gebhart/patrepeval huggingface dataset:
Combined selection of Gpc-B1 and Glu-B1 locus encoding the Bx7OE subunit for improving end-use quality of hard white wheat (2021)

Wheat in Canada is classified into nine different market classes based on attributes that impact end-use functionality. The Canada Western Hard White Spring (CWHWS) class was created in 2001 to diversify wheat production. The quality requirements of the CWHWS class demand strong gluten properties but lower grain protein (GP) content levels compared to the premium CWRS class. Generally, GP and grain yield are negatively correlated, so a reduction in GP would allow CWHWS cultivars to express greater yield potential. However, lowering GP can result in weaker gluten strength. This study investigated the combined use of Gpc-B1 and Bx7OE to increase GP while maintaining the dough strength in hard white wheat lines. Additionally, the effects of these introgressions on agronomic traits (grain yield, days to heading, days to maturity, plant height, test weight, and thousand kernel weight) were evaluated. Seven populations (each comprising 40 RILs, all varying for presence of Bx7OE, and five populations carrying all possible combinations of Gpc-B1 and Bx7OE) were developed using marker-assisted selection and elite cultivars or advanced breeding lines as parents and tested in three field environments in Saskatchewan, Canada. End-use quality was measured on grain (protein content, kernel hardness), and flour (protein, ash, protein loss, color, and farinograph). Results from our study showed a 0.8–1.1% increase in GP content relative to CWHWS cultivars (used as checks in the study) and dough strength properties similar to CWRS cultivar ‘CDC Teal’ (representing uppermost limit of dough strength in CWRS class at the time). Except for a slight increase in plant height (still comparable to elite cultivars), no deleterious effects on agronomic or other quality traits were observed. We conclude that combined selection of Gpc-B1 DIC with Bx7OE is effective in developing CWHWS lines with a desirable end-use quality.
Deriving State Machines from TinyOS Programs Using Symbolic Execution (2008)

The most common programming languages and platforms for sensor networks foster a low-level programming style. This design provides fine-grained control over the underlying sensor devices, which is critical given their severe resource constraints. However, this design also makes programs difficult to understand, maintain, and debug. In this paper, we describe an approach to automatically recover the high-level system logic from such low-level programs, along with an instantiation of the approach for nesC programs running on top of the TinyOS operating system. We adapt the technique of symbolic execution from the program analysis community to handle the event-driven nature of TinyOS, providing a generic component for approximating the behavior of a sensor network application or system component. We then employ a form of predicate abstraction on the resulting information to automatically produce a finite state machine representation of the component. We have used our tool, called FSMGen, to automatically produce compact and fairly accurate state machines for several TinyOS applications and protocols. We illustrate how this high-level program representation can be used to aid programmer understanding, error detection, and program validation.
A genome-wide case-only test for the detection of digenic inheritance in human exomes (2020)

Abstract Whole-exome sequencing (WES) has facilitated the discovery of genetic lesions underlying monogenic disorders. Incomplete penetrance and variable expressivity suggest a contribution of additional genetic lesions to clinical manifestations and outcome. Some monogenic disorders may therefore actually be digenic. However, only a few digenic disorders have been reported, all discovered by candidate gene approaches applied to at least one locus. We propose here a novel two-locus genome-wide test for detecting digenic inheritance in WES data. This approach uses the gene as the unit of analysis and tests all pairs of genes to detect pairwise gene x gene interactions underlying disease. It is a case-only method, which has several advantages over classic case-control tests, in particular by avoiding recruitment and bias of controls. Our simulation studies based on real WES data identified two major sources of type I error inflation in this case-only test: linkage disequilibrium and population stratification. Both were corrected by specific procedures. Moreover, our case-only approach is more powerful than the corresponding case-control test for detecting digenic interactions in various population stratification scenarios. Finally, we validated our unbiased, genome-wide approach by successfully identifying a previously reported digenic lesion in patients with craniosynostosis. Our case-only test is a powerful and timely tool for detecting digenic inheritance in WES data from patients. Significance statement Despite a growing number of reports of rare disorders not fully explained by monogenic lesions, digenic inheritance has been reported for only 54 diseases to date. The very few existing methods for detecting gene x gene interactions from next-generation sequencing data were generally studied in rare-variant association studies with limited simulation analyses for short genomic regions, under a case-control design. We describe the first case-only approach designed specifically to search for digenic inheritance, which avoids recruitment and bias related to controls. We show, through both extensive simulation studies on real WES datasets and application to a real example of craniosynostosis, that our method is robust and powerful for the genome-wide identification of digenic lesions.
A distributed solution for proportional fairness optimization in load coupled OFDMA networks (2016)

