gebhart/patrepeval huggingface dataset:
An analytic dosimetry study for the use of radionuclide-liposome conjugates in internal radiotherapy. (2001)

This study provides a dosimetric evaluation for the use of some liposome systems as carriers in targeted radionuclide therapy. Although much further work must be undertaken before any clinical application is considered, these results suggest that radionuclide targeting using liposomes is feasible and may have the advantage of reduced red marrow absorbed dose.
Physical Insights on BJT-Based 1T DRAM Cells (2009)

The basic operation of BJT-based floating-body 1T DRAM cells on SOI is analyzed with supportive numerical device simulation. Extreme sensitivity of the charging process (write ldquo1rdquo) to the offset (Delta <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">WB</sub> ) between the word-line and bit-line voltage pulses is revealed and explained. The necessity of a positive Delta <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</i> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">WB</sub> for successful write ldquo1rdquo is related to establishing a high gate capacitance, which is the predominant charge-storage element in the BJT-based cell. Such charging underlies why a fully depleted (FD) cell, e.g., a FinFET, can work for BJT-based DRAM, without an independent bias for accumulation charge that is necessary in conventional FD-MOSFET DRAM cells for charge storage and data sensing. Furthermore, a bulk-accumulation effect in the BJT-based DRAM cell is revealed and described. It undermines the BJT operation and leads to ineffective charging and significant loss of sense margin when the cell body thickness is scaled.
Bacteriophages infecting dairy propionibacteria (1995)

Nineteen bacteriophages infecting P freudenreichii have been isolated from 32 Swisstype cheeses. They ail present a similar morphology and belong to the B1 group of Bradley's classification. According to their restriction patterns, obtained with the endonuclease Ps~, they can be grouped into 3 clusters, 1 of which contains the majority of the phages. Sixteen of the 32 cheeses studied were infected with bacteriophages. We observed that ail the cheeses made from raw milk and ripened in a warm curing room for several weeks which are known to contain high concentrations of propionibacteria, were infected with bacteriophages. Moreover, the multiplication of bacteriophages occurred in cheese during the multiplication stage of propionibacteria in a warm curing room. We have shown that raw milk contains bacteriophages and thus it can be a source of phages in factories. However, these bacteriophages are sensitive to the milk heat treatment used for cheesemaking. bacteriophage 1 Propionibacterium 1Swiss-type cheese Rsum -Bactriophages infectant les bactries propioniques laitires. Dix-neuf bactriophages actifs sur P freudenreichii ont t isols partir de 32 fromages pte presse cuite. Leur morphologie est similaire et permet de les classer dans le groupe B1 de la classification de Bradley. L'tude du profil de restriction de leur chromosome obtenu avec l'endonuclase Pstl a permis de les classer en 3 groupes, dont un en rassemble la grande majorit. Seize fromages parmi les 32 tudis taient contamins par des bactriophages. Nous avons remarqu que tous les fromages faits avec du lait cru, affins en cave chaude et qui par consquent montrent une haute concentration en bactries propionlaues, contenaient des bactriophages. De plus, la multiplication de ceux-ci se produisait paralllement celle des bactries lors de l'affinage. Nous avons aussi montr que le lait cru pouvait vhiculer des bactriophages et donc constituer une voie d'entre des phages dans les usines. Ces phages sont cependant sensibles aux traitements thermiques appliqus au lait avant la fabrication fromagre. bactriophage IPropionibacterium Ifromage pte presse cuite
New edge-directed interpolation (2001)

This paper proposes an edge-directed interpolation algorithm for natural images. The basic idea is to first estimate local covariance coefficients from a low-resolution image and then use these covariance estimates to adapt the interpolation at a higher resolution based on the geometric duality between the low-resolution covariance and the high-resolution covariance. The edge-directed property of covariance-based adaptation attributes to its capability of tuning the interpolation coefficients to match an arbitrarily oriented step edge. A hybrid approach of switching between bilinear interpolation and covariance-based adaptive interpolation is proposed to reduce the overall computational complexity. Two important applications of the new interpolation algorithm are studied: resolution enhancement of grayscale images and reconstruction of color images from CCD samples. Simulation results demonstrate that our new interpolation algorithm substantially improves the subjective quality of the interpolated images over conventional linear interpolation.
The emerging phenomenon of electronic cigarettes (2012)

