Miracle-dz/UniFAR-FTUs huggingface dataset:
Telomere Maintenance Mechanisms in Soft Tissue Sarcomas

1.1 Telomeres and tumorigenesis 1.1.1 Telomere structure Human chromosomes, which are composed of linear double-stranded DNA, are capped at their ends by nucleoprotein complexes called telomeres (reviewed in (Martinez & Blasco, 2011)). This telomeric cap prevents end-to-end fusion events between chromosomes, and protects chromosome ends from being recognized as double-stranded breaks by the DNA damage machinery in the cell. Telomeric DNA is composed of tandem 5’TTAGGG repeats at each end of the chromosome, extending up to tens of kilobases. Poorly understood endprocessing reactions after replication result in a 3’ overhang on the G-rich strand, which invades the upstream double-stranded telomeric DNA to form a displacement (D)-loop such that the end of the chromosome is buried thereby preventing detection by the cellular DNA damage response (Greider, 1999). Telomeric DNA is in complex with a number of proteins that act to stabilize the structure and mediate telomeric functions of capping and length regulation (Figure 1). Double-stranded (ds) telomeric repeats are bound directly by TRF1 (Zhong et al., 1992) and TRF2 (Bilaud et al., 1997; Broccoli et al., 1997), while the POT1-TPP1 heterodimer binds to the single-stranded (ss) telomeric DNA (de Lange, 2005; Lei et al., 2002). The dsand ss-telomeric DNA complexes are linked through their interaction with TIN2 (Abreu et al., 2010; Kim et al., 1999; O'Connor et al., 2006), together forming the telomeric shelterin complex (de Lange, 2005). Additional proteins necessary for telomeric function are recruited by interactions with components of the shelterin complex (reviewed in (Martinez & Blasco, 2011)). Mammalian telomeres have been shown to contain characteristics of heterochromatin, including the presence of homologues of the heterochromatin binding protein HP1 (Koering et al., 2002; Sharma et al., 2003), enriched tri-methylation of histone H3 lysine 9 (H3K9) and histone H4 lysine 20 (H4K20) (Garcia-Cao et al., 2004), and methylation of CpG dinucleotides in subtelomeric DNA repeats (Gonzalo et al., 2006). Studies in telomerase knockout mice demonstrated that as telomeres become shorter the heterochromatic marks are lost and replaced by marks characteristic of open chromatin, such as increased acetylation of histone tails (Benetti et al., 2007), suggesting that a minimum telomere length is necessary to maintain the appropriate chromatin structure at chromosome ends. Alterations in the level of epigenetic modifications, such as tri-methylation of H3K9 and H4K20 via knockout of the relevant modifying enzymes, led to increased telomere length
RANS/PDF and LES/FDF for prediction of turbulent premixed flames

Probability density function (PDF) and filtered density function (FDF)methodologies are developed and implemented, respectively, forReynolds-averaged Navier-Stokes (RANS) and large eddy simulation (LES) ofturbulent premixed flames. RANS predictions are made of a lean premixedbluff-body flame via the joint velocity-scalar-frequency PDF model. LES of apremixed Bunsen-burner flame is conducted via the scalar FDF methodology. Bothsimulations employ finite rate kinetics via a reduced methane chemistrymechanism to account for combustion. Prediction results are compared withexperimental data, and are shown to capture some of the intricate physics ofturbulent premixed combustion.
Field-effect polymer gating of low-dimensionality carbon-based materials

The work focuses on the modification of the transport properties of low-dimensional carbon based materials by tuning their surface charge carrier density (up to values of induced charge exceeding 2·10^14 carriers/cm^2) via electrochemical gating with an innovative polymer electrolyte solution. Main subjects of the study are single- and few-layer graphene systems produced by micro-mechanical exfoliation and by CVD growth respectively. Attempts to modulate the superconducting critical temperature of the graphite intercalated compounds CaC6 are also made. In addition, polymer gating was also studied on highly oriented pyrolytic graphite, for the first time, to study its properties under high charge induction
Highly sensitive and fast protein detection with Coomassie brilliant blue in sodium dodecyl sulfate-polyacrylamide gel electrophoresis

