gebhart/patrepeval huggingface dataset:
Quantifying the Activity of <em>cis</em>-Regulatory Elements in the Mouse Retina by Explant Electroporation (2011)

Transcription factors within cellular gene networks control the spatiotemporal pattern and levels of expression of their target genes by binding to cis-regulatory elements (CREs), short (˜300-600 bp) stretches of genomic DNA which can lie upstream, downstream, or within the introns of the genes they control. CREs (i.e., enhancers/promoters) typically consist of multiple clustered binding sites for both transcriptional activators and repressors(1-3). They serve as logical integrators of transcriptional input giving a unitary output in the form of spatiotemporally precise and quantitatively exact promoter activity. Most studies of mammalian cis-regulation to date have relied on mouse transgenesis as a means of assaying the enhancer function of CREs(4-5). This technique is time-consuming, costly and, on account of insertion site effects, largely non-quantitative. On the other hand, quantitative assays for mammalian CRE function have been developed in tissue culture systems (e.g., dual luciferase assays), but the in vivo relevance of these results is often uncertain. Electroporation offers an excellent alternative to traditional mouse transgenesis in that it permits both spatiotemporal and quantitative assessment of cis-regulatory activity in living mammalian tissue. This technique has been particularly useful in the analysis of cis-regulation in the central nervous system, especially in the cerebral cortex and the retina(6-8). While mouse retinal electroporation, both in vivo and ex vivo, has been developed and extensively described by Matsuda and Cepko(6-7,9), we have recently developed a simple approach to quantify the activity of photoreceptor-specific CREs in electroporated mouse retinas(10). Given that the amount of DNA that is introduced into the retina by electroporation can vary from experiment to experiment, it is necessary to include a co-electroporated 'loading control' in all experiments. In this respect, the technique is very similar to the dual luciferase assay used to quantify promoter activity in cultured cells. When assaying photoreceptor cis-regulatory activity, electroporation is usually performed in newborn mice (postnatal day 0, P0) which is the time of peak rod production(11-12). Once retinal cell types become post-mitotic, electroporation is much less efficient. Given the high rate of rod birth in newborn mice and the fact that rods constitute more than 70% of the cells in the adult mouse retina, the majority of cells that are electroporated at P0 are rods. For this reason, rod photoreceptors are the easiest retinal cell type to study via electroporation. The technique we describe here is primarily useful for quantifying the activity of photoreceptor CREs.
Randomized Phase III Trial of Paclitaxel/Carboplatin With or Without PF-3512676 (Toll-Like Receptor 9 Agonist) As First-Line Treatment for Advanced Non–Small-Cell Lung Cancer (2011)

Addition of PF-3512676 to paclitaxel/carboplatin did not improve OS or PFS versus paclitaxel/carboplatin alone for first-line treatment of patients with advanced NSCLC but did increase toxicity. This regimen cannot be recommended for treating patients with advanced NSCLC.
Nonvolatile Memory Device Using Mobile Protons via Insertion Hydrogen Neutral Beam Treatment Process between SiO<sub>2</sub> Deposition Processes at Room Temperature (2014)

We demonstrated the nonvolatile memory functionality of nano-crystalline silicon (nc-Si) thin film transistors (TFTs) using mobile protons that are generated by very short time hydrogen neutral beam (H-NB) treatment at room temperature (25 °C). The whole memory fabrication process kept under 50 °C (except SiO 2 deposition process; 300 °C). These nc-Si devices exhibited reproducible hysteresis, reversible switching, and nonvolatile memory behaviors in comparison with those of the conventional FET devices. Our study will further provide a useful route of creating memory functionality and incorporating proton-based storage elements onto a probability of next generation flexible memorable electronics such as low power consumption flexible display panel.
Development of strong elasticoluminescence from ferroelectric phase (2005)

