gebhart/patrepeval huggingface dataset:
Energetic Mapping of Transition State Analogue Interactions with Human and Plasmodium falciparum Purine Nucleoside Phosphorylases (2005)

Human purine nucleoside phosphorylase (huPNP) is essential for human T-cell division by removing deoxyguanosine and preventing dGTP imbalance. Plasmodium falciparum expresses a distinct PNP (PfPNP) with a unique substrate specificity that includes 5'-methylthioinosine. The PfPNP functions both in purine salvage and in recycling purine groups from the polyamine synthetic pathway. Immucillin-H is an inhibitor of both huPNP and PfPNPs. It kills activated human T-cells and induces purine-less death in P. falciparum. Immucillin-H is a transition state analogue designed to mimic the early transition state of bovine PNP. The DADMe-Immucillins are second generation transition state analogues designed to match the fully dissociated transition states of huPNP and PfPNP. Immucillins, DADMe-Immucillins and related analogues are compared for their energetic interactions with human and P. falciparum PNPs. Immucillin-H and DADMe-Immucillin-H are 860 and 500 pM inhibitors against P. falciparum PNP but bind human PNP 15-35 times more tightly. This common pattern is a result of kcat for huPNP being 18-fold greater than kcat for PfPNP. This energetic binding difference between huPNP and PfPNP supports the k(chem)/kcat binding argument for transition state analogues. Preferential PfPNP inhibition is gained in the Immucillins by 5'-methylthio substitution which exploits the unique substrate specificity of PfPNP. Human PNP achieves part of its catalytic potential from 5'-OH neighboring group participation. When PfPNP acts on 5'-methylthioinosine, this interaction is not possible. Compensation for the 5'-OH effect in the P. falciparum enzyme is provided by improved leaving group interactions with Asp206 as a general acid compared with Asn at this position in huPNP. Specific atomic modifications in the transition state analogues cause disproportionate binding differences between huPNP and PfPNPs and pinpoint energetic binding differences despite similar transition states.
Preamble-Based SNR Estimation in Frequency Selective Channels for Wireless OFDM Systems (2009)

Orthogonal frequency division multiplexing (OFDM) offers high data rates and robust performance in frequency selective channels by link adaptation utilizing information about the channel quality. A crucial parameter required for adaptive transmission is the signal-to-noise ratio (SNR). In this paper, we propose a novel SNR estimation algorithm for wireless OFDM systems based on the reuse of the synchronization preamble. The periodic structure of the preamble is utilized for the computationally efficient SNR estimation algorithm, based on the second-order moments of received preamble samples. The performance of the proposed algorithm is compared with the MMSE algorithm and two preamble-based algorithms found in the literature. It is shown that the proposed algorithm is robust against frequency selectivity and may therefore be used for subchannel SNR estimation.
Gauge Equivariant Convolutional Networks and the Icosahedral CNN (2019)

The principle of equivariance to symmetry transformations enables a theoretically grounded approach to neural network architecture design. Equivariant networks have shown excellent performance and data efficiency on vision and medical imaging problems that exhibit symmetries. Here we show how this principle can be extended beyond global symmetries to local gauge transformations. This enables the development of a very general class of convolutional neural networks on manifolds that depend only on the intrinsic geometry, and which includes many popular methods from equivariant and geometric deep learning. We implement gauge equivariant CNNs for signals defined on the surface of the icosahedron, which provides a reasonable approximation of the sphere. By choosing to work with this very regular manifold, we are able to implement the gauge equivariant convolution using a single conv2d call, making it a highly scalable and practical alternative to Spherical CNNs. Using this method, we demonstrate substantial improvements over previous methods on the task of segmenting omnidirectional images and global climate patterns.
Aqueous Suspension Polymerization of Isobutene Initiated by 1,2-C<sub>6</sub>F<sub>4</sub>[B(C<sub>6</sub>F<sub>5</sub>)<sub>2</sub>]<sub>2</sub> (2004)

Lewis acidic, chelating diborane 1 forms stable oxonium acids 2 in the presence of excess MeOH or water. Diborane 1 is shown to be an effective co-initiator for the suspension polymerization of isobutene in aqueous media at sufficiently low temperatures. Poly(isobutene) or butyl rubber is obtained at moderate to high conversion and with Mw < 200 K and PDI approximately 2 under these conditions.
Lockin Thermography with Optical or Ultrasound Excitation (2010)