The need for novel and more effective approaches to tobacco control is unquestionable. The electronic cigarette is a battery-powered electronic nicotine delivery system that looks very similar to a conventional cigarette and is capable of emulating smoking, but without the combustion products accountable for smoking's damaging effects. Smokers who decide to switch to electronic cigarettes instead of continuing to smoke would achieve large health gains. The electronic cigarette is an emerging phenomenon that is becoming increasingly popular with smokers worldwide. Users report buying them to help quit smoking, to reduce cigarette consumption, to relieve tobacco withdrawal symptoms due to workplace smoking restrictions and to continue to have a 'smoking' experience but with reduced health risks. The focus of the present article is the health effects of using electronic cigarettes, with consideration given to the acceptability, safety and effectiveness of this product to serve as a long-term substitute for smoking or as a tool for smoking cessation.
Tracking the dose distribution in radiation therapy by accounting for variable anatomy (2004)

The goal of this research is to calculate the daily and cumulative dose distribution received by the radiotherapy patient while accounting for variable anatomy, by tracking the dose distribution delivered to tissue elements (voxels) that move within the patient. Non-linear image registration techniques (i.e., thin-plate splines) are used along with a conventional treatment planning system to combine the dose distributions computed for each 3D computed tomography (CT) study taken during treatment. For a clinical prostate case, we demonstrate that there are significant localized dose differences due to systematic voxel motion in a single fraction as well as in 15 cumulative fractions. The largest positive dose differences in rectum, bladder and seminal vesicles were 29%, 2% and 24%, respectively, after the first fraction of radiation treatment compared to the planned dose. After 15 cumulative fractions, the largest positive dose differences in rectum, bladder and seminal vesicles were 23%, 32% and 18%, respectively, compared to the planned dose. A sensitivity analysis of control point placement is also presented. This method provides an important understanding of actual delivered doses and has the potential to provide quantitative information to use as a guide for adaptive radiation treatments.
Over‐expression of secreted proteins from mammalian cell lines (2014)

Secreted mammalian proteins require the development of robust protein over-expression systems for crystallographic and biophysical studies of protein function. Due to complex disulfide bonds and distinct glycosylation patterns preventing folding and expression in prokaryotic expression hosts, many secreted proteins necessitate production in more complex eukaryotic expression systems. Here, we elaborate on the methods used to obtain high yields of purified secreted proteins from transiently or stably transfected mammalian cell lines. Among the issues discussed are the selection of appropriate expression vectors, choice of signal sequences for protein secretion, availability of fusion tags for enhancing protein stability and purification, choice of cell line, and the large-scale growth of cells in a variety of formats.
Aminoglycoside‐Resistance Mechanisms for Cystic FibrosisPseudomonas aeruginosaIsolates Are Unchanged by Long‐Term, Intermittent, Inhaled Tobramycin Treatment (2000)

Aminoglycoside-resistance mechanisms were characterized in Pseudomonas aeruginosa isolates from cystic fibrosis (CF) patients during a recent clinical trial of inhaled tobramycin. Impermeability, in which bacteria have reduced susceptibility to all aminoglycosides, was the predominant mode of resistance in isolates obtained both before and after 6 months of cyclic treatment with tobramycin or placebo administered by aerosol. Enzymatic resistance mechanisms were found in fewer than 10% of resistant isolates. P. aeruginosa from individual patients could be grouped on the basis of genetic relatedness. When enzymatic resistance was involved, all isolates in a group had elevated tobramycin MICs. When impermeability occurred, MICs of a genotypic group varied from susceptible to resistant. These findings suggest that impermeability resistance occurs in only a fraction of the P. aeruginosa population in lungs of persons with CF and that this form of resistance arises by a process involving multiple small changes in MIC.
More than an interface: scsi vs. ata (2003)

