gebhart/patrepeval huggingface dataset:
Dynamic re-optimization of a fed-batch fermentor using heuristic dynamic programming (1999)

Traditionally, fed-batch biochemical process optimization and control uses complicated theoretical off-line optimizers, with no online model adaptation or re-optimization. This study demonstrates the applicability, effectiveness, and economic potential of a simple phenomenological model for modeling, and an adaptive critic design, heuristic dynamic programming, for online re-optimization and control of an aerobic fed-batch fermentor. The results are compared with those obtained using a heuristic random optimizer.
PhyloDet: a scalable visualization tool for mapping multiple traits to large evolutionary trees (2009)

http://research.microsoft.com/cue/phylodet/
Near- and far-field optical properties of embedded scatters in AgOx-type super-resolution near-field structures. (2004)

In recent near-field optical recording techniques, the super-resolution near-field structures (super-RENS) have been successfully demonstrated to overcome the diffraction limit. To realize the possibility of replacing the conventional near-field optical probe by the super-RENS, and to understand the relations between the near-field enhancements and detectable far-field signals, we use the two-dimensional finite-difference time-domain (FDTD) method to study the near-field and far-field properties of different types of embedded scatters in the AgOx-type super-RENS.
A Fuel Vapor Model (FVSMOD) for Evaporative Emissions System Design and Analysis (1998)

&lt;div class="htmlview paragraph"&gt;A fuel vapor system model (FVSMOD) has been developed to simulate vehicle evaporative emission control system behavior. The fuel system components incorporated into the model include the fuel tank and pump, filler cap, liquid supply and return lines, fuel rail, vent valves, vent line, carbon canister and purge line. The system is modeled as a vented system of liquid fuel and vapor in equilibrium, subject to a thermal environment characterized by underhood and underbody temperatures and heat transfer parameters assumed known or determined by calibration with experimental liquid temperature data. The vapor/liquid equilibrium is calculated by simple empirical equations which take into account the weathering of the fuel, while the canister is modeled as a 1-dimensional unsteady absorptive and diffusive bed. Both fuel and canister submodels have been described in previous publications. This paper presents the system equations along with validation against experimental data. Some typical vapor system applications are also presented including a simulation of the EPA three day enhanced evaporative test procedure.&lt;/div&gt;
A proof-of-concept screen for identification of novel natural product modulators involved in mouse Treg/Th17 differentiation by using high-throughput Flow Cytometry (124.2) (2012)

Abstract The recent discovery of two novel subsets of CD4+ T lymphocytes (Th17 and Treg) has led to a paradigm shift in the understanding of how autoimmune responses are mediated and regulated. Interestingly, both Th17 and Treg cells can develop from the same naïve CD4+ T cell precursors and in some circumstances they can convert to each other. Several recent publications highlight the role of the aryl hydrocarbon receptor (Ahr) in regulating Treg and Th17 cell differentiation and possible application to human diseases. Depending on the ligands, Ahr activation can control naïve CD4+ T cell differentiation towards either a Treg (TCDD) or a Th17 (FICZ) phenotype. Identifying novel agents that promote or inhibit differentiation of naïve CD4+ T cells to Treg or Th17 could be beneficial in the area of Oncology and autoimmune diseases. Here we describe an assay developed for identification of new modulators based on T cell differentiation by using high-throughput flow cytometry. With TGF-β or TGF-β/IL-6 stimulation isolated mouse naïve CD4 cells can be differentiated efficiently into Treg or Th17 lineages. Treg or Th17-specific expression was detected by intracellular staining of FoxP3 or IL-17, respectively. A proof-of-concept screening against 1600 pure natural products (NPs) was performed and seventeen Th17 specific hits were identified
Critical Review on Sulphide Scale Formation, Removal and Inhibition (2020)

