gebhart/patrepeval huggingface dataset:
Sequence occurrence and structural uniqueness of a G-quadruplex in the human c-kit promoter (2007)

The 22-nt c-kit87 promoter sequence is unique within the human genome. Its fold and tertiary structure have recently been determined by NMR methods [Phan,A.T., Kuryavyi,V., Burge,S., Neidle,S. and Patel,D.J. (2007) Structure of an unprecedented G-quadruplex scaffold in the c-kit promoter. J. Am. Chem. Soc., 129, 4386-4392], and does not have precedent among known DNA quadruplexes. We show here using bioinformatics and molecular dynamics simulations methods that (i) none of the closely related sequences (encompassing all nucleotides not involved in the maintenance of structural integrity) occur immediately upstream (<100 nt) of a transcription start site, and (ii) that all of these sequences correspond to the same stable tertiary structure. It is concluded that the c-kit87 tertiary structure may also be formed in a very small number of other loci in the human genome, but the likelihood of these playing a significant role in the expression of particular genes is very low. The c-kit87 quadruplex thus fulfils a fundamental criterion of a 'good' drug target, in that it possesses distinctive three-dimensional structural features that are only present in at most a handful of other genes.
The isolation and characterization of renal cancer initiating cells from human Wilms' tumour xenografts unveils new therapeutic targets (2012)

There are considerable differences in tumour biology between adult and paediatric cancers. The existence of cancer initiating cells/cancer stem cells (CIC/CSC) in paediatric solid tumours is currently unclear. Here, we show the successful propagation of primary human Wilms' tumour (WT), a common paediatric renal malignancy, in immunodeficient mice, demonstrating the presence of a population of highly proliferative CIC/CSCs capable of serial xenograft initiation. Cell sorting and limiting dilution transplantation analysis of xenograft cells identified WT CSCs that harbour a primitive undifferentiated-NCAM1 expressing-"blastema" phenotype, including a capacity to expand and differentiate into the mature renal-like cell types observed in the primary tumour. WT CSCs, which can be further enriched by aldehyde dehydrogenase activity, overexpressed renal stemness and genes linked to poor patient prognosis, showed preferential protein expression of phosphorylated PKB/Akt and strong reduction of the miR-200 family. Complete eradication of WT in multiple xenograft models was achieved with a human NCAM antibody drug conjugate. The existence of CIC/CSCs in WT provides new therapeutic targets.
An Unique Methodology to Estimate The Thermal Time Constant and Dynamic Self Heating Impact for Accurate Reliability Evaluation in Advanced FinFET Technologies (2018)

The increasing impact of self-heating effect (SHE) in complex FinFET structure is a serious reliability concern. Although the evaluation of SHE has become extremely arduous; this work proposes an in-situ layout based experimental solution to find out the precise thermal time constant (T <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH</inf> ) due to SHE on advanced FinFET devices, even with the application of very pragmatic ‘circuit-like’ gate and drain input waveforms. Using this precise T <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TH</inf> , the accurate dynamic thermal profile is found out from SPICE simulations. Finally, the true degradations due to different reliability mechanisms are evaluated including SHE impact and successfully compared with measured FinFET silicon data.
Highly-branched vertically-oriented graphene nanosheets with dense open graphitic edge planes as Pt support for methanol oxidation (2013)

Vertically-oriented graphene (VG) with predominantly edge plane structure is considered as a promising catalyst support candidate for the methanol oxidation reaction (MOR) in direct methanol fuel cells (DMFCs). Inspired by the fact that catalyst nanoparticles are spontaneously attached to the exposed graphene edges, a novel highly-branched vertically-oriented graphene (HBVG) based catalyst support is proposed in the current work. With employing atmospheric normal glow discharge (ANGD) and microwave plasma-enhanced chemical vapor deposition (PECVD) methods, HBVG and maze-like VG (MVG) are synthesized on the surface of carbon paper (CP), respectively. Pt nanoparticles are deposited on pristine CP, HBVG-CP, and MVG-CP with the same route of repeated double-potential pulse electrodeposition (RDPE). Experimental results show that HBVG-CP with dense open graphitic edge planes can desirably provide a considerable number of nuclei sites for the fast nucleation and well dispersion of Pt nanoparticles. Meanwhile, a certain amount of oxygen-containing functional groups on the HBVG surface will benefit the rapid removal of CO and accumulated carbonaceous species. Based on the electrochemical measurements on Pt utilization efficiency, catalytic activity, CO tolerance, and long-term stability, Pt/HBVG-CP is demonstrated to be able to present enhanced catalytic performance over the Pt/CP and Pt/MVG-CP counterparts, holding a great potential for fuel cell applications.
Composite induction consolidation apparatus and method (2023)

