gebhart/patrepeval huggingface dataset:
Mutational Analysis of Active Site Residues Essential for Sensing of Organic Hydroperoxides by <i>Bacillus subtilis</i> OhrR (2007)

Bacillus subtilis OhrR is the prototype for the one-Cys family of organic peroxide-sensing regulatory proteins. Mutational analyses indicate that the high sensitivity of the active site cysteine (C15) to peroxidation requires three Tyr residues. Y29 and Y40 from the opposing subunit of the functional dimer hydrogen bond with the reactive Cys thiolate, and substitutions at these positions reduce or eliminate the ability of OhrR to respond to organic peroxides. Y19 is also critical for peroxide sensing, and the Ala substitution mutant (OhrR Y19A) is less susceptible to oxidation at the active site C15 in vivo. The Y19A protein also displays decreased sensitivity to peroxide-mediated oxidation in vitro. Y19 is in van der Waals contact with two residues critical for protein function, F16 and R23. The latter residue makes critical contact with the DNA backbone in the OhrR-operator complex. These results indicate that the high sensitivity of the OhrR C15 residue to oxidation requires interactions with the opposed Tyr residues. Oxidative modification of C15 likely disrupts the C15-Y29'-Y40' hydrogen bond network and thereby initiates conformational changes that reduce the ability of OhrR to bind to its operator site.
Static leakage reduction through simultaneous V/sub t//T/sub ox/ and state assignment (2005)

Standby leakage current minimization is a pressing concern for mobile applications that rely on standby modes to extend battery life. In this paper, we propose new leakage current reduction methods in standby mode. First, we propose a combined approach of sleep-state assignment and threshold voltage (V/sub t/) assignment in a dual-V/sub t/ process for subthreshold leakage (I/sub sub/) reduction. Second, for the minimization of gate oxide leakage current (I/sub gate/) which has become comparable to I/sub sub/ in 90-nm technologies, we extend the above method to a combined sleep-state, V/sub t/ and gate oxide thickness (T/sub ox/) assignments approach in a dual-V/sub t/ and dual-T/sub ox/ process to minimize both I/sub sub/ and I/sub gate/. By combining V/sub t/ or V/sub t//T/sub ox/ assignment with sleep-state assignment, leakage current can be dramatically reduced since the circuit is in a known state in standby mode and only certain transistors are responsible for leakage current and need to be considered for high-V/sub t/ or thick-T/sub ox/ assignment. A significant improvement in the leakage/performance tradeoff is therefore achievable using such combined methods. We formulate the optimization problem for simultaneous state/V/sub t/ and state/V/sub t//T/sub ox/ assignments under delay constraints and propose both an exact method for its optimal solution as well as two practical heuristics with reasonable run time. We implemented and tested the proposed methods on a set of synthesized benchmark circuits and show substantial leakage current reduction compared to the previous approaches using only state assignment or V/sub t/ assignment alone.
Stress evolution due to electromigration in confined metal lines (1993)

Electromigration is an important concern in very large scale integrated circuits. In narrow, confined metal interconnects used at the chip level, the electromigration flux is resisted by the evolution of mechanical stresses in the interconnects. Solutions for the differential equation governing the evolution of back stresses are presented for several representative cases, and the solutions are discussed in the light of experimental as well as theoretical developments from the literature.
Recovery of cortical effective connectivity and recovery of consciousness in vegetative patients (2012)