Abstract Sulphide scales, namely iron sulphide (FeS), zinc sulphide (ZnS) and lead sulphide (PbS), are increasingly being encountered in gas/oil wells. These scales can present serious safety concerns, impair well productivity and limit access to downhole tools. There are many published research studies addressing sulphide scale removal and inhibition. However, there is an incomplete understanding of the governing processes of sulphide scale formation and prevention. Furthermore, there are contradictory results in the literature on issues such as the removal procedures and inhibition tests for sulphide scales. Therefore, the main objective of this paper is to critically review the published work on sulphide scale formation, removal and inhibition, to address the factors that control them and to discuss some of the apparent discrepancies in published experimental studies. The review discusses the formation mechanisms of different sulphide scales in relation to the sources and levels of Fe, Zn, Pb and the sulphide species. The experimental procedures used by different researchers to evaluate sulphide scale dissolvers and inhibitors are described, along with the performance results for the chemistries tested to remove or prevent sulphide scales. Hydrochloric acid has been shown to outperform rival chemistries for dissolving sulphide scales, however the associated high corrosion rate and H2S generation has necessitated the development of other dissolvers to overcome such drawbacks. Several dissolvers based on chelating agent chemistries combined with catalysts provided high dissolution rates, and the dissolution results and the reaction mechanisms will be discussed in some detail. Multiple factors have been shown to play a significant role in the inhibition efficiency of sulphide scale inhibitors including pH, salinity, temperature, scale formation sequence and mechanism, and the initial concentrations of sulphide species and scaling metals. In addition, there is a developing understanding of the significance of scale inhibitor consumption in these systems. Understanding the formation mechanism is essential for accurate interpretation of scale-related issues in the field and for providing the correct treatment strategy. A more complete knowledge of these issues will lead to the further development of reliable procedures for generating dissolution and inhibition results and consequently improving the scale dissolver and inhibitor chemistries themselves.
20‐3: Novel Host‐Guest System for Drastic Improvement in the Lifetime of a Deep‐Red OLED that Satisfies the Red Chromaticity of the BT.2020 Standard (2018)

We developed a novel host‐guest system that increases the lifetime of a deep‐red phosphorescent OLED covering the wide color gamut of the BT.2020 standard. An OLED that employs this host‐guest system has a ~5.4 times longer lifetime than an OLED that employs the conventional system.
Itraconazole inhibits endothelial cell migration by disrupting inositol pyrophosphate-dependent focal adhesion dynamics and cytoskeletal remodeling (2023)

The antifungal drug itraconazole has been repurposed to anti-angiogenic agent, but the mechanisms of action have been elusive. Here we report that itraconazole disrupts focal adhesion dynamics and cytoskeletal remodeling, which requires 5-diphosphoinositol 1,2,3,4,6-pentakisphosphate (5-InsP<sub>7</sub>). We find that inositol hexakisphosphate kinase 1 (IP6K1) binds Arp2 and generates 5-InsP<sub>7</sub> to recruit coronin, a negative regulator of the Arp2/3 complex. IP6K1 also produces focal adhesion-enriched 5-InsP<sub>7</sub>, which binds focal adhesion kinase (FAK) at the FERM domain to promote its dimerization and phosphorylation. Itraconazole treatment elicits displacement of IP6K1/5-InsP<sub>7</sub>, thus augments 5-InsP<sub>7</sub>-mediated inhibition of Arp2/3 complex and reduces 5-InsP<sub>7</sub>-mediated FAK dimerization. Itraconazole-treated cells display reduced focal adhesion dynamics and actin cytoskeleton remodeling. Accordingly, itraconazole severely disrupts cell motility, an essential component of angiogenesis. These results demonstrate critical roles of IP6K1-generated 5-InsP<sub>7</sub> in regulating focal adhesion dynamics and actin cytoskeleton remodeling and reveal functional mechanisms by which itraconazole inhibits cell motility.
Prospects for Optical Clocks with a Blue-Detuned Lattice (2009)

We investigated the properties of optical lattice clocks operated with a repulsive light-shift potential. The magic wavelength, where light-shift perturbation for the clock transition cancels, was experimentally determined to be 389.889(9) nm for 87Sr. The hyperpolarizability effects on the clock transition were investigated theoretically. With minimal trapping field perturbation provided by the blue-detuned lattice, the fractional uncertainty due to the hyperpolarizability effects was found to be 2x10;{-19} in the relevant clock transition.
Surface plasmon resonance imaging for detection of drug metabolites in water (2019)

