gebhart/patrepeval huggingface dataset:
Potentiation of chemotherapeutic drugs by energy metabolism inhibitors 2‐deoxyglucose and etomoxir (2008)

Inhibition of energy production as a strategy for potentiation of anticancer chemotherapy was investigated using 1 glycolysis inhibitor and 1 fatty acid beta-oxidation inhibitor-2-deoxyglucose and etomoxir, respectively, both known to be clinically well tolerated. Eighteen anticancer drugs were screened for potentiation by these inhibitors. 2-deoxyglucose potentiated acute apoptosis (24 hr) induced mainly by some, but not all, genotoxic drugs, whereas etomoxir had effect only on cisplatin. By contrast, etomoxir did potentiate the overall, 48 hr effects of some genotoxic drugs, and was in addition more efficient than deoxyglucose in potentiating the overall effects of several non-genotoxic drugs. Both types of potentiation were largely lost in the absence of p53. Because cisplatin was potentiated by both energy inhibitors in both types of assay, it was investigated at additional concentrations and over longer time. Both energy inhibitors strongly potentiated non-apoptotic concentrations of cisplatin in p53-wildtype as well as in p53-deficient, cisplatin-resistant HCT-116 colon carcinoma cells. Reduced ATP levels correlated with, but were not sole determinants, the antiproliferative effects. We conclude that the long-term effects of cisplatin potentiation are important and either p53-independent or improved by a lack of p53. We also conclude that although the potentiated drugs as yet have no obvious mechanistic factor in common, the strategy holds promise with genotoxic as well non-genotoxic anticancer drugs.
Fermentor temperature as a tool for control of high-density perfusion cultures of mammalian cells (1997)

Temperature is a key environmental variable whose potential in animal cell fermentor optimization is not yet fully utilized. The scarce literature data suggests that reduced fermentor temperature results in an improved viability and shear resistance, higher cell density and titer in batch cultures, and reduction in glucose/lactate metabolism. Due to the arrest of the cells in the G1 phase, the specific growth rate was found to decrease at temperatures below 37.0 degrees C. The response of the specific production rate was cell line dependent: in some cases it increased 2-to-3-fold, but decreased in other cases. The controlable slowdown of cell metabolism at lower temperature can be used in optimization of perfusion mammalian cell cultures with several potential advantages, including higher cell density in oxygen limited reactors, lower perfusion rate, improved product quality, simplified pH control, and others. To evaluate this strategy, a series of long-term experiments in 15 L perfusion bioreactors culturing recombinant hamster cells at 20.0 x 10(6) cells/mL were conducted. The temperature was changed over a range of set points, and maintained at each of these for a long period of time. Steady state process data was collected and analyzed. The effect of temperature on the following characteristics of the perfusion process was studied: cell growth, glucose/lactate metabolism, glutamine/ammonia metabolism, cell respiration, cell density at constant oxygen transfer rate, proteolytic activity, and product quality (glycosylation and molecule fragmentation). The results suggest that temperature is a variable with a significant potential in optimization of perfusion cultures. Properly selected temperature set point will contribute to the overall improvement of process performance. (c) 1997 John Wiley & Sons, Inc. Biotechnol Bioeng 55: 328-338, 1997.
Performance of the APTIMA Combo 2 Assay for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Female Urine and Endocervical Swab Specimens (2003)

The greater sensitivity of nucleic acid amplification tests (NAATs) for Chlamydia trachomatis and Neisseria gonorrhoeae permits the use of urine and other noninvasive specimens, which can increase the reach and decrease the costs of public health screening programs aimed at controlling these infections. This study evaluated the performance of the APTIMA Combo 2 assay, a multiplex assay based on the transcription-mediated amplification reaction, for the simultaneous detection of both pathogens in endocervical swab and urine specimens from females. Combo 2 assay results were compared with patient infected status, which were available by using other commercial NAATs. Sensitivity and specificity for C. trachomatis were 94.2 and 97.6%, respectively, in swabs and 94.7 and 98.9%, respectively, in first-catch urine (FCU). Sensitivity and specificity for N. gonorrhoeae were 99.2 and 98.7%, respectively, in swabs and 91.3 and 99.3%, respectively, in FCU. The assay reliably detected both infections in coinfected patients. The Combo 2 assay can be recommended for use with endocervical swab and urine specimens from females, especially for screening tests for asymptomatic women in sexually transmitted disease surveillance programs. This Food and Drug Administration-cleared assay can be a useful tool in efforts to reduce the prevalence and incidence of C. trachomatis and N. gonorrhoeae infections in sexually active women and to prevent their costly and serious sequelae.
Danazol Suppresses Both Spontaneous and Activated Human Lymphocyte‐Mediated Cytotoxicity (1992)

