gebhart/patrepeval huggingface dataset:
Distribution of Mitochondrial NADH Fluorescence Lifetimes:  Steady-State Kinetics of Matrix NADH Interactions (2005)

The lifetimes of fluorescent components of matrix NADH in isolated porcine heart mitochondria were investigated using time-resolved fluorescence spectroscopy. Three distinct lifetimes of fluorescence were resolved: 0.4 (63%), 1.8 (30%), and 5.7 (7%) ns (% total NADH). The 0.4 ns lifetime and the emission wavelength of the short component were consistent with free NADH. In addition to their longer lifetimes, the remaining pools also had a blue-shifted emission spectrum consistent with immobilized NADH. On the basis of emission frequency and lifetime data, the immobilized pools contributed >80% of NADH fluorescence. The steady-state kinetics of NADH entering the immobilized pools was measured in intact mitochondria and in isolated mitochondrial membranes. The apparent binding constants (K(D)s) for NADH in intact mitochondria, 2.8 mM (1.9 ns pool) and >3 mM (5.7 ns pool), were on the order of the estimated matrix [NADH] (approximately 3.5 mM). The affinities and fluorescence lifetimes resulted in an essentially linear relationship between matrix [NADH] and NADH fluorescence intensity. Mitochondrial membranes had shorter emission lifetimes in the immobilized poo1s [1 ns (34%) and 4.1 ns (8%)] with much higher apparent K(D)s of 100 microM and 20 microM, respectively. The source of the stronger NADH binding affinity in membranes is unknown but could be related to high order structure or other cofactors that are diluted out in the membrane preparation. In both preparations, the rate of NADH oxidation was proportional to the amount of NADH in the long lifetime pools, suggesting that a significant fraction of the bound NADH might be associated with oxidative phosphorylation, potentially in complex 1.
Thermal modeling and characterization of Package with Through-Silicon-Vias (TSV) Interposer (2011)

Numerical simulation of micro-bumped flip chips mounted on a TSV interposer is conducted to study the thermal performance of the package. The 3D package, which consists of two chips, each dissipating 4W, is evaluated under various conditions with its thermal resistances θ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">ja</sub> θ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">jb</sub> , θ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">jc</sub> and θ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">jma</sub> determined according to JEDEC or MIL-STD standard. Instead of building the detailed model, equivalent thermal conductivity model is adopted for anisotropic bump-underfill layers, silicon interposer and the substrates. Effects of design parameters to the waste heat dissipation, such as the density of TSV in the interposer and the presence of mold encapsulation are investigated. In addition, maximum power dissipation of the package is explored. These modeling results are useful for design optimisation, and also to provide thermal design guideline for a reliable, high performance, and cost-effective 3D package.
Robustness of sub-70 nm dynamic circuits: analytical techniques and scaling trends (2002)

We present an accurate (to within 3%, across two process generations), three parameter, closed form, time-domain technique for evaluating the noise response of domino circuits. We evaluate the robustness of scaled topologies to show that conventional domino circuits will cease to be useful around the 70 nm generation. The paper concludes with possible device/circuit approaches to extend domino circuit usefulness.
Strategies to Improve Recruitment to a De-escalation Trial: A Mixed-Methods Study of the OPTIMA Prelim Trial in Early Breast Cancer (2020)

This is the first study illuminating the tension between oncologists' routine practices and recruitment to de-escalation trials. Although time and resources are required, these challenges can be addressed through specific feedback and training as the trial is underway.
WikiAnalytics: Ad-hoc querying of highly heterogeneous structured data (2010)

Searching and extracting meaningful information out of highly heterogeneous datasets is a hot topic that received a lot of attention. However, the existing solutions are based on either rigid complex query languages (e.g., SQL, XQuery/XPath) which are hard to use without full schema knowledge, without an expert user, and which require up-front data integration. At the other extreme, existing solutions employ keyword search queries over relational databases, as well as over semistructured data, which are too imprecise to specify exactly the user's intent. To address these limitations, we propose an alternative search paradigm in order to derive tables of precise and complete results from a very sparse set of heterogeneous records. Our approach allows users to disambiguate search results by navigation along conceptual dimensions that describe the records. Therefore, we cluster documents based on fields and values that contain the query keywords. We build a universal navigational lattice (UNL) over all such discovered clusters. Conceptually, the UNL encodes all possible ways to group the documents in the data corpus based on where the keywords hit. We describe, WikiAnalytics, a system that facilitates data extraction from the Wikipedia infobox collection. WikiAnalytics provides a dynamic and intuitive interface that lets the average user explore the search results and construct homogeneous structured tables, which can be further queried and mashed up (e.g., filtered and aggregated) using the conventional tools.
ChemInform Abstract: Unnatural Amino Acids for the Design of Functional Proteins: Biomimetic Catalysis Using Coenzyme Amino Acids (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Modeling HCCI using CFD and Detailed Chemistry with Experimental Validation and a Focus on CO Emissions (2007)

