gebhart/patrepeval huggingface dataset:
Effects of cisplatin on the induction of apoptosis in proliferating hepatoma cells and nonproliferating immature thymocytes. (1993)

A 2-h exposure of JB1 rat hepatoma cells in late log phase of growth to 50 microM cis-diamminedichloroplatinum (II) (cisplatin) resulted in the asynchronous detachment of cells from the monolayer over 4 days. Detached but not monolayer cells exhibited condensed chromatin and DNA fragmentation, which is indicative of endonuclease activation, the hallmarks of apoptosis in epithelial cells. The number of cisplatin-treated cells identified as apoptotic at any one time was never > 1% of the total cell number present on addition of drug. Two days after drug addition there was a decrease from 85% to 29% cells in G1 phase of the cell cycle, cells in S phase increased from 9% to 18%, and cells in G2/M phase increased from 6% to 51% with respect to untreated cells. Previous studies by Eastman and colleagues demonstrated that cisplatin-induced apoptosis of Chinese hamster ovary cells occurred in the G2 phase of the cell cycle [A. Eastman, Cancer Cells (Cold Spring Harbor), 2: 275-280, 1990]. Continuous exposure of JB1 cells to cycloheximide (1 microM) during and after exposure to cisplatin prevented both drug-induced changes in cell cycle distribution and the engagement of apoptosis. Freshly isolated immature rat thymocytes are known to be exquisitely sensitive to the induction of apoptosis by multiple stimuli including dexamethasone, etoposide, and irradiation. However, no significant increase in the amount of apoptosis above control levels was observed up to 36 h after a 2-h exposure to 50 microM cisplatin. JB1 cells have a doubling time of 24 h, whereas > 90% of immature rat thymocytes are noncycling. The data presented here provide indirect evidence that initiation of cisplatin-induced apoptosis may need to be coupled to a cell cycle-mediated event.
Facile autoplast generation and transformation in Bacillus thuringiensis subsp. kurstaki (1987)

We describe a method for maximizing the rate of conversion of Bacillus thuringiensis subsp. kurstaki vegetative cells to osmotically fragile forms in the absence of exogenously added enzymes. Optimal generation of autoplasts occurred in 50 mM sodium acetate buffer (pH 7.0) at 37 degrees C with 10% (wt/vol) polyethylene glycol as an osmotic stabilizer. The maximum autolytic rate resulted in a conversion of greater than 90% of bacilli to spherical autoplasts in 6 min. Autoplasts regained bacillary morphology upon plating on DM3-G regeneration medium, with reversion frequencies ranging from 1.2 x 10(-1) to 5.3 x 10(-3). The autoplasts could efficiently take up exogenously added plasmid DNA. The presence of plasmids was verified by Southern hybridization analysis.
Achieving predictable performance through better memory controller placement in many-core CMPs (2009)

In the near term, Moore's law will continue to provide an increasing number of transistors and therefore an increasing number of on-chip cores. Limited pin bandwidth prevents the integration of a large number of memory controllers on-chip. With many cores, and few memory controllers, where to locate the memory controllers in the on-chip interconnection fabric becomes an important and as yet unexplored question. In this paper we show how the location of the memory controllers can reduce contention (hot spots) in the on-chip fabric and lower the variance in reference latency. This in turn provides predictable performance for memory-intensive applications regardless of the processing core on which a thread is scheduled. We explore the design space of on-chip fabrics to find optimal memory controller placement relative to different topologies (i.e. mesh and torus), routing algorithms, and workloads.
Surface Initiated Polymerization from Nanoparticle Surfaces (2003)

Abstract The synthesis, characterization, and development of new nanoparticle materials have both scientific and technological significance. Surface initiated polymerization (SIP) from nanoparticle surfaces involves the growth of end‐tethered polymer brushes where the length or thickness can be more than twice the radius of gyration (Rg) compared to a free polymer in solution. Different mechanisms are possible on a variety of initiators, reaction conditions, monomers, and nanoparticles. Important differences to solution and bulk polymerization can be observed where the nanoparticles with grafted initiators behave as macroinitiators. In turn, the development of these materials will allow the preparation of thermodynamically and kinetically stable nanocomposites and colloids. Through the careful use of surface sensitive spectroscopic and microscopic techniques, much has been gained from the direct and in‐situ analysis of grafted polymers on the nanoparticles with regards to the kinetics and mechanism of the polymerization process. Parallels can be drawn to SIP on flat surfaces where surface sensitive spectroscopic and microscopic measurements are complementary to analysis methods for colloidal particles. Thus, this review surveys the different polymerization mechanisms and procedures towards forming core‐shell types of hybrid inorganic–organic polymer nanoscale materials.
Perspectives for the Treatment of Infections with Flaviviridae (2000)

