gebhart/patrepeval huggingface dataset:
Long-Term Sphere Culture Cannot Maintain a High Ratio of Cancer Stem Cells: A Mathematical Model and Experiment (2011)

Acquiring abundant and high-purity cancer stem cells (CSCs) is an important prerequisite for CSC research. At present, researchers usually gain high-purity CSCs through flow cytometry sorting and expand them by short-term sphere culture. However, it is still uncertain whether we can amplify high-purity CSCs through long-term sphere culture. We have proposed a mathematical model using ordinary differential equations to derive the continuous variation of the CSC ratio in long-term sphere culture and estimated the model parameters based on a long-term sphere culture of MCF-7 stem cells. We found that the CSC ratio in long-term sphere culture presented as gradually decreased drift and might be stable at a lower level. Furthermore, we found that fitted model parameters could explain the main growth pattern of CSCs and differentiated cancer cells in long-term sphere culture.
Copy Number and SNP Arrays in Clinical Diagnostics (2011)

The ability of chromosome microarray analysis (CMA) to detect submicroscopic genetic abnormalities has revolutionized the clinical diagnostic approach to individuals with intellectual disability, neurobehavioral phenotypes, and congenital malformations. The recognition of the underlying copy number variant (CNV) in respective individuals may allow not only for better counseling and anticipatory guidance but also for more specific therapeutic interventions in some cases. The use of CMA technology in prenatal diagnosis is emerging and promises higher sensitivity for several highly penetrant, clinically severe microdeletion and microduplication syndromes. Genetic counseling complements the diagnostic testing with CMA, given the presence of CNVs of uncertain clinical significance, incomplete penetrance, and variable expressivity in some cases. While oligonucleotide arrays with high-density exonic coverage remain the gold standard for the detection of CNVs, single-nucleotide polymorphism (SNP) arrays allow for detection of consanguinity and most cases of uniparental disomy and provide a higher sensitivity to detect low-level mosaic aneuploidies.
Enabling Loop Fusion and Tiling for Cache Performance by Fixing Fusion-Preventing Data Dependences (2005)

This paper presents a new approach to enabling loop fusion and tiling for arbitrary affine loop nests. Given a set of multiple loop nests, we present techniques that automatically eliminate all the fusion-preventing dependences by means of loop tiling and array copying. Applying our techniques iteratively to multiple loop nests yields a single loop nest that can be tiled for cache locality. Our approach handles LU, QR, Cholesky and Jacobi in a unified framework. Our experimental evaluation on an SGI Octane2 system shows that the benefit from the significantly reduced L1 and L2 cache misses has far more than offset the branching and loop control overhead introduced by our approach.
Advances in the Catalytic Production and Utilization of Sorbitol (2013)

Recently, research on the production and transformation of sorbitol has become exciting in chemical industry and in catalysis studies for its broad applications. It opens up a new path for achieving sustainable energy supply and chemicals production. Here we mainly review the catalytic routes for the synthesis of sorbitol and conversion of sorbitol into high value-added compounds such as lower alcohols, paraffins, isosorbide, and other derivatives. Meanwhile, some promising and valuable research directions are suggested based on the major challenges emerged in current research, such as the development of efficient magnetic catalysts, microwave heating, and other hydrogen sources.
Apoptosis regulating proteins as targets of therapy for haematological malignancies (1999)

