gebhart/patrepeval huggingface dataset:
Abstract 5169: Roles of lipogenesis in cancer stem-like cells at early stage of breast cancer (2012)

Abstract Ductal carcinoma in situ (DCIS) is considered an early stage of breast cancer and it is the precursor of invasive breast carcinoma. However, the transition from normal breast epithelial cells to DCIS is still not clearly elucidated. In order to determine the role of lipogenesis in normal to DCIS transition, we investigated the roles of SREBP1, a major transcription regulator of lipogenesis and its downstream lipogenic genes such as ACLY, ACC1 and FAS, by isolating cancer stem-like cells (CSCs) from DCIS.com cell line which forms typical DCIS lesions in animals by using the well-established cell surface markers, CD24−/CD44+/ESA+. We found that lipid synthesis was significantly upregulated in CSCs from DCIS.com in contrast to the corresponding population from normal breast epithelial cells (MCF10A). Furthermore, we found that this elevation of lipogenesis is indeed caused by the overexpression of SREBP1 which co-ordinately induces the overexpression of the downstream lipogenic genes. The CSCs obtained from DCIS.com were also found to be more tumorigenic than the parental cells as shown by the limiting dilution analysis. To determine the role of elevated level of SREBP1 and lipogenesis in the transition of normal breast epithelial cells to DCIS phenotype, we overexpressed SREBP1 in MCF10A and examined the transforming properties. Our in vitro data showed that MCF10A-SREBP1 cells indeed expressed a significantly higher level of SREBP1 and other lipogenic genes and this elevated level of lipogenesis resulted in the increased cell proliferation, increased mammospheres forming ability and enhanced cellular growth in 3D culture. These data suggest that increased lipogenesis in breast CSCs plays critical roles in DCIS formation. We also examined the effects of Resveratrol on CSCs from DCIS.com. Resveratrol significantly reduced the total lipid content by inhibiting SREBP1 and in turn other lipogenic genes and induced a series of pro-apoptotic genes such as DAPK2 and BNIP3 causing the death of CSCs from DCIS. The mammosphere forming ability of CSCs from DCIS was also blocked by Resveratrol. We also observed that Resveratrol indeed significantly suppressed the formation of DCIS by inhibiting lipogenesis and by upregulating DAPK2 and BNIP3 in our animal model of human DCIS. Collectively, our results indicate that lipogenic genes ACLY, ACC-1, FAS and SREBP1 are significantly up regulated in early stage of breast tumorigenesis and they confer proliferative and growth advantages to these cells. Lipogenesis targeting effect of Resveratrol on CSCs from DCIS provides us with a strong rationale to use this agent for chemo-prevention against DCIS. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5169. doi:1538-7445.AM2012-5169
The Role of Participation in Systems. (2000)

ABSTRACT The use of participational approaches to system design has been debated for a number of years. In some situations it seems that participational approaches are not a suitable or practical method by which to design an Information System or to analyse a problem. Within this paper we describe a framework in which participation plays an active and effective role and describe a method that was used to effectively design information systems and implement computer security countermeasures. Keywords: participational approach, SIM-ETHICS, Information System.
Using droplet-based microfluidics to improve the catalytic properties of RNA under multiple-turnover conditions (2015)

In vitro evolution methodologies are powerful approaches to identify RNA with new functionalities. While Systematic Evolution of Ligands by Exponential enrichment (SELEX) is an efficient approach to generate new RNA aptamers, it is less suited for the isolation of efficient ribozymes as it does not select directly for the catalysis. In vitro compartmentalization (IVC) in aqueous droplets in emulsions allows catalytic RNAs to be selected under multiple-turnover conditions but suffers severe limitations that can be overcome using the droplet-based microfluidics workflow described in this paper. Using microfluidics, millions of genes in a library can be individually compartmentalized in highly monodisperse aqueous droplets and serial operations performed on them. This allows the different steps of the evolution process (gene amplification, transcription, and phenotypic assay) to be uncoupled, making the method highly flexible, applicable to the selection and evolution of a variety of RNAs, and easily adaptable for evolution of DNA or proteins. To demonstrate the method, we performed cycles of random mutagenesis and selection to evolve the X-motif, a ribozyme which, like many ribozymes selected using SELEX, has limited multiple-turnover activity. This led to the selection of variants, likely to be the optimal ribozymes that can be generated using point mutagenesis alone, with a turnover number under multiple-turnover conditions, k(ss) cat, ∼ 28-fold higher than the original X-motif, primarily due to an increase in the rate of product release, the rate-limiting step in the multiple-turnover reaction.
Correlation between Optical and Psychophysical Parameters as a Function of Defocus (2002)