The family Flaviviridae contains three genera: Hepacivirus, Flavivirus, and Pestivirus. Worldwide, more than 170 million people are chronically infected with Hepatitis C virus and are at risk of developing cirrhosis and/or liver cancer. In addition, infections with arthropod-borne flaviviruses (such as dengue fever, Japanese encephalitis, tick-borne encephalitis, St. Louis encephalitis, Murray Valley encephalitis, West Nile, and yellow fever viruses) are emerging throughout the world. The pestiviruses have a serious impact on livestock. Unfortunately, no specific antiviral therapy is available for the treatment or the prevention of infections with members of the Flaviviridae. Ongoing research has identified possible targets for inhibition, including binding of the virus to the cell, uptake of the virus into the cell, the internal ribosome entry site of hepaciviruses and pestiviruses, the capping mechanism of flaviviruses, the viral proteases, the viral RNA-dependent RNA polymerase, and the viral helicase. In light of recent developments, the prevalence of infections caused by these viruses, the disease spectrum, and the impact of infections, different strategies that could be pursued to specifically inhibit viral targets and animal models that are available to study the pathogenesis and antiviral strategies are reviewed.
Ferromagnetic properties of potassium clusters incorporated into zeolite LTA (1993)

Ferromagnetic properties are reported for K clusters incorporated into the \ensuremath{\alpha} cage (supercage) of zeolite LTA. In LTA, \ensuremath{\alpha} cages are arrayed in a simple cubic structure with a lattice constant of 12.3 \AA{}. The average 4s-electron number per cluster, n, is systematically changed from 0.8 to 7.3 by controlling the K loading density. Ferromagnetism is observed for 2--3n6--7. The magnetization shows a peak at n\ensuremath{\sim}5, and the average magnetic moment amounts to 0.24${\mathrm{\ensuremath{\mu}}}_{\mathit{B}}$ per cluster at 100 Oe and 1.7 K. The Curie temperature is n dependent and less than 7 K. Magnetic properties are basically interpreted in terms of the model of itinerant electron ferromagnetism. Narrow energy bands due to the electron transfer between adjacent clusters play an important role in the construction of a model. The magnetic properties exhibit spin-glass and reentrant spin-glass phenomena depending on the K loading density.
OIL: an ontology infrastructure for the Semantic Web (2001)

Researchers in artificial intelligence first developed ontologies to facilitate knowledge sharing and reuse. Ontologies play a major role in supporting information exchange across various networks. A prerequisite for such a role is the development of a joint standard for specifying and exchanging ontologies. The authors present OIL, a proposal for such a standard. Ontologies applied to the World Wide Web are creating the Semantic Web.
E. coli Expression and Purification of Fab Antibody Fragments (2009)

The Fab molecule was the first generated antibody fragment and still dominates basic research and clinical applications. This unit describes the E. coli expression and purification of Fab antibody fragments with and without a His tag, and is designed to yield sufficient protein for the evaluation and characterization of a panel of Fab selected from a Fab library by phage display.
Characterization of common neoantigenic epitopes generated in plasminogen activator inhibitor‐1 after cleavage of the reactive center loop or after complex formation with various serine proteinases (1995)