Thermography is a well established non-destructive testing (NDT) technique providing images of temperature distributions. If the temperature field on a sample surface is modulated by periodical injection of heat either from outside or inside the sample, the time dependence of the temperature field provides information on thermal features hidden underneath the surface. Using the Fourier-transform, this information is finally compressed into a phase and an amplitude image. Phase images are more robust than amplitude images, because surface features and reflections are effectively suppressed.
With excitation by ultrasound, the heating mechanism is local conversion of elastic energy into heat which occurs preferably due to local friction losses caused e.g. by the relative motion of boundaries in a crack. As intact material and boundaries are suppressed in such an image, it displays defects selectively. The techniques and their applications are illustrated by examples that were obtained on various industry-relevant components.
Multi‐way versus one‐way constraints in user interfaces: Experience with the deltablue algorithm (1993)

Abstract The efficient satisfaction of constraints is essential to the performance of constraint‐based user interfaces. In the past, most constraint‐based user interfaces have used one‐way rather than multi‐way constraints because of a widespread belief that one‐way constraints were more efficient. In this paper we argue that many user interface construction problems are handled more naturally and elegantly by multi‐way constraints than by one‐way constraints. We present pseudocode for an incremental multi‐way constraint satisfaction algorithm, DeltaBlue, and describe experience in using the algorithm in two user interface toolkits. Finally, we provide performance figures demonstrating that multi‐way constraint solvers can be entirely competitive in performance with one‐way constraint solvers.
On-Line Monitoring When the Process Yields a Linear Profile (2000)

Control charts monitor processes where performance is measured by one or multiple quality characteristics. Some processes, however, are characterized by a profile or a function. Here we focus on monitoring a process in semiconductor manufacturing that is characterized by a linear function. While the linear function is the simplest, it occurs frequently, for example in calibration studies. Two monitoring approaches are proposed: (1) monitor parameters, slope and intercept, with multivariate T2 and (2) monitor average residuals between sample and reference lines with EWMA and R charts. Simulation studies indicate that both methods work well. Both methods are extendable to complex functions.
Reversible Infrared Actuation of Carbon Nanotube–Liquid Crystalline Elastomer Nanocomposites (2008)

Nanocomposite films comprising polymer-functionalized single-walled carbon-nanotubes (SWNTs) and liquid crystal elastomers (LCEs) show a reversible IR-induced strain (∼−30%) at very low SWNT loading levels (≤0.2 wt%). SWNTs can efficiently transform absorbed IR light into thermal energy, thereby serving as a nanoscale heat-source and thermal- conduction pathway. The absorbed thermal-energy induced a nematic– isotropic phase-transition, generating a shape change in the nanocomposite film. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2089/2008/adma200702953_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Enhanced susceptibility of <i>Prnp</i>‐deficient mice to kainate‐induced seizures, neuronal apoptosis, and death: Role of AMPA/kainate receptors (2007)

Normal physiologic functions of the cellular prion protein (PrPc) are still elusive. This GPI-anchored protein exerts many functions, including roles in neuron proliferation, neuroprotection or redox homeostasis. There are, however, conflicting data concerning its role in synaptic transmission. Although several studies report that PrPc participates in NMDA-mediated neurotransmission, parallel studies describe normal behavior of PrPc-mutant mice. Abnormal axon connections have been described in the dentate gyrus of the hippocampi of PrPc-deficient mice similar to those observed in epilepsy. A study indicates increased susceptibility to kainate (KA) in these mutant mice. We extend the observation of these studies by means of several histologic and biochemical analyses of KA-treated mice. PrPc-deficient mice showed increased sensitivity to KA-induced seizures in vivo and in vitro in organotypic slices. In addition, we show that this sensitivity is cell-specific because interference experiments to abolish PrPc expression increased susceptibility to KA in PrPc-expressing cells. We indicate a correlation of susceptibility to KA in cells lacking PrPc with the differential expression of GluR6 and GluR7 KA receptor subunits using real-time RT-PCR methods. These results indicate that PrPc exerts a neuroprotective role against KA-induced neurotoxicity, probably by regulating the expression of KA receptor subunits.
Escher's art, Smith chart, and hyperbolic geometry (2006)