This paper sets out to clear up a misconception prominent in the storage community today, that SCSI disc drives and IDE (ATA) disc drives are the same technology internally, and differ only in their external interface and in their suggested retail price. The two classes of drives represent two different product lines aimed at two different markets. In fact, both classes contain a range of products that address a variety of features and usage patterns beyond simply the interface used to talk to the device. The target market and final product specification are taken into account from the earliest design decision through the manufacturing and testing process. This paper attempts to clarify the differences by illuminating some of these design choices and their consequences on final device characteristics. This will hopefully allow the community to build better storage systems with better knowledge of the trade-offs being made and the performance characteristics that result.
Characterization of the Schizosaccharomyces pombe ral2 gene implicated in activation of the ras1 gene product. (1989)

Mutations in the Schizosaccharomyces pombe ral2 gene cause a phenotype indistinguishable from that of the ras1-defective mutant. Using cloned ral2 DNA, we disrupted the chromosomal gene. The disruptants showed the same phenotype as the original ral2 isolates, i.e., they had spherical cells, had no detectable mating activity, and exhibited no response to the mating pheromone, but their vegetative growth was apparently normal. Sequence analysis of the ral2 gene suggests that it encodes a polypeptide of 611 amino acid residues whose predicted amino acid sequence shows no strong homology to any known protein. Either multiple copies or even a single copy of the ras1Val-17 allele, which is an activated form of ras1, restored rodlike cell morphology and ability to respond to the mating factor to ral2 mutants. These results suggest that the ral2 and ras1 gene products interact intimately and that the ral2 gene product is involved in activation of the ras1 protein in S. pombe.
Frozen and freeze‐dried solvent/detergent treated plasma: Two different pharmaceutical formulations with comparable quality (2022)

The two pharmaceutical forms of OctaplasLG (frozen and freeze-dried) have comparable biochemical quality. Key features of OctaplasLG Lyo are rapid reconstitution time and storage flexibility, which may improve logistics and utilization, and have particular advantages in emergency situations and pre-hospital settings.
Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes (2009)

We have developed a protocol to assemble in one step and one tube at least nine separate DNA fragments together into an acceptor vector, with 90% of recombinant clones obtained containing the desired construct. This protocol is based on the use of type IIs restriction enzymes and is performed by simply subjecting a mix of 10 undigested input plasmids (nine insert plasmids and the acceptor vector) to a restriction-ligation and transforming the resulting mix in competent cells. The efficiency of this protocol allows generating libraries of recombinant genes by combining in one reaction several fragment sets prepared from different parental templates. As an example, we have applied this strategy for shuffling of trypsinogen from three parental templates (bovine cationic trypsinogen, bovine anionic trypsinogen and human cationic trypsinogen) each divided in 9 separate modules. We show that one round of shuffling using the 27 trypsinogen entry plasmids can easily produce the 19,683 different possible combinations in one single restriction-ligation and that expression screening of a subset of the library allows identification of variants that can lead to higher expression levels of trypsin activity. This protocol, that we call 'Golden Gate shuffling', is robust, simple and efficient, can be performed with templates that have no homology, and can be combined with other shuffling protocols in order to introduce any variation in any part of a given gene.
Progress towards butyrate-producing pharmabiotics: Butyricicoccus pullicaecorum capsule and efficacy in TNBS models in comparison with therapeutics (2013)

We read with interest the commentary of Philippe Marteau1 on our study2 in which the author rightly questions the therapeutic value of butyrate-producing bacteria as pharmabiotics in humans because of their difficulty to grow in vitro. While indeed lactic acid bacteria are easy to grow but seem to have limited efficacy, the butyrate-producing bacteria from Clostridium cluster IV and XIVa are promising candidates as pharmabiotics, provided that the strains can be cultured and formulated in a stable way. Butyricicoccus pullicaecorum easily grows under anaerobic conditions in M2GSC medium reaching 108 cfu/mL after 24 h incubation. Our group further evaluated the survival and viability of B pullicaecorum in hydroxypropylmethylcellulose (HPMC) capsules after they were anaerobically lyophilised in horse serum supplemented with 7.5% trehalose and 1 mg/mL cysteine HCl and only observed a reduction of 1 log after 7 months. Now, after 15 months of storage at 4°C, still 107 …
Gene activation by recruitment of the RNA polymerase II holoenzyme. (1996)

