gebhart/patrepeval huggingface dataset:
T-linker-specific ligation PCR (T-linker PCR): an advanced PCR technique for chromosome walking or for isolation of tagged DNA ends (2003)

Dozens of PCR-based methods are available for chromosome walking from a known sequence to an unknown region. These methods are of three types: inverse PCR, ligation-mediated PCR and randomly primed PCR. However, none of them has been generally applied for this purpose, because they are either difficult or inefficient. Here we describe a simple and efficient PCR strategy--T-linker-specific ligation PCR (T-linker PCR) for gene or chromosome walking. The strategy amplifies the template molecules in three steps. First, genomic DNA is digested with 3' overhang enzymes. Secondly, primed by a specific primer, a strand of the target molecule is replicated by Taq DNA polymerase and a single A tail is generated on the 3' unknown end of the target molecule, and then a 3' overhang-T linker (named T-linker) is specifically ligated onto the target. Thirdly, the target is amplified by two rounds of nested PCR with specific primers and T-linker primers. T-linker PCR significantly improves the existing PCR methods for walking because it uses specific T/A ligation instead of arbitrary ligation or random annealing. To show the feasibility and efficiency of T-linker PCR, we have exploited this method to identify vector DNA or T-DNA insertions in transgenic plants.
Topoisomerase I and II cleavage of adenovirus DNA in vivo: both topoisomerase activities appear to be required for adenovirus DNA replication (1990)

Sites of topoisomerase I and II cleavage across large portions of the adenovirus type 5 genome were mapped by using the drugs camptothecin and VM26, respectively. These drugs prolong the half-lives of the covalent DNA-protein intermediates in which the DNA is transiently cleaved, and so treatment with protein denaturants after exposure to the drugs leads to DNA strand scission at the site of topoisomerase cleavage. Strong topoisomerase II cleavage sites occurred in clusters throughout the regions examined, including both transcribed regions and transcriptional control regions. The efficiency of topoisomerase II cleavage increased as the rate of adenovirus DNA replication increased and then decreased with the decreasing rate of replication late in the infection cycle. The increase was not dependent on expression of the E1A gene, whose products activate transcription of the early viral genes. Positions of topoisomerase II cleavage sites did not vary during the infection. Topoisomerase I cleavage sites were also found throughout the examined regions, with the strongest sites occurring near the ends of the transcription units. Topoisomerase I cleavage in the E1 region occurred much more frequently than topoisomerase II cleavage, was not dependent on E1A gene expression, and remained at a similar level from the early viral phase into the late viral phase. Treatment of infected cells with either drug prevented efficient replication of adenovirus DNA. Inhibition of topoisomerase I activity led to an immediate cessation of adenovirus DNA replication, while inhibition of topoisomerase II blocked replication only after completion of approximately one additional round.
Pan-PCR, a Computational Method for Designing Bacterium-Typing Assays Based on Whole-Genome Sequence Data (2012)

With increasing rates of antibiotic resistance, bacterial infections have become more difficult to treat, elevating the importance of surveillance and prevention. Effective surveillance relies on the availability of rapid, cost-effective, and informative typing methods to monitor bacterial isolates. PCR-based typing assays are fast and inexpensive, but their utility is limited by the lack of targets which are capable of distinguishing between strains within a species. To identify highly informative PCR targets from the growing base of publicly available bacterial genome sequences, we developed pan-PCR. This computer algorithm uses existing genome sequences for isolates of a species of interest and identifies a set of genes whose patterns of presence or absence provide the best discrimination between strains in this species. A set of PCR primers targeting the identified genes is then designed, with each PCR product being of a different size to allow multiplexing. These target DNA regions and PCR primers can then be utilized to type bacterial isolates. To evaluate pan-PCR, we designed an assay for the emerging pathogen Acinetobacter baumannii. Taking as input a set of 29 previously sequenced genomes, pan-PCR identified 6 genetic loci whose presence or absence was capable of distinguishing all the input strains. This assay was applied to a set of patient isolates, and its discriminatory power was compared to that of multilocus sequence typing (MLST) and whole-genome optical maps. We found that the pan-PCR assay was capable of making clinically relevant distinctions between strains with identical MLST profiles and showed a discriminatory power similar to that of optical maps. Pan-PCR represents a tool capable of exploiting available genome sequence data to design highly discriminatory PCR assays. The ease of design and implementation makes this approach feasible for diagnostic facilities of all sizes.
Elevated Levels of Cyclin D1 Protein in Response to Increased Expression of Eukaryotic Initiation Factor 4E (1993)