The analysis of surface water, groundwater, drinking water as well as sewage is important to get information about the contamination of the water cycle. Currently, these time-consuming investigations require special equipment, like for example hyphenated mass spectrometry. Surface plasmon resonance (SPR) is a faster alternative as it is highly sensitive to changes in the dielectric medium next to a thin metal layer and makes it a quasi-universal detector. Therefore, and due to the labelfree nature, SPR is a widely used sensing tool for real‐time monitoring of molecular interactions of various analytes. SPR imaging (SPRi) has several advantages to standard surface plasmon resonance, as it allows to observe many analytes in parallel as well as the integration of referencing technologies. However, the homogenous illumination of a large area (several millimeters) with a small light source is challenging and demands new approaches. Allopurinol, a drug used to lower the blood concentration of urate and hence decrease the affection of gout, gets metabolized to oxipurinol in the body and dropped out almost entirely by urinary excretion. After wastewater treatment, concentrations of oxipurinol up to 21.7 &mu;g&bull;L<sup>-1</sup> are detected. Further tracking of oxipurinol in the urban water cycle showed its presence in rivers and streams or even in groundwater. Therefore, the high biological stability of oxipurinol allows this molecule to be used as a marker for domestic wastewater in the environment. For the detection of oxipurinol by SPR graphene was used as receptive layer, as the analyte can bind via &pi;-stacking to this surface. An SPRi technique was developed and compared to conventional SPR system for the detection of oxipurinol.
Amylin and Bone Metabolism in Streptozotocin-Induced Diabetic Rats (2001)

Amylin (AMY) is a 37 amino acid peptide cosecreted with insulin (INS) by pancreatic beta-cells and absent in type 1 diabetes, a condition frequently associated with osteopenia. AMY binds to calcitonin receptors, lowers plasma calcium concentration, inhibits osteoclast activity, and stimulates osteoblasts. In the present study, we examined the effects of AMY replacement on bone loss in a streptozotocin (STZ)-induced rodent model type 1 diabetes. Of 50 male Wistar rats studied, 40 were made diabetic with intraperitoneal STZ (50 mg/kg; plasma glucose concentrations > 11 mM within 5 days). Ten nondiabetic control (CONT) rats received citrate buffer without STZ. Diabetic rats were divided into four groups (n = 10/group) and injected subcutaneously with rat AMY (45 mg/kg), INS (12 U/kg), both (same doses), or saline (STZ; diabetic controls) once per day. After 40 days of treatment and five 24-h periods of urine collection for deoxypyridinoline (DPD), the animals were killed, blood was sampled, and femurs were removed. The left femur was tested for mechanical resistance (three-point bending). The right femur was tested for total, diaphyseal (cortical bone), and metaphyseal (trabecular bone) bone densities using dual-energy X-ray absorptiometry (DXA). Bone was ashed to determine total bone mineral (calcium) content. None of the treatments had any significant effect on femoral length and diameter. Untreated diabetic rats (STZ; 145+/-7N) had lower bone strength than did nondiabetic CONT (164+/-38; p < 0.05). Total bone mineral density (BMD; g/cm2) was significantly lower in STZ (0. 2523+/-0.0076) than in CONT (0.2826+/-0.0055), as were metaphyseal and diaphyseal densities. Diabetic rats treated with AMY, INS, or both had bone strengths and bone densities that were indistinguishable from those in nondiabetic CONT. Changes in bone mineral content paralleled those for total BMD (T-BMD). Plasma osteocalcin (OC) concentration, a marker for osteoblastic activity, was markedly lower in untreated diabetic rats (7. 6+/-0.9 ng/ml); p < 0.05) than in nondiabetic CONT (29.8+/-1.7; p < 0.05) or than in AMY (20.1+/-0.7; p < 0.05). Urinary DPD excretion, a marker for bone resorption, was similar in untreated and AMY-treated diabetic rats (35.0+/-3.1 vs. 35.1+/-4.4 nmol/mmol creatinine), intermediate in rats treated with INS (49.9+/-2.7), and normalized in diabetic rats treated with both agents (58.8+/-8.9 vs. 63.2+/-4.5 in CONT). Thus, in our STZ rat model of diabetic osteopenia, addition of AMY improved bone indices apparently by both inhibiting resorption and stimulating bone formation.
<title>Proxy-Assisted Power-Friendly Streaming to Mobile Devices</title> (2003)