The single amino acid "P" (potentiator) mutation in the holoenzyme component GAL11 creates an interaction between that protein and the dimerization region of GAL4. That interaction triggers strong gene activation when the GAL4 fragment is tethered to DNA. Here we show that, among a series of variants of the GAL4 dimerization region and different GAL11P alleles, the strength of the interaction as quantitated in vitro correlates with the degree of activation in vivo; swapping the protein fragments bearing the GAL4 dimerization region and the GAL11P mutation such that the latter is tethered to DNA and the former is attached to the holoenzyme does not diminish gene activation; gene activation in this system is squelched by overproduction of either a fragment bearing the GAL4 dimerization region or a fragment of GAL11 bearing a P mutation; and neither GAL11 nor GAL11P is a target of an acidic activating region. These results argue that the GAL4-GAL11P interaction triggers gene activation simply by recruiting the holoenzyme to DNA. Consistent with this view, we also show that fusion of LexA to another holoenzyme component, SRB2, creates an activator, and that an SRB2 mutant predicted on genetic grounds to interact especially efficiently with a holoenzyme containing a specific mutant form of polymerase also activates more efficiently when tethered to DNA.
Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group (1998)

The Bacillus cereus group comprises the four valid species Bacillus cereus, Bacillus mycoides, Bacillus thuringiensis and bacillus anthracis. Some isolates of B. cereus are known to be psychrotolerant (growth at 7 degrees C or below). Here, specific sequence differences are described between the 16S rDNA, the 23S rDNA, the 16S-23S rDNA spacer region and the genes of the major cold-shock protein homologue cspA in a variety of psychrotolerant and mesophilic B. cereus and B. mycoides strains. Randomly amplified polymorphic DNA analysis using three different primers clearly separated psychrotolerant strains of both species from the rest of the B. cereus group, as did inverse PCR patterns of the rDNA operons. These data strongly support a hitherto unrecognized fifth sub-group within the B. cereus species group comprising psychrotolerant, but not mesophilic, B. cereus strains. Despite the latter finding, the DNA sequences investigated exhibited a high degree of sequence similarity indicating a close relationship between the species of the B. cereus group. Considering the unusual importance of B. cereus in both food poisoning and food spoilage and to avoid merging all species of the group, a new species, Bacillus weihenstephanensis sp. nov., comprising psychrotolerant 'cereus' strains, is proposed. Isolates of the new species grow at 4-7 degrees C but not at 43 degrees C and can be identified rapidly using rDNA or cspA targeted PCR. The type strain is B. weihenstephanensis WSBC 10204T (= DSM 11821T).
Use of micro Raman spectroscopy for the quantitative determination of polyethylene density using partial least‐squares calibration (1995)

Abstract A series of polyethylene samples were analysed using a micro Raman system. The data were analysed using a commercial partial least‐squares package and correlated with the polymer density. A correlation coefficient of up to 0.98 was obtained, depending on the spectral region used. A standard error of prediction of 2.15 kg m −3 was obtained and the densities of ‘blind’ samples were predicted with good accuracy.
Transcriptome Profiling of Human and Murine ESCs Identifies Divergent Paths Required to Maintain the Stem Cell State (2005)

Human embryonic stem cells (hESCs) are an important source of stem cells in regenerative medicine, and much remains unknown about their molecular characteristics. To develop a detailed genomic profile of ESC lines in two different species, we compared transcriptomes of one murine and two different hESC lines by massively parallel signature sequencing (MPSS). Over 2 million signature tags from each line and their differentiating embryoid bodies were sequenced. Major differences and conserved similarities between species identified by MPSS were validated by reverse transcription polymerase chain reaction (RT-PCR) and microarray. The two hESC lines were similar overall, with differences that are attributable to alleles and propagation. Human-mouse comparisons, however, identified only a small (core) set of conserved genes that included genes known to be important in ESC biology, as well as additional novel genes. Identified were major differences in leukemia inhibitory factor, transforming growth factor-beta, and Wnt and fibroblast growth factor signaling pathways, as well as the expression of genes encoding metabolic, cytoskeletal, and matrix proteins, many of which were verified by RT-PCR or by comparing them with published databases. The study reported here underscores the importance of cross-species comparisons and the versatility and sensitivity of MPSS as a powerful complement to current array technology.
New Class of Inhibitors of Amyloid-β Fibril Formation (2002)