Plasminogen activator inhibitor-1 (PAI-1), an important risk factor for thrombotic diseases, is a member of the superfamily of serine proteinase inhibitors. To define structural rearrangements occurring during interaction between PAI-1 and its target proteinases we have raised monoclonal antibodies against the PAI-1/t-PA complex. Thirteen out of 401 monoclonal antibodies reacted preferentially with the PAI-1/t-PA complex as compared to free PAI-1 or free t-PA. Detailed characterization revealed the presence of two non-overlapping neoantigenic epitopes in the PAI-1/t-PA complex. Both neoantigenic epitopes were also exposed after complex formation between PAI-1 and either urokinase-type plasminogen activator, plasmin or thrombin as well as after cleavage of the reactive site loop of non-inhibitory substrate type PAI-1 variants. Thus, we have identified two neoantigenic epitopes, localized entirely in PAI-1, and commonly exposed after complex formation of active PAI-1 with various proteinases or after cleavage of substrate PAI-1. These monoclonal antibodies should facilitate further studies on the mechanism of interaction between various PAI-1 forms and its target proteinases.
Evolutionary conservation of sequence and expression of the bHLH protein Atonal suggests a conserved role in neurogenesis (1996)

atonal is a Drosophila proneural gene that belongs to the family of basic helix-loop-helix (bHLH)- containing proteins. It is expressed in the chordotonal organs and photoreceptor cells, and flies that lack Atonal protein are ataxic and blind. Here we report the cloning of atonal homologs from red flour beetle, puffer fish, chicken, mouse, and human. The bHLH domain is conserved throughout evolution, while the entire coding region is highly similar in mammals. Both the chicken and the mouse homologs are expressed early in embryogenesis in the hind brain, and specifically in cells predicted to give rise to the external granular layer of the cerebellum. In addition, these genes are expressed throughout the dorsal part of the spinal cord, in patterns different from those found for other genes, like LH-2 and wnt-1. The mouse homolog (Math1) maps to mouse chromosome 6, and the human homolog (HATH1) to human chromosome 4q22. Two neurological mouse mutants, Lc and chp, were found to map to the vicinity of Math1, but are not caused by mutations in Math1. The evolutionary conservation of this gene and its mRNA expression patterns during embryogenesis suggests that it plays a key role in the development of the vertebrate central nervous system.
Modular Structure of the TIM23 Preprotein Translocase of Mitochondria (2001)

The TIM23 complex mediates import into mitochondria of nuclear encoded preproteins with a matrix-targeting signal. It is composed of the integral membrane proteins Tim17 and Tim23 and the peripheral membrane protein Tim44, which recruits mitochondrial Hsp70 to the sites of protein import. We have analyzed the functions of these constituents using a combined genetic and biochemical approach. Depletion of either Tim17 or Tim23 led to loss of import competence of mitochondria and to a reduction in the number of preprotein-conducting channels. Upon depletion of Tim44, mitochondria also lost their ability to import proteins but maintained normal numbers of import channels. In the absence of Tim44 precursor protein was specifically recognized. The presequence was translocated in a Delta psi-dependent manner across the inner membrane and cleaved by matrix-processing peptidase. However, the preprotein did not move further into the matrix but rather underwent retrograde sliding out of the TIM23 complex. Thus, the TIM23 complex is composed of functionally independent modules. Tim17 and Tim23 are necessary for initiating translocation, whereas Tim44 and mitochondrial Hsp70 are indispensable for complete transport of preproteins and for unfolding of folded domains of preproteins.
Ghrelin Modulates Lateral Amygdala Neuronal Firing and Blocks Acquisition for Conditioned Taste Aversion (2013)

Ghrelin is an orexigenic brain-gut hormone promoting feeding and regulating energy metabolism in human and rodents. An increasing number of studies have reported that ghrelin and its identified receptor, the growth hormone secretagogue receptor 1a (GHS-R1a), produces remarkably wide and complex functions and biological effects on specific populations of neurons in central nervous system. In this study, we sought to explore the in vivo effects of acute ghrelin exposure on lateral amygdala (LA) neurons at the physiological and behavioral levels. In vivo extracellular single-unit recordings showed that ghrelin with the concentration of several nanomolars (nM) stimulated spontaneous firing of the LA neurons, an effect that was dose-dependent and could be blocked by co-application of a GHS-R1a antagonist D-Lys3-GHRP-6. We also found that D-Lys3-GHRP-6 inhibited spontaneous firing of the LA neurons in a dose-dependent manner, revealing that tonic GHS-R1a activity contributes to orchestrate the basal activity of the LA neurons. Behaviorally, we found that microinfusion of ghrelin (12 ng) into LA before training interfered with the acquisition of conditioned taste aversion (CTA) as tested at 24 h after conditioning. Pre-treatment with either purified IgG against GHS-R1a or GHS-R1a antagonist blocked ghrelin's effect on CTA memory acquisition. Ghrelin (12 ng) had no effect on CTA memory consolidation or the expression of acquired CTA memory; neither did it affect the total liquid consumption of tested rats. Altogether, our data indicated that ghrelin locally infused into LA blocks acquisition of CTA and its modulation effects on neuronal firing may be involved in this process.
Evidence that transcriptional activation by p53 plays a direct role in the induction of cellular senescence. (1996)