Cyclin D1 is a G1-specific cyclin that has been linked to lymphoid, parathyroid, and breast tumors. Recent studies suggested that high protein levels of cyclin D1 are not always produced when cyclin D1 mRNA is overexpressed in transfected cells, suggesting that posttranscriptional events may be important in cyclin D1 regulation. The mRNA cap-binding protein (eukaryotic initiation factor 4E [eIF-4E]) is a potential regulatory of several posttranscriptional events, and it can itself induce neoplastic transformation. Consequently, we examined eIF-4E as a potential regulator of cyclin D1. Overexpression of cyclin D1 mRNA in NIH 3T3 cells did not increase cyclin D1 protein. In contrast, overexpression of eIF-4E markedly increased the amount of cyclin D1 protein in NIH 3T3 cells. This increase was specific to cyclin D1 in comparison with the retinoblastoma gene product, c-Myc, actin, and eukaryotic initiation factor 2 alpha. We also examined cyclin D1 protein in cells expressing an estrogen receptor-Myc fusion protein because we previously found that eIF-4E increases after induction of c-myc function. In these cells, increased levels of eIF-4E protein were closely followed by increases in levels of cyclin D1 protein, but the level of cyclin D1 mRNA was not increased. We conclude that increases in cyclin D1 levels may result from increased expression of eIF-4E, and this regulation may be one determinant of cyclin D1 levels in the cell.
Identification of a single base change in ribosomal RNA leading to erythromycin resistance. (1992)

The molecular basis of a mutation conferring an erythromycin-resistance phenotype was explored, as an approach to the role of 23 S rRNA in the peptidyl-transferase activity of 50 S ribosomal subunits. Mutagenization of an Escherichia coli strain, which carried the multicopy plasmid pLC7-21 containing the rrnH operon, led to the production of an erythromycin-resistant strain. Plasmid pBFL1 isolated from this mutant was able to transform the sensitive RecA- strain EM4 and to induce a "dissociated" type of antibiotic resistance. Two ribosome populations occurred in EM4/pBFL1: normal particles coded for by the seven rrn chromosomal genes and mutated particles containing rRNA of plasmid origin. The latter particles displayed in vitro lower affinity and susceptibility to erythromycin than wild type particles. The mutation within plasmid pBFL1 was mapped by a multiple primer extension technique. Three synthetic primers were used to sequence the central loop in domain V of 23 S rRNA, leading to identification of a C to U transition at position 2611. This base change was proved to be responsible for the erythromycin-resistance phenotype by the plasmid-plasmid marker rescue technique. A molecular explanation for the rrn mutations leading, respectively, to undissociated and to dissociated types of resistance to the MLSb (macrolide-lincosamide-synergimycin B) group of antibiotics is proposed. These results and some literature data support the notion that rRNA bases involved in antibiotic resistance play a conformational role in the ribosomal binding sites for the MLSb antibiotics.
Engineering Thermotolerant Biocatalysts for Biomass Conversion to Products (2010)