Patients surviving severe brain injury may regain consciousness without recovering their ability to understand, move and communicate. Recently, electrophysiological and neuroimaging approaches, employing simple sensory stimulations or verbal commands, have proven useful in detecting higher order processing and, in some cases, in establishing some degree of communication in brain-injured subjects with severe impairment of motor function. To complement these approaches, it would be useful to develop methods to detect recovery of consciousness in ways that do not depend on the integrity of sensory pathways or on the subject's ability to comprehend or carry out instructions. As suggested by theoretical and experimental work, a key requirement for consciousness is that multiple, specialized cortical areas can engage in rapid causal interactions (effective connectivity). Here, we employ transcranial magnetic stimulation together with high-density electroencephalography to evaluate effective connectivity at the bedside of severely brain injured, non-communicating subjects. In patients in a vegetative state, who were open-eyed, behaviourally awake but unresponsive, transcranial magnetic stimulation triggered a simple, local response indicating a breakdown of effective connectivity, similar to the one previously observed in unconscious sleeping or anaesthetized subjects. In contrast, in minimally conscious patients, who showed fluctuating signs of non-reflexive behaviour, transcranial magnetic stimulation invariably triggered complex activations that sequentially involved distant cortical areas ipsi- and contralateral to the site of stimulation, similar to activations we recorded in locked-in, conscious patients. Longitudinal measurements performed in patients who gradually recovered consciousness revealed that this clear-cut change in effective connectivity could occur at an early stage, before reliable communication was established with the subject and before the spontaneous electroencephalogram showed significant modifications. Measurements of effective connectivity by means of transcranial magnetic stimulation combined with electroencephalography can be performed at the bedside while by-passing subcortical afferent and efferent pathways, and without requiring active participation of subjects or language comprehension; hence, they offer an effective way to detect and track recovery of consciousness in brain-injured patients who are unable to exchange information with the external environment.
Optimized Metal–Organic-Framework Nanospheres for Drug Delivery: Evaluation of Small-Molecule Encapsulation (2014)

We have developed a general synthetic route to encapsulate small molecules in monodisperse zeolitic imid-azolate framework-8 (ZIF-8) nanospheres for drug delivery. Electron microscopy, powder X-ray diffraction, and elemental analysis show that the small-molecule-encapsulated ZIF-8 nanospheres are uniform 70 nm particles with single-crystalline structure. Several small molecules, including fluorescein and the anticancer drug camptothecin, were encapsulated inside of the ZIF-8 framework. Evaluation of fluorescein-encapsulated ZIF-8 nanospheres in the MCF-7 breast cancer cell line demonstrated cell internalization and minimal cytotoxicity. The 70 nm particle size facilitates cellular uptake, and the pH-responsive dissociation of the ZIF-8 framework likely results in endosomal release of the small-molecule cargo, thereby rendering the ZIF-8 scaffold an ideal drug delivery vehicle. To confirm this, we demonstrate that camptothecin encapsulated ZIF-8 particles show enhanced cell death, indicative of internalization and intracellular release of the drug. To demonstrate the versatility of this ZIF-8 system, iron oxide nanoparticles were also encapsulated into the ZIF-8 nanospheres, thereby endowing magnetic features to these nanospheres.
Ramped Versus Square Injection Rate Experiments in a Heavy-Duty Diesel Engine (2020)

<div class="section abstract"><div class="htmlview paragraph">CO<sub>2</sub> regulations on heavy-duty transport are introduced in essentially all markets within the next decade, in most cases in several phases of increasing stringency. To cope with these mandates, developers of engines and related equipment are aiming to break new ground in the fields of combustion, fuel and hardware technologies. In this work, a novel diesel fuel injector, Delphi’s DFI7, is utilized to experimentally investigate and compare the performance of ramped injection rates versus traditional square fueling profiles. The aim is specifically to shift the efficiency and NO<sub>x</sub> tradeoff to a more favorable position. The design of experiments methodology is used in the tests, along with statistical techniques to analyze the data. Results show that ramped and square rates - after optimization of fueling parameters - produce comparable gross indicated efficiencies. Tests were carried out at 1200 and 1425 rpm; for the latter engine speed peak efficiency was attained at considerably lower NO<sub>x</sub> levels by applying a ramped injection rate. Particulate matter emissions, on the other hand, are generally lower with the use of square profiles. Heat release analysis further reveals that ignition delays in ramped rate operation are quite long, hinting at vastly different spray behavior. The relatively low loads applied in this work only sustain the delays further. Altogether, this causes the potential of the rate shaping capabilities to be underexploited, as direct control over the burn rate is limited with the combustion system used in this work. The results emphasize the need to carefully select ramp slopes for a particular engine geometry, load and speed point, and additional operating parameter settings.</div></div>
A multiclass input-regulation throttle (1990)