Department of Chemistry, Sungkyunkwan University, Suwon 440-746, KoreaReceived August 12, 2002Key Words : Coomasie brilliant blue, 2-Dimensional gel electrophoresis, ProteomicsDetection of proteins in sodium dodecyl sulfate-polyacryl-amide gel electrophoresis (SDS-PAGE) is an important firststep for protein analysis. For years, various experimentalefforts have been directed to develop and improve theprotein detection methods
Studies on the structural changes of myoglobin in tuna meat discoloration

報告番号: ; 学位授与年月日: 2013-03-25 ; 学位の種別: 課程博士 ; 学位の種類: 博士（農学） ; 学位記番号: 博農第3914号 ; 研究科・専攻: 農学生命科学研究科水圏生物科学専攻
Spiroconjugation in 1-, 2-, and 3-Dimensions: The Foundations of a Spiro Quantum Chemistry

A recent paper has described the structure of a hypothetical 3-,4-connected net termed glitter. This is a model of an allotrope of carbon in the form of a synthetic metal. That paper pointed to the importance of through-space pσ interactions of adjacent olefin units in the net in understanding the electronic structure at the Fermi level. The present communication elucidates the role of spiroconjugation in understanding features of the electronic band structure and density of states of glitter. With this analysis of spiroconjugation in the 1-dimensional polyspiroquinoid polymer and the 3-dimensional glitter lattice, the foundations have been laid for a new type of quantum chemistry herein called spiro quantum chemistry. Spiro quantum chemistry complements traditional quantum chemistry which is focused on linear polyenes, circular annulenes, polyhexes, 2-dimensional graphene sheets and related structures including fullerenes, by focusing on spiroconjugated hydrocarbon structures in 1-, 2- and 3-D, including linear spiro[n]quinoids and polyspiroquinoid in 1-D, circular cyclospiro[n]quinoids, spiro[m,n]graphene fragments and spirographene in 2-D and [m,n,o]glitter fragments and glitter in 3-D.
High-Temperature Test Facility for Reactor In-Core Sensor Testing

Abstract An in-reactor test facility has been designed and built at The Ohio State University Research Reactor to evaluate the static and dynamic performance of nuclear reactor in-core sensors in environmental and neutronic conditions comparable to those expected in a high-temperature gas reactor. The primary objective for design and construction of this facility was to evaluate the performance of prototype constant-temperature power sensors. The facility can test sensors and materials over a wide range of temperatures up to 800°C, over a range of Reynolds numbers that can be varied to evaluate thermal-dynamic response, and at a reasonable neutron flux value that can be oscillated nearly 7% (up to 100 Hz eventually) to deterministically evaluate sensor transfer functions. Testing has demonstrated that this facility safely performs its desired functions with the current limitation of a 50-Hz maximum neutron flux oscillation speed.
THE IMPACT OF INFLAMMATION ON THE REGULATION OF INTRACELLULAR CALCIUM IN CUTANEOUS NOCICEPTIVE NEURONS

The most effective way to treat clinical pain is to target the subpopulation of primary afferent neurons responsible. However, clinical pain is heterogeneous, reflecting, in part, differences in the relative contribution of different subpopulations of afferents. The functional heterogeneity of primary afferents is reflected in the heterogeneous regulation of intracellular Ca2+ ([Ca2+]i). Because the regulation of [Ca2+]i contributes to neuronal function, injury-induced changes in neuronal function may be due to dysregulation in the regulation of [Ca2+]i. Thus, the persistent inflammation-induced increase in the magnitude and duration of depolarization-evoked Ca2+ transient in a subset of putative nociceptive cutaneous DRG neurons served as the focus of this thesis. I first ruled out the contribution of Ca2+-induced Ca2+ release to the inflammation-induced increase in the evoked Ca2+ transient. Results of these experiments also indicated the presence of tightly segregated Ca2+ regulatory domains where Ca2+ transients evoked via Ca2+ influx and release from intracellular stores are functionally isolated. Parametric analysis demonstrated that inflammation-induced changes in evoked Ca2+ had a high threshold for activation, thus I focused on low affinity Ca2+ extrusion mechanism, Na+/Ca2+ exchanger (NCX). I demonstrated that NCX regulates the decay of the evoked transient in the same subset of putative nociceptive afferents modified by inflammation, and can influence axonal [Ca2+]i levels, resting membrane potential, and nociceptive threshold. Finally, I confirmed a role for NCX in response to persistent inflammation, such that the increase in the duration of the evoked transient is due to a loss of NCX in the cell body due to an increase in unidirectional NCX3 trafficking to the peripheral terminals. These observations serve as the basis for my current working hypothesis that the inflammation-induced changes in trafficking of NCX3, underlie three major aspects of the inflammatory response: an increase in transmitter release from the central terminal to contribute to inflammatory hyperalgesia, a change in gene expression secondary to altered Ca2+ transients in the cell body, and a decrease in the neurogenic inflammatory response in the periphery secondary to a decrease in transmitter release. Increasing NCX function may be a potentially novel therapeutic strategy for treatment of inflammatory pain.
Large Protein Folding and Dynamics Studied by Advanced Hydrogen Exchange Methods

