gebhart/patrepeval huggingface dataset:
POWER SYSTEM AGENTS: THE MOBILE AGENTS 2006 FIELD TEST AT MDRS (2006)

During the Mars Society&amp;apos;s Mars Desert Research Station (MDRS) Rotation 49 (April 23-May 7, 2006), we field tested and significantly extended a prototype monitoring and advising system for the habitat crew that integrates data from the MDRS power system. A distributed, wireless network of functionally specialized agents interact with the crew to provide alerts, access and interpret historical data (through voice command), and display troubleshooting procedures. In practical application during two weeks, the system generated speech over loudspeakers and headsets to alert the crew about the need to investigate generator-inverter-battery problems that had not yet come to their attention. This field test accomplished a milestone for the “CEV Agent-Mediated Situational Awareness ” task in NASA’s Exploration Technology Development Program 12B, Human-Systems Interaction.
Tumor necrosis factor-α antagonist diminishes osteocytic RANKL and sclerostin expression in diabetes rats with periodontitis (2017)

Type 1 diabetes with periodontitis shows elevated TNF-α expression. Tumor necrosis factor (TNF)-α stimulates the expression of receptor activator of nuclear factor-κB ligand (RANKL) and sclerostin. The objective of this study was to determine the effect of TNF-α expression of osteocytic RANKL and sclerostin in type 1 diabetes rats with periodontitis using infliximab (IFX), a TNF-α antagonist. Rats were divided into two timepoint groups: day 3 and day 20. Each timepoint group was then divided into four subgroups: 1) control (C, n = 6 for each time point); 2) periodontitis (P, n = 6 for each time point); 3) diabetes with periodontitis (DP, n = 8 for each time point); and 4) diabetes with periodontitis treated with IFX (DP+IFX, n = 8 for each time point). To induce type 1 diabetes, rats were injected with streptozotocin (50 mg/kg dissolved in 0.1 M citrate buffer). Periodontitis was then induced by ligature of the mandibular first molars at day 7 after STZ injection (day 0). IFX was administered once for the 3 day group (on day 0) and twice for the 20 day group (on days 7 and 14). The DP group showed greater alveolar bone loss than the P group on day 20 (P = 0.020). On day 3, higher osteoclast formation and RANKL-positive osteocytes in P group (P = 0.000 and P = 0.011, respectively) and DP group (P = 0.006 and P = 0.017, respectively) than those in C group were observed. However, there was no significant difference in osteoclast formation or RANKL-positive osteocytes between P and DP groups. The DP+IFX group exhibited lower alveolar bone loss (P = 0.041), osteoclast formation (P = 0.019), and RANKL-positive osteocytes (P = 0.009) than that of the DP group. On day 20, DP group showed a lower osteoid area (P = 0.001) and more sclerostin-positive osteocytes (P = 0.000) than P group. On days 3 and 20, the DP+IFX group showed more osteoid area (P = 0.048 and 0.040, respectively) but lower sclerostin-positive osteocytes (both P = 0.000) than DP group. Taken together, these results suggest that TNF-α antagonist can diminish osteocytic RANKL/sclerostin expression and osteoclast formation, eventually recovering osteoid formation. Therefore, TNF-α might mediate alveolar bone loss via inducing expression of osteocytic RANKL and sclerostin in type 1 diabetes rats with periodontitis.
Synthesis and Characterization of Novel Titanium(III) and -(IV) Alkyls and Carbenes Supported by Amide Ligands. Crystal Structure of [(Cy2N)2Ti(.mu.-CH2)]2 (1994)