Strehl ratio is well correlated with the psychophysical estimates of the visual performance for moderate amount of defocus (within 1 D), whereas the other parameter (log_Vol D-P) is well correlated for larger ranges of defocus (within 2 D) and for different pupil diameters. These results suggest that optical measurements could be used for clinical testing of ophthalmic optics.
Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering (2011)

High-throughput sequencing of 16S rRNA genes has increased our understanding of microbial community structure, but now even higher-throughput methods to the Illumina scale allow the creation of much larger datasets with more samples and orders-of-magnitude more sequences that swamp current analytic methods. We developed a method capable of handling these larger datasets on the basis of assignment of sequences into an existing taxonomy using a supervised learning approach (taxonomy-supervised analysis). We compared this method with a commonly used clustering approach based on sequence similarity (taxonomy-unsupervised analysis). We sampled 211 different bacterial communities from various habitats and obtained ∼1.3 million 16S rRNA sequences spanning the V4 hypervariable region by pyrosequencing. Both methodologies gave similar ecological conclusions in that β-diversity measures calculated by using these two types of matrices were significantly correlated to each other, as were the ordination configurations and hierarchical clustering dendrograms. In addition, our taxonomy-supervised analyses were also highly correlated with phylogenetic methods, such as UniFrac. The taxonomy-supervised analysis has the advantages that it is not limited by the exhaustive computation required for the alignment and clustering necessary for the taxonomy-unsupervised analysis, is more tolerant of sequencing errors, and allows comparisons when sequences are from different regions of the 16S rRNA gene. With the tremendous expansion in 16S rRNA data acquisition underway, the taxonomy-supervised approach offers the potential to provide more rapid and extensive community comparisons across habitats and samples.
An Improved Bimolecular Fluorescence Complementation Assay with a High Signal-To-Noise Ratio (2010)

Protein-protein interactions (PPIs) play crucial roles in various biological processes. Among biochemical, genetic, and imaging approaches that have been used for the study of PPIs, visualization of PPIs in living cells is the key to understanding their cellular functions. The bimolecular fluorescence complementation (BiFC) assay represents one of these imaging tools for direct visualization of PPIs in living cells. The BiFC assay is based on the structural complementation of two nonfluorescent N- and C-terminal fragments of a fluorescent protein when they are fused to a pair of interacting proteins. Although over 10 different fluorescent proteins have been used for BiFC assays, the two nonfluorescent fragments from all of these fluorescent proteins can spontaneously self-assemble, which contributes to background fluorescence and decreases the signal-to-noise (S/N) ratio in the BiFC assay. Here we report the identification of a mutation, I152L, that can specifically reduce self-assembly and decrease background fluorescence in a Venus-based BiFC system. This mutation allows a 4-fold increase in the S/N ratio of the BiFC assay in living cells. This improved Venus-based BiFC system will facilitate PPI studies in various biological research fields.
A generic graph-based multidimensional recommendation framework and its implementations (2012)

As the volume of information on the Web is explosively growing, recommender systems have become essential tools for helping users to find what they need or prefer. Most existing systems are two-dimensional in that they only exploit User and Item dimensions and perform a typical form of recommendation 'Recommending Item to User'. Yet, in many applications, the capabilities of dealing with multidimensional information and of adapting to various forms of recommendation requests are very important. In this paper, we take a graph-based approach to accomplishing such requirements in recommender systems and present a generic graph-based multidimensional recommendation framework. Based on the framework, we propose two homogeneous graph-based and one heterogeneous graph-based multidimensional recommendation methods. We expect our approach will be useful for increasing recommendation performance and enabling flexibility of recommender systems so that they can incorporate various user intentions into their recommendation process. We present our research result that we have reached and discuss remaining challenges and future work.
Tumor glycolysis as a target for cancer therapy: progress and prospects (2013)

