gebhart/patrepeval huggingface dataset:
‘Once bit, twice shy’ (2015)

Abstract This chapter discusses the issues surrounding a bill introduced by MP William Edward Forster into the House of Commons on 17 February 1870. This bill provided for England's first national system of elementary education. The bill gave voluntary organizations twelve months in which to increase the accommodation provided by their schools. Only at the end of this period, in places where school accommodation was still deficient, were school boards to be set up, chosen by town councils in the boroughs and by parish vestries elsewhere. Such boards would have the power to levy rates, build schools, employ teachers, and compel the attendance of children. On the issue of religious teaching in these board schools, Forster was ready to make a concession to the advocates of ‘unsectarian’ religious teaching.
Automatic communication coalescing for irregular computations in UPC language (2012)

Partitioned Global Address Space (PGAS) languages appeared to address programmer productivity in large scale parallel machines. However, fine grain accesses on shared structures have been identified as one of the main bottlenecks of PGAS languages. Manual or compiler assistance code optimization is required to avoid fine grain accesses. The downside of manually applying code transformations is the increased program complexity and hindering of the programmer productivity. On the other hand, compiler optimizations of fine grain accesses require knowledge of physical data mapping and the use of parallel loop constructs. This paper presents an optimization for prefetching and coalescing of shared accesses at runtime. Larger messages decrease the impact of remote access latency and increase the efficiency of the network communication. We have implemented our optimization for the Unified Parallel C (UPC) language. An experimental evaluation on a distributed-memory environment using a Power7 cluster demonstrates the benefits of our optimization.
Multi-Ethnic Comparisons of Diabetes in Heart Failure with Reduced Ejection Fraction: Insights from the HF-ACTION trial and the ASIAN-HF Registry (2018)

There is marked heterogeneity in the prevalence and correlates of DM among different ethnic groups with HF worldwide. Subgroups particularly predisposed to DM warrant special attention, since DM increases the combined risk of morbidity and mortality in all ethnicities with HF.
Overview of the National Jet Fuels Combustion Program (2017)

This paper provides an overview of the National Jet Fuels Combustion Program led by the Federal Aviation Administration, the U.S. Air Force Research Laboratory, and the NASA. The program follows from basic research from the U.S. Air Force Office of Scientific Research and results from the engine-company-led Combustion Rules and Tools program funded by the U.S. Air Force. The overall objective of this fuels program was to develop combustion-related generic test and modeling capabilities that can improve the understanding of the impact of fuel chemical composition and physical properties on combustion, leading to accelerating the approval process of new alternative jet fuels. In this paper, the motivation and objectives for the work, participating universities, gas-turbine-engine companies, other federal agencies, and international partners are described. This paper provides an in-depth discussion on the benefits to the fuels approval process, the rationale in selecting conventional and alternative fuels to study, the referee rig used for fuel testing, and the modeling approaches. High-level results are also briefly discussed, and will be covered in detail in separate university-led papers. Lastly, an Appendix reviewing past programs, events, and workshops that lay the groundwork for this program is also included for reference.
Cyber Resilience for the Internet of Things: Implementations With Resilience Engines and Attack Classifications (2022)

Recently, the number of publicized attacks on IoT devices has noticeably grown. This is in part due to the increasing deployment of embedded systems into various domains, including critical infrastructure, which makes them a valuable asset and a compromise can cause significant damages. In this case, it is often required to send an engineer to manually recover the devices, as the attack leaves them out of reach of standard remote management solutions. To avoid this costly process, the concept of <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">cyber resilience</i> has gained traction in recent years in both academia and industry. Its core idea is to enable compromised devices to recover themselves to a trusted state without human intervention. Initial guidelines and architectures to realize cyber resilience have been published by standardization entities like NIST and TCG, and in multiple academic papers. While the initial works focused on guaranteed recovery, recent proposals included attack detection to speed up the recovery process. In this work, we build on top of these ideas and present an extended resilience architecture. We present new implementations of resilience engines with a focus on secure and reliable data acquisition for attack detection and classification. Our attack classification engine enables tailored, more efficient recovery responses.
Further characterization of a novel EP2 and EP3 receptor dual agonist, ONO‐8055, on lower urinary tract function in normal and lumbar canal stenosis rats (2019)