Multi-zone CFD simulations with detailed kinetics were used to model engine experiments performed on a diesel engine that was converted for single cylinder, HCCI operation, here using iso-octane as the fuel. The modeling goals were to validate the method (multi-zone combustion modeling) and the reaction mechanism (LLNL 857 species iso-octane), both of which performed very well. The purpose of this paper is to document the validation findings and to set the ground work for further analysis of the results by first looking at CO emissions characteristics with varying equivalence ratio.
The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods (2011)

The Protein Structure Initiative's Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org ) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI's high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology.
How to Mobilize Mmwave: A Joint Beam and Channel Tracking Approach (2018)

Maintaining reliable millimeter wave (mmWave) connections to many fast-moving mobiles is a key challenge in the theory and practice of 5G systems. In this paper, we develop a new algorithm that can jointly track the beam direction and channel coefficient of mm Wave propagation paths using phased antenna arrays. Despite the significant difficulty in this problem, our algorithm can simultaneously achieve fast tracking speed, high tracking accuracy, and low pilot overhead. In static scenarios, this algorithm can converge to the minimum Cramér-Rao lower bound of beam direction with high probability. Simulations reveal that this algorithm greatly outperforms several existing algorithms. Even at SNRs as low as 5dB, our algorithm is capable of tracking a mobile moving at an angular velocity of 5.45 degrees per second and achieving over 95% of channel capacity with a 32-antenna phased array, by inserting only 10 pilots per second.
Physiologic Effects of Exogenous Dextrose in Murine Klebsiella pneumoniae Sepsis Vary by Route of Provision (2020)

Sepsis is characterized by a dysregulated immune response to infection. Nutrition is important in the care of septic patients, but the effects of specific nutrients on inflammation in sepsis are not well defined. Our prior work has shown benefits from early enteral dextrose infusion in a preclinical endotoxemia model of sepsis. In the current study, we extend our initial work to examine the effects of dextrose infusions, varying by route of administration, on inflammation and glycemic control in a more clinically relevant and translational model of <i>Klebsiella pneumoniae</i> (KP) bacteremia. Ten-week old C57BL6/J male mice (<i>n</i> = 31) underwent the implantation of indwelling vascular catheters, followed by inoculation with oropharyngeal KP. The mice were randomized 24 h after inoculation to (1) intravenous (IV) dextrose, (2) enteral dextrose, or (3) enteral saline (control) to study the effects on systemic inflammation, hemodynamics, and glycemic control. At 72 h, 77% of the control mice died, whereas IV dextrose induced 100% mortality, associated with increased inflammation, hyperglycemia, and hypotension. Enteral dextrose reduced mortality to 27%, promoted euglycemia, and reduced inflammation compared to IV dextrose. We conclude, in a bacteremic model of sepsis, that enteral (but not IV) dextrose administration is protective, suggesting that the route of nutrient support influences inflammation in sepsis.
A novel platform simulating irregular motion to enhance assessment of respiration‐correlated radiation therapy procedures (2005)

Respiratory motion continues to present challenges in the delivery of radiation therapy to tumors in the thorax and abdomen by causing movement of structures within those areas. Several approaches to account for this movement in the planning and delivery of treatment have been developed over the past several years. To assist in the development and assessment of various techniques for respiration-correlated radiation therapy, a platform capable of programmable irregular longitudinal motion has been designed and fabricated to simulate intrafractional respiratory motion. A sliding platform and the base on which it was mounted were constructed from polycarbonate plastic, and a stepper motor provided platform motion. Respiratory motion data, either artificially generated on a spreadsheet or extracted from respiratory monitoring files, were converted to a format appropriate for driving the stepper motor. Various phantoms were placed on top of the platform and used in studies related to respiration-correlated radiation therapy. Several applications of the platform were demonstrated, such as improving the quality of acquisition of time-dependent computed tomography image datasets, comparing various methods of acquiring such datasets, and implementing feedback-guided breath hold treatment delivery procedures. This study showed that a platform capable of programmable irregular motion is a useful tool for the development and assessment of procedures related to the effects of respiratory motion in radiation therapy.
The Effects of Granularity and Adaptivity on Private/Shared Classification for Coherence (2015)