Reaction of (Cy(2)N)(2)Ti(mu-Cl)(2)Li(TMEDA) (1) [TMEDA = N,N,N',N'-tetramethylethylene-diamine] with MeLi formed different complexes depending on the stoichiometric ratio of the reactants used. The novel Ti(III) complex (Cy(2)N)(2)Ti(mu-Me)(2)Li(TMEDA) (2) was formed when 2 equiv of the organolithium reagent was used, while a tetravalent complex, (Cy(2)N)(2)-TiMe(2) (3), was formed when a stiochiometric ratio of 1:1 was used. Complex 3 rapidly decomposed in toluene at 60 degrees C to form the bridging methylene complex (Cy(2)N)(2)Ti(mu-CH2)(2)-Ti(NCy(2))(2) (5). The structures of 2, 3, and 5 were elucidated by X-ray diffraction analysis. Crystal data are as follows. 2: C32H66N4TiLi, M = 561.74, monoclinic, P2(1)/n, a 12.505(5) Angstrom, b = 19.333(9) Angstrom, c = 15.393(5) Angstrom, beta = 109.10(2)degrees, V = 3517(3) Angstrom(3), Z = 4, T = -160 degrees C, Mo K alpha, R = 0.066, R(w) = 0.061 for 3644 reflections and 343 parameters. Non-hydrogen atoms were refined anisotropically. 3: C26H50N2Ti, M = 438.59, monoclinic, P2(1)/n, a = 9.906(4) Angstrom, b = 18.520(6) Angstrom, c = 14.271(4) Angstrom, beta = 96.87(3)degrees, V = 2599(3) Angstrom(3), Z = 4, T = -161 degrees C, Mo K alpha, R = 0.053, R(w) = 0.065 for 3132 reflections and 263 parameters. Non-hydrogen atoms were refined anisotropically. 5: C50H92N2Ti2, M = 845.10, monoclinic, P2/n, a = 13.6190(9) Angstrom, b = 12.484(1) Angstrom, c 14.811(1) Angstrom, beta = 96.510(3)degrees, V 2501.9(6) Angstrom(3), Z = 2, T = -160 degrees C, Mo K alpha, R = 0.057, R(w) = 0.065 for 2637 reflections and 343 parameters. Non-hydrogen atoms were refined anisotropically.
Organic Gas Sensor with an Improved Lifetime for Detecting Breath Ammonia in Hemodialysis Patients (2017)

In this work, a TFB (poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-(4,4'-(N-(4-s-butylphenyl)diphenylamine)]) sensor with a cylindrical nanopore structure exhibits a high sensitivity to ammonia in ppb-regime. The lifetime and sensitivity of the TFB sensor were studied and compared to those of P3HT (poly(3-hexylthiophene)), NPB (N,N'-di(1-naphthyl)-N,N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine), and TAPC (4,4'-cyclohexylidenebis[N,N-bis(4-methylphenyl) benzenamine]) sensors with the same cylindrical nanopore structures. The TFB sensor outstands the others in sensitivity and lifetime and it shows a sensing response (current variation ratio) of 13% to 100 ppb ammonia after 64 days of storage in air. A repeated sensing periods testing and a long-term measurement have also been demonstrated for the test of robustness. The performance of the TFB sensor is stable in both tests, which reveals that the TFB sensor can be utilized in our targeting clinical trials. In the last part of this work, we study the change of ammonia concentration in the breath of hemodialysis (HD) patients before and after dialysis. An obvious drop of breath ammonia concentration can be observed after dialysis. The reduction of breath ammonia is also correlated with the reduction of blood urea nitrogen (BUN). A correlation coefficient of 0.82 is achieved. The result implies that TFB sensor may be used as a real-time and low cost breath ammonia sensor for the daily tracking of hemodialysis patients.
Telomerase and Cell Immortality: Applications in Research and Medicine (2001)

This article has no abstract.
Sub-Nyquist Radar: Principles and Prototypes (2018)

In the past few years, new approaches to radar signal processing have been introduced which allow the radar to perform signal detection and parameter estimation from much fewer measurements than that required by Nyquist sampling. These systems - referred to as sub-Nyquist radars - model the received signal as having finite rate of innovation and employ the Xampling framework to obtain low-rate samples of the signal. Sub-Nyquist radars exploit the fact that the target scene is sparse facilitating the use of compressed sensing (CS) methods in signal recovery. In this chapter, we review several pulse-Doppler radar systems based on these principles. Contrary to other CS-based designs, our formulations directly address the reduced-rate analog sampling in space and time, avoid a prohibitive dictionary size, and are robust to noise and clutter. We begin by introducing temporal sub-Nyquist processing for estimating the target locations using less bandwidth than conventional systems. This paves the way to cognitive radars which share their transmit spectrum with other communication services, thereby providing a robust solution for coexistence in spectrally crowded environments. Next, without impairing Doppler resolution, we reduce the dwell time by transmitting interleaved radar pulses in a scarce manner within a coherent processing interval or "slow time". Then, we consider multiple-input-multiple-output array radars and demonstrate spatial sub-Nyquist processing which allows the use of few antenna elements without degradation in angular resolution. Finally, we demonstrate application of sub-Nyquist and cognitive radars to imaging systems such as synthetic aperture radar. For each setting, we present a state-of-the-art hardware prototype designed to demonstrate the real-time feasibility of sub-Nyquist radars.
EVOLUTIONARY-GENETIC ALGORITHM FOR SOLVING 2-D STEADY-STATE CONDUCTION PROBLEMS (2003)