Danazol is an effective drug in the treatment of endometriosis. Previous reports suggest that it can act by influencing the immune system. Thus, in this study we evaluated whether danazol is able to affect the expression of natural and activated cytotoxicity by human peripheral blood lymphocytes (PBL). A cytotoxicity assay by 51Cr release was performed to determine the effect of danazol on lymphocyte cytotoxic response toward an erythroleukemic cell line (K562). A significant suppression of spontaneous cytotoxicity was observed when lymphocytes were pretreated for 18 h with danazol at the concentration of 5 x 10(-6) M. In addition, danazol could significantly inhibit both IL-2- and INF alpha-activated cytotoxicity at the concentration of 10(-5) M. Following 18 h exposure to danazol, PBL were able to completely recover their spontaneous but not activated cytotoxic potential upon further in vitro incubation (18 h) in absence of the drug. The biological significance of danazol as an inhibitor of immune function under experimentally defined conditions is discussed in relation to its possible role in vivo.
Compaction of DNA Induced by Like-Charge Protein: Opposite Salt-Effect against the Polymer-Salt-Induced Condensation with Neutral Polymer (2010)

We observed the collapsing transition of a DNA molecule in a crowding environment with a water-soluble negatively charged protein, albumin. We performed fluorescence microscopic observation to monitor the change in the conformation of individual giant DNA molecules. It is found that DNA molecules exhibit compact conformation above critical concentrations of the negatively charged protein. We interpret this transition in terms of depletion interaction, segregation of different polymers driven by excluded volume interaction. Interestingly, coexisting salt causes retardation on the collapsing transition, being opposite to the well-known phenomenon of DNA compaction in a crowding solution of neutral polymer, polymer-salt-induced-condensation of DNA (psi-condensation). The possible biological significance of the transition of higher-order structure on DNA in a concentrated protein solution is discussed in relation to the highly crowded conditions in living cells.
LRFU: a spectrum of policies that subsumes the least recently used and least frequently used policies (2001)

Efficient and effective buffering of disk blocks in main memory is critical for better file system performance due to a wide speed gap between main memory and hard disks. In such a buffering system, one of the most important design decisions is the block replacement policy that determines which disk block to replace when the buffer is full, In this paper, we show that there exists a spectrum of block replacement policies that subsumes the two seemingly unrelated and independent Least Recently Used (LRU) and Least Frequently Used (LFU) policies. The spectrum is called the LRFU (Least Recently/Frequently Used) policy and is formed by how much more weight we give to the recent history than to the older history. We also show that there is a spectrum of implementations of the LRFU that again subsumes the LRU and LFU implementations. This spectrum is again dictated by how much weight is given to recent and older histories and the time complexity of the implementations lies between O(1) (the time complexity of LRU) and O(log(2) n) (the time complexity of LFU), where n is the number of blocks in the buffer, Experimental results from trace-driven simulations show that the performance of the LRFU is at least competitive with that of previously known policies for the workloads we considered.
Scalable color image coding with Matching Pursuit (2004)