Lignocellulosic biomass is a promising feedstock for producing renewable chemicals and transportation fuels as petroleum substitutes. Fermentation of the cellulose in biomass in an SSF process requires that the properties of the microbial biocatalyst match the fungal cellulase activity optima for cost-effective production of products. Fermentation of the pentose sugars derived from hemicellulose in biomass is an additional asset of an ideal biocatalyst. The microbial biocatalyst used by the industry, yeast, lacks the ability to ferment pentose sugars. The optimum temperature for growth and fermentation of yeast is about 35°C. The optimum temperature for commercially available cellulase enzymes for depolymerization of cellulose in biomass to glucose for fermentation is 50-55 °C. Because of the mismatch in the temperature optima for the enzyme and yeast, SSF of cellulose to ethanol (cellulosic ethanol) with yeast is conducted at a temperature that is close to the optimum for yeast. We have shown that by increasing the temperature of SSF to 50-55 °C using thermotolerant B. coagulans, the amount of cellulase required for SSF of cellulose to products can be reduced by 3-4 –fold compared to yeast-based SSF at 35°C with a significant cost savings due to lower enzyme loading. Thermotolerant Bacillus coagulans strains ferment hemicellulose-derived pentose sugars completely to L(+)-lactic acid, the primary product of fermentation. We have developed genetic tools to engineer B. coagulans for fermentation of all the sugars in biomass to ethanol. Using these tools, we have altered the fermentation properties of B. coagulans to produce ethanol as the primary product. The thermotolerant property of B. coagulans has been shown to also lower the cellulase requirement and associated cost in SSF of cellulose to lactic acid compared to lactic acid bacteria. Lactic acid is a potential petroleum substitute for bio-based renewable plastics production. This study has led to the development of B. coagulans as a thermotolerant microbial biocatalyst for production of ethanol as a transportation fuel and lactic acid as a starting material for bio-based plastics in a cost-effective manner from renewable biomass.
Pharmacology and Biological Efficacy of a Recombinant, Humanized, Single-Chain Antibody C5 Complement Inhibitor in Patients Undergoing Coronary Artery Bypass Graft Surgery With Cardiopulmonary Bypass (1999)

A single-chain antibody specific for human C5 is a safe and effective inhibitor of pathological complement activation in patients undergoing CPB. In addition to significantly reducing sC5b-9 formation and leukocyte CD11b expression, C5 inhibition significantly attenuates postoperative myocardial injury, cognitive deficits, and blood loss. These data suggest that C5 inhibition may represent a novel therapeutic strategy for preventing complement-mediated inflammation and tissue injury.
Cloning and expression of myelin-associated oligodendrocytic basic protein. A novel basic protein constituting the central nervous system myelin. (1994)

We have screened genes predominantly expressed in the rat spinal cord, and we report here cloning of the most abundant unknown gene. It is a novel member of the central nervous system (CNS) myelin-constituting proteins, myelin-associated oligodendrocytic basic protein (MOBP). MOBP is abundantly expressed specifically in oligodendrocytes at the mRNA level only next to myelin basic protein (MBP) and proteolipid protein. Two isoforms have been confirmed. One of them has proline-rich tandem repeats and has 84% homology with human counterpart in terms of predicted amino acid sequences. The cDNA-derived primary structure predicts a small, soluble, basic protein. The immunoelectron microscopy has shown that MOBP is expressed throughout compact myelin. All these characteristics are similar to MBP. One definite difference between MBP and MOBP is that MOBP is expressed exclusively in the CNS myelin. These findings suggest that MOBP shares some important functions with MBP in the CNS myelin such as myelin compaction.
Pharmacokinetics and Toxicity of a p-Boronophenylalanine—Cyclodextrin Formulation Delivered by Intravenous Infusion to Dogs (1994)

Boron-neutron capture therapy (BNCT) is a potentially important treatment for metastatic malignant melanoma. Effective BNCT requires the selective uptake of a boron compound by tumor cells. Para-boronophenylalanine (BPA) is of particular interest for BNCT since it is selectively delivered to melanoma tissue. However, its use is limited by its poor solubility in water at physiological pH. To facilitate the delivery of BPA to melanoma tissue sites, BPA's aqueous solubility was increased by forming a host-guest complex with 2-hydroxypropyl-β-cyclodextrin (HP-β-CD). An in vivo study was carried out in dogs to examine BPA levels in plasma and selected tissues after i.v. infusion of BPA. Two BPA formulations were used: BPA in a pH 7.4 phosphate buffer and in an HP-β-CD formulation. The pharmacokinetic profiles of BPA in both formulations were determined. The plasma concentrations of boron for the BPA/HP-β-CD formulation were much higher than those for the BPA/buffer formulation. The area under each plasma boron concentration-time curve for BPA/HP-β-CD was 20.7 times that for BPA/buffer. Thus, the delivery of BPA into the blood circulation was significantly enhanced due to the increase in BPA solubility.
Resolution independent curve rendering using programmable graphics hardware (2005)