The amyloid hypothesis suggests that the process of amyloid-beta protein (Abeta) fibrillogenesis is responsible for triggering a cascade of physiological events that contribute directly to the initiation and progression of Alzheimer's disease. Consequently, preventing this process might provide a viable therapeutic strategy for slowing and/or preventing the progression of this devastating disease. A promising strategy to achieve prevention of this disease is to discover compounds that inhibit Abeta polymerization and deposition. Herein, we describe a new class of small molecules that inhibit Abeta aggregation, which is based on the chemical structure of apomorphine. These molecules were found to interfere with Abeta1-40 fibrillization as determined by transmission electron microscopy, Thioflavin T fluorescence and velocity sedimentation analytical ultracentrifugation studies. Using electron microscopy, time-dependent studies demonstrate that apomorphine and its derivatives promote the oligomerization of Abeta but inhibit its fibrillization. Preliminary structural activity studies demonstrate that the 10,11-dihydroxy substitutions of the D-ring of apomorphine are required for the inhibitory effectiveness of these aporphines, and methylation of these hydroxyl groups reduces their inhibitory potency. The ability of these small molecules to inhibit Abeta amyloid fibril formation appears to be linked to their tendency to undergo rapid autoxidation, suggesting that autoxidation product(s) acts directly or indirectly on Abeta and inhibits its fibrillization. The inhibitory properties of the compounds presented suggest a new class of small molecules that could serve as a scaffold for the design of more efficient inhibitors of Abeta amyloidogenesis in vivo.
Identification of a Regulated Alkaline Phosphatase, a Cell Surface-Associated Lipoprotein, inMycobacterium smegmatis (2003)

Although alkaline phosphatases are common in a wide variety of bacteria, there has been no prior evidence for alkaline phosphatases in Mycobacterium smegmatis. Here we report that transposon insertions in the pst operon, encoding homologues of an inorganic phosphate transporter, leads to constitutive expression of a protein with alkaline phosphatase activity. DNA sequence analysis revealed that M. smegmatis does indeed have a phoA gene that shows high homology to other phoA genes. The M. smegmatis phoA gene was shown to be induced by phosphate starvation and thus negatively regulated by the pst operon. Interestingly, the putative M. smegmatis PhoA has a hydrophobic N-terminal domain which resembles a lipoprotein signal sequence. The M. smegmatis PhoA was demonstrated to be an exported protein associated with the cell surface. Furthermore, immunoprecipitation of PhoA from [(14)C]acetate-labeled M. smegmatis cell lysates demonstrated that this phosphatase is a lipoprotein.
Tissue distribution of HRF20, a novel factor preventing the membrane attack of homologous complement, and its predominant expression on endothelial cells in vivo. (1990)

A 20,000 molecular weight (MW) homologous restriction factor (HRF20), detected by 1F5 monoclonal antibody (mAb), is present on blood cell surfaces and inhibits the terminal stage of the formation of membrane attack complexes by homologous complement activation. The tissue distribution of HRF20 was studied by immunohistochemical analysis using 1F5. HRF20 was predominantly expressed on endothelial cells of systemic arteries, veins and capillaries, as well as on the surface of cultured human umbilical vein endothelial cells. HRF20 was also detected, to a lesser extent, on the Schwann sheath of peripheral nerve fibres, ependymal cells and certain epithelial cells such as acinar cells of the salivary gland, bronchial epithelium, renal tubules and squamous epithelium. The distribution pattern of HRF20 differed somewhat from that of decay-accelerating factor (DAF), which is another membrane inhibitor of homologous complement activation.