AbstractThis paper presents a new scalable and highly exible color imagecoder based on a Matching Pursuit expansion. The Matching Pursuitalgorithm provides an intrinsically progressive stream and the proposedcoder allows us to reconstruct color information from the rst bit received.In order to eciently capture edges in natural images, the dictionary ofatoms is built by translation, rotation and anisotropic re nement of awavelet-like mother function. This dictionary is moreover invariant un-der shifts and isotropic scaling, thus leading to very simple spatial resiz-ing operations. This exibility and adaptivity of the MP coder makesit appropriate for asymmetric applications with heterogeneous end userterminals. 1 Introduction Most visual coding schemes generally rst compress luminance image compo-nents, and then extend coding to color components. They use color spaces withluminance and chrominance channels, where the latter may easily be down-sampled, due to the fact that they carry much less information than the lu-minance component. Moreover, in the classical coding paradigm, decorrelationbetween channels is generally seen as an advantage. However, when a similarstrategy is applied to scalable color image coding, it often causes colors to onlyappear after a certain time, or with important distortion.In this paper, we present a scalable color image coder, based on MatchingPursuit, that codes color information altogether, from the rst information bit.The proposed image representation algorithm takes advantage of the correlationbetweenthe color channels, insteadof tryingto reduceit, as opposed to commoncoding schemes. The Matching Pursuit representation uses anisotropic re ne-ment of wavelet-like mother functions, since such a dictionary has been shownto perform very well at low bit rates for gray scale images and is moreover in-trinsically scalable [1]. The coder then chooses the same basis function for thethree channels, and just recomputes the projection coecient for each channel.Such an algorithm can be thought of as a vector greedy algorithm [2] tryingto simultaneously approximate all three channels. Using a common waveform2
Human islet amyloid polypeptide transgenic mice as a model of non‐insulin‐dependent diabetes mellitus (NIDDM) (1993)

To model islet amyloidogenesis in NIDDM and explore the glucoregulatory role of islet amyloid polypeptide (IAPP), we have created transgenic mice containing a rat insulin-I promoter-human IAPP fusion gene. Expression of human IAPP was localized to the islets of Langerhans, anterior pituitary and brain in transgenic animals; blood IAPP levels were elevated 5-fold while fasting glucose levels remained normal. Amyloid deposits have not been detected in transgenic islets suggesting that other co-existing abnormalities in NIDDM may be required for the formation of islet amyloid. These animals provide a unique model for exploring this hypothesis and other proposed functions of IAPP.
The role of PI3K/AKT, MAPK/ERK and NFκβ signalling in the maintenance of human embryonic stem cell pluripotency and viability highlighted by transcriptional profiling and functional analysis (2006)

Understanding the molecular mechanism by which pluripotency is maintained in human embryonic stem cells (hESC) is important for the development of improved methods to derive, culture and differentiate these into cells of potential therapeutic use. Large-scale transcriptional comparison of the hES-NCL1 line derived from a day 8 embryo with H1 line derived from a day 5 embryo (WiCell Inc.) showed that only 0.52% of the transcripts analysed varied significantly between the two cell lines. This is within the variability range that has been reported when hESC derived from days 5-6 embryos have been compared with each other. This implies that transcriptional differences between the cell lines are likely to reflect their genetic profile rather than the embryonic stage from which they were derived. Bioinformatic analysis of expression changes observed when these cells were induced to differentiate as embryoid bodies suggested that quite a few of the downregulated genes were components of signal transduction networks. Subsequent analysis using western blotting, flow cytometry and antibody arrays implicated components of the PI3K/AKT kinase, MAPK/ERK and NFkappabeta pathways and confirmed that these components are decreased upon differentiation. Disruption of these pathways in isolation using specific inhibitors resulted in loss of pluripotency and/or loss of viability suggesting the importance of such signalling pathways in embryonic stem cell maintenance.
Acidolysis of Wood in Ionic Liquids (2010)

Three wood species including Eucalyptus grandis (E. grandis), Southern pine (S. pine), and Norway spruce thermomechanical pulp (N. spruce TMP) were dissolved in the ionic liquid (IL) 1-allyl-3-methylimidazolium chloride ([Amim]Cl), and then they were pretreated with small amounts of hydrochloric acid, as a function of time. The materials regenerated from the IL solutions were determined to contain significantly higher amounts of lignin than the original wood. Detailed analyses of the recovered IL revealed the presence of typical wood degradation compounds, such as 5-hydroxymethylfurfural, furan-2-carboxylic acid, catechol, methylcatechol, methylguaiacol, acetoguaiacone, and acetol. The acidic pretreatment of these wood species in IL resulted in not only the near-complete hydrolysis of cellulose and hemicelluloses but also in a significant amount of lignin degradation. Aqueous reactions (under identical acid concentrations) showed a remarkably lower efficiency, demonstrating that ILs offer a unique environment for the acid-catalyzed dehydration chemistry, which is known to occur when polysaccharides and/or wood are subjected to an acid treatment.
Stro-1 Positive and Stro-1 Negative Human Mesenchymal Stem Cells Express Different Levels of Immunosuppression. (2005)