Most chemotherapeutic agents used in the treatment of haematological malignancies cause cell death by inducing apoptosis through undefined means. The discovery of the proteins involved in apoptosis and the description of apoptotic pathways suggest new potential targets for therapeutic intervention. Both 'intrinsic' and 'extrinsic' pathways can be activated separately, but activation of caspases appears central to most apoptotic pathways. Novel approaches attempt to induce apoptosis by directly targeting a portion of an apoptotic pathway. Agents that trigger signalling of Fas or tumour necrosis factor- (TNF-) related apoptosis inducing ligand (TRAIL) receptor seek to induce the extrinsic pathway at the cell surface. The BCL-2 family of proteins seems central to the regulation of those apoptotic pathways that involve mitochondrial sequestration or the release of cytochrome c, with subsequent activation of Apaf-1, caspase-9 and caspase-3. The activity of this family may depend upon both the phosphorylation state of different members and the relative level of pro- and anti-apoptotic members. New agents such as the staurosporine analogue UCN-01 and bryostatin are thought to affect apoptosis induction by altering BCL-2 phosphorylation. Others, such as BCL-2 antisense and ATRA attempt to modulate the protein levels to promote apoptosis. Direct activation of caspase-3 is a probable target, but as yet no agent with this direct function is in trial. Clinical trials of several agents have been completed or are underway. It is likely that agents that target particular points in apoptosis pathways will have antileukaemia/lymphoma activity, however, the optimal utilisation may involve combination with other more conventional agents that also activate apoptosis.
Inductive tissue engineering with protein and DNA-releasing scaffolds (2005)

Cellular differentiation, organization, proliferation and apoptosis are determined by a combination of an intrinsic genetic program, matrix/substrate interactions, and extracellular cues received from the local microenvironment. These molecular cues come in the form of soluble (e.g. cytokines) and insoluble (e.g. ECM proteins) factors, as well as signals from surrounding cells that can promote specific cellular processes leading to tissue formation or regeneration. Recent developments in the field of tissue engineering have employed biomaterials to present these cues, providing powerful tools to investigate the cellular processes involved in tissue development, or to devise therapeutic strategies based on cell replacement or tissue regeneration. These inductive scaffolds utilize natural and/or synthetic biomaterials fabricated into three-dimensional structures. This review summarizes the use of scaffolds in the dual role of structural support for cell growth and vehicle for controlled release of tissue inductive factors, or DNA encoding for these factors. The confluence of molecular and cell biology, materials science and engineering provides the tools to create controllable microenvironments that mimic natural developmental processes and direct tissue formation for experimental and therapeutic applications.
Regulation of Aurora B Expression by the Bromodomain Protein Brd4 (2009)

The bromodomain protein Brd4 plays critical roles in cellular proliferation and cell cycle progression. In this study, we investigated the involvement of Brd4 in cell cycle regulation and observed aberrant chromosome segregation and failures in cytokinesis in cancer cells as well as in primary keratinocytes in which Brd4 has been knocked down by RNA interference. Suppression of Brd4 protein levels in proliferating cells decreased Aurora B protein and transcript levels and abolished its chromosomal distribution. In contrast, exogenous Brd4 expression stimulated Aurora B promoter reporter activity and upregulated endogenous Aurora B expression. Aurora B kinase is a chromosomal passenger protein that is essential for chromosome segregation and cytokinesis. Either overexpression of Aurora B or its inactivation can induce defects in centrosome function, spindle assembly, chromosome alignment, and cytokinesis in various cancer cells. The impaired regulation of Aurora B expression in human cells by Brd4 knockdown or overexpression coincided with mitotic catastrophe and multinucleation that are typically observed when Aurora B is inactivated or overexpressed. Overall, our data suggest that Brd4 is essential for the maintenance of the cell cycle progression mediated at least in part through the control of transcription of the Aurora B kinase cell cycle regulatory gene.
Plasmid copy number control: isolation and characterization of high-copy-number mutants of plasmid pE194 (1979)

A plasmid, pE194, obtained from Staphylococcus aureus confers resistance to macrolide, lincosamide, and streptogramin type B ("MLS") antibiotics. For full expression, the resistance phenotype requires a period of induction by subinhibitory concentrations of erythromycin. A copy number in the range of 10 to 25 copies per cell is maintained during cultivation at 32 degrees C. It is possible to transfer pE194 to Bacillus subtilis by transformation. In B. subtilis, the plasmid is maintained at a copy number of approximately 10 per cell at 37 degrees C, and resistance is inducible. Tylosin, a macrolide antibiotic which resembles erythromycin structurally and to which erythromycin induces resistance, lacks inducing activity. Two types of plasmid mutants were obtained and characterized after selection on medium containing 10 microgram of tylosin per ml. One mutant class appeared to express resistance constitutively and maintained a copy number indistinguishable from that of the parent plasmid. The other mutant type had a 5- to 10-fold-elevated plasmid copy number (i.e., 50 to 100 copies per cell) and expressed resistance inducibly. Both classes of tylosin-resistant mutants were shown to be due to alterations in the plasmid and not to modifications of the host genome.
Inhibiting mutations in the transforming growth factor beta type 2 receptor in recurrent human breast cancer. (2001)