The purpose of this article is to point out a conceptual link between an artistic creation by the well-known Dutch artist M.C. Escher (1898-1972), called Circle Limit IV (woodcut, 1960), and the most commonly used graphical aid in microwave engineering work, called the Smith chart (1939-1944), created by the U.S. engineer P.H. Smith (1905-1987)
CD39 Modulates Hematopoietic Stem Cell Recruitment and Promotes Liver Regeneration in Mice and Humans After Partial Hepatectomy (2012)

We demonstrate CD39 to be a novel HSC marker that defines a functionally distinct stem cell subset in mice and humans. HSCs are mobilized after liver resection, limit inflammation, and boost regeneration in a CD39-dependent manner. These observations have implications for monitoring and indicate future therapeutic avenues.
A New Cluster of Genes Within the Human Major Histocompatibility Complex (1989)

A 435-kilobase (kb) DNA segment, which is centromeric to HLA-B in the human major histocompatibility complex, was isolated by chromosome walking with overlapping cosmids. Within the cloned region, the genes for the tumor necrosis factors (TNFs) alpha and beta and HLA-B were 210 kb apart. The human homolog of a mouse gene, B144, was located next to TNF alpha. Moreover, the presence of additional genes was suggested by a large cluster of CpG islands. With cosmid probes, several distinct transcripts were detected in RNA samples from a variety of cell lines. Altogether, five novel genes were identified by isolation of corresponding complementary DNA clones. These "HLA-B-associated transcripts" (BATs) were mapped to different locations within a 160-kb region that includes the genes for TNF alpha and TNF beta. The presence of the genes for BAT1 and BAT5 in the vicinity of HLA-B again raises the question of which gene in this region determines susceptibility to ankylosing spondylitis.
Catalytic Effect of Nanoparticle 3d-Transition Metals on Hydrogen Storage Properties in Magnesium Hydride MgH<sub>2</sub> Prepared by Mechanical Milling (2005)

We examined the catalytic effect of nanoparticle 3d-transition metals on hydrogen desorption (HD) properties of MgH(2) prepared by mechanical ball milling method. All the MgH(2) composites prepared by adding a small amount of nanoparticle Fe(nano), Co(nano), Ni(nano), and Cu(nano) metals and by ball milling for 2 h showed much better HD properties than the pure ball-milled MgH(2) itself. In particular, the 2 mol % Ni(nano)-doped MgH(2) composite prepared by soft milling for a short milling time of 15 min under a slow milling revolution speed of 200 rpm shows the most superior hydrogen storage properties: A large amount of hydrogen ( approximately 6.5 wt %) is desorbed in the temperature range from 150 to 250 degrees C at a heating rate of 5 degrees C/min under He gas flow with no partial pressure of hydrogen. The EDX micrographs corresponding to Mg and Ni elemental profiles indicated that nanoparticle Ni metals as catalyst homogeneously dispersed on the surface of MgH(2). In addition, it was confirmed that the product revealed good reversible hydriding/dehydriding cycles even at 150 degrees C. The hydrogen desorption kinetics of catalyzed and noncatalyzed MgH(2) could be understood by a modified first-order reaction model, in which the surface condition was taken into account.
Comparison of the performance of direct current atmospheric pressure glow microdischarges operated between a small sized flowing liquid cathode and miniature argon or helium flow microjets (2013)

Low power direct current atmospheric glow microdischarges were sustained between miniature Ar or He flow nozzle microjets and a small-sized flowing liquid cathode as new excitation microsources for optical emission spectrometry. The morphology of emission spectra of both microdischarges was compared and the effect of the flow rate of both gases on their performance and the emission characteristic related to molecular bands and atomic lines of selected metals (Ca, Cd, Cu, Fe, K, Li, Mg, Mn, Na and Zn) were studied using optical emission spectrometry. It was established that in the microdischarge with the miniature He flow microjet there were more convenient conditions for the quenching of the band emission originating from OH, N2, NH and NO molecules as compared to those with the Ar microjet. The background level and its fluctuation in the vicinity of analytical lines of metals were lower, while their signal to noise ratios were higher. Under compromised conditions, selected figures of merit for the better microdischarge with the He microjet were evaluated. The detection limits assessed for Ca, K, Li, Mg and Na were within the range of 0.001 to 0.077 mg L−1. These metals were determined in six samples of tap water. The accuracy of this analysis, expressed as the relative error with reference to values determined with flame atomic absorption spectrometry (Ca, Mg) and flame atomic emission spectrometry (K, Li, Na), ranged from −2.1 to +10.1%. In addition, recoveries of metals added to the analyzed tap water samples varied from 90.6 to 106.9%. The precision of the analysis was within 0.2–4.6%.
Risk factors for depression in elderly people: a prospective study (1992)