An input-regulation throttle to allocate capacity among multiple classes of jobs, where the allocation is enforced only when the total offered load is beyond capacity, is presented. The design uses a rate control throttle with a dedicated token bank for each class and a single, shared overflow bank. The per-class blocking and throughput are computed by alternative, approximate analyses. For the important special case of two priority classes of Poisson job arrivals, an exact analysis is given. The simple fluid approximation does surprisingly well, except in the case of roughly equal token and job arrival rates and small bank capacities. The stochastic Markov-chain-Poisson approximation yields only modest improvement over the fluid approximation. Thus, approximations that reasonably capture at least the second moment of the overflow processes are needed for accurate estimates of blocking for the important case in which the offered load is near the regulated limit. The two-parameter approximation with simulation for fine tuning seems adequate for most engineering purposes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
ES cell pluripotency and germ-layer formation require the SWI/SNF chromatin remodeling component BAF250a (2008)

ATP-dependent chromatin remodeling complexes are a notable group of epigenetic modifiers that use the energy of ATP hydrolysis to change the structure of chromatin, thereby altering its accessibility to nuclear factors. BAF250a (ARID1a) is a unique and defining subunit of the BAF chromatin remodeling complex with the potential to facilitate chromosome alterations critical during development. Our studies show that ablation of BAF250a in early mouse embryos results in developmental arrest (about embryonic day 6.5) and absence of the mesodermal layer, indicating its critical role in early germ-layer formation. Moreover, BAF250a deficiency compromises ES cell pluripotency, severely inhibits self-renewal, and promotes differentiation into primitive endoderm-like cells under normal feeder-free culture conditions. Interestingly, this phenotype can be partially rescued by the presence of embryonic fibroblast cells. DNA microarray, immunostaining, and RNA analyses revealed that BAF250a-mediated chromatin remodeling contributes to the proper expression of numerous genes involved in ES cell self-renewal, including Sox2, Utf1, and Oct4. Furthermore, the pluripotency defects in BAF250a mutant ES cells appear to be cell lineage-specific. For example, embryoid body-based analyses demonstrated that BAF250a-ablated stem cells are defective in differentiating into fully functional mesoderm-derived cardiomyocytes and adipocytes but are capable of differentiating into ectoderm-derived neurons. Our results suggest that BAF250a is a key component of the gene regulatory machinery in ES cells controlling self-renewal, differentiation, and cell lineage decisions.
Expressing Transactions with Savepoints as Non-Markovian Theories of Actions. (2003)

Flat transactions with savepoints are a variation of the classical flat transactions that allows the user to go undo work done so far back to a certain point within the transaction.
Social and Behavioral Aspects of Energy use (1993)

Human interactions with wildlife are a defining experience of human existence. These interactions can be positive or negative. People compete with wildlife for food and resources, and have eradicated dangerous species; co-opted and domesticated valuable ...Read More
Early Role of CD4+ Th1 Cells and Antibodies in HER-2 Adenovirus Vaccine Protection against Autochthonous Mammary Carcinomas (2005)