We propose a novel distributed downlink technique for proportional fairness optimization in load coupled orthogonal frequency multiple access (OFDMA) networks where the power allocation, the rate allocation and resources assignment are jointly optimized. Building upon recent results on nonlinear interference models for OFDMA-based wireless systems, we pose the problem of finding proportionally fair rates as a convex network utility optimization problem for which solutions can be computed efficiently and are known to be energy efficient. Furthermore, we propose a distributed optimality-achieving implementation based on a message passing protocol between base stations. Simulations show a potential for improvements in terms of network utility and energy consumption.
Saturation of multiplication mechanism in silicon avalanche photodiodes used for single electron detection (1998)

We have examined the multiplication factor of silicon avalanche photodiodes designed for fast timing detection of monoenergetic electrons. The multiplication mechanism was found to be saturated. The highly concentrated space charge generated by a primary electron causes the saturation. This was confirmed by a Monte Carlo simulation of electron trajectories in silicon and an experiment exploiting a subpicosecond laser pulse with a variable illuminating spot size to simulate an electron bombardment.
Development of an Ectopic huLiver Model for Plasmodium Liver Stage Infection (2022)

Abstract Early Plasmodium falciparum and P. vivax infection requires parasite replication within host hepatocytes, referred to as liver stage (LS). However, limited understanding of infection dynamics in human LS exists due to species-specificity challenges. Reported here is a reproducible, easy-to-manipulate, and moderate-cost in vivo model to study human Plasmodium LS in mice; the ectopic huLiver model. Ectopic huLiver tumors were generated through subcutaneous injection of the HC-04 cell line and shown to be infectible by both freshly dissected sporozoites and through the bite of infected mosquitoes. Evidence for complete LS development was supported by the transition to blood-stage infection in mice engrafted with human erythrocytes. Additionally, this model was successfully evaluated for its utility in testing antimalarial therapeutics, as supported by primaquine acting as a causal prophylactic against P. falciparum. Presented here is a new platform for the study of human Plasmodium infection with the potential to aid in drug discovery.
Temporal Patterns of Δ4C-21 Steroids in Coexisting, Genetically Dissimilar Twin Lamb Fetuses throughout Late Gestation* (1984)

We have examined the relationships among fetal maturity, adrenal steroidogenesis, and initiation of parturition using embryo transfer procedures. Ovine embryos, genetically coded for relatively short [145.5 +/- 1.4 days; Finnish Landrace (Finn)] and long [150.7 +/- 1.3 days; Rambouillet (Ra)] gestational periods, were transferred to a common recipient, thereby facilitating comparative endocrine studies in genetically dissimilar fetuses with a common intrauterine environment. Maternal and fetal plasma samples were obtained daily from chronic fetal lamb preparations in six mixed breed (MB), three Finn, and three Ra single breed (SB) pregnancies during the last trimester and assayed for cortisol, desoxycortisol, and progesterone by RIA. Mean +/- SEM gestational lengths of the forenamed pregnancies were 141.5 +/- 0.7, 141.7 +/- 0.7, and 149.3 +/- 0.9 days, respectively. Time-trend analysis of C-21 steroid data showed an increase in Finn and Ra SB fetal plasma cortisol of 1.0 ng/ml X day at 9.03 +/- 1.0 and 9.58 +/- 1.10 days prepartum, respectively. Significant (P less than or equal to 0.05) differences in the number of days of incremental change (T*) were noted between Finn (10.56 +/- 0.67) and Ra (4.82 +/- 1.08) siblings in MB pregnancies at increment rates of 1.0 ng/ml X day. Similarly, significant (P less than or equal to 0.05) differences in T* values were observed between Finn (8.31 +/- 0.38 days) and RA (4.63 +/- 1.0 days) siblings at 2.0 ng/ml X day. While Finn and Ra SB fetal desoxycortisol T* values were similar at 0.5 and 0.1 ng/ml X day, significant differences (P less than or equal to 0.05) were noted in Finn and Ra cofetuses in the MB pregnancy. Prepartal changes in maternal and fetal progesterone concentrations were correlated, and a direct parallelism was noted between fetal sibling progesterone concentrations. These results are consistent with the view that the fetal genome has a principal role in the timing of parturition.
Optical Design of DEI/ABI System at the HEX Beamline at the NSLS-II (2021)