This agonist did not augment bladder contractility or urethral relaxation in normal rats.
Halogenation dictates the architecture of amyloid peptide nanostructures (2017)

Amyloid peptides yield a plethora of interesting nanostructures though difficult to control. Here we report that depending on the number, position, and nature of the halogen atoms introduced into either one or both phenylalanine benzene rings of the amyloid β peptide-derived core-sequence KLVFF, four different architectures were obtained in a controlled manner. Our findings demonstrate that halogenation may develop as a general strategy to engineer amyloidal peptide self-assembly and obtain new amyloidal nanostructures.
Recent advances in understanding NRF2 as a druggable target: development of pro-electrophilic and non-covalent NRF2 activators to overcome systemic side effects of electrophilic drugs like dimethyl fumarate (2017)

Dimethyl fumarate (DMF) is an electrophilic compound previously called BG-12 and marketed under the name Tecfidera <sup>®</sup>. It was approved in 2013 by the US Food and Drug Administration and the European Medicines Agency for the treatment of relapsing multiple sclerosis. One mechanism of action of DMF is stimulation of the nuclear factor erythroid 2-related factor 2 (NRF2) transcriptional pathway that induces anti-oxidant and anti-inflammatory phase II enzymes to prevent chronic neurodegeneration. However, electrophiles such as DMF also produce severe systemic side effects, in part due to non-specific S-alkylation of cysteine thiols and resulting depletion of glutathione. This mini-review presents the present status and future strategy for NRF2 activators designed to avoid these side effects. Two modes of chemical reaction leading to NRF2 activation are considered here. The first mode is S-alkylation (covalent reaction) of thiols in Kelch-like ECH-associated protein 1 (KEAP1), which interacts with NRF2. The second mechanism involves non-covalent pharmacological inhibition of protein-protein interactions, in particular domain-specific interaction between NRF2 and KEAP1 or other repressor proteins involved in this transcriptional pathway. There have been significant advances in drug development using both of these mechanisms that can potentially avoid the systemic side effects of electrophilic compounds. In the first case concerning covalent reaction with KEAP1, monomethyl fumarate and monoethyl fumarate appear to represent safer derivatives of DMF. In a second approach, pro-electrophilic drugs, such as carnosic acid from the herb <i>Rosmarinus officinalis</i>, can be used as a safe pro-drug of an electrophilic compound. Concerning non-covalent activation of NRF2, drugs are being developed that interfere with the direct interaction of KEAP1-NRF2 or inhibit BTB domain and CNC homolog 1 (BACH1), which is a transcriptional repressor of the promoter where NRF2 binds.
Magnetic Resonance Imaging Volumetric Analysis of the Putamen in Children With ADHD (2006)

A reversal of symmetry in the putamen (as found in the caudate) may relate to ADHD symptomology as well as to psychopathic traits.
Label‐Free Protein Glycosylation Analysis Using NanoMonitor—An Ultrasensitive Electrochemical Biosensor (2021)

Glycans (oligosaccharide chains attached to glycoproteins) are a promising class of biomarkers, found in body fluids such as serum, saliva, urine, etc., that can be used for the diagnosis of disease conditions. Subtle changes in glycans resulting from altered glycosylation machinery have been reported during various diseases, including carcinogenesis. In this article, we detail protocols for the rapid, label-free analysis of glycans using a previously developed highly sensitive and selective electrochemical impedance spectroscopy-based biosensing diagnostic platform called "NanoMonitor." The glycosensor operation is based on the specific affinity capture of the target glycans on the sensor surface by glycan-binding proteins known as lectins. This glycan-lectin binding activity modulates the impedance of the electrical double layer at the buffer-electrode interface. Protocols for the preparation of glycoprotein samples and glycosylation analysis using NanoMonitor and lectin-based ELISA are described here. The data obtained using these protocols show that NanoMonitor is capable of distinguishing between glycoform variants of the glycoprotein fetuin and glycoproteins derived from cultured human pancreatic cancer cells with high sensitivity (orders of magnitude higher than lectin-based ELISA) and selectivity. The results obtained indicate that NanoMonitor protocols can be further developed to enable use of NanoMonitor as a handheld electronic biosensor device for routine multiplexed detection of glycan biomarkers from clinical samples. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparing the NanoMonitor surface for glycan biosensing Support Protocol: Synthesis of glycoform variants of fetuin Basic Protocol 2: Performing Electrochemical Impedance Spectroscopy (EIS) for analyzing glycoprotein structures.
Sparse Signal Reconstruction from Noisy Compressive Measurements using Cross Validation (2007)