HER-2 is an oncogenic tumor-associated Ag that is overexpressed in several human tumors including breast and ovarian cancer. The efficacy and mechanism of a HER-2-expressing recombinant adenoviral vaccine to protect against tumorigenesis was examined using HER-2 transgenic (BALB-neuT) mice, which develop spontaneous breast tumors in all 10 mammary glands, and also using a transplantable mouse tumor model. Vaccination beginning at 6-8 wk of age (through 19 wk of age) prevented development of spontaneous mammary tumors even after 50 wk, whereas the animals in the control groups had tumors in all mammary glands by 25 wk. Such long-term protection after the last boost has not been achieved previously in this transgenic mouse in which the oncogene is continuously spawning tumorigenesis. Using beta(2)-microglobulin-knockout, IFN-gamma-knockout, and B cell-deficient mice, CD4(+) and CD8(+) cell depletion, and Ab transfer studies, we show that induction of anti-HER-2/neu Abs are both necessary and sufficient for protection, and the IgG2a isotype is most effective. In contrast, CD8(+) T cells are not necessary at all, and CD4(+) T cells are necessary for only 36-48 h after immunization to provide help for B cells but not as effector cells. Equal protection in immunized mice deficient in FcgammaRI/III excluded an FcR-mediated mechanism. Anti-HER-2 serum not only inhibited growth of mammary tumor cell lines expressing HER-2 in vitro but also protected mice from tumors in vivo, suggesting a direct action of Ab on the tumor cells. Such a vaccine may provide Ab-mediated protection against HER-2-expressing breast cancers in humans.
Variation with age and disease of an amyloid A protein-related serum component. (1975)

A C T Using the radioactively-labeled alkaline- degraded acid-soluble fraction of amyloid (["SI] DAA), we developed a radioimmunoassay for the previously described amyloid-related component of the human serum (SAA). Screening the sera of 228 normal in- dividuals and of 297 patients with a variety of illnesses, we found that SAA is a component of all human sera, including cord blood (mean 9457 ng/ml). The con- centration of this component increases significantly with the aging process, reaching very high levels in the eighth and nine decades. It is also elevated in all cases of amyloidosis (except for those associated with nephrotic syndrome) as well as in many patients with myeloma, macroglobulinemia, lymphoma, carcinoma, rheumatoid arthritis, and tuberculosis. A marked in- crease was noted in the early stages of a variety of acute inflammatory and infectious states with a re- turn to normal levels paralleling clinical improvement and faster than the erythrocyte sedimentation rate. The possible implications of this component in the genesis of amyloid and in the immune process are discussed.
A study on smoothing effect on output fluctuation of distributed wind power generation (2003)

Wind power generation in Japan has shown a marked increase in recent years. This increase has aroused growing concerns about the adverse effects of wind power generation on power system control, operation, and planning, because wind power output cannot be controlled and fluctuates much more than that of the conventional power plants. However, if wind power generators am distributed over a wide area, a "smoothing effect" an output fluctuation of distributed wind turbines could be expected because of the stochastic nature of wind. This paper examines the smoothing effect of output fluctuation of dispersed wind turbines. The remits reveal that the output of a single wind turbine fluctuates almost its rated power in ten minutes and little smoothing effect is expected in a wind farm scale (i.e., within sum kilometers) for a period of 10 minutes. On the other hand, a smoothing effect can be expected for a wider area in 100 minutes.
Metal Borohydrides as Electrolytes for Solid-State Li, Na, Mg, and Ca Batteries: A First-Principles Study (2017)

Metal borohydrides are a family of materials that were recently discovered to have extraordinary ionic conductivities, making them promising candidates as electrolytes for solid-state batteries (SSBs). In fact, various groups have measured the ionic conductivities and assembled batteries using specific borohydrides. However, there are no comprehensive studies assessing the thermodynamic properties or discussing the suitability of metal borohydrides as electrolytes in SSBs, especially for beyond-lithium applications. In this work, we investigate the electrochemical stability, interfacial characteristics, mechanical properties, and ionic conductivities of Li, Na, Ca, and Mg borohydrides using first-principles calculations. Our results suggest that Li and Na borohydrides are unstable at high voltages. However, the corresponding decomposition products, i.e., B12H122–-containing phases, have wide electrochemical windows which protect the electrolyte, leading to large electrochemical windows as wide as 5 V. In addition, our simulations indicate that metal borohydrides are ductile, suggesting facile processing. However, their low shear moduli may result in metal dendrite formation. For Ca and Mg borohydrides, while they possess reasonably good electrochemical stability, the low cationic diffusivity may impede their practical use. Finally, the anion rotation barrier was shown to correlate with the superionic phase transition temperature, suggesting that anion mixing may be a potential approach to achieve room-temperature superionic conductivity.
Using Semantics-Enabled Information Retrieval in Requirements Tracing: An Ongoing Experimental Investigation (2010)