In 1982-1983 a random sample of 1486 people aged 65 years and above was generated from general practitioner lists; 1070 were interviewed in the community using the Geriatric Mental State and a Social History questionnaire. The cohort was followed up by interview 3 years later. At year 3 the diagnostic computer program AGECAT diagnosed 44 incident cases of depression. Information from the depressed group's initial and further interviews was compared with a control group (which excluded cases of affective or organic mental illness). Univariate analysis yielded three factors that were significantly associated with the development of depression 3 years later: a lack of satisfaction with life; feelings of loneliness; and smoking. Multivariate analysis confirmed their independent effects and revealed 2 further factors attaining significance: female gender and a trigger factor, bereavement of a close figure within 6 months of the third-year diagnosis. Some other factors traditionally associated with depression, such as poor housing, marital status and living alone, failed to attain significance as risk factors.
TOCTTOU vulnerabilities in UNIX-style file systems: an anatomical study (2005)

Due to their non-deterministic nature, Time of Check To Time of Use (TOCTTOU) vulnerabilities in Unix-style file systems (e.g., Linux) are difficult to find and prevent. We describe a comprehensive model of TOCTTOU vulnerabilities, enumerating 224 file system call pairs that may lead to successful TOCTTOU attacks. Based on this model, we built kernel monitoring tools that confirmed known vulnerabilities and discovered new ones (in often-used system utilities such as rpm, vi, and emacs). We evaluated the probability of successfully exploiting these newly discovered vulnerabilities and analyzed in detail the system events during such attacks. Our performance evaluation shows that the dynamic monitoring of system calls introduces non-negligible overhead in microbenchmark of those file system calls, but their impact on application benchmarks such as Andrew and PostMark is only a few percent.
The optimal projection equations for model reduction and the relationships among the methods of Wilson, Skelton, and Moore (1985)

First-order necessary conditions for quadratically optimal reduced-order modeling of linear time-invariant systems are derived in the form of a pair of modified Lyapunov equations coupled by an oblique projection which determines the optimal reduced-order model. This form of the necessary conditions considerably simplifies previous results of Wilson [1] and clearly demonstrates the quadratic extremality and nonoptimality of the balancing method of Moore [2]. The possible existence of multiple solutions of the optimal projection equations is demonstrated and a relaxation-type algorithm is proposed for computing these local extrema. A component-cost analysis of the model-error criterion similar to the approach of Skelton [3] is utilized at each iteration to direct the algorithm to the global minimum.
Increased fructose 1,6-bisphosphate aldolase in plastids enhances growth and photosynthesis of tobacco plants (2012)

The Calvin cycle is the initial pathway of photosynthetic carbon fixation, and several of its reaction steps are suggested to exert rate-limiting influence on the growth of higher plants. Plastid fructose 1,6-bisphosphate aldolase (aldolase, EC 4.1.2.13) is one of the nonregulated enzymes comprising the Calvin cycle and is predicted to have the potential to control photosynthetic carbon flux through the cycle. In order to investigate the effect of overexpression of aldolase, this study generated transgenic tobacco (Nicotiana tabacum L. cv Xanthi) expressing Arabidopsis plastid aldolase. Resultant transgenic plants with 1.4-1.9-fold higher aldolase activities than those of wild-type plants showed enhanced growth, culminating in increased biomass, particularly under high CO₂ concentration (700 ppm) where the increase reached 2.2-fold relative to wild-type plants. This increase was associated with a 1.5-fold elevation of photosynthetic CO₂ fixation in the transgenic plants. The increased plastid aldolase resulted in a decrease in 3-phosphoglycerate and an increase in ribulose 1,5-bisphosphate and its immediate precursors in the Calvin cycle, but no significant changes in the activities of ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) or other major enzymes of carbon assimilation. Taken together, these results suggest that aldolase overexpression stimulates ribulose 1,5-bisphosphate regeneration and promotes CO₂ fixation. It was concluded that increased photosynthetic rate was responsible for enhanced growth and biomass yields of aldolase-overexpressing plants.
Germline mutations 657del5 of the <i>NBS1</i> gene contribute significantly to the incidence of breast cancer in Central Poland (2006)