Members of the transforming growth factor beta (TGF-beta) family are potent inhibitors of the growth of many epithelial cell types. Transmembrane signaling by TGF-beta occurs via a complex of the serine/threonine kinases TGF-beta type 1 receptor and TGF-beta type 2 receptor (TGFBR2), and inactivating mutations in the latter have recently been detected in some primary tumors and in several types of tumor-derived cell lines. The most common mutations that have been identified in TGFBR2 are frameshifts in a repetitive polyadenine region in replication error-positive colorectal carcinomas that result in a truncated protein and absence of receptor expression at the cell surface. A number of point mutations in the highly conserved serine/threonine kinase domain of TGFBR2 have also been reported, some of which have been correlated with either loss of trans-phosphorylation of TGF-beta type 1 receptor or constitutive activation of trans-phosphorylation. No TGFBR2 mutations have been reported in human breast tumors, but anomalous expression of TGF-beta in breast carcinomas suggests that TGF-beta signaling may be defective. We have therefore systematically examined unmatched sets of 17 primary and 17 recurrent breast tumor samples for mutations in TGFBR2, restricted to those regions of the gene in which mutations have previously been reported. None of the previously reported mutations was detected, but four novel mutations (V387M, N435S, V447A, and L452M) were found in the kinase domain in recurrent tumors. No mutations were detected in primary tumors. TGF-beta signaling was significantly inhibited by each of the N435S, V447A, and L452M mutations.
Differential Protein Stability and ALK Inhibitor Sensitivity of EML4-ALK Fusion Variants (2012)

Our results might explain some of the heterogeneous responses of ALK-positive tumors to ALK kinase inhibition observed in the clinic. Thus, targeted therapy of ALK-positive lung cancer should take into account the precise ALK genotype. Furthermore, combining ALK and HSP90 inhibitors might enhance tumor shrinkage in EML4-ALK-driven tumors.
Physical parameters of helium-rich subdwarf B stars from spectral energy distributions (2003)

We present effective temperatures and angular radii for eleven helium-rich subdwarf B stars. These are measured using spectral energy distributions from archival IUE spectra and existing optical and infrared photometry. The data have been analysed using a grid of high-gravity helium-rich LTE model atmospheres and a -minimization procedure. The parameters derived here allow for independent verification of the parameters derived from the analysis of optical spectra.
Mechanism-based inactivation of ribonuclease A (1995)

The first example of a mechanism-based inhibitor of a phosphodiesterase is reported. Although the inactivation brought about by the fluoride <b>4</b> is not complete, this compound provides a useful starting point for the synthesis of other more potent inhibitors of ribonuclease A, as well as inhibitors of other nucleases. In addition, an inexpensive method is described for the synthesis of phosphate diesters that cannot be synthesized using standard phosphoramidite methodology. Phosphitylation of the target alcohol with a dialkyl chlorophosphite, followed by activation of the resulting trialkyl phosphite with I<sub>2</sub>, yields an iodophosphate. The resulting iodophosphate can then be coupled to a second alcohol, phenol, or enolate to give a phosphate triester, which after subsequent deprotection affords the desired phosphate diester. The novel phosphorylation chemistry presented should greatly facilitate the synthesis of other similar mechanism-based phosphodiesterase inhibitors.
Spreadsheets for images (1994)