Protein folding studies over the past 50 years have been largely focused on small proteins (< 200 residues) leading to a dearth of information about large protein folding. Regardless of protein size, research has generally lacked the structural tools with necessary temporal resolution to provide mechanistic insight into the process. This goal requires incisive information on transient kinetic intermediate conformations that describe the folding pathway. In this work special challenges that hinder large protein folding studies are addressed, and advancements to both HX NMR and HX MS experiments are described that provide unparalleled temporal resolution of structure formation than has been previously possible. These various advanced hydrogen exchange methods are used to study folding behaviors of the large, 370-residue, twodomain maltose binding protein from E. coli and provide a description of its folding pathway in structural detail. This work sheds light on two basic unresolved problems regarding the mechanisms of protein folding, the first being the enigmatic nature of the initial folding collapse event seen in many proteins, and the second concerning the nature of the folding pathway. We find that from an initially heterogeneous hydrophobic collapse, an obligatory intermediate emerges with a 7-second time constant followed by an apparent sequential pathway to the native state. These results add the largest protein studied at structural resolution todate to the list of proteins known to fold through obligatory, native-like intermediates in distinct pathways and this work highlights strategies that may be employed to interrogate other large systems in future work. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Biochemistry & Molecular Biophysics First Advisor S. Walter Englander Second Advisor Feng Gai
Raman spectra of L‐isoleucine crystals

Single crystals of L-isoleucine, C6H13O2N, have been studied by Raman spectroscopy at temperatures from 17 to 290 K over the spectral range 20–3300 cm−1. No evidence of a structural phase transition in this temperature range is found, although some splitting of bands associated with the internal modes has been observed. A tentative assignment of the modes is also given. Copyright © 2006 John Wiley & Sons, Ltd.
In vitro imaging of cells using peptide-conjugated quantum dots

Efficient intracellular delivery of quantum dots (QDs) in living cells and elucidating the mechanism of the delivery are essential for advancing the applications of QDs to in vivo imaging and in vivo photodynamic therapy. Here, we demonstrate that clathrin-mediated endocytosis is the most dominant pathway for the delivery of peptide-conjugated QDs. We selected an insect neuropeptide, allatostatin (AST1), conjugated with CdSe-ZnS QDs, and investigated the delivery of the conjugate in living cells. We evaluated the contributions of clathrin-mediated endocytosis, receptormediated endocytosis, and charge-based cell penetration to the delivery of QD605-AST1 conjugates by flow cytometry and fluorescence video microscopy. The delivery was suppressed by ~57% in inhibiting phosphoinositide 3-kinase with wortmannin, which blocks the formation of clathrin-coated vesicles, and by ~45% in incubating the cells at 4°C. Also, we identified clathrin-mediated endocytosis by two-color experiment to find colocalization of QD560-labeled clathrin heavy-chain antibody and QD605-AST1. We further observed reduction of the galanin receptor-mediated delivery of QD605-AST1 by ~8% in blocking the cells with a galanin antagonist, and reduction of charge-based cell penetration delivery by ~30% in removing the positive charge in the peptide from arginine and suppressing the cell-surface negative charge from glycosaminoglycan.
The relationship between skin surface temperature measured via non-contact thermal imaging and intra-muscular temperature of the rectus femoris muscle