Classification of data into private and shared has proven to be a catalyst for techniques to reduce coherence cost, since private data can be taken out of coherence and resources can be concentrated on providing coherence for shared data. In this article, we examine how granularity—page-level versus cache-line level—and adaptivity—going from shared to private—affect the outcome of classification and its final impact on coherence. We create a classification technique, called Generational Classification , and a coherence protocol called Generational Coherence, which treats data as private or shared based on cache-line generations. We compare two coherence protocols based on self-invalidation/self-downgrade with respect to data classification. Our findings are enlightening: (i) Some programs benefit from finer granularity, some benefit further from adaptivity, but some do not benefit from either. (ii) Reducing the amount of shared data has no perceptible impact on coherence misses caused by self-invalidation of shared data, hence no impact on performance. (iii) In contrast, classifying more data as private has implications for protocols that employ write-through as a means of self-downgrade, resulting in network traffic reduction—up to 30%—by reducing write-through traffic.
The Full Function Test Explosive Generator (2009)

We have conducted three tests of a new pulsed power device called the Full Function Test (FFT). These tests represented the culmination of an effort to establish a high energy pulsed power capability based on high explosive pulsed power (HEPP) technology. This involved an extensive computational modeling, engineering, fabrication, and fielding effort. The experiments were highly successful and a new US record for magnetic energy was obtained.
Examining a DNA Replication Requirement for Bacteriophage λ Red- and Rac Prophage RecET-Promoted Recombination in Escherichia coli (2016)

Bacteriophage homologous recombination systems are widely used for in vivo genetic engineering in bacteria. Single- or double-stranded linear DNA substrates containing short flanking homologies to chromosome targets are used to generate precise and accurate genetic modifications when introduced into bacteria expressing phage recombinases. Understanding the molecular mechanism of these recombination systems will facilitate improvements in the technology. Here, two phage-specific systems are shown to require exposure of complementary single-strand homologous targets for efficient recombination; these single-strand regions may be created during DNA replication or by single-strand exonuclease digestion of linear duplex DNA. Previously, in vitro studies reported that these recombinases promote the single-strand annealing of two complementary DNAs and also strand invasion of a single DNA strand into duplex DNA to create a three-stranded region. Here, in vivo experiments show that recombinase-mediated annealing of complementary single-stranded DNA is the predominant recombination pathway in E. coli.
Electrodeposition of tungsten from EMPyrCl-ZnCl<sub>2</sub> melts at 150ºC (2010)

Electrodeposition of tungsten has been achieved at 150°C, which is the lowest temperature to this day, by using a new molten salt (ionic liquid), N-ethyl-N-methylpyrrolidinium chloride (EMPyrCl)-ZnCl2. Metallic tungsten was electrodeposited on a nickel substrate by potentiostatic electrolysis at 0.01 V vs. Zn(II)/Zn in an equimolar EMPyrCl-ZnCl2 melt after adding KF and WCl4. A denser and smoother tungsten film was obtained by the same electrolysis condition when WCl6 was used as a tungsten ion source.
Adjusting the functional properties of niobium carbide (2016)

The process window and range of functional properties of NbC is wide, because micro-hardness, hot hardness, sliding wear resistance, elastic modulus and toughness can be tailored by the C/Nb ratio, because Nb4C3, Nb6C5 and other short and long range ordered phases occur in the region of homogeneity of NbCx (0,75≤ x ≤1.0) in the binary Phase diagram, and by the type of binder. Further improvements enable the addition of secondary carbides. Supporting results from literature and different grades with varying C/Nb ratio or binder types were illuminated. Thus, the NbC system offers to producers a wider process window, than WC. The impact of these tailored properties on sliding wear and cutting performance was illuminated by tribological and machining results. NbC can be synthesized by carbothermal conversion of Nb2O5 or be metallurgically grown in melts and leached out as coarse NbC cubes. NbC provides comparably lower friction in many relevant tribo-contacts and displays low wear. NbC and Nb2O5 have so far no REACH classification related to human toxicology and are not listed as substances of very high concern contrary to WO3 and Co3O4.
Molecular Targeting of Immunosuppressants Using a Bifunctional Elastin-Like Polypeptide (2019)