Since multimedia applications are known to be resource-hungry and mobile devices are resource-poor, in this paper, we propose techniques to reduce the energy consumption of streaming media applications running on mobile hosts. Our proposed techniques are proxy-based and involve power-friendly transformations on the requested streams so as to limit the energy required for receiving and decoding this data. Additionally, our proxy employs intelligent network transmission techniques to reduce the energy needs for network reception of streaming data. We implement our techniques into a prototype proxy and client and demonstrate their efficacy via an experimental evaluations. Our results show that our power-friendly transformations are effective over a range of bit rates and stream resolutions, while our intelligent transmission techniques can reduce the potential energy wastage during network reception by 65-98%.
Differential cross section measurement of charged current νe interactions without final-state pions in MicroBooNE (2022)

In this paper we present the first measurements of an exclusive electron neutrino cross section with the MicroBooNE experiment using data from the Booster neutrino beamline at Fermilab. These measurements are made for a selection of charged-current electron neutrinos without final-state pions. Differential cross sections are extracted in energy and angle with respect to the beam for the electron and the leading proton. The differential cross section as a function of proton energy is measured using events with protons both above and below the visibility threshold. This is done by including a separate selection of electron neutrino events without reconstructed proton candidates in addition to those with proton candidates. Results are compared to the predictions from several modern generators, and we find the data agrees well with these models. The data shows best agreement, as quantified by the $p$-value, with the generators that predict a lower overall cross section, such as GENIE v3 and NuWro.
Cross Evaluation of Speech Enhancement Methods under Different Noise Conditions (2019)

In this paper, we present a cross evaluation of different a priori SNR estimation methods as well as different time-frequency analysis processing using a subjective listening test. The noisy signal is corrupted by different types of background noise i.e. babble and pink, and varying levels of input SNR (0 dB and 10 dB). The signals are processed using Short Time Fourier Transform (STFT) or Critical Band (CB) processing. After estimating the clean speech signal, it was presented to 10 participants for evaluation using a subjective listening test according to (ITU-TP.835) methodology. The results demonstrate that the participants preferred the speech signal processed using CB for low SNR levels and non-stationary background noise, which means that critical band based frequency scale is more useful in adverse noisy conditions.
1422: Injection of Muscle-Derived Cells at Site of Cavernous Nerve Injury Facilitates Recovery in a Rat Model for Post-Radical Prostatectomy Erectile Dysfunction (2004)

INTRODUCTION AND OBJECTIVE: The cavernous nerve plays a crucial role in initiating and sustaining erections. Injury to this nerve during radical prostatectomy commonly results in postoperative erectile dysfunction. The goal of our experiments is to determine whether the injection of muscle-derived cells (MDC) at the site of nerve injury can promote cavernous nerve regeneration and consequently enhance the recovery of erectile function.
Genome-wide expression analysis in Arabidopsis (2000)

Conference Abstract| October 01 2000 Genome-wide expression analysis in Arabidopsis Marc Zabeau; Marc Zabeau 1K.L. Ledeganckstraat 35, 9000 Gent Search for other works by this author on: This Site PubMed Google Scholar Peter Breyne; Peter Breyne 1K.L. Ledeganckstraat 35, 9000 Gent Search for other works by this author on: This Site PubMed Google Scholar Paul Van Hummelen Paul Van Hummelen 1K.L. Ledeganckstraat 35, 9000 Gent Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (2000) 28 (5): A112. https://doi.org/10.1042/bst028a112c Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation Marc Zabeau, Peter Breyne, Paul Van Hummelen; Genome-wide expression analysis in Arabidopsis. Biochem Soc Trans 1 October 2000; 28 (5): A112. doi: https://doi.org/10.1042/bst028a112c Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Society Transactions Search Advanced Search This content is only available as a PDF. © 2000 Biochemical Society2000 Article PDF first page preview Close Modal You do not currently have access to this content.
Fast High-Fidelity Measurements of the Ground and Excited States of a dc-SQUID Phase Qubit (2006)