A composite induction consolidation apparatus includes a base mandrel and a ferromagnetic base mandrel facesheet having a specific Curie temperature carried by the base mandrel. The base mandrel facesheet is adapted to support a composite part and allow ambient air pressure to compact the composite part against the base mandrel facesheet. At least one magnetic induction coil is provided in the base mandrel.
Controlling the electrical, optical, and morphological properties of sol–gel spin-coated indium tin oxide films (2021)

In this research, transparent conductive films of indium tin oxide (ITO) were deposited by solution processing sol–gel ink through spin coating on soda-lime glass and sheet glass substrates. The processing parameters evaluated include the deposition humidity, spin coating speed, and ink concentration. The optical transmittance of the ITO thin films was collected by UV–vis spectrophotometry, while the electrical properties were studied by sheet resistance measurements and impedance spectroscopy (IS) using an in-plane configuration. The lowest sheet resistance achieved for a single layer film is 104 Ω/□, with a corresponding low frequency impedance magnitude of 2 × 105. These values were obtained at medium humidity values while maintaining high optical transparency (&amp;gt;90%) in the visible light region. High humidity values were found to affect the substrate wetting property of the ITO ink and increased the possibility of hydrolysis during deposition, resulting in the formation of non-uniform surface patterns. A spin coating speed of 4000 rpm or more is required to obtain a uniform ITO film with desirable electrical and optical properties. Once the optimum combination of parameters is obtained, the sheet resistance and impedance magnitude can be reduced to ∼102 Ω/□ through multilayer deposition and annealing in a reducing atmosphere with minimal effect on the optical transmittance (&amp;gt;90%) and surface morphology, making these materials useful as electrodes for electro-optic applications. When the optimal values of the main deposition parameters are used, the ink concentration was found to have minimal effect on the quality and properties of the ITO films.
Evidence for in vitro extensive proliferation of adult hepatocytes and biliary epithelial cells (2023)

Over the last several years, a method has emerged that endows adult hepatocytes with in vitro proliferative capacity, producing chemically induced liver progenitors (CLiPs). However, there is a growing controversy regarding the origin of these cells. Here, we provide lineage tracing-based evidence that adult hepatocytes acquire proliferative capacity in vitro using rat and mouse models. Unexpectedly, we also found that the CLiP method allows biliary epithelial cells to acquire extensive proliferative capacity. Interestingly, after long-term culture, hepatocyte-derived cells (hepCLiPs) and biliary epithelial cell-derived cells (bilCLiPs) become similar in their gene expression patterns, and they both exhibit differentiation capacity to form hepatocyte-like cells. Finally, we provide evidence that hepCLiPs can repopulate injured mouse livers, reinforcing our earlier argument that CLiPs can be a cell source for liver regenerative medicine. This study advances our understanding of the origin of CLiPs and motivates the application of this technique in liver regenerative medicine.
The physical origins of low surface tensions (1999)

The minimum surface tension and respreadability of a surfactant monolayer is limited by a two to three dimensional instability called collapse. Liquid-condensed or solid phase monolayers collapse via fracture followed by loss of material. Liquid-expanded monolayers collapse by solubilization into the subphase. Monolayers that retain a continuous LE phase network surrounding islands of LC or S phase collapse at lower surface tensions via a localized, large amplitude buckling. The buckled regions coexist with the flat monolayer, remain attached to the interface and are reversibly reincorporated into the monolayer upon expansion. Synthetic replacement surfactants must be designed to reproduce this unique phase behavior for optimal function.
Time delay estimation: Compressed sensing over an infinite union of subspaces (2010)