Recently, we have found a new phenomenon, named elasticoluminescence, in which intensive visible light can be emitted by the application of mechanical stress in the elastic deformation region. This phenomenon, contrary to piezoelectricity, can sense changes in mechanical stress without any electrical contacts or electrodes. Elastico-deformation luminescence has been investigated systematically using precisely controlled pure-phase of various oxides and their mixed phases. This study reveals that only certain ferroelectric phases produce strong elastico-deformation luminescence; other pure-phases of non-piezoelectricity show no deformation luminescence. Correlation of deformation luminescence and crystal structure has been found. This finding can be applied in designing strong elastico-deformation-luminescent materials. Strong elasticoluminescence materials and/or coatings can give real-time stress images, so that it is a prospective candidate for developing a new non-destructive evaluation technology.
Relationship between age and health care utilization in patients with myelodysplastic syndrome receiving supportive care. (2011)

6560 Background: Myelodysplastic syndrome (MDS) is rare in people under 50. Little is known about the disease in this group, particularly among those patients who receive supportive care only. Methods: This was a descriptive cohort study using a large commercial claims database. The study included patients with an initial MDS claim (ICD-9-CM 238.72-238.75) between 2/1/2007 and 7/31/2008, who were continuously enrolled for 6 months prior to and 12 months following the index claim. Patients were excluded it they were treated with either hypomethylating agents (HMA) or thalidomide analogues (TA). Once identified, patients were stratified into two group, those aged <50 and those ≥50. Demographic variables and utilization and costs were calculated in the pre- and postindex period, respectively. Results: The study identified 1,209 patients newly diagnosed with MDS and continuously enrolled in the health plan. After excluding 76 (6.3%) who were treated with HMA/TA, the final cohort contained 1,133 patients. Of these, 221 (19.5%) were <50 and 912 (80.5%) were ≥50. In the first year after diagnosis, patients <50 had significantly fewer office visits than the older group (17.5 vs. 24.2, p<.001) but were no different in the proportion hospitalized (25.8% vs. 29.2%, respectively, p=.52) or in length of stay (7.8 vs. 9.0 days, p=.42). Mean total health care charges were $30,177 (SD $53,550, Md $9,622) for patients <50 and $31,832 (SD $63,658, Md $12,248) for those ≥ 50 (p=.69). Conclusions: Despite MDS being classified as a disease of the elderly, the results showed that among the commercially insured, 1 in 5 diagnosed with MDS was under 50. Although NCCN guidelines support HMA treatment, the vast majority received supportive care only. In addition, for both age groups, hospitalizations were common, and total healthcare costs were high but did not differ between the two groups. This suggests similar levels of diseases severity. Further studies of the characteristics of patients with early onset MDS appear warranted.
Properties and Application of Double-Walled Carbon Nanotubes Sorted by Outer-Wall Electronic Type (2011)

Double-walled carbon nanotubes (DWNTs) can adopt four distinct permutations arising from the electronic type (metallic or semiconducting) of their inner and outer walls. This polydispersity limits the utility of DWNTs in applications such as thin film electronics. We demonstrate that density gradient ultracentrifugation can be employed to address this source of heterogeneity by producing DWNTs with well-defined outer-wall electronic types. Optical absorption measurements of sorted DWNTs reveal outer-wall purities of 96% and 98% for sorted semiconducting and metallic samples, respectively. Electrical characterization of semiconducting and metallic outer-wall DWNTs in thin film transistors directly confirms the efficacy of these separations, with semiconducting DWNT devices yielding on/off ratios 2 orders of magnitude higher than comparable metallic DWNT devices.
Complete Replacement of the Mitochondrial Genotype in a <i>Bos indicus</i> Calf Reconstructed by Nuclear Transfer to a <i>Bos taurus</i> Oocyte (2001)