Abstract Mesenchymal stem cells (MSC) have been shown to elicit immunosuppressive effect on allogeneic lymphocyte response. However, MSC are heterogeneous and data on the inhibitory abilities of different MSC subsets are lacking. The Stro-1 antigen potentially defines a more pure and more primitive MSC subset We compared the suppressive property of expanded Stro-1+ and Stro-1− MSC when add to mixed lymphocyte reactions (MLR) or to mitogen response assays. Results showed that T lymphocyte proliferation was significantly more inhibited by expanded Stro-1+ (11.0%~63.7% of maximal response) than by expanded stro-1− MSC (35.5%~106% of maximal response) (p&amp;lt;0.01). Results indicated that as few as 1,000 expanded Stro-1+ MSC could induce a similar inhibition of lymphocyte proliferation than 10 times more (10,000 cells) expanded Stro-1− MSC −. Stro-1+ MSC was the main population responsible for T cell inhibition. The expression of genes coding for inhibitors of T-cell activation and proliferation (IL-10, LIF, IDO, TGF-b1, HGF, HLA-G), for adhesion molecules (VCAM, LFA-3), and for chemotactic factors (IL-8, SDF-1) was analysed by semi-quantitative real time RT-PCR in the Stro1+ and Stro1- MSC. Results are expressed as a fold increase in the mRNA level in expanded Stro-1+ compared to Stro-1− MSC. IL-10 (0.24 fold p=0.002) and TGF-β1 (0.43 fold, p=0.03) were down regulated in expanded Stro-1+ compared to Stro-1− MSC. LIF (106 fold, p=0.025), IDO (6130 fold, p=0.04), HGF (24 fold, p=0.01), and HLA-G (260 fold, p= 0.02) were up regulated in expanded Stro-1+ compared to Stro-1− MSC. VCAM-1 and LFA-3 were up regulated in expanded Stro-1+ compared to Stro-1− MSC (28.2 fold, p=0.03 and 298.4 fold, p=0.04 for VCAM-1 and LFA-3 respectively): IL-8 was over expressed in expanded Stro-1+ (4.9 fold, p=0.0015). There was no significant difference between expanded Stro-1+ and Stro-1− MSC for SDF-1. These results suggest that LIF, IDO, HGF, HLA-G inhibitory factors and VCAM1, LFA-3 adhesion molecules are mainly responsible for the different T cell inhibition observed between Stro-1+ and Stro-1− MSC. These findings suggest that in clinics a Stro-1+ pre-selection of MSC might produce a more effective immunosuppression especially for the prevention and the treatment of graft versus host disease.
Markerless EPID image guided dynamic multi-leaf collimator tracking for lung tumors (2013)

Compensation of target motion during the delivery of radiotherapy has the potential to improve treatment accuracy, dose conformity and sparing of healthy tissue. We implement an online image guided therapy system based on soft tissue localization (STiL) of the target from electronic portal images and treatment aperture adaptation with a dynamic multi-leaf collimator (DMLC). The treatment aperture is moved synchronously and in real time with the tumor during the entire breathing cycle. The system is implemented and tested on a Varian TX clinical linear accelerator featuring an AS-1000 electronic portal imaging device (EPID) acquiring images at a frame rate of 12.86 Hz throughout the treatment. A position update cycle for the treatment aperture consists of four steps: in the first step at time t = t0 a frame is grabbed, in the second step the frame is processed with the STiL algorithm to get the tumor position at t = t0, in a third step the tumor position at t = ti + δt is predicted to overcome system latencies and in the fourth step, the DMLC control software calculates the required leaf motions and applies them at time t = ti + δt. The prediction model is trained before the start of the treatment with data representing the tumor motion. We analyze the system latency with a dynamic chest phantom (4D motion phantom, Washington University). We estimate the average planar position deviation between target and treatment aperture in a clinical setting by driving the phantom with several lung tumor trajectories (recorded from fiducial tracking during radiotherapy delivery to the lung). DMLC tracking for lung stereotactic body radiation therapy without fiducial markers was successfully demonstrated. The inherent system latency is found to be δt = (230 ± 11) ms for a MV portal image acquisition frame rate of 12.86 Hz. The root mean square deviation between tumor and aperture position is smaller than 1 mm. We demonstrate the feasibility of real-time markerless DMLC tracking with a standard LINAC-mounted (EPID).
Effects of hormones and growth factors on human mammary epithelial cells in collagen gel culture. (1981)