We present a method for resolution independent rendering of paths and bounded regions, defined by quadratic and cubic spline curves, that leverages the parallelism of programmable graphics hardware to achieve high performance. A simple implicit equation for a parametric curve is found in a space that can be thought of as an analog to texture space. The image of a curve's Bézier control points are found in this space and assigned to the control points as texture coordinates. When the triangle(s) corresponding to the Bézier curve control hull are rendered, a pixel shader program evaluates the implicit equation for a pixel's interpolated texture coordinates to determine an inside/outside test for the curve. We extend our technique to handle anti-aliasing of boundaries. We also construct a vector image from mosaics of triangulated Bézier control points and show how to deform such images to create resolution independent texture on three dimensional objects.
Structural and functional characterization of a C‐type lectin‐like antifreeze protein from rainbow smelt (Osmerus mordax) (2002)

Antifreeze proteins (AFPs) are produced by several cold-water fish species. They depress physiological freezing temperatures by inhibiting growth of ice crystals and, in so doing, permit the survival of these fish in seawater cooler than their normal freezing temperatures. The type II AFP from rainbow smelt (Osmerus mordax), which is a member of the C-type lectin superfamily, was characterized in terms of its Ca2+-binding quaternary structure and the role of its single N-linked oligosaccharide. The protein core of the smelt AFP, shown through sequence homology to be a C-type lectin carbohydrate-recognition domain, was found to be protease resistant. Smelt AFP was also shown to bind Ca2+, as determined by ruthenium red staining and a conformational change on Ca2+ binding detected by intrinsic fluorescence. The N-linked oligosaccharide was found to have no effect on protease resistance, dimerization, or antifreeze activity. Thus its role, if any, in the antifreeze function of this protein remains unknown. Smelt AFP was also shown to be a true intermolecular dimer composed of two separate subunits. This dimerization did not require the presence of N-linked oligosaccharide or bound Ca2+. Smelt AFP dimerization has implications for the effective solution concentration and measurement of its activity. This finding may also lead to new interpretation of the mechanism of ice-growth inhibition by this AFP.
Structure of the human laminin B1 chain gene. (1990)

The exon-intron structure of the human laminin B1 chain gene was determined from genomic clones that spanned 90 kilobase pairs (kb), including 80 kb of the structural gene, about 1 kb of the 5'-flanking region, and 9 kb of the 3'-flanking region. DNA sequencing and heteroduplex analyses demonstrated that the gene consists of 34 exons. The intron sizes vary from 92 base pairs to more than 15,000 base pairs. The clones did not completely contain introns 13 and 14 and, therefore, the exact size of the gene remains to be determined. The first exon encodes a 5'-untranslated region, with the ATG translation start codon being in exon 2. The promoter region does not contain TATA or CAAT boxes, but it has four GC boxes. Additionally, two GC boxes are located in the 5'-untranslated sequence. A glucocorticoid response element-like sequence and a sequence resembling the binding sequence for transcription factor AP-2 are present in the 5'-flanking region. Another potential AP-2 binding sequence is located in the 5'-untranslated sequence of exon 1. A TGACC motif present in the binding region for the retinoic acid response element of the mouse laminin B1 gene promoter is also present in the human counterpart. The overall exon pattern of the gene correlates only slightly with the highly conserved structural domains and internal repeats of the B1 polypeptide chain. Furthermore, the exon profile differs considerably from that of the laminin B2 gene. A HincII/HpaI restriction fragment length polymorphism was identified in exon 31.
Role of P-selectin in total hepatic ischemia and reperfusion. (1995)

P-selectin has a significant role in ischemia and reperfusion injury of the liver. Early modulation of the interaction between P-selectin and its ligand decreased neutrophil adhesion and migration and consequently diminished damage to the liver.
β-Hydroxy-β-methylbutyrate free acid reduces markers of exercise-induced muscle damage and improves recovery in resistance-trained men (2013)