Recent studies have demonstrated that heterozygous carriers of the NBS1 657del5 mutation have an increased risk for familial and bilateral breast cancer, but similar studies in consecutive breast cancer patients were inconclusive. Here, in a study of 562 nonselected breast cancer patients from Central Poland, we found 11 (1.96%) 657del5 mutation carriers vs. 3.47 expected (OR 3.21, 95%CI: 1.36-7.61, p = 0.0107) and only 9 (1.6%) carriers of the 5382insC mutation of the BRCA1 gene, most frequently found among breast cancer patients in Poland. No carriers of R215W, another pathogenic mutation of the NBS1 gene, were found in the present study. All carriers of the 657del5 mutation had sporadic breast tumors while 5 of 9 5382insC carriers had a family history of breast/ovarian cancer or bilateral breast carcinoma. In the pooled group of patients from the present and our previous study, carried out also in patients from Central Poland, we obtained the following risk estimates (OR) for 657del5 carriers, as related to the age at breast cancer diagnosis: < 40 years: 8.36; (95%CI: 2.57-27.27) p = 0.0003; < 50 years: 4.27 (95%CI: 1.67-10.89) p = 0.003; > or = 50 years: 2.40 (95%CI: 0.91-6.35) p = 0.1250; all ages: 3.13 (95% CI: 1.40-7.00) p = 0.0066. These findings demonstrate conclusively that NBS1 657del5 mutation carriers have a significantly, though moderately increased, age-related risk of breast cancer, and imply that in populations with a high 657del5 carrier frequency this mutation may contribute substantially to the overall incidence of breast cancer, particularly in younger age groups.
Pharmacodynamics and Pharmacokinetics of Propofol in a Medium-Chain Triglyceride Emulsion (2002)

Differences between the two propofol formulations were slight and not clinically significant. Similar gender differences in plasma concentrations and awaking times were found for both formulations.
Selective Nucleic Acid Removal via Exclusion (SNARE): Capturing mRNA and DNA from a Single Sample (2013)

The path from gene (DNA) to gene product (RNA or protein) is the foundation of genotype giving rise to phenotype. Comparison of genomic analyses (DNA) with paired transcriptomic studies (mRNA) is critical to evaluating the pathogenic processes that give rise to human disease. The ability to analyze both DNA and mRNA from the same sample is not only important for biologic interrogation but also to minimize variance (e.g., sample loss) unrelated to the biology. Existing methods for RNA and DNA purification from a single sample are typically time-consuming and labor intensive or require large sample sizes to split for separate RNA and DNA extraction procedures. Thus, there is a need for more efficient and cost-effective methods to purify both RNA and DNA from a single sample. To address this need, we have developed a technique, termed SNARE (Selective Nucleic Acid Removal via Exclusion), that uses pinned oil interfaces to simultaneous purify mRNA and DNA from a single sample. A unique advantage of SNARE is the elimination of dilutive wash and centrifugation processes that are fundamental to conventional methods where sample is typically discarded. This minimizes loss and maximizes recovery by allowing nondilutive reinterrogation of the sample. We demonstrate that SNARE is more sensitive than commercially available kits, robustly and repeatably achieving mRNA and DNA purification from extremely low numbers of cells for downstream analyses. In addition to sensitivity, SNARE is fast, easy to use, and cost-effective and requires no laboratory infrastructure or hazardous chemicals. We demonstrate the clinical utility of the SNARE with prostate cancer circulating tumor cells to demonstrate its ability to perform both genomic and transcriptomic interrogation on rare cell populations that would be difficult to achieve with any current method.