Requirements tracing is a central activity for software systems quality management. However, in large-scale evolving systems, maintaining traceability information manually can become a tedious task. To address this problem, several dynamic techniques were introduced to provide automatic traceability links generation. These techniques are usually based on information retrieval (IR) methods which link different artifacts based on their syntactic information. This paper reports an ongoing experimental investigation of using semantics-enabled IR methods to generate traceability links. Our goal is to explore dynamic, accurate, and conceptually rich ways to generate and maintain traceability information.
Targeted disruption of the Ca <sup>2+</sup> channel β <sub>3</sub> subunit reduces N- and L-type Ca <sup>2+</sup> channel activity and alters the voltagedependent activation of P/Q-type Ca <sup>2+</sup> channels in neurons (1998)

In comparison to the well characterized role of the principal subunit of voltage-gated Ca2+ channels, the pore-forming, antagonist-binding alpha1 subunit, considerably less is understood about how beta subunits contribute to neuronal Ca2+ channel function. We studied the role of the Ca2+ channel beta3 subunit, the major Ca2+ channel beta subunit in neurons, by using a gene-targeting strategy. The beta3 deficient (beta3-/-) animals were indistinguishable from the wild type (wt) with no gross morphological or histological differences. However, in sympathetic beta3-/- neurons, the L- and N-type current was significantly reduced relative to wt. Voltage-dependent activation of P/Q-type Ca2+ channels was described by two Boltzmann components with different voltage dependence, analogous to the "reluctant" and "willing" states reported for N-type channels. The absence of the beta3 subunit was associated with a hyperpolarizing shift of the "reluctant" component of activation. Norepinephrine inhibited wt and beta3-/- neurons similarly but the voltage sensitive component was greater for N-type than P/Q-type Ca2+ channels. The reduction in the expression of N-type Ca2+ channels in the beta3-/- mice may be expected to impair Ca2+ entry and therefore synaptic transmission in these animals. This effect may be reversed, at least in part, by the increase in the proportion of P/Q channels activated at less depolarized voltage levels.
Improving Low Bit-Rate Video Coding using Spatio-Temporal Down-Scaling (2014)

Good quality video coding for low bit-rate applications is important for transmission over narrow-bandwidth channels and for storage with limited memory capacity. In this work, we develop a previous analysis for image compression at low bit-rates to adapt it to video signals. Improving compression using down-scaling in the spatial and temporal dimensions is examined. We show, both theoretically and experimentally, that at low bit-rates, we benefit from applying spatio-temporal scaling. The proposed method includes down-scaling before the compression and a corresponding up-scaling afterwards, while the codec itself is left unmodified. We propose analytic models for low bit-rate compression and spatio-temporal scaling operations. Specifically, we use theoretic models of motion-compensated prediction of available and absent frames as in coding and frame-rate up-conversion (FRUC) applications, respectively. The proposed models are designed for multi-resolution analysis. In addition, we formulate a bit-allocation procedure and propose a method for estimating good down-scaling factors of a given video based on its second-order statistics and the given bit-budget. We validate our model with experimental results of H.264 compression.
Hydrogen Storage in Wind Turbine Towers: Design Considerations; Preprint (2003)

The paramount considerations associated with a hydrogen tower are corrosion (in the form of hydrogen embrittlement) and structural failure (through bursting or fatigue life degradation). Although hydrogen embrittlement (HE) requires more research and experimentation, it does not appear to prohibit the use of turbine towers for hydrogen storage. Furthermore, the structural modifications required to store hydrogen in a tower are technically feasible. We discovered that hydrogen towers have a''crossover pressure'' at which their critical mode of failure crosses over from fatigue to bursting. The crossover pressure for many turbine towers is between 10 and 15 atm. The cost of hydrogen storage per unit of storage capacity is lowest near the crossover pressure. Above the crossover pressure, however, storage costs rise quickly.