Altered energy metabolism is a biochemical fingerprint of cancer cells that represents one of the "hallmarks of cancer". This metabolic phenotype is characterized by preferential dependence on glycolysis (the process of conversion of glucose into pyruvate followed by lactate production) for energy production in an oxygen-independent manner. Although glycolysis is less efficient than oxidative phosphorylation in the net yield of adenosine triphosphate (ATP), cancer cells adapt to this mathematical disadvantage by increased glucose up-take, which in turn facilitates a higher rate of glycolysis. Apart from providing cellular energy, the metabolic intermediates of glycolysis also play a pivotal role in macromolecular biosynthesis, thus conferring selective advantage to cancer cells under diminished nutrient supply. Accumulating data also indicate that intracellular ATP is a critical determinant of chemoresistance. Under hypoxic conditions where glycolysis remains the predominant energy producing pathway sensitizing cancer cells would require intracellular depletion of ATP by inhibition of glycolysis. Together, the oncogenic regulation of glycolysis and multifaceted roles of glycolytic components underscore the biological significance of tumor glycolysis. Thus targeting glycolysis remains attractive for therapeutic intervention. Several preclinical investigations have indeed demonstrated the effectiveness of this therapeutic approach thereby supporting its scientific rationale. Recent reviews have provided a wealth of information on the biochemical targets of glycolysis and their inhibitors. The objective of this review is to present the most recent research on the cancer-specific role of glycolytic enzymes including their non-glycolytic functions in order to explore the potential for therapeutic opportunities. Further, we discuss the translational potential of emerging drug candidates in light of technical advances in treatment modalities such as image-guided targeted delivery of cancer therapeutics.
Performance Evaluation of Three-Phase Grid-Connected Photovoltaic Inverters Using Electrolytic or Polypropylene Film Capacitors (2014)

In grid-connected photovoltaic (PV) power stations, improving the life expectancy and long-term reliability of three-phase PV inverters is urgently needed to match the significantly higher lifetime of the PV modules. A key contribution toward such improvement is replacing the conventional electrolytic film capacitors by metallized polypropylene film ones. This paper presents a detailed evaluation of a conventional three-phase grid-connected PV inverter performance when replacing the electrolytic capacitor with a minimum value of metallized polypropylene film capacitor. Although the minimum dc bus capacitance leads to higher voltage ripples, such ripples were found to be within acceptable limits to operate the inverter satisfactorily. Simulation and experimental results are presented for a 5-kW grid-connected inverter prototype with a nominal dc voltage of 457 V to confirm the theoretical considerations.
Modelling of a microfluid ultrasonic particle separator (2006)