We have investigated the fidelity and speed of single-shot current-pulse measurements of the three lowest energy states of the dc SQUID phase qubit. We apply a short (2ns) current pulse to one junction of a Nb/AlOx/Nb SQUID that is in the zero voltage state at 25 mK and measure if the system switches to the finite voltage state. By plotting the switching rate versus pulse size we can determine average occupancy of the levels down to 0.01%, quantify small levels of leakage, and find the optimum pulse condition for single-shot measurements. Our best error rate is 3% with a measurement fidelity of 94%. By monitoring the escape rate during the pulse, the pulse current in the junction can be found to better than 10 nA on a 0.1 ns time scale. Theoretical analysis of the system reveals switching curves that are in good agreement with the data, as well as predictions that the ultimate single-shot error rate for this technique can reach 0.4% and the fidelity 99.2%.
On the origin of the fading memory effect in ReRAMs (2017)

Redox-based resistive switching devices can be switched between a high resistance state and a low resistance state in a reversible manner. An important requirement is the stable operation between these two states for a high amount of switching cycles. In this work the switching dynamics of these devices are investigated by means of device simulation. Hereby, we discuss the conditions for which a fading memory effect appears. In this case the switching dynamics of set and reset process needs to be identical. Using sinusoidal input voltages fading memory behavior is observed in the simulation results. The final steady-state oscillation between two resistance states is only determined by the input voltage signal and not by the initial state of the device. Moreover, it is found that the time to reach the steady-state oscillation, the oscillation amplitude and its mean value depend on a device inherent series resistance. This result opens a way for tuning the resulting reliable operation window for memory operation by means of device engineering.
Evaluation and Medical Management of Patients with Cystine Nephrolithiasis: A Consensus Statement (2020)

<b><i>Purpose:</i></b> Cystinuria is a genetic disorder with both autosomal recessive and incompletely dominant inheritance. The disorder disrupts cystine and other dibasic amino acid transport in proximal tubules of the kidney, resulting in recurrent kidney stone formation. Currently, there are no consensus guidelines on evaluation and management of this disease. This article represents the consensus of the author panel and will provide clinicians with a stepwise framework for evaluation and clinical management of patients with cystinuria based on evidence in the existing literature. <b><i>Materials and Methods:</i></b> A search of MEDLINE<sup>®</sup>/PubMed<sup>®</sup> and Cochrane databases was performed using the following key words: "cystine nephrolithiasis," "cystinuria," "penicillamine, cystine," and "tiopronin, cystine." In total, as of May 2018, these searches yielded 2335 articles, which were then evaluated for their relevance to the topic of evaluation and management of cystinuria. Evidence was evaluated by the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) system. <b><i>Results:</i></b> Twenty-five articles on the topic of cystinuria or cystine nephrolithiasis were deemed suitable for inclusion in this study. The literature supports a logical evaluation process and step-wise treatment approach beginning with conservative measures: fluid intake and dietary modification. If stone formation recurs, proceed to pharmacotherapeutic options by first alkalinizing the urine and then using cystine-binding thiol drugs. <b><i>Conclusions:</i></b> The proposed clinical pathways provide a framework for efficient evaluation and treatment of patients with cystinuria, which should improve overall outcomes of this rare, but highly recurrent, form of nephrolithiasis.
Molecular mechanism and potential target indication of TAK-931, a novel CDC7-selective inhibitor (2019)

Replication stress (RS) is a cancer hallmark; chemotherapeutic drugs targeting RS are widely used as treatments for various cancers. To develop next-generation RS-inducing anticancer drugs, cell division cycle 7 (CDC7) has recently attracted attention as a target. We have developed an oral CDC7-selective inhibitor, TAK-931, as a candidate clinical anticancer drug. TAK-931 induced S phase delay and RS. TAK-931-induced RS caused mitotic aberrations through centrosome dysregulation and chromosome missegregation, resulting in irreversible antiproliferative effects in cancer cells. TAK-931 exhibited significant antiproliferative activity in preclinical animal models. Furthermore, in indication-seeking studies using large-scale cell panel data, TAK-931 exhibited higher antiproliferative activities in <i>RAS</i>-mutant versus <i>RAS</i>-wild-type cells; this finding was confirmed in pancreatic patient-derived xenografts. Comparison analysis of cell panel data also demonstrated a unique efficacy spectrum for TAK-931 compared with currently used chemotherapeutic drugs. Our findings help to elucidate the molecular mechanisms for TAK-931 and identify potential target indications.