Due to the exclusively maternal inheritance of mitochondria, mitochondrial genotypes can be coupled to a particular nuclear genotype by continuous mating of founder females and their female offspring to males of the desired nuclear genotype. However, backcrossing is a gradual procedure that, apart from being lengthy, cannot ascertain that genetic and epigenetic changes will modify the original nuclear genotype. Animal cloning by nuclear transfer using host ooplasm carrying polymorphic mitochondrial genomes allows, among other biotechnology applications, the coupling of nuclear and mitochondrial genotypes of diverse origin within a single generation. Previous attempts to use Bos taurus oocytes as hosts to transfer nuclei from unrelated species led to the development to the blastocyst stage but none supported gestation to term. Our aim in this study was to determine whether B. taurus oocytes support development of nuclei from the closely related B. indicus cattle and to examine the fate of their mitochondrial genotypes throughout development. We show that indicus:taurus reconstructed oocytes develop to the blastocyst stage and produce live offspring after transfer to surrogate cows. We also demonstrate that, in reconstructed embryos, donor cell-derived mitochondria undergo a stringent genetic drift during early development leading, in most cases, to a reduction or complete elimination of B. indicus mtDNA. These results demonstrate that cross-subspecies animal cloning is a viable approach both for matching diverse nuclear and cytoplasmic genes to create novel breeds of cattle and for rescuing closely related endangered cattle.
Renaturation of guanidine‐unfolded tryptophan synthase by multi‐mixing stopped‐flow dilution in D<sub>2</sub>O (1988)

Guanidine hydrochloride (GdnHCl) at high concentrations, e.g. 4 to 8 M, has been used extensively to promote reversible denaturation of several proteins. The refolding is induced by removal of the denaturing agent by diluting the denatured protein at least 50-100-fold in a 'renaturation buffer'. Fast kinetic studies, using a stopped-flow apparatus to achieve such dilutions, are difficult for two reasons: firstly, injecting widely different volumes of the two reagents does not afford a proper mixing. Secondly, the density differences existing between the concentrated GdnHCl solution and the renaturation buffer often causes important mixing and redistribution artefacts particularly in vertical stopped-flows. Here, it is shown that these difficulties can be overcome by using a multi-mixing stopped-flow to achieve 2 successive 7-fold dilutions and by using heavy water (D2O) to adjust the density of the renaturation buffer. This enabled us to study the appearance of a short-lived intermediate during the folding of the beta 2-subunit of Escherichia coli tryptophan synthase.
Effect of particle size distributions on the rheology of concentrated bimodal suspensions (1994)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Chingyi Chang, Robert L. Powell; Effect of particle size distributions on the rheology of concentrated bimodal suspensions. J. Rheol. 1 January 1994; 38 (1): 85–98. https://doi.org/10.1122/1.550497 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentThe Society of RheologyJournal of Rheology Search Advanced Search |Citation Search
Hierarchical Capacity Planning With Reconfigurable Kits in Global Semiconductor Assembly and Test Manufacturing (2007)

Kits (such as accessories, fixtures, jigs, etc.) are widely used in production for many industries. They are normally product- and machine-specific, so a large kit inventory must be maintained when the product-mix variation is high. Fortunately, many kits are reconfigurable. That means they can be dissembled into components and then these components themselves (or together with some other components) can be reassembled into new types of kits. Therefore, we can save money and improve supply chain responsiveness by purchasing components instead of entire kits. However, research on capacity planning with reconfigurable kits has not been reported. We proposed a two-level hierarchical planning methodology to generate a complete capacity planning solution using mixed-integer linear programming. MaxIt covers mid-range monthly planning and automated capacity allocation system covers short-range weekly planning. These systems are integrated to generate optimal capacity plans considering kit components. This methodology has been successfully implemented in Intel's global semiconductor assembly and test manufacturing since 2004. In this paper, we present the hierarchical modeling framework and focus on MaxIt modeling with kit reconfiguration. We also verify the methodology by numerical experiments in a real production environment.
CXCL12/CXCR4/CXCR7 Chemokine Axis in the Central Nervous System: Therapeutic Targets for Remyelination in Demyelinating Diseases (2017)

The chemokine CXCL12 plays a vital role in regulating the development of the central nervous system (CNS) by binding to its receptors CXCR4 and CXCR7. Recent studies reported that the CXCL12/CXCR4/CXCR7 axis regulates both embryonic and adult oligodendrocyte precursor cells (OPCs) in their proliferation, migration, and differentiation. The changes in the expression and distribution of CXCL12 and its receptors are tightly associated with the pathological process of demyelination in multiple sclerosis (MS), suggesting that modulating the CXCL12/CXCR4/CXCR7 axis may benefit myelin repair by enhancing OPC recruitment and differentiation. This review aims to integrate the current findings of the CXCL12/CXCR4/CXCR7 signaling pathway in the CNS and to highlight its role in oligodendrocyte development and demyelinating diseases. Furthermore, this review provides potential therapeutic strategies for myelin repair by analyzing the relevance between the pathological changes and the regulatory roles of CXCL12/CXCR4/CXCR7 during MS.
On Difference and Understanding: The Use and Abuse of the Study of Islam (2000)