Particles within an ultrasonic standing wave experience an acoustic force causing the particles to\nmove to certain positions within the acoustic field. This phenomenon can be used to manipulate\nparticles and so provides a means to separate, concentrate or trap particles, cells or spores. The\nwork described is applied to a micro-engineered flow-through device for processing small samples\nand incorporates a fluid filled chamber of depth typically between 100 and 200μm, and therefore\napproaches microfluidic dimensions. The successful design and subsequent performance of such\ndevices rely on the predictability of particle trajectories which are influenced predominantly by\nacoustic and fluid flow fields. Therefore, the majority of this research seeks an understanding of\nthe nature of these fields and, in turn, reliable simulation of particle trajectories.\nComputational fluid dynamics (CFD) modelling is used to develop a robust 2-dimensional\nmodel of the device’s microchannels and is used to predict the presence of eddy regions, associated\nwith the etch fabrication techniques, which are likely to disrupt the separation process. Based on\na geometric study, simulations and subsequent test results on a fabricated device have revealed\ngeometric modifications which minimise these eddy flows and promote the existence of laminar\nflow within the main channel of the device.\nFinite element analysis (FEA) provides a method to investigate the 2-dimensional characteristics\nof the acoustic field and reveals variations in acoustic pressure across the width of the device,\ngiving rise to lateral radiation forces frequently reported in similar ultrasonic devices. This work\ninvestigates acoustic enclosure modes in 2 or 3-dimensions as a possible cause of these lateral\nvariations, with modelled results matching well with experiment.\nA particle force model has also been developed which predicts the motion of particles through\nthe device, and by which concentration and separation performance may be calculated. This tool is\nused to investigate acoustic design, operating conditions and separation performance for both the\nmicro-engineered device and a device based on a quarter-wavelength, providing valuable insight\ninto various trends observed.\nThe novelty in this work is the application of macro-scale numerical techniques to microengineered\nultrasonic particle manipulators and the execution of an extensive analysis of the design\nand operation of such devices. These analyses have demonstrated, and therefore have explained,\nvarious phenomena associated with the fluid and acoustic fields, and how they influence particle\nseparation performance. The development of similar devices can be aided by the use of the\nnumerical simulation methods featured throughout this thesis.
An Effective Procedure for the Acylation of Azaindoles at C-3 (2002)

Conditions for attachment of acetyl chloride, benzoyl chloride, and chloromethyl oxalate to the 3-position of 4-, 5-, 6-, or 7-azaindoles were explored. Best results were achieved with an excess of AlCl(3) in CH(2)Cl(2) followed by the addition of an acyl chloride at room temperature.
Mack Forster Award Lecture Receptor nuclear medicine: vasointestinal peptide and somatostatin receptor scintigraphy for diagnosis and treatment of tumour patients (1997)

The multiple aspects of radioligand-receptor interactions do not only show a major impact of certain cell surface-bound receptors in the pathophysiology of human disease: the concept of radioligand-receptor interactions has also been extended to the clinic. In particular, naturally occurring peptides, when radiolabelled, are clinically useful for the imaging diagnosis of human disease and have future implications for the treatment of tumour expressing certain target receptors using radiolabelled peptide tracers. The finding that receptors for VIP (vasoactive intestinal peptide) and SST (somatostatin) are overexpressed on tumour cells presents a breakthrough into this direction. Recent data indicate that [123I]-VIP receptor scintigraphy is clinically useful for the in vivo localization of small primary adenocarcinomas, liver metastases and certain endocrine tumours of the gastrointestinal tract. After the successful clinical introduction of the SST analogues [123I]-Tyr3-octreotide and [111In]-DTPA-D-Phe1-octreotide for localization diagnosis of neuroendocrine tumours in 1989, P829, labelled with the more cost-effective radionuclide 99mTc, nowadays promises to be a potential novel diagnostic imaging agent for tumours expressing SST/VIP receptors. Furthermore, the novel SST analogue [90Y]-MAURITIUS is entering the clinic for treatment of VIP/SST receptor-expressing tumours.
An objective measurement of brace usage for the treatment of adolescent idiopathic scoliosis (2010)

Effectiveness of orthotic treatment for scoliosis depends on how much time and how well the orthosis is worn. Questionnaires and clinical judgment are subjective methods to wear compliance. Even though using a temperature sensor can objectively record how long the orthosis has been used, it may not be able to answer the orthosis effectiveness without knowing the wear tightness. Custom made thoracolumbosacral orthoses (TLSO) were instrumented with low power wireless data acquisition systems to measure the time and loads imposed by the pressure pad during daily activities. Force measurements were recorded at 1 sample/min and the system was able to record data up to 4 months without patient-involvement. Ten subjects (9F, 1M), age between 9 and 13.5 years, average 11.6±1.3 years, who prescribed a new TLSO and full-time brace wear were took part in this study over 4.4±1.0 months. Long-term logging of loads within a spinal orthosis is a reliable method to measure compliance objectively. The monthly quantity of brace wear ranged from 33% to 82%, average 60.0±4.3%. The monthly average loads imposed by the pressure pads varied from 39% to 78% relative to the reference level, average 64.3±4.6%. There was a statistically significant decrease in force, but increase in wear time over the period after the brace fitting session. This information may help to better understand the effectiveness of bracing and to predict the brace treatment outcomes.
In Vitro and in Vivo Imaging Studies of a New Endohedral Metallofullerene Nanoparticle (2006)