Abstract Genetic algorithms that can solve problems in conduction heat transfer have in the past encountered difficulties with increasing mesh resolution. The reasons for these difficulties were identified to be due to the np-hard nature of the problem. They were successfully resolved by means of a novel "genetic engineering" operator. As the data show, the new algorithm displays good convergence and can solve much finer meshes than previously possible. In addition, the algorithm was tested on different boundary conditions, such as fixed temperature, convection, and prescribed heat flux. Finally, the effect of different parameters and operators on the accuracy of the results was studied.
The differential extension in dsDNA bound to Rad51 filaments may play important roles in homology recognition and strand exchange (2013)

RecA and Rad51 proteins play an important role in DNA repair and homologous recombination. For RecA, X-ray structure information and single molecule force experiments have indicated that the differential extension between the complementary strand and its Watson-Crick pairing partners promotes the rapid unbinding of non-homologous dsDNA and drives strand exchange forward for homologous dsDNA. In this work we find that both effects are also present in Rad51 protein. In particular, pulling on the opposite termini (3' and 5') of one of the two DNA strands in a dsDNA molecule allows dsDNA to extend along non-homologous Rad51-ssDNA filaments and remain stably bound in the extended state, but pulling on the 3'5' ends of the complementary strand reduces the strand-exchange rate for homologous filaments. Thus, the results suggest that differential extension is also present in dsDNA bound to Rad51. The differential extension promotes rapid recognition by driving the swift unbinding of dsDNA from non-homologous Rad51-ssDNA filaments, while at the same time, reducing base pair tension due to the transfer of the Watson-Crick pairing of the complementary strand bases from the highly extended outgoing strand to the slightly less extended incoming strand, which drives strand exchange forward.
In vitro and in vivo activities of the carbonic anhydrase inhibitor, dorzolamide, against vancomycin-resistant enterococci (2021)

Vancomycin-resistant enterococci (VRE) are a serious public health threat and a leading cause of healthcare-associated infections. Bacterial resistance to antibiotics recommended for the treatment of enterococcal infections complicates the management of these infections. Hence, there is a critical need for the discovery of new anti-VRE agents. We previously reported carbonic anhydrase inhibitors (CAIs) as new potent VRE inhibitors. In the present study, the activity of the CAI, dorzolamide was evaluated against VRE both in vitro and in vivo. Dorzolamide exhibited potent activity against a panel of clinical VRE isolates, with minimum inhibitory concentration (MIC) values ranging from 1 µg/mL to 8 µg/mL. A killing kinetics experiment determined that dorzolamide exhibited a bacteriostatic effect against VRE, which was similar to the drug of choice (linezolid). Dorzolamide interacted synergistically with gentamicin against four strains of VRE, and exhibited an additive interaction with gentamicin against six VRE strains, reducing gentamicin's MIC by several folds. Moreover, dorzolamide outperformed linezolid in an in vivo VRE colonization reduction mouse model. Dorzolamide significantly reduced the VRE burden in fecal samples of mice by 2.9-log<sub>10</sub> (99.9%) and 3.86-log<sub>10</sub> (99.99%) after 3 and 5 days of treatment, respectively. Furthermore, dorzolamide reduced the VRE count in the cecal (1.74-log<sub>10</sub> (98.2%) reduction) and ileal contents (1.5-log<sub>10</sub> (96.3%)) of mice, which was superior to linezolid. Collectively, these results indicate that dorzolamide represents a promising treatment option that warrants consideration as a supplement to current therapeutics used for VRE infections.
Abstract 18673: JNK Inhibition Restores Endothelial Function in Type 2 Diabetes Mellitus (2015)