Sampling theorems for signals that lie in a union of subspaces have been receiving growing interest. A recent model that describes analog signals over a union is that of a union of shift-invariant (SI) subspaces. Until now, sampling and recovery algorithms have been developed only for a finite union of SI subspaces. Here we extend this paradigm to a special case of an infinite union, in which the SI subspaces are generated by pulses with unknown delays, taken from a continuous interval. We develop a unified approach to time delay recovery of the pulses, from low rate samples of the signal taken at the lowest possible rate. In particular, we derive sufficient conditions on the pulses and the sampling filters in order to ensure perfect recovery of the signal. We then show that by properly manipulating the low-rate samples, the time delays can be recovered using the well-known ESPRIT algorithm.
Analysis of the Kirk Effect in Silicon-Based Bipolar Transistors With a Nonuniform Collector Profile (2005)

In this paper, the Kirk effect has been analyzed for silicon-based bipolar transistors (BJTs) with a nonuniform collector profile. We show that, for any arbitrary collector doping profile, the Kirk effect starts when the electron concentration equals the average doping concentration in the depletion region. We present a basic guideline for determining the collector current density at the onset of Kirk effect (J/sub K/) for any collector doping profile and simple expressions for J/sub K/ and the electrical field in the collector drift region for the case of a linearly graded collector drift region. These analytical expressions are verified with device simulations. The Kirk effect for this kind of transistor is substantially different from that presented previously for transistors having a uniform collector drift region. For example, the possibility of the onset of the Kirk effect in a partially depleted collector occurs, while in a uniform collector profile the effect can only occur in a fully depleted collector. Our expressions can be used to do approximate analytical calculations for optimizing future BJTs.
Nitrogen-Doped Graphene Oxide Electrocatalysts for the Oxygen Reduction Reaction (2019)

Platinum group metal-free (PGM-free) electrocatalysts for the oxygen reduction reaction (ORR) often exhibit a complex functionalized graphitic structure. Because of this complex structure, limited understanding exists about the design factors for the synthesis of high-performing materials. Graphene, a two-dimensional hexagonal structure of carbon, is amenable to structural and functional group modifications, making it an ideal analogue to study crucial properties of more complex graphitic materials utilized as electrocatalysts. In this paper, we report the synthesis of active nitrogen-doped graphene oxide catalysts for the ORR in which their activity and four-electron selectivity are enhanced using simple solvent and electrochemical treatments. The solvents, chosen based on Hansen’s solubility parameters, drive a substantial change in the morphology of the functionalized graphene materials by (i) forming microporous holes in the graphitic sheets that lead to edge defects and (ii) inducing 3D structure in the graphitic sheets that promotes ORR. Additionally, the cycling of these catalysts has highlighted the multiplicity of the active sites, with different durability, leading to a highly selective catalyst over time, with a minimal loss in performance. High ORR activity was demonstrated in an alkaline electrolyte with an onset potential of ∼1.1 V and half-wave potential of 0.84 V vs RHE. Furthermore, long-term stability potential cycling showed minimal loss in half-wave potential (<3%) in both N2- and O2-saturated solutions with improved selectivity toward the four-electron reduction after 10000 cycles. The results described in this work provide additional understanding about graphitic electrocatalysts in alkaline media that may be utilized to further enhance the performance of PGM-free ORR electrocatalysts.
Diffusion and dynamical transition in hierarchical systems (1987)