Why do we study Islam, and how should we do it? As usual, what appears like a simple question poses the most intricate problems. Compared to the 'how', the 'why' is relatively easy: culture is very much in fashion, and it has been so for a while. The 'cultural turn' is widely debated, not only in the humanities, but also in the social sciences. This includes the discipline I was first trained in and remain attached to: history. The cultural turn has made an impact on sociology and political science, and to a lesser extent on economics and law. Its strong appeal has certainly to do with politics, for there can be little doubt that the demise of the Soviet Empire and the intensification of ethnic conflict in many parts of the world have contributed towards giving so high a profile to matters of culture and identity. The fact that there should be a link to politics (and I hasten to emphasize that I do not subscribe to monocausal explanations) need not render the interest in culture and identity, variously and often ill-defined, suspect or illegitimate: I at least can see nothing intrinsically wrong with an approach that looks at politics, society, law and the economy with a greater awareness of, and sensitivity to, cultural norms and aspirations. But there are disturbing aspects to this preoccupation with culture, if it is not an outright obsession; aggressive ethnic assertiveness on one hand, and the talk about a potential if not inescapable 'clash of civilizations' on the other, are among them. The latter in particular would not have found such fertile ground and reached so wide an audience, had it not been for the cultural turn in academic as well as in what is commonly considered to be 'real' life.
Bacterial Kidney Disease of Salmonid Fish (1981)

Human coronavirus (HCoV) infection causes respiratory diseases with mild to severe outcomes. In the last 15 years, we have witnessed the emergence of two zoonotic, highly pathogenic HCoVs: severe acute respiratory syndrome coronavirus (SARS-CoV) and ...Read More
The Circadian Clock Component BMAL1 Is a Critical Regulator of p21 Expression and Hepatocyte Proliferation (2007)

Most living organisms show circadian (approximately 24 h) rhythms in physiology and behavior. These oscillations are generated by endogenous circadian clocks, present in virtually all cells where they control key biological processes. Although circadian gating of mitosis has been reported for many years in some peripheral tissues, the underlying molecular mechanisms have remained poorly understood. Here we show that the cell cycle inhibitor p21WAF1/CIP1 is rhythmically expressed in mouse peripheral organs. This rhythmic pattern of mRNA and protein expression was recapitulated in vitro in serum-shocked differentiated skeletal muscle cells. p21WAF1/CIP1 circadian expression is dramatically increased and no longer rhythmic in clock-deficient Bmal1-/- knock-out mice. Biochemical and genetic data show that oscillation of p21WAF1/CIP1 gene transcription is regulated by the antagonistic activities of the orphan nuclear receptors REV-ERBalpha/beta and RORalpha4/gamma, which are core clock regulators. Importantly, p21WAF1/CIP1 overexpressing Bmal1-/- primary hepatocytes exhibit a decreased proliferation rate. This phenotype could be reversed using small interfering RNA-mediated knockdown of p21WAF1/CIP1. These data establish a novel molecular link between clock and cell cycle genes and suggest that the G1 progression phase is a target of the circadian clock during liver cell proliferation.
Effect of halothane on sinus rhythm of dog heart in situ. (1987)

Effect of halothane on sinus rhythm was investigated using a direct perfusion technique of the canine SA node artery in situ. Halothane was dissolved in a fat emulsion and administered to the SA node artery in doses between 148.8 micrograms and 2976 micrograms. Both the solvent itself and a stabilizer of halothane produced no change in the heart rate. Halothane induced a biphasic chronotropic response in all doses: an initial sinus acceleration of 2 to 5 sec duration followed by a long-lasting sinus deceleration. Both responses were dose-related. The positive response was not substantially affected by prior administration of propranolol or tetrodotoxin or in reserpinized dogs. Atropine or tetrodotoxin also failed to cause any change in the negative response. Therefore, both responses were assumed to have resulted from a direct action of halothane on the SA node, but the detailed mechanism underlying the positive response remains to be further clarified.
MAO Knock-Out Mice and Behavior (2000)