Introduction: Diabetes mellitus type 2 is an increasingly public health problem and it is a major cause in the development of cardiovascular diseases. Endothelial dysfunction is a key mechanism that contributes to the pathogenesis of cardiovascular diseases and is a well-known feature of clinical diabetes. Prior studies have demonstrated an impaired nitric oxide bioavailability and a reduced endothelium-dependent vasodilation under diabetic conditions and in animal models, JNK activity has been widely described to be involved in systemic insulin resistance. Hypothesis: Our study aimed to evaluate the involvement of JNK in endothelial dysfunction, studying its potential role in altered eNOS activation and NO synthesis in diabetic patients. Methods: We measured endothelial function and JNK activity in freshly isolated endothelial cells from diabetic patients (n=38) and nondiabetic controls (n=40). Results: ECs from diabetic patients displayed impaired eNOS activation and reduced NO release after insulin and A23187 stimulation, consistent with the presence of endothelial dysfunction. JNK activation was higher in diabetic (**P=0.003), and was associated with lower flow-mediated dilation (r=-0.53, *P=0.02). In endothelial cells from diabetic patients, treatment with JNK chemical inhibitor (SP600125) restored eNOS activation and insulin response (***P&lt;0.001). Nitric oxide bioactivity after A23187 stimuli with diabetes was also recovered in endothelial cells from patients with diabetes. Conclusions: In summary, our data suggest that JNK activation contributes to vascular insulin resistance and endothelial dysfunction in patients with type 2 diabetes and may represent a target in novel therapeutic opportunities.
3D simulations of an industrial ICP reactor with comparison to experimental data (2003)

Summary form only given, as follows. Coil design and gas flow patterns determine spatial uniformity of plasma and its composition in inductively coupled plasma (ICP) reactors for semiconductor manufacturing. Attempts of 3D ICP simulations have been reported over the last few years, however these simulations have remained a difficult and time-consuming task. We have performed 3D simulations of an industrial ICP reactor (Panasonic Pantheon E800 Dry Etcher) using a filament model to set up complicated multi-spiral RF coil and gas injectors.
Replication Data for: Latent Representation Learning for Structural Characterization of Catalysts (2022)

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.
Development of gold nanoparticle-aptamer-based LSPR sensing chips for the rapid detection of Salmonella typhimurium in pork meat (2017)

A non-labeled, portable plasmonic biosensor-based device was developed to enable the ultra-sensitive and selective detection of Salmonella typhimurium in pork meat samples. Specifically, a plasmonic sensor, using the self-assembly of gold nanoparticles (AuNPs) to achieve a regulated diameter of 20 nm for the AuNP monolayers, was used to conduct high-density deposition on a transparent substrate, which produced longitudinal wavelength extinction shifts via a localized surface plasmon resonance (LSPR) signal. The developed aptamers conjugated to the LSPR sensing chips revealed an ultra-sensitive upper limit of detection (LOD) of approximately 10<sup>4</sup> cfu/mL for S. typhimurium in pure culture under the optimal assay conditions, with a total analysis time of 30-35 min. When the LSPR sensing chips were applied on artificially contaminated pork meat samples, S. typhimurium in the spiked pork meat samples was also detected at an LOD of 1.0 × 10<sup>4</sup> cfu/mL. The developed method could detect S. typhimurium in spiked pork meat samples without a pre-enrichment step. Additionally, the LSPR sensing chips developed against S. typhimurium were not susceptible to any effect of the food matrix or background contaminant microflora. These findings confirmed that the developed gold nanoparticle-aptamer-based LSPR sensing chips could facilitate sensitive detection of S. typhimurium in food samples.
β3AR-Dependent Brain-Derived Neurotrophic Factor (BDNF) Generation Limits Chronic Postischemic Heart Failure (2023)

BDNF loss underscores chronic postischemic heart failure. TrkB agonists can improve ischemic LV dysfunction via replenished myocardial BDNF content. Direct cardiac β3AR stimulation, or β-blockers (via upregulated β3AR), is another BDNF-based means to fend off chronic postischemic heart failure.
Supplementary Figure 4 from DCLK1-Isoform2 Alternative Splice Variant Promotes Pancreatic Tumor Immunosuppressive M2-Macrophage Polarization (2023)

&lt;p&gt;DCLK1-isoform2 staining is positively and negatively correlated with CD8 T cell staining. Fixed tumor tissues with CD8+ T-cell high ("T-cell high",) CD8+ T-cell mild ("T-cell mild") and CD8+ T-cell low ("T-cell low") from an autochthonous mouse model of pancreatic adenocarcinoma were stained for Dclk1. Bar graph representing the percentage positive staining intensity of DCLK1 between the tissue samples, quantified using ImageJ.&lt;/p&gt;
The GATA1-HS2 Enhancer Allows Persistent and Position-Independent Expression of a β-globin Transgene (2011)