Compressive sensing is a new data acquisition technique that aims to measure sparse and compressible signals at close to their intrinsic information rate rather than their Nyquist rate. Recent results in compressive sensing show that a sparse or compressible signal can be reconstructed from very few incoherent measurements. Although the sampling and reconstruction process is robust to measurement noise, all current reconstruction methods assume some knowledge of the noise power or the acquired signal to noise ratio. This knowledge is necessary to set algorithmic parameters and stopping conditions. If these parameters are set incorrectly, then the reconstruction algorithms either do not fully reconstruct the acquired signal (underfitting) or try to explain a significant portion of the noise by distorting the reconstructed signal (overfitting). This paper explores this behavior and examines the use of cross validation to determine the stopping conditions for the optimization algorithms. We demonstrate that by designating a small set of measurements as a validation set it is possible to optimize these algorithms and reduce the reconstruction error. Furthermore we explore the trade-off between using the additional measurements for cross validation instead of reconstruction.
An Indirect Impedance Technique to Determine Reinforcing Steel Properties (2014)

Studies have shown that the application of an electric field to the surface of an electrolytic medium can indirectly polarize a metal within the solution. 1,2,3,4 This technique can be applied to the study of reinforcing steel in concrete, and in this particular paper, to the study of post-tensioning steel in grouted cylinder tendons used in bridge construction. With the use of Electrochemical Impedance Spectroscopy, a ﬁnite-element model has been developed to solve for the frequency-dependent potential distribution through a cylindrical grout specimen containing one axially-located steel strand. Impedance simulations were performed at diﬀerent steel corrosion states while incorporating the kinetics at the current-injecting electrodes. Following the procedure of Huang et al. 5 , the electrode kinetics are expressed as an oscillating current density as the summation of a charging and faradaic current. The grout is modeled as a uniform conductivity media and Laplace’s equation is used to solve for the potential distribution. The impedance is simulated over a range of frequencies as the potential difference between two reference electrodes divided by the current of the working electrode. The results are compared to experimental measurements throughout the hydration process. The effectiveness of this method relies on the use of accurate representations of the steel surface impedance. Passive film models developed from rotating disk experiments in simulated pore solution are used to describe the steel boundary condition in the finite element model. The simulated results incorporating these models show a similar impedance response as the measured impedance of an aged cylinder put through a wetting and drying cycle. Barring an accurate model, this technique has the potential to effectively determine the interface properties of the embedded steel from the overall response of the system. References J. Zhang, P. J. Monteiro, F.H. Morrison, “Noninvasive surface measurement of corrosion of reinforcing bar in concrete: Part I Experimental results”, ACI Materials Journal, 98 (2001) pg. 116-125. M Keddam, X. R. Novoa, V. Vivier, “The concept of floating electrode for contact-less electrochemical measurements: Application to reinforcing steel-bar corrosion in concrete,” Corrosion Science, 51 (2009) pg. 1795-1801. C. Andrade, I. Martnez, “Metal corrosion rate determination of diﬀerent solutions and reinforced concrete specimens by means of a noncontacting corrosion method,” Corrosion 66 (2010) pg. 056001-056001. C. Andrade, J. Sanchez, I. Martinez, N. Rebolledo, Analogue circuit of the inductive polarization resistance,” Electrochimica Acta 56 (2011) pg. 1874-1880. V. M. W. Huang, V. Vivier, M. E. Orazem, N. Pbre, B. Tribollet, “The apparent constant-phase-element behavior of a disk electrode with faradaic reactions a global and local impedance analysis,” Journal of the Electrochemical Society 154 (2007) C99-C107.
Enteric Bacterial Invasion Of Intestinal Epithelial Cells <em>In Vitro</em> Is Dramatically Enhanced Using a Vertical Diffusion Chamber Model (2013)