We have recently found a phase transition in the dynamics of a particle that diffuses in the presence of a hierarchical array of barriers. The transition occurs as R, a parameter that controls the relative size of the barriers, is varied. For R&gt;${R}_{c}$, the system is diffusive; as R\ensuremath{\rightarrow}${R}_{c}^{+}$ the diffusion constant vanishes. For R${R}_{c}$, the system is subdiffusive; the mean-square displacement grows slower than linearly with time, with an exponent that varies continuously with R. Analytic as well as numerical renormalization-group methods are introduced and used to solve some specific models; however, the tools developed here are applicable to more general situations as well. In one dimension we present, in addition to a renormalization-group solution for the asymptotic behavior, several new results; in particular, scaling arguments that predict transient behavior as well. We show that the asymptotic regime is approached algebraically, on time scales that obey a law of a Vogel-Fulcher form near the transition. Higher-dimensional systems that also have such a transition are introduced and studied. Finally, possible connections to many-body systems such as dynamic spin models and glassy materials are suggested and discussed.
Academic-Practice Collaborations in Automation and Control: Keys for Success (2022)

This study identifies the keys for successful collaboration between the communities of academia and practice in the field of automation and control. The findings are based on the analysis of 85 different collaborations reported in a survey of the international control community conducted by the Industry and Education Committees at IFAC. Addressing a joint problem, understanding and respecting each other, frequent communication, and adequate funding are among the top attributes of successful collaboration. A complete list of the top 10 keys for success is provided in the conclusion section.
Layer pseudospin skyrmions and topological moir\'e bands in twisted homobilayers (2018)

We show that moir\'e bands of homobilayer van der Waals materials can be topologically nontrivial, and illustrate the tendency by studying valence band states in the $\pm K$ valleys of twisted semiconducting transition metal dichalcogenides (TMDs). Because of the large spin-orbit splitting at their monolayer valence band maxima, the low energy bands of TMD homobilayers can be described using a two-band model with a layer-pseudospin magnetic field $\boldsymbol{\Delta}(\boldsymbol{r})$ that has the periodicity of the moir\'e pattern. We show that for balanced bilayers $\boldsymbol{\Delta}(\boldsymbol{r})$ has a topologically non-trivial skyrmion lattice texture in real space, and that the topmost moir\'e valence bands provide an accurate realization of the Kane-Mele quantum spin-Hall model. When the bilayer is polarized by a vertical displacement potential, the band Chern numbers are driven to zero before $\boldsymbol{\Delta}(\boldsymbol{r})$ becomes topologically trivial. Because the bands narrow at small twist angles, a rich set of broken symmetry insulating states can occur when the number of electrons per moir\'e unit cell is an integer.
Development of vacuum underfill technology for a 3D chip stack (2011)

We developed a vacuum underfill technology for 3D chip stacks and for flip chips in high performance system integration. We fabricated a 3D prototype chip stack using the vacuum underfill technology to apply the adhesive. The underfill was injected into each 6 µm gaps in a 3-layer chip stack and no voids were detected in acoustic microscopy images. Electrical tests and thermal reliability tests were used to measure the resistance of the vertical interconnections and the impact of the underfill. The results showed there was minimal difference in the average interconnection resistance of the chip stack with and without underfill.
Multivariate genetic determinants of EEG oscillations in schizophrenia and psychotic bipolar disorder from the BSNIP study (2015)

Schizophrenia (SZ) and psychotic bipolar disorder (PBP) are disabling psychiatric illnesses with complex and unclear etiologies. Electroencephalogram (EEG) oscillatory abnormalities in SZ and PBP probands are heritable and expressed in their relatives, but the neurobiology and genetic factors mediating these abnormalities in the psychosis dimension of either disorder are less explored. We examined the polygenic architecture of eyes-open resting state EEG frequency activity (intrinsic frequency) from 64 channels in 105 SZ, 145 PBP probands and 56 healthy controls (HCs) from the multisite BSNIP (Bipolar-Schizophrenia Network on Intermediate Phenotypes) study. One million single-nucleotide polymorphisms (SNPs) were derived from DNA. We assessed eight data-driven EEG frequency activity derived from group-independent component analysis (ICA) in conjunction with a reduced subset of 10,422 SNPs through novel multivariate association using parallel ICA (para-ICA). Genes contributing to the association were examined collectively using pathway analysis tools. Para-ICA extracted five frequency and nine SNP components, of which theta and delta activities were significantly correlated with two different gene components, comprising genes participating extensively in brain development, neurogenesis and synaptogenesis. Delta and theta abnormality was present in both SZ and PBP, while theta differed between the two disorders. Theta abnormalities were also mediated by gene clusters involved in glutamic acid pathways, cadherin and synaptic contact-based cell adhesion processes. Our data suggest plausible multifactorial genetic networks, including novel and several previously identified (DISC1) candidate risk genes, mediating low frequency delta and theta abnormalities in psychoses. The gene clusters were enriched for biological properties affecting neural circuitry and involved in brain function and/or development.
Simultaneous Data Reconciliation and Parameter Estimation in Bulk Polypropylene Polymerizations in Real Time (2006)