Gene therapy of genetic diseases requires persistent and position-independent expression of a therapeutic transgene. Transcriptional enhancers binding chromatin-remodeling and modifying complexes may play a role in shielding transgenes from repressive chromatin effects. We tested the activity of the HS2 enhancer of the GATA1 gene in protecting the expression of a β-globin minigene delivered by a lentiviral vector in hematopoietic stem/progenitor cells. Gene expression from proviruses carrying GATA1-HS2 in both LTRs was persistent and resistant to silencing at most integration sites in the in vivo progeny of human hematopoietic progenitors and murine long-term repopulating stem cells. The GATA1-HS2-modified vector allowed correction of murine β-thalassemia at low copy number without inducing clonal selection of erythroblastic progenitors. Chromatin immunoprecipitation studies showed that GATA1 and the CBP acetyltransferase bind to GATA1-HS2, significantly increasing CBP-specific histone acetylations at the LTRs and β-globin promoter. Recruitment of CBP by the LTRs thus establishes an open chromatin domain encompassing the entire provirus, and increases the therapeutic efficacy of β-globin gene transfer by reducing expression variegation and epigenetic silencing.
An improved FORTRAN 77 recombinant DNA database management system with graphic extensions in GKS (1986)

We have improved an existing clone database management system written in FORTRAN 77 and adapted it to our software environment. Improvements are that the database can be interrogated for any type of information, not just keywords. Also, recombinant DNA constructions can be represented in a simplified 'shorthand', whereafter a program assembles the full nucleotide sequence from the contributing fragments, which may be obtained from nucleotide sequence databases. Another improvement is the replacement of the database manager by programs, running in batch to maintain the databank and verify its consistency automatically. Finally, graphic extensions are written in Graphical Kernel System, to draw linear and circular restriction maps of recombinants. Besides restriction sites, recombinant features can be presented from the feature lines of recombinant database entries, or from the feature tables of nucleotide databases. The clone database management system is fully integrated into the sequence analysis software package from the Pasteur Institute, Paris, and is made accessible through the same menu. As a result, recombinant DNA sequences can directly be analysed by the sequence analysis programs.
Millimeter wave picocellular system evaluation for urban deployments (2013)

With the severe spectrum shortage in conventional cellular bands, millimeter wave (mmW) frequencies between 30 and 300 GHz have been attracting considerable attention as a possible candidate for next-generation micro- and picocellular wireless networks. The mmW frequency bands offer orders of magnitude greater spectrum than current cellular microwave frequencies currently deployed below 3 GHz. However, even with typical microcellular radii of 100m to 200m, the propagation of mmW signals in outdoor non line-of-sight (NLOS) links remains challenging and the feasibility of such mmW networks is far from clear. This paper uses recent real-world measurements at 28 GHz to provide the first systematic assessment of mmW picocellular networks. It is found that, even with its limited propagation characteristics, mmW systems can offer an order of magnitude increase in capacity over current state-of-the-art 4G cellular networks with similar cell density. However, it is also shown that such mmW networks will operate in an extremely power-limited regime where the full spatial and bandwidth degrees of freedom are not fully utilized. This power-limited regime contrasts significantly with current bandwidth-limited cellular systems, requiring alternate technologies for mmW systems that may unlock further gains that mmW frequency bands offer.
mRNA 5′ terminal sequences drive 200-fold differences in expression through effects on synthesis, translation and decay (2022)

Abstract mRNA regulatory sequences control gene expression at multiple levels including translation initiation and mRNA decay. The 5′ terminal sequences of mRNAs have unique regulatory potential because of their proximity to key post-transcriptional regulators. Here we have systematically probed the function of 5′ terminal sequences in gene expression in human cells. Using a library of reporter mRNAs initiating with all possible 7-mer sequences at their 5′ ends, we find an unexpected impact on transcription that underlies 200-fold differences in mRNA expression. Library sequences that promote high levels of transcription mirrored those found in native mRNAs and define two basic classes with similarities to classic Initiator (Inr) and TCT core promoter motifs. By comparing transcription, translation and decay rates, we identify sequences that are optimized for both efficient transcription and growth-regulated translation and stability, including variants of terminal oligopyrimidine (TOP) motifs. We further show that 5′ sequences of endogenous mRNAs are enriched for multi-functional TCT/TOP hybrid sequences. Together, our results reveal how 5′ sequences define two general classes of mRNAs with distinct growth-responsive profiles of expression across synthesis, translation and decay.