The interactions of bacterial pathogens with host cells have been investigated extensively using in vitro cell culture methods. However as such cell culture assays are performed under aerobic conditions, these in vitro models may not accurately represent the in vivo environment in which the host-pathogen interactions take place. We have developed an in vitro model of infection that permits the coculture of bacteria and host cells under different medium and gas conditions. The Vertical Diffusion Chamber (VDC) model mimics the conditions in the human intestine where bacteria will be under conditions of very low oxygen whilst tissue will be supplied with oxygen from the blood stream. Placing polarized intestinal epithelial cell (IEC) monolayers grown in Snapwell inserts into a VDC creates separate apical and basolateral compartments. The basolateral compartment is filled with cell culture medium, sealed and perfused with oxygen whilst the apical compartment is filled with broth, kept open and incubated under microaerobic conditions. Both Caco-2 and T84 IECs can be maintained in the VDC under these conditions without any apparent detrimental effects on cell survival or monolayer integrity. Coculturing experiments performed with different C. jejuni wild-type strains and different IEC lines in the VDC model with microaerobic conditions in the apical compartment reproducibly result in an increase in the number of interacting (almost 10-fold) and intracellular (almost 100-fold) bacteria compared to aerobic culture conditions. The environment created in the VDC model more closely mimics the environment encountered by C. jejuni in the human intestine and highlights the importance of performing in vitro infection assays under conditions that more closely mimic the in vivo reality. We propose that use of the VDC model will allow new interpretations of the interactions between bacterial pathogens and host cells.
Differential effects of FSH and testosterone on the maintenance of spermatogenesis in the adult hypophysectomized rat (1989)

In order to clarify further the role of FSH in the maintenance of spermatogenesis, adult rats were treated with purified human FSH (2 X 5 IU/day per rat), testosterone (1.5 cm silicone elastomer implant) or a combination of both hormones for 2 weeks following hypophysectomy. After hypophysectomy alone, no elongate spermatids were observed and the numbers of pachytene spermatocytes and round spermatids observed were reduced when compared with untreated controls. Testosterone supplementation alone qualitatively maintained the formation of elongate spermatids in most seminiferous tubules, whilst in FSH-treated rats increased numbers of round spermatids and pachytene spermatocytes were observed when compared with hypophysectomized animals. Formation of elongate spermatids, however, did not occur under FSH treatment alone. A combination of FSH and testosterone treatment maintained spermatogenesis in an almost quantitative fashion. Numbers of pachytene spermatocytes and round spermatids were maintained at about 80% of levels seen in intact control animals. Treatment with FSH or testosterone alone maintained testis weights at significantly higher levels than those seen in hypophysectomized controls (FSH, 0.79 +/- 0.05 g; testosterone, 0.81 +/- 0.07 g; hypophysectomized, 0.50 +/- 0.04 g). Animals treated with FSH and testosterone showed testis weights 20% below control values (1.22 +/- 0.05 vs 1.51 +/- 0.06 g; P less than 0.05). No increases in intratesticular or intratubular androgen concentrations or in testosterone: dihydrotestosterone ratios were observed in any of the hormone-treated groups when compared with hypophysectomized controls. In all hypophysectomized animals testicular androgen concentrations were reduced to less than 5% of control values. The results obtained in this study suggest that FSH is involved in the maintenance of spermatogenesis in the adult rat and that the effects of FSH are not mediated through changes in intratesticular androgens. Low levels of testosterone in combination with FSH can almost quantitatively maintain spermatogenesis in adult rats.
Synthesis, Structural Characterization, and Reactivity of Zirconium Complexes Containing Trimethylenemethane-Based Ligands (1997)