The purpose of the present study was to determine the effects of short-term supplementation with the free acid form of b-hydroxyb-methylbutyrate (HMB-FA) on indices of muscle damage, protein breakdown, recovery and hormone status following a high-volume resistance training session in trained athletes. A total of twenty resistance-trained males were recruited to participate in a high-volume resistance training session centred on full squats, bench presses and dead lifts. Subjects were randomly assigned to receive either 3 g/d of HMB-FA or a placebo. Immediately before the exercise session and 48 h post-exercise, serum creatine kinase (CK), urinary 3-methylhistadine (3-MH), testosterone, cortisol and perceived recovery status (PRS) scale measurements were taken. The results showed that CK increased to a greater extent in the placebo (329%) than in the HMB-FA group (104%) (P¼0·004, d ¼ 1·6). There was also a significant change for PRS, which decreased to a greater extent in the placebo (9·1 (SEM 0·4) to 4·6 (SEM 0·5)) than in the HMB-FA group (9·1 (SEM 0·3) to 6·3 (SEM 0·3)) (P¼0·005, d ¼ 20·48). Muscle protein breakdown, measured by 3-MH analysis, numerically decreased with HMB-FA supplementation and approached significance (P¼0·08, d ¼ 0·12). There were no acute changes in plasma total or free testosterone, cortisol or C-reactive protein. In conclusion, these results suggest that an HMB-FA supplement given to trained athletes before exercise can blunt increases in muscle damage and prevent declines in perceived readiness to train following a high-volume, muscle-damaging resistance-training session.
Mild Intraoperative Hypothermia during Surgery for Intracranial Aneurysm (2005)

Intraoperative hypothermia did not improve the neurologic outcome after craniotomy among good-grade patients with aneurysmal subarachnoid hemorrhage.
Supporting multimedia information presentation in a distributed, heterogeneous environment (2002)

A design overview of a distributed object-oriented system is given which supports the distributed processing of multimedia information with special regard to information presentation in an environment of heterogeneous networks and workstations. Essential features of the system are an object model designed for the handling of multimedia information and the adaptation of presentation and transport of multimedia information to the capabilities and available resources of the workstations and underlying networks. This adaptation is done by a distributed support layer. Using environment information, this layer makes an information presentation and transport service available to the applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Label-Free Cell-Based Assays with Optical Biosensors in Drug Discovery (2006)

Once viewed solely as a tool for low throughput and kinetic analysis of biomolecular interactions, optical biosensors are gaining widespread uses in drug discovery because of recent advances in instrumentation and experimental design. These advances have expanded the capabilities of optical biosensors to meet the needs at many points in the drug discovery process. Concurrent shifts in drug discovery paradigms have seen the growing use of whole cell systems for drug screens, thus creating both a need in drug discovery and a solution in optical biosensors. This article reviews important advances in optical biosensor instrumentation, and highlights the potential of optical biosensors for drug discovery with an emphasis on whole cell sensing in both high throughput and high content fashions.
An immersive 3D video-conferencing system using shared virtual team user environments (2002)

Videoconferencing is going to become attractive for geo-graphically distributed team collaboration, specifically to avoid travelling and to increase flexibility. Against this background this paper presents a next generation system - a 3D videoconference providing immersive tele-presence and natural representation of all participants in a shared virtual meeting space to enhance quality of human-centred communication. This system is based on the principle of a shared virtual table environment, which guarantees correct eye contact and gesture reproduction. The key features of our system are presented and compared to other approaches like tele-cubicles. Furthermore the current system design and details of the real-time hardware and software concept are explained.
Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. (1989)

The CYC1 gene of Saccharomyces cerevisiae is positively regulated by the HAP2 and HAP3 proteins, which form a heteromeric complex that binds to a CCAAT box in the upstream activation site, UAS2, and which activate transcription in a nonfermentable carbon source. We carried out a genetic analysis to identify additional trans-acting regulatory factors exerting their effects through UAS2. We present the identification and characterization of a new locus, HAP4, which is shown to encode a subunit of the DNA-binding complex at UAS2. In the hap4 mutant, the binding of HAP2 and HAP3 (HAP2/3) is not observed in vitro. The HAP4 gene is regulated transcriptionally by a carbon source, suggesting that it encodes a regulatory subunit of the bound complex. The sequence of HAP4 shows a highly acidic region, which innactivated the protein when deleted. Replacement of this region with the activation domain of GAL4 restored activity, suggesting that it provides the principal activation domain to the bound HAP2/3/4 complex.