Diffraction Enhanced Imaging (DEI) or Analyzer Based Imaging (ABI) uses a perfect crystal monochromator and matching analyzer to achieve sensitivity to x-ray refraction and ultra small-angle scattering on the order of 0.01 micro-radians. As such, a thermal bump caused by heat-load in the order of 1 W is detrimental. The heat load at the HEX (High Energy Engineering X-ray) super-conducting wiggler (SCW) beamline, under construction at the NSLS-II, is on the order of 1 kW. How to reconcile the three orders of magnitude difference between the HEX source power and the DEI/ABI requirements? The solution involves using a double-crystal bent-Laue monochromator as pre-monochromator to prepare a beam with a large divergence and bandwidth that is matched to a flat crystal post-monochromator. We show through phase-space (x-ray energy vs. angle as viewed by a flat crystal) analysis and Dumond diagrams that there is indeed a unique bending radius that matches the double-crystal bent-Laue monochromator in phase space to the flat Bragg crystal. The matched system has a desirable feature that the phase space of the bent crystal’s output beam is much larger than that of the flat crystal, making the combined system stable. Based on these considerations, here we present our optical design for performing DEI/ABI at the HEX beamline
Spatial control of the recombination zone in ambipolar light-emitting polymer transistors (2006)

Ambipolar organic field-effect transistors (FET) are interesting as building blocks for low power complementary circuits in organic electronics. Another intriguing feature of ambipolar FETs is the recombination of holes and electrons within the channel, which leads to the formation of excitons that can relax radiatively and thus emit light. We have recently demonstrated that ambipolar charge transport is a generic feature in a wide range of polymer semiconductors when appropriate injection electrodes and trapfree dielectrics are used. Among these materials are those that are generally used in light-emitting diodes and thus show high photoluminescence efficiencies. Here we demonstrate ambipolar light-emitting field-effect transistors based on the conjugated polymer OC<sub>1</sub>C<sub>10-</sub>PPV (poly(2-methoxy-5-(3,7-dimethyloctoxy)-p-phenylenevinylene)) as the semiconducting and emissive layer. OC<sub>1</sub>C<sub>10-</sub> PPV shows efficient electron and hole transport with field-effect mobilities of 3&#8901;10<sup>-3</sup> cm<sup>2</sup>/Vs and 6&#8901;10<sup>-4</sup> cm<sup>2</sup>/Vs, respectively. Electrons and holes are injected from calcium and gold source and drain electrodes, respectively, and recombine radiatively within the transistor channel leading to visible light emission. We can actively control the position of the recombination zone through the applied gate and source-drain bias in both constant and variable current mode and thus move the emission zone from the source through the channel to the drain electrode and vice versa. The intensity of light emitted from the channel is proportional to the drain current with efficiencies comparable to those of LEDs based on OC<sub>1</sub>C<sub>10-</sub>PPV.
High‐Quality Epitaxial Film Growth of Superconducting Sodium‐Cobalt Oxyhydrate, Na 0.3 CoO 2 · 1.3H 2 O (2006)

This chapter contains sections titled: Introduction Experimental Results and Discussion Conclusion
Synchrotron microbeam x-ray radiation damage in semiconductor layers (2008)

Radiation induced structural damage is observed in silicon-on-insulator (SOI) and SiGe on SOI samples illuminated with monochromatic (11.2keV) x-ray microbeams approximately 250nm in diameter. The x-ray diffraction peaks from the irradiated layers irreversibly degrade with time, indicating permanent structural damage to the crystal lattice. The size of the damaged regions is almost an order of magnitude larger than the beam size. The magnitude of damage decreases as one moves away from the center of the illuminated volume. We discuss the threshold dosage required for damage initiation and possible mechanisms for the observed damage.
PK/PD Disconnect Observed with a Reversible Endothelial Lipase Inhibitor (2018)

Screening of a small set of nonselective lipase inhibitors against endothelial lipase (EL) identified a potent and reversible inhibitor, <i>N</i>-(3-(3,4-dichlorophenyl)propyl)-3-hydroxy-1-methyl-2-oxo-1,2-dihydropyridine-4-carboxamide (<b>5</b>; EL IC<sub>50</sub> = 61 nM, EL<sub>HDL</sub> IC<sub>50</sub> = 454 nM). Deck mining identified a related hit, <i>N</i>-(3-(3,4-dichlorophenyl)propyl)-4-hydroxy-1-methyl-5-oxo-2,5-dihydro-1<i>H</i>-pyrrole-3-carboxamide (<b>6a</b>; EL IC<sub>50</sub> = 41 nM, EL<sub>HDL</sub> IC<sub>50</sub> = 1760 nM). Both compounds were selective against lipoprotein lipase (LPL) but nonselective versus hepatic lipase (HL). Optimization of compound <b>6a</b> for EL inhibition using HDL as substrate led to <i>N</i>-(4-(3,4<b>-</b>dichlorophenyl)butan-2-yl)-1-ethyl-4-hydroxy-5-oxo-2,5-dihydro-1<i>H</i>-pyrrole-3-carboxamide (<b>7c</b>; EL IC<sub>50</sub> = 148 nM, EL<sub>HDL</sub> IC<sub>50</sub> = 218 nM) having improved PK over compound <b>6a</b>, providing a tool molecule to test for the ability to increase HDL-cholesterol (HDL-C) levels in vivo using a reversible EL inhibitor. Compound <b>7c</b> did not increase HDL-C in vivo despite achieving plasma exposures targeted on the basis of enzyme activity and protein binding demonstrating the need to develop more physiologically relevant in vitro assays to guide compound progression for in vivo evaluation.
Loss of m 1 acp 3 Ψ ribosomal RNA modification is a major feature of cancer (2019)