Abstract This work presents the implementation of a methodology for dynamic data reconciliation and simultaneous estimation of quality and productivity parameters in real time, using data from an industrial bulk Ziegler‐Natta propylene polymerization process. A phenomenological model of the real process, based on mass and energy balances, was developed and implemented for interpretation of actual plant data. The resulting nonlinear dynamic optimization problem was solved using a sequential approach on a time window specifically tuned for the studied process. Despite the essentially isothermal operation conditions, obtained results show that inclusion of energy balance constraints allows for increase of information redundancy and, as a consequence, for computation of better parameter estimates than the ones obtained when the energy balance constraints are not considered (Prata et al ., 2005). Examples indicate that the proposed technique can be used very effectively for monitoring of polymer quality and identification of process malfunctions in real time even when laboratory analyses are scarce.
Decreased Activation Rate of Insulin-Stimulated Glucose Transport in Adipocytes From Obese Subjects (1989)

Recent studies from our laboratory have shown that the rate at which insulin activates glucose disposal in vivo is much slower in obese subjects compared with lean controls. To determine if this was caused by an abnormality in activation of insulin-stimulated glucose transport at the cellular level, we measured the rate at which insulin stimulated glucose transport in human adipocytes from obese volunteers. Basal rates of 3-O-methylglucose transport in the absence of insulin were lower (0.20 +/- 0.04 vs. 0.40 +/- 0.11 pmol.10(-5) cells.10 s-1, P less than .25) in adipocytes from obese subjects (n = 10) than in lean control subjects (n = 5), but this did not achieve statistical significance. Maximal insulin-stimulated (4300 pM insulin) glucose transport rates were significantly decreased in obesity (2.81 +/- 0.81 vs. 1.15 +/- 0.20 pmol.10(-5) cells.10 s-1, P less than .005). It took longer for adipocytes from obese subjects to achieve half-maximal activation of insulin-stimulated glucose transport than those from lean subjects (15 +/- 2 vs. 9.4 +/- 1.2 min, P less than .05). The slower overall rates of activation of maximal insulin-stimulated glucose transport observed in adipocytes from obese subjects mirror the slower rates of stimulation of glucose disposal in vivo, which suggests that the in vivo findings are caused by a cellular abnormality in insulin action at a step beyond the binding of insulin to its receptor.(ABSTRACT TRUNCATED AT 250 WORDS)
Diffusion Analysis across Grain Boundary in Al-3.7 mass%Cu Alloy Using Analytical Electron Microscopy (2003)

An Al–3.7 mass%Cu alloy was subjected to aging treatment at selected temperatures in the range from 453 to 548 K. Diffusion coefficients of Cu in the alloy were then determined from Cu concentration profiles measured across the grain boundary. A high spatial resolution analytical electron microscope (AEM) capable of forming a 1 nm probe was used to measure the concentration profiles. As the aging temperature is lower, the diffusion coefficients tend to deviate from the values extrapolated from the higher annealing temperatures. It is suggested that this deviation is due to the presence of quenched-in excess vacancies. The concentration profiles were also measured for the boundaries having different misorientation angles. It is shown that the concentration profiles are essentially the same regardless of the misorientation angles and of the boundary characters except for the misorientation angles smaller than a few degrees.