Wild-type p53 is necessary for the growth arrest of human diploid fibroblasts (HDF) (and many other cell types) at the end of their proliferative lifespan. Although p53 may actively mediate senescence, possibly in response to telomere erosion, it is however equally possible that it is merely a permissive factor required for response to some other inducer. To address this question, we have generated stable transfectants of early passage HDF, represented here by clone LacZ21, in which expression of a beta-galactosidase reporter construct reflects p53 transactivation activity. During continuous passage, the proportion of beta-gal positive LacZ21 cells remained below 2% for 25 population doublings (pd), first became significantly increased after 29 pd, and thereafter increased rapidly, reaching a maximum of 88% in fully-senescent cells (32 pd), which exceeded the response observed following an optimum dose (20 J/m2) of u.v. radiation. Correspondingly, the proportion of cells incorporating bromodeoxyuridine (BrdU) (initially 45-50%) began to fall at 29 pd and thereafter dropped rapidly to below 1% by pd 32. There was therefore a near-perfect reciprocal relationship between reporter construct expression and DNA synthesis as cells approached senescence. Furthermore, a dominant-negative p53 mutant (introduced by retroviral transduction) rescued LacZ21 cells from senescence and generated colonies with extended lifespan in which beta-gal expression was totally abolished. These data, although not excluding the need for other p53 functions, strongly suggest that p53-mediated transactivation of growth regulatory genes is a direct trigger, rather than a permissive factor, for cellular senescence.
Evaluation of Pre-Treatment Serum Levels of IL-7 and GM-CSF in Colorectal Cancer Patients. (2014)

Survival of Colorectal cancer (CRC) patients is considerably stage-dependent; therefore, early diagnosis is a pivotal factor in decreasing mortality and morbidity associated with this cancer. GM-CSF and IL-7 are reported to increase in different cancers and we aimed to investigate the pre-treatment serum levels of GM-CSF and IL-7 in Iranian patients with colorectal cancer. 127 patients (68 males and 59 females) entered this study before receiving chemotherapy or radiotherapy. A control group of 50 healthy age/sex matched individuals (27 males and 23 females) were included in the study. The serum levels of GM-CSF and IL-7 were measured using commercial enzyme linked immunosorbent assays. A significantly higher level of GM-CSF was found in the sera of patients with colorectal cancer compared to healthy age/sex matched controls (P=0.013). However, there was no significant difference between the levels of IL-7 in sera of patients and controls. We observed a significant elevation in the level of GM-CSF in poorly differentiated tumors (P=0.024). Also a significant correlation between lymphatic invasion and the level of GM-CSF in sera of CRC patients was detected (P=0.01). We found an increase of the level of IL-7 in four patients presenting moderate stages of tumor concomitant with a decrease of the level of GM-CSF. It can be concluded that the increase of the level of GM-CSF is accompanied by CRC progression in Iranian patients. Potential therapeutic effect of IL-7 in this disease, however, needs further investigations.
Entrepreneurial Growth and Ownership under Market Socialism in China: A Longitudinal Case Study of Small Business Growth (2012)