Elastin-Like Polypeptides (ELP) are environmentally responsive protein polymers which are easy to engineer and biocompatible, making them ideal candidates as drug carriers. Our team has recently utilized ELPs fused to FKBP12 to carry Rapamycin (Rapa), a potent immunosuppressant. Through high affinity binding to Rapa, FKBP carriers can yield beneficial therapeutic effects and reduce the off-site toxicity of Rapa. Since ICAM-1 is significantly elevated at sites of inflammation in diverse diseases, we hypothesized that a molecularly targeted ELP carrier capable of binding ICAM-1 might have advantageous properties. Here we report on the design, characterization, pharmacokinetics, and biodistribution of a new ICAM-1-targeted ELP Rapa carrier (IBPAF) and its preliminary characterization in a murine model exhibiting elevated ICAM-1. Lacrimal glands (LG) of male NOD mice, a disease model recapitulating the autoimmune dacryoadenitis seen in Sjögren's Syndrome patients, were analyzed to confirm that ICAM-1 was significantly elevated in the LG relative to control male BALB/c mice (3.5-fold, <i>p</i> < 0.05, <i>n</i> = 6). In vitro studies showed that IBPAF had significantly higher binding to TNF-α-stimulated bEnd.3 cells which overexpress surface ICAM-1, relative to nontargeted control ELP (AF)(4.0-fold, <i>p</i> < 0.05). A pharmacokinetics study in male NOD mice showed no significant differences between AF and IBPAF for plasma half-life, clearance, and volume of distribution. However, both constructs maintained a higher level of Rapa in systemic circulation compared to free Rapa. Interestingly, in the male NOD mouse, the accumulation of IBPAF was significantly higher in homogenized LG extracts compared to AF at 2 h (8.6 ± 6.6% versus 1.3 ± 1.3%, respectively, <i>n</i> = 5, <i>p</i> < 0.05). This accumulation was transient with no differences detected at 8 or 24 h. This study describes the first ICAM-1 targeted protein-polymer carrier for Rapa that specifically binds to ICAM-1 in vitro and accumulates in ICAM-1 overexpressing tissue in vivo, which may be useful for molecular targeting in diverse inflammatory diseases where ICAM-1 is elevated.
Abstract 1314: Molecular profiling and characterization of patient-derived human pancreatic tumor xenograft models, and application for drug discovery and preclinical development of cancer therapeutics (2012)

Abstract A major obstacle that has hampered the development and assessment of novel anticancer therapies is the inability of the conventional xenograft models to reliably predict clinical efficacy. This is in part due the fact that the cell lines used for these studies are cultured on plastic for extensive passages and lack the human extracellular matrix component that is critical for cancer-stromal cell interactions. Models are needed which more accurately reflect tumor heterogeneity and interaction with the tumor microenvironment in order to more accurately reflect tumor complexity and predict response to therapies in the clinic. This has led to the development of models by directly engrafting cancer patient-derived tumor tissues into immunodeficient mice with the aim of retaining histopathological features and molecular characteristics of the original tumor. A vital question relating to patient-derived tumor xenografts is whether tumor characteristics are maintained during passaging. We have established a number of proprietary pancreatic cancer patient-derived xenografts. Studies were performed to molecularly characterize the xenograft models and to confirm they retain similarity to the original tumors. Original patient tumors and corresponding serial xenograft passages were examined for growth, histopathological features and protein expression, as well as genomic and tumor biomarker status. Examination of these patient-derived xenograft models demonstrated that tumor morphology is maintained upon passaging. Immunohistochemical and qPCR analysis of targets of interest showed that expression levels are consistent between tumors and xenograft passages. Although slight differences were observed in genomic profiles for some individual models after engraftment in mice, whole genome profiling by microarray and aCGH revealed that individual tumor models retain organ-specific characteristics and that xenografts remain stable throughout passaging. Core sets of significantly expressed genes and genomic aberrations were maintained, with some additional changes observed during passaging. Retention of the characteristics of the original donor tumors within the xenograft models, such as tumor architecture and molecular signatures will afford the use of models which more accurately reflect patient tumor biology. Comprehensive molecular characterization of our models was utilized to investigate differential response to our proprietary drug candidates. Expanded testing in multiple models can potentially provide important pre-clinical translational information to help guide clinical trial design regarding patient subpopulations that may be more likely to respond to therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1314. doi:1538-7445.AM2012-1314