We describe a data visualization system based on spreadsheets. Cells in our spreadsheet contain graphical objects such as images, volumes, or movies. Cells may also contain widgets such as buttons, sliders, or curve editors. Objects are displayed in miniature inside each cell. Formulas for cells are written in a general-purpose programming language (Tcl) augmented with operators for array manipulation, image processing, and rendering.
Enterovirus infections are associated with the induction of β‐cell autoimmunity in a prospective birth cohort study (2002)

Enterovirus infections have been associated with the manifestation of clinical type 1 diabetes in a number of reports, and recent prospective studies have suggested that enterovirus infections may initiate the autoimmune process, leading to the disease. In the present study, we analyzed the role of enterovirus infections in a Finnish birth cohort study, Diabetes Prediction and Prevention (DIPP), in which all newborn infants are screened for diabetes-associated HLA-DQB1 alleles, and those with an increased genetic risk are invited for prospective follow-up. Enterovirus infections were diagnosed by serology and reverse transcriptase-polymerase chain reaction (RT-PCR) from serum samples taken from birth every 3-6 months. Case children included 41 infants who became positive for diabetes-associated autoantibodies during the observation. Control children comprised altogether 196 infants who remained autoantibody negative and were matched for the time of birth, sex, and HLA-DQB1 alleles. Enterovirus infections were more frequent in case children than in control children (P = 0.004), and the average enterovirus antibody levels were also higher in the case children (P = 0.003). Enterovirus infections were particularly frequent during the 6-month period preceding the first detection of autoantibodies: 51% of the case children compared with 28% of the control children had an infection in that time interval (P = 0.003). There was no difference in the frequency of adenovirus infections between the groups (P = 0.9). The present results imply that enterovirus infections are associated with the appearance of beta-cell autoantibodies. A possible causal relationship is supported by the clustering of infections to the time when autoantibodies appeared.
Right Bipyramids of Silver:  A New Shape Derived from Single Twinned Seeds (2006)

Silver nanoparticles with a single (111) twin were selectively nucleated and grown for the first time to produce right bipyramids 75-150 nm in edge length. Key to the production of single twinned seeds was the addition of NaBr to a polyol synthesis in which AgNO3 is reduced by ethylene glycol in the presence of poly(vinyl pyrrolidone). Examination of nanoparticles at different stages of the reaction with electron microscopy revealed that the spherical, single twinned seeds grew to become right bipyramids through enlargement of their (100) facets. The UV-vis-NIR spectrum exhibited by right bipyramids is distinct from that of any other silver nanostructure, and their sharp corners make these new nanoparticles especially promising for enhancement of Raman scattering.
A myocardium tropic adeno-associated virus (AAV) evolved by DNA shuffling and in vivo selection (2009)

To engineer gene vectors that target striated muscles after systemic delivery, we constructed a random library of adeno-associated virus (AAV) by shuffling the capsid genes of AAV serotypes 1 to 9, and screened for muscle-targeting capsids by direct in vivo panning after tail vein injection in mice. After 2 rounds of in vivo selection, a capsid gene named M41 was retrieved mainly based on its high frequency in the muscle and low frequency in the liver. Structural analyses revealed that the AAVM41 capsid is a recombinant of AAV1, 6, 7, and 8 with a mosaic capsid surface and a conserved capsid interior. AAVM41 was then subjected to a side-by-side comparison to AAV9, the most robust AAV for systemic heart and muscle gene delivery; to AAV6, a parental AAV with strong muscle tropism. After i.v. delivery of reporter genes, AAVM41 was found more efficient than AAV6 in the heart and muscle, and was similar to AAV9 in the heart but weaker in the muscle. In fact, the myocardium showed the highest gene expression among all tissues tested in mice and hamsters after systemic AAVM41 delivery. However, gene transfer in non-muscle tissues, mainly the liver, was dramatically reduced. AAVM41 was further tested in a genetic cardiomyopathy hamster model and achieved efficient long-term delta-sarcoglycan gene expression and rescue of cardiac functions. Thus, direct in vivo panning of capsid libraries is a simple tool for the de-targeting and retargeting of viral vector tissue tropisms facilitated by acquisition of desirable sequences and properties.
Epithelial antimicrobial peptides in host defense against infection (2000)