The new functionalized trimetallic nitride endohedral metallofullerene species Gd(3)N@C(80)[DiPEG5000(OH)(x)] is an effective proton relaxation agent, as demonstrated with in vitro relaxivity and MR imaging studies, in infusion experiments with agarose gel and in vivo rat brain studies simulating clinical conditions of direct intraparenchymal drug delivery for the treatment of brain tumors.
DNA Repair in Humans (1995)

DNA repair is an important molecular defense system against agents that cause cancer, degenerative diseases, and aging. Several repair systems in humans protect the genome by repairing modified bases, DNA adducts, cross links, and double strand breaks. These repair systems, base excision, nucleotide excision, and recombination, are intimately connected to transcription and to cell cycle checkpoints. In addition, genotoxic stress induces a set of cellular reactions mediated by the p53 tumor suppressor and the Ras oncogene. These genotoxic response reactions may help the cell survive or enter apoptosis. Damage-response reactions may be utilized as targets of anticancer chemotherapy.
Penicillin-Binding Proteins and Cell Wall Composition in β-Lactam-Sensitive and -Resistant Strains of Staphylococcus sciuri (2007)

A close homologue of the acquired Staphylococcus aureus mecA gene is present as a native gene in Staphylococcus sciuri. We determined the patterns of penicillin-binding proteins (PBPs) and the peptidoglycan compositions of several S. sciuri strains to explore the functions of this mecA homologue, named pbpD, in its native S. sciuri environment. The protein product of pbpD was identified as PBP4 with a molecular mass of 84 kDa, one of the six PBPs present in representatives of each of three subspecies of S. sciuri examined. PBP4 had a low affinity for nafcillin, reacted with a monoclonal antibody raised against S. aureus PBP2A, and was greatly overproduced in oxacillin-resistant clinical isolate S. sciuri SS37 and to a lesser extent in resistant laboratory mutant K1M200. An additional PBP inducible by oxacillin and corresponding to S. aureus PBP2A was identified in another oxacillin-resistant clinical isolate, S. sciuri K3, which harbors an S. aureus copy of mecA. Oxacillin resistance depended on the overtranscribed S. sciuri pbpD gene in strains SS37 and K1M200, while the resistance of strain K3 depended on the S. aureus copy of mecA. Our data provide evidence that both S. aureus mecA and S. sciuri pbpD can function as resistance determinants in either an S. aureus or an S. sciuri background and that the protein products of these genes, S. aureus PBP2A and S. sciuri PBP4, can participate in the biosynthesis of peptidoglycan, the muropeptide composition of which depends on the bacterium "hosting" the resistance gene.
Draft Genome Sequence of the Clinical Isolate Acinetobacter nosocomialis Strain M2 (2013)

We report the 3.78-Mbp high-quality draft assembly of the genome from a clinical isolate of Acinetobacter nosocomialis called strain M2 (previously known as Acinetobacter baumannii strain M2).
Visualizing Implanted Tumors in Mice with Magnetic Resonance Imaging Using Magnetotactic Bacteria (2009)

Magnetotactic bacteria can produce positive magnetic resonance imaging contrast and colonize mouse tumor xenografts, providing a potential tool for improved magnetic resonance imaging visualization in preclinical and translational studies to track cancer.
The impact of sex and sex hormones on lung physiology and disease: lessons from animal studies (2007)

Numerous animal studies have revealed significant effects of sex and sex hormones on normal lung development, lung physiology, and various lung diseases. The primary goal of this review is to summarize knowledge to date on the effects of sex and sex hormones on lung development, physiology, and disease in animals. Specific emphasis will be placed on fibrosis, allergic airway disease, acute lung injury models, respiratory infection, and lung toxicology studies.