Monoamine oxidase A and B (MAO-A and MAO-B) are important isoenzymes which catalyze the oxidation deamination of biogenic and dietary amines in the brain and in the periphery with the production of hydrogen peroxide (H20 2) (1,2). MAO-A has higher affinity for the substrates serotonin (5-HT), norepinephrine (NE), dopamine (DA), and the inhibitor clorgyline whereas MAO-B has higher affinity for phenylethylamine (PEA), benzylamine, and the inhibitor deprenyl (3). These isoenzymes are made of different polypeptides (4,5) located on the X chromosome (6,7) and have identical intron and exon organization (8). Different cysteines are important for the catalytic activity of MAO-A and B (9), and distinct domains confer their substrate specificity (10). The different cis and trans ele­ ments in the promotor suggest that the regulation of these two genes is different (11,12). A line of transgenic mice has been generated in which the gene that encodes MAO-A is disrupted. MAO-A knock-out (KO) mice have elevated brain levels of 5-HT, NE, and DA and manifest aggressive behavior similar to men with a deletion of MAO-A (4,13,14). Emotional learning and memory are also increased in MAO-A KO mice (15). We have also generated mice deficient in MAO-B by homologous recombination. MAO-B KO mice do not exhibit aggres­ sion and only levels of PEA are increased. Mice lacking MAO-B are also resistant to the Parkinsongenic neurotoxin l-methyl-4-phenyl-l,2,3,6-tetrahydropyridine (MPTP) (16). Both MAO-A (17) and MAO-B KO (16) mice show increased reactivity to stress. Thus, studies of MAO-A and MAO-B KO mice have clearly shown that MAO-A and B have distinct functions in neurotransmitter metabolism and behavior. These KO mice are valuable models for investigating the role of monoamines in psychoses, neurodegenerative, and stress-related disorders. In thischapter we will discuss the behavior and monoamine metabolism of mice defi­ cient in MAO-A and B and future research directions using KO mice.
Dance Dance Convolution (2017)

Dance Dance Revolution (DDR) is a popular rhythm-based video game. Players perform steps on a dance platform in synchronization with music as directed by on-screen step charts. While many step charts are available in standardized packs, players may grow tired of existing charts, or wish to dance to a song for which no chart exists. We introduce the task of learning to choreograph. Given a raw audio track, the goal is to produce a new step chart. This task decomposes naturally into two subtasks: deciding when to place steps and deciding which steps to select. For the step placement task, we combine recurrent and convolutional neural networks to ingest spectrograms of low-level audio features to predict steps, conditioned on chart difficulty. For step selection, we present a conditional LSTM generative model that substantially outperforms n-gram and fixed-window approaches.
Molecular allelokaryotyping of pediatric acute lymphoblastic leukemias by high-resolution single nucleotide polymorphism oligonucleotide genomic microarray (2007)

Pediatric acute lymphoblastic leukemia (ALL) is a malignant disease resulting from accumulation of genetic alterations. A robust technology, single nucleotide polymorphism oligonucleotide genomic microarray (SNP-chip) in concert with bioinformatics offers the opportunity to discover the genetic lesions associated with ALL. We examined 399 pediatric ALL samples and their matched remission marrows at 50,000/250,000 SNP sites using an SNP-chip platform. Correlations between genetic abnormalities and clinical features were examined. Three common genetic alterations were found: deletion of ETV6, deletion of p16INK4A, and hyperdiploidy, as well as a number of novel recurrent genetic alterations. Uniparental disomy (UPD) was a frequent event, especially affecting chromosome 9. A cohort of children with hyperdiploid ALL without gain of chromosomes 17 and 18 had a poor prognosis. Molecular allelokaryotyping is a robust tool to define small genetic abnormalities including UPD, which is usually overlooked by standard methods. This technique was able to detect subgroups with a poor prognosis based on their genetic status.