Cryotherapy; the application of cold to achieve therapeutic objective, is the most commonly used technique in the acute management of musculoskeletal injuries. Despite superficial application, the deeper tissues are ordinarily the target tissues of cryotherapy application. The relationship between skin surface temperature (Tsk) and intra muscular temperature (Tim) are currently poorly understood. Following clinically relevant 15 minute application of crushed ice (CI) to the Rectus Femoris muscle, Tsk data were collected using Non-contact thermal imaging (TI), simultaneously with Tim by thermistor probe. The relationship between the 2 parameter’s was investigated. A strong negative quadratic relationship was established, suggesting that intramuscular cooling occurred as Tsk increased. The time period following removal of cold modality should therefore be considered an important part of cryotherapy treatment sessions to achieve full therapeutic benefit.
Heteronuclear decoupling in rotating solids

A simple two pulse phase modulation (TPPM) scheme greatly reduces the residual linewidths arising from insufficient proton decoupling power in double resonance magic angle spinning (MAS) experiments. Optimization of pulse lengths and phases in the sequence produces substantial improvements in both the resolution and sensitivity of dilute spins (e.g., 13C) over a broad range of spinning speeds at high magnetic field. The theoretical complications introduced by large homo‐ and heteronuclear interactions among the spins, as well as the amplitude modulation imposed by MAS, are explored analytically and numerically. To our knowledge, this method is the first phase‐switched sequence to exhibit improvement over continuous‐wave (cw) decoupling in a strongly coupled homogeneous spin system undergoing sample spinning.
Phthalimide-based π-conjugated small molecules with tailored electronic energy levels for use as acceptors in organic solar cells

The design, synthesis, and characterization of seven phthalimide-based organic π-conjugated small molecules are reported. The new materials are based on a phthalimide–thiophene–CORE–thiophene–phthalimide architecture. The CORE units utilized were phthalimide (M2), diketopyrrolopyrrole (M3), isoindigo (M4), naphthalene diimide (M5), perylene diimide (M6), and difluorobenzothiadiazole (M7); they were specifically selected to progressively increase the electron affinity of the resulting compound. A small molecule with no core (M1) was synthesized for comparison. Each material was synthesized through optimized direct heteroarylation cross-coupling procedures using bench top solvents in air. Combinations of UV-visible spectroscopy (UV-vis), cyclic voltammetry (CV), differential scanning calorimetry (DSC), ultraviolet photoelectron spectroscopy (UPS) and density functional theory (DFT) were used to characterize each material. The use of various core acceptor building blocks with differing electron affinities resulted in the series M1–M7 having a range of energetically deep LUMO levels and a range of HOMO–LUMO gap energies. Meanwhile, the melting and crystallization temperatures of the molecules M1–M7 were also found to vary according to the change in central acceptor unit. Compounds M1–M7 were employed as acceptors in combination with either the polymeric donor P3HT or small molecule donor DTS(FBTTh2)2 to understand how the LUMO levels of each acceptor influences the open circuit voltage (Voc). It was found that, in general, Voc was only weakly related to the offset between the HOMO energy level of the donor and LUMO level of the acceptor used, with a Voc of up to 1.2 V being achieved for M1.
Desenvolvimento e estudo da estabilidade físico-química de emulsões múltiplas A/O/A E O/A/O acrescidas de filtros químicos e manteiga de karité