How firms grow is still a mystery and a definitive explanation remains elusive. This is especially the case for emerging economies, where the development of research into business growth has been notably slow whilst emerging business ventures are developing at hyper speed. Since most empirical studies have focused on the quantitative differences in growth across firms, this paper adopts a longitudinal case study approach to explore the qualitative differences in terms of how various types of firm achieve their growth outcomes in the organisational development process over a prolonged period of time. Through a theoretical lens which focuses on growth process approaches, this study not only demonstrates that entrepreneurial processes take different forms and dimensions in different contexts, but it also provides insight into the interactions of various organisational factors underpinning the strategies and changes that lead to contrasting growth outcomes. Case study findings assert that the ownership factor is a key contingent factor that shapes management structure and resources which, in turn, affect particular entrepreneurial outcomes. Furthermore, a combination of leadership style and the approach to knowledge management also play critical roles in the learning process which tends to determine the strategy choice of either high or low value added product strategy. The findings of this research are that small firms with a low value product strategy can improve their survival chances and growth through the vertical broadening of a product portfolio in synchrony with increasing production and technology advancement. The case study companies show a tendency to reinforce their industry position by adopting contrasting choices for growth. The paper addresses the challenges and managerial implications for Western company managers in different growth contexts.
Porcine models of coronary atherosclerosis and vulnerable plaque for imaging and interventional research (2009)

Animal models facilitate our understanding of human disease by providing a controlled environment permitting testing of mechanisms of disease, diagnostic technologies and therapeutic interventions. The ideal animal model should display coronary lesions resembling those seen in human atherosclerosis. No suitable large animal model of high-risk (vulnerable) plaque exists. Lack of such a model has hampered studies designed to validate imaging technologies and to scrutinise the effects of therapeutic interventions in atherosclerotic arteries. Several porcine models of advanced human-like coronary atherosclerosis exist. In this review some of the most promising porcine models are discussed, focusing on their applicability in the development and validation of coronary imaging technologies and interventional devices. In the evolving era of technological development, the availability and use of such animal models of advanced human-like coronary atherosclerosis and vulnerable plaque will become critically important in the preclinical testing of emerging technologies in interventional cardiology.
Differential Detection of Skeletal Troponin I Isoforms in Serum of a Patient with Rhabdomyolysis: Markers of Muscle Injury? (2002)

Unlike the extensive research devoted to the development of troponin-based diagnostic assays for myocardial disease, much less effort has been expended on the development of a counterpart for skeletal muscle disorders. The consensus that the cardiac troponins [cardiac troponin I (cTnI) and/or cTnT] should be used for diagnosis of myocardial infarction (MI), as well as for diagnosis and management of unstable angina, is based on their superior tissue specificity over such conventional markers as creatine kinase [(CK); see Refs. (1)(2)]. Although CK is the most common serum marker for skeletal muscle injury, it is not ideal for several reasons, including lack of tissue specificity, inability to reveal damage to specific skeletal fiber types (fast or slow), and inappropriately low values when glutathione concentrations are decreased because of liver or multiple-organ failure (3). Skeletal troponin I (sTnI), with its two distinct isoforms [fast (fsTnI) and slow (ssTnI)], like cTnI and cTnT, may have a similar advantage over conventional markers for detecting skeletal-muscle injury.

In 1996, Rama et al. (4) described an experimental immunoenzymatic assay for sTnI using antibodies that cross-react with both sTnI and cTnI. The assumption of the investigators was that the concentrations of cTnI in patients with skeletal injury would be negligible. Others have since used this assay (5)(6)(7). For example, Onuoha et al. (7) found that serum sTnI reflects the severity and type of orthopedic and soft tissue injury. However, because this assay does not differentiate between the two isoforms of sTnI, which have a sequence homology of ∼56%, information about selective damage to particular fiber types is unavailable. Posttranslational modifications to the analyte, such as degradation, are also undetected by this assay.

We applied our Western blot–direct serum analysis (WB-DSA) procedure (8), originally developed and successfully used for the detection …
Photoinduced Reduction of PtIV within an Anti‐Proliferative PtIV–Texaphyrin Conjugate (2014)

Abstract Invited for the cover of this issue are the groups of Jonathan Sessler at The University of Texas at Austin and Zahid Siddik at The University of Texas M.D. Anderson Cancer Center in Houston, Texas. The cover picture depicts a tumor‐targeting texaphyrin platinum(IV) conjugate that undergoes controlled reduction and subsequent release of the platinum moiety that can then bind DNA. This conjugate is found to inhibit cell proliferation in ovarian cancer cell lines. Read the full text of the article at 10.1002/chem.201403094 .