General synthetic routes to zirconium metallocene-like complexes containing derivatives of the dianionic trimethylenemethane (TMM) ligand are presented. One approach consists of reacting the dilithium salts of TMM, tribenzylidenemethane (TBM), tert-butyltribenzylidenemethane (t-Bu-TBM), and dibenzylidenemethylenemethane (DBM) with either Cp*ZrCl3 or CpZrCl3(DME). In the case of the small TMM fragment, the product is the zwitterionic Cp*(TMM)Zr(μ-Cl)2Li(TMEDA) (1). Larger TMM derivatives give discrete salts such as [Cp*(TBM)ZrCl2][Li(TMEDA)2] (2), [Cp(TBM)ZrCl2][Li(TMEDA)2] (3), [Cp(t-Bu-TBM)ZrCl2][Li(TMEDA)2] (4), [Cp*(t-Bu-TBM)ZrCl2][Li(TMEDA)2] (5), and [Cp*(exo-endo-DBM)ZrCl2][Li(TMEDA)2] (6). The reaction of TBM(LiTMEDA)2 with Cp*ZrCl2CH2Ph affords [Cp*(TBM)ZrCl(CH2Ph)][Li(TMEDA)2] (9); thus the retention of LiCl(TMEDA)2 by zirconium is strong. Structural characterization of these complexes reveals crowded environments around the zirconium, especially when both TBM and Cp* are coordinated. It is also possible to take advantage of intramolecular σ-bond metathesis reactions to convert coordinated allyl ligands to TMM-related fragments. For example, [Cp*(TMM)Zr]2(μ-CH2) (10) is derived from Cp*(η3-CH2C(Me)CH2)ZrMe2, and Cp*(TBM)ZrMe(THF) (12) is from Cp*(PhCH2C(CHPh)2)ZrMe2 (11). Formation of the methylpropargyl complex Cp*(TBM)Zr(η3-CH2CCMe) (13) from Cp*(TBM)ZrMe(THF) and 2-butyne instead of a butenyl derivative is a consequence of steric constraints. Activation of 2−6 with methylaluminoxane affords homogeneous catalyst mixtures for polymerization of ethylene and 1,5-hexadiene and copolymerization of ethylene with 1-hexene. There is a strong correlation between catalyst precursor structure and reactivity. Polyethylene can also be prepared by pressurizing a vessel containing only Cp*(TBM)ZrMe(THF).
Negative pattern fabrication using laser exposure of positive photoresist (1998)

The method of simultaneous positive and negative pattern formation on a single positive photoresist layer is described. A negative photoresist pattern was fabricated by using local laser exposure to crosslink a positive resist layer, consecutive UV flood exposure, and resist developing. The positive pattern is obtained on the same photoresist layer in the areas masked from the UV flood exposure. Effects of laser energy and resist processing parameters on height and width of negative type resist structures were investigated. Metal line grid structures with lines in the region of 3 to 30 micrometers in width were manufactured on a 5' X 5' glass substrate using this technique. The proposed method of positive/negative pattern formation significantly reduces the number of technological steps in the fabrication of diffractive elements for dual-wavelength applications.
Coupled Reservoir-Geomechanical Modeling and Stability Analysis during CO 2 Injection into Minjur Sandstone Reservoir (2018)

The continuous emission of carbon dioxide to the environment has caused major climatic changes and is the main cause of the global warming. In order to mitigate the level of carbon dioxide in the atmosphere, the excess amount of carbon dioxide needs to be permanently stored in the deep sedimentary rocks. The pore pressure buildup during carbon dioxide injection process needs to be monitored in order to prevent the failure of the reservoir and hence the leakage of the stored carbon dioxide. In this paper, coupled geomechanical modeling and stability analysis are performed for the Minjur Sandstone reservoir in Saudi Arabia. The pore pressure buildup and ground uplift was calculated during carbon dioxide injection into the reservoir. The Mohr-Coulomb failure criterion was utilized to perform the stability analysis of the reservoir. The stability analysis was performed for the reservoir which suggested safe carbon dioxide injection parameters based on the changes in the pore pressure and horizontal stresses in the reservoir.
Simple estimate of electron-phonon coupling in small fullerenes (1999)

Simple scaling arguments show how contributions to the electron-phonon coupling strength vary with the number of atoms in a carbon fullerene. Smaller fullerenes have higher curvature, which yields larger electron-phonon coupling. The enhancement in coupling is inversely proportional to the number of atoms in the fullerene molecule. Recent ab initio theoretical results on ${\mathrm{C}}_{36}$ fit well within this simple model.