RESUMO. O objetivo deste trabalho foi desenvolver e avaliar a estabilidade fisico-quimica de emulsoes multiplas A/O/A e O/A/O acrescidas de filtros quimicos e manteiga de karite. As formulacoes foram preparadas pelo metodo de duas etapas e permaneceram em observacao durante uma semana para analise visual, sendo que a mais estavel foi selecionada para prosseguimento dos estudos. A avaliacao da estabilidade foi realizada em diferentes temperaturas (estufa, geladeira e temperatura ambiente) durante 30 dias, avaliando-se as caracteristicas organolepticas, pH e viscosidade. Os resultados evidenciaram que a formulacao mantida em temperatura ambiente e em geladeira apresentou maior estabilidade fisico-quimica e menor variacao de viscosidade no periodo analisado, sendo que a temperatura influenciou nos valores de viscosidade. Conclui-se que e possivel formular emulsoes multiplas A/O/A estaveis com metoxicinamato de isoamila e manteiga de karite. SUMMARY. “Development and Study of the Physicochemical Stability of W/O/W and O/W/O Multiple Emulsions increased of Chemical Filters and Shea Butter”. The aim of this work was to develope and evaluate the physical-chemistry stability of W/O/W and O/W/O multiple emulsions increased of chemical filters and shea butter. The formulations were prepared using the two-step procedure and remained in observation during one week for visual analysis, and the most steady was selected for continuation the studies. The stability evaluation was performed at different temperatures (oven, refrigerator and room temperature) over 30 days and its organoleptic characteristics, pH and viscosity were evaluated. The results evidenced that the formulation kept at room temperature and refrigerator presented greater physical-chemistry stability and minor variation of viscosity in the analyzed period, the temperature influencing in the viscosity values. It was concluded that is possible to formulate A/O/A multiple emulsions steady with isoamyl methoxycinnamate and shea butter.
Four ways to introduce structure in fluidized bed reactors

Just like for fixed bed reactors, the rational structuring of fluidized beds is interesting from the point of view of process intensification. Structuring can facilitate scale-up and increase conversion and selectivity by controlling the size and the spatial distribution of the bubbles. We present four approaches to structure fluidized beds: oscillating the gas flow, imposing an electric field to induce interparticle forces, distributing the gas injection, and optimizing distributed particle properties such as particle size. Experimentally, we show that these methods can indeed lead to a drastic reduction of the bubble diameter in bubbling fluidized beds for a range of operating conditions. For two methodologies, imposing an electric field and distributing the gas injection, also a considerable increase in conversion is demonstrated.
Sol-gel processing of PZT thin films: A review of the state-of-the-art and process optimization strategies

Abstract Sol-gel processing has been widely employed for the fabrication of lead zirconate titanate (PZT) thin films. To successfully optimize thin film material properties for different applications, we must develop a fundamental understanding of the processing-property relationships inherent in the sol-gel fabrication process. In the asprepared state, sol-gel thin films are amorphous, have large organic contents, and can possess significant porosity. The preparation of thin films with acceptable properties requires that we effectively control densification and crystallization of the as-deposited film. We have determined that this “structural evolution” into the dense, crystalline ceramic phase may be affected by many aspects of the preparation process. In this paper we review the effects that tailored solution precursor characteristics and heat-treatment ramp rate can have on structural evolution. Specific examples are presented for process variation effects on the densification of thin films in the mod.
UVTRAN: An Ultraviolet Transmission and Lidar Simulation Model.

Abstract : UVTRAN is a user friendly, ultraviolet and visible wavelength, propagation and lidar model. The computer program is available as both a generic FORTRAN code and as a mighty interactive Visual Basic Ver. 3, MS Windows. The transmission code currently uses a modified Koshmeider aerosol model for the aerosol attenuation. It uses a modified Rayleigh scattering model for the attenuation due to molecular scattering, and it uses average molecular absorption data for ozone, oxygen and trace gas attenuation. The wavelength range is 200 to 700 nm. The principle inputs are: range in kilometers, visibility in kilometers, and wavelength in nanometers. Other inputs are: gas concentration in parts per billion, the wavelength interval for calculations, and the range information (starting and ending ranges), and the interval for the range calculation. Default values are built into the model if the user does not know sensible values to use. The last values used in a calculation are saved and can be reused for the next calculations. A 1976 standard atmosphere is used for gas concentration but can be user defined. The Windows version of the program has plotting capability while the FORTRAN version allows the information to be printed to a data file and plotted externally. This version also has options for viewing and printing the date. The lidar model includes the UVTRAN model for the two-way atmospheric attenuation of the beam. The lidar model performs standard elastic back scattering calculations as a function of range, and it will also perform fluorescence lidar calculations. Inputs are the same for the UVTRAN model, but also include the likar inputs such as back scattering cross section (or fluorescence back scattering) and the lidar system parameters (wavelength, power, mirror size, system efficiency).