Studies on growth regulation were performed on normal human mammary epithelial cells obtained from a number of different sources: ( a ) reduction mammoplasties; ( b ) areas away from the primary lesion in mastectomies; and ( c ) colostrums. These cells were embedded inside collagen gels and cultured in Ham's F-12 medium containing serum, insulin, cortisol, cholera toxin, and urine extract or epidermal growth factor. Sustained growth leading to an increase of 10- to 30-fold in cell number over the initial value in 2 to 3 weeks has been accomplished in primary culture. Similar growth was also achieved in secondary culture after passaging the cultures with a split of one to eight. The relative contributions of the supplements to overall growth have been assessed by deletion experiments. The magnitude of effect of deleting any single additive was variable among the samples tested, but, in all cases, omission of any one additive resulted in reduction of the final cell number. This suggests that each of the additives must be involved in the stimulation of growth of normal mammary epithelial cells in culture. The three-dimensional outgrowths derived from single cells and small clumps were of different morphologies. In general, the outgrowth ranged in morphology from a duct-like appearance to a spherical mass. Colostrums gave rise to predominantly spherical mass-type outgrowths, whereas mammoplasties and mastectomies gave rise to more heterogeneous types. These differences in outgrowth morphology may be a reflection of the possibility that different cell types may give rise to different colony shapes. The collagen gel system provides a reproducible and consistent method for sustained three-dimensional growth of human normal mammary epithelial cells in primary culture and has been used to analyze growth regulation as well as morphogenesis in the present study.
Temporal regulation of human cytomegalovirus transcription at immediate early and early times after infection (1981)

The immediate early transcripts of human cytomegalovirus originated from restricted regions of the viral genome. In contrast, transcription at early times was complementary to all regions of the viral genome that were fractionated by restriction endonuclease treatment followed by agarose gel electrophoresis. The viral genome was also extensively transcribed when 2 h of protein synthesis or longer was permitted after infection in permissive cells treated with an inhibitor of viral DNA replication or in nonpermissive cells of animal origin that permit little or no viral DNA replication. The size and in vitro translation products of the cytomegalovirus-specified mRNA's at immediate early and early times after infection were determined. Discrete size classes of virus-specified polyadenylated RNA accumulated on the polyribosomes of cells infected in the presence of an inhibitor of protein synthesis. When 2 or 24 h of protein synthesis occurred after infection, there were changes in the relative abundance of the virus-specified RNAs that accumulated on polyribosomes. Treatment of nonpermissive cells had little effect on the size classes of viral RNA found associated with the polyribosomes at early times after infection. These viral mRNA's were assumed to represent early viral gene expression. In vitro translation of the viral mRNA isolated from polyribosomes at immediate early and early times after infection identified many of the virus-specified gene products and demonstrated (i) a switch from immediate early to early viral gene expression and (ii) a prolonged phase of early viral gene expression. The data also indicated that the initiation of viral RNA synthesis does not depend on the formation of viral protein, but that de novo viral protein synthesis may influence the extent of transcription of the viral genome.
Vector Expansion in a Large Collection. (1992)

This paper investigates whether a completely automatic, statistical expansion technique that uses a general-purpose thesaurus as a source of related concepts is viable for large collection. The retrieval results indicate that the particular expansion technique used here improved the performance of some queries, but degrades the performance of other queries. The variability of the method is attributable to two main factors: the choice of concepts that are expanded and the confounding effects expansion has on cencept weights. Addressing these problems will require both a better method for determining the important concepts of a text and a better method for determining the correct sense of an ambiguous word