chromatography, gel filtration, and affinity chromatography using anti-interferon anti-body. The preparation was labeled with 125I at a later step of purification, which served as an index of protein concentration. Two main species of interferon molecules differing in molecular weight were separated from each other, and the final preparations obtained were shown to be essentially pure by polyacrylamide gel electrophoresis in the absence as well as in the presence of sodium dodecyl sulfate. The highest specific activities obtained were 2.6 X 10(9) and 7.3 X 10(8) international units/mg of protein (determined by 125I radioactivity) for the 40,000- and 24,000-dalton species, respectively. The preparations at different steps of purification, including those of the highest purity, were tested for the anti-cell growth activity. Their activities were found to be indistinguishable from each other when compared at the same antiviral doses, indicating that the anti-cell growth activity is carried by the interferon molecules themselves.
High-throughput SNP analysis for genetic association studies. (2003)

Single nucleotide polymorphisms (SNPs) are the most common type of genetic variation, and millions of SNPs are now documented. Because of their dense distribution across the genome, SNPs are viewed as ideal markers for large-scale genome-wide association studies to discover genes in common complex diseases, such as cancer. To enable such studies, researchers have constructed appropriate sets of SNP markers, by selecting SNPs that are common in major human populations and by charting the patterns of co-occurrence of SNPs, which could further guide marker selection. High-throughput SNP analysis technologies have also been developed, which can analyze thousands of SNPs in thousands of samples. As SNP analysis techniques and SNP marker sets are improving, researchers have begun to carry out large-scale genome scans for disease genes, with encouraging first results.
High levels of bcl‐2 protein in circulating t lymphocytes, but not b lymphocytes, of patients with systemic lupus erythematosus (1994)

Although the occurrence of circulating T lymphocytes with abnormally high bcl-2 expression is not specific for SLE, it is evidence for a dysregulation of lymphocytic programmed cell death in this autoimmune disease.
Catheter Ablation in Patients With Multiple and Unstable Ventricular Tachycardias After Myocardial Infarction (2001)

A 4- to 5-cm line of RF lesions abolishes all inducible VTs in more than 50% of patients. Less ablation is required if a reentry circuit isthmus is identified even when multiple and unstable VTs are present.
Subtype selectivity of peptide analogs for all five cloned human somatostatin receptors (hsstr 1-5). (1994)

Recent reports (Raynor et al) have claimed the identification of potent somatostatin (SST) agonists exhibiting binding affinities of 1-2 pM and up to 30,000 fold binding selectivity for several of the 5 cloned sstr subtypes. These conclusions, however, are based on binding comparisons of sstr subtypes from different species expressed in different cell lines and studied with different radioligands. To eliminate the effect of species and/or methodological variations, we have investigated agonist selectivity of 32 synthetic SST analogs for all 5 hsstrs stably expressed in CHO-K1 cells under identical binding conditions. We show that hsstr2, 3, 5 react potently with hexapeptide as well as cyclic and linear octapeptide analogs and belong to a similar sstr subclass. hsstr1 and 4 react poorly with these analogs and belong to a separate subclass. The present generation of SST analogs exhibit a modest-50 fold increase in binding potency compared to SST-14 for 2 subtypes (hsstr2, 3), and relative selectivity for only 1 subtype (hsstr2) which is at best only 35 fold. The potency and degree of selectivity of these analogs is several orders of magnitude less than that reported earlier and suggests the need for caution in using these compounds as putative superagonists or subtype selective compounds for any of the individual sstrs.
The use of synthetic oligodeoxynucleotide primers in cloning and sequencing segment 8 of influenza virus (A/PR/8/34) (1981)

Complete double-stranded DNA copies of the RNA genes of the human influenza virus A/PR/8/34 have been synthesized by using two synthetic oligodeoxynucleotide primers. The gene encoding the non-structural proteins NS1 and NS2, prepared with these primers, has been cloned into the bacteriophage M13mp7 and sequenced. The sequence is compared with that from another human strain and from an avian strain.