One component of host defense at mucosal surfaces seems to be epithelium-derived antimicrobial peptides. Antimicrobial peptides are classified on the basis of their structure and amino acid motifs. Peptides of the defensin, cathelicidin, and histatin classes are found in humans. In the airways, alpha-defensins and the cathelicidin LL-37/hCAP-18 originate from neutrophils. beta-Defensins and LL-37/hCAP-18 are produced by the respiratory epithelium and the alveolar macrophage and secreted into the airway surface fluid. Beside their direct antimicrobial function, antimicrobial peptides have multiple roles as mediators of inflammation with effects on epithelial and inflammatory cells, influencing such diverse processes as proliferation, immune induction, wound healing, cytokine release, chemotaxis, protease-antiprotease balance, and redox homeostasis. Further, antimicrobial peptides qualify as prototypes of innovative drugs that might be used as antibiotics, anti-lipopolysaccharide drugs, or modifiers of inflammation.
Computer-generated relief gratings as space-variant polarization elements (1992)

A method for exploiting nonuniform ultrahigh spatial-frequency relief gratings as space-variant polarization elements is presented. In this method the local direction of the gratings determines the polarization angles, while the period of the gratings is controlled to ensure continuity of the grating function for any desired polarization operation. We illustrate the method with a specific space-variant half-wave plate for laser radiation of 10.6 μm.
Internal models engaged by brain-computer interface control (2012)

Internal models have been proposed to explain the brain's ability to compensate for sensory feedback delays by predicting the sensory consequences of movement commands. Single-neuron studies in the oculomotor and vestibulo-ocular systems have provided evidence of internal models, as have behavioral studies in the skeletomotor system. Here, we present evidence of internal models from simultaneously recorded population activity underlying closed-loop brain-computer interface (BCI) control. We studied cursor-based BCI control by a nonhuman primate implanted with a multi-electrode array in motor cortex. Using a novel BCI task, we measured the visual feedback processing delay to be about 130 milliseconds. By examining the task-based appropriateness of the population activity at different time lags, we found evidence that the subject compensates for the feedback delay by predicting upcoming cursor positions, suggesting the use of an internal forward model. Lastly, we examined the time course of internal model adaptation after altering the mapping between population activity and cursor movements. This study suggests that closed-loop BCI experiments combined with novel statistical analyses can provide insight into the neural substrates of feedback motor control and motor learning.
EWS/FLI-1 antagonists induce growth inhibition of Ewing tumor cells in vitro. (1996)

Among primitive neuroectodermal tumors, Ewing tumors are characterized by a gene rearrangement recombining the 5'-EWS gene portion with one of two ETS-related proto-oncogenes, FLI-1 or ERG, in roughly 90 and 10% of cases, respectively. We attempted to antagonize EWS/FLI-1 function in Ewing tumor cell lines. As a control, a cell line derived from another small round cell tumor of neuroectodermal origin, neuroblastoma, was used. This cell line was found to express almost identical patterns of ETS proteins except for EWS/FLI-1 and a novel, ELF-related gene product. Stable expression of antisense EWS/FLI-1 cDNA resulted in decreased endogenous EWS/FLI-1 RNA levels and growth reduction of ET cells but not of neuroblastoma cells. DNA-binding FLI-1 derivatives localizing to the nucleus in which the 5'-EWS regulatory domain was replaced by bacterial beta-galactosidase dominantly modulated transcriptional transactivation from a degenerate ETS-binding motif. Transient transfection of these dominant-negative recombinants resulted in a significant decrease in the relative number of mitoses in four Ewing tumor cell lines tested but not in the neuroblastoma cell line. The presented evidence for modulation of tumor cell proliferation by EWS/FLI-1 antagonists suggests a causal role for EWS/FLI-1-mediated gene activation in the malignant transformation of the enigmatic Ewing tumor-precursor cell.