Summary The ribosome is an RNA-protein complex essential for translation in all domains of life. The structural and catalytic core of the ribosome is its ribosomal RNA (rRNA). While mutations in ribosomal protein (RP) genes are known drivers of oncogenesis, oncogenic rRNA variants have remained elusive. We discovered a cancer-specific single nucleotide variation in 18S rRNA at nucleotide 1248.U in up to 45.9% of colorectal carcinoma (CRC) patients and present across &gt;22 cancer types. This is the site of a unique hyper-modified base, 1-methyl-3-α-amino-α-carboxyl-propyl pseudouridine (m 1 acp 3 Ψ), a &gt;1 billion years conserved RNA modification at the ribosome’s peptidyl decoding-site. A sub-set of CRC tumors we term ‘hypo-m 1 acp 3 Ψ’, show sub-stoichiometric m 1 acp 3 Ψ-modification unlike normal control tissues. A m 1 acp 3 Ψ knockout model and hypo-m 1 acp 3 Ψ patient tumors share a translational signature, characterized by highly abundant ribosomal proteins. Thus, m 1 acp 3 Ψ-deficient rRNA forms an uncharacterized class of ‘onco-ribosome’ which may serve as a chemotherapeutic target for treating cancer patients.
Synthesis and Structural Characterization of the Yttrium Containing Isopolytungstate [YW10O36]9− (2008)

Abstract The yttrium containing isopolytungstate [YW 10 O 36 ] 9− ( 1 ) has been synthesized and isolated in the form of its hydrated sodium salt Na 9 [YW 10 O 36 ]·35H 2 O ( Na‐1 ). The title compound has been structurally characterized in the solid state by single‐crystal X‐ray crystallography, IR spectroscopy, thermogravimetric analysis and in solution by 183 W and 89 Y NMR spectroscopy. The X‐ray analysis shows that Na‐1 crystallizes in the triclinic system, space group $P{\bar 1}$ , with a = 12.7625(9), b = 13.0825(10), c = 20.496(2) Å, α = 82.856(5), β = 74.520(4), γ = 88.822(4)°, V = 3272.1(4) Å 3 and Z = 2. Solution 183 W NMR shows the expected 2 lines at –1.3 ppm and –14.3 ppm, respectively, with an intensity ratio of 1:4, and 89 Y NMR shows a singlet at –12.9 ppm.
Experimental investigations of the effects of cutting angle on chattering of a flexible manipulator (1991)

When a machine tool is mounted at the tip of a robotic manipulator, the manipulator becomes more flexible (the natural frequencies are lowered). Moreover, for a given flexible manipulator, its compliance will be different depending on feedback gains, configurations, and direction of interest. Here, the compliance of a manipulator is derived analytically, and its magnitude is represented as a compliance ellipsoid. Then, using a two-link flexible manipulator with an abrasive cut off saw, the experimental investigation shows that the chattering varies with the saw cutting angle due to different compliance. The main work is devoted to finding a desirable cutting angle which reduces the chattering.
Why do we need a Sparse Global Time-Base in Dependable Real-time Systems? (2007)

In many hi-dependability applications (such as a fly-by-wire system) triple-modular redundancy (TMR) is deployed to mask arbitrary failures of any of its constituent components. A TMR system will only work properly if the three replicated channels are synchronized, operate independently and exhibit a deterministic behavior. Determinism requires that two inputs that are presented to the three independent channel at the same instant must be ordered in the same way by all three channels, i.e., simultaneity must be resolved consistently at the system level. In order to resolve this issue of system-wide consistent temporal ordering of events, a global time base of known precision-as established by the IEEE 1588 standard-is of utmost utility. Given such a global time-base of known precision, one can establish a global sparse time model that supports the consistent ordering of events.
Heterogeneous distribution of adrenergic receptors in coronary arteries and their influence on coronary arterial tone. (1985)

In-vitro experiments, using canine large (o.d. 1-2 mm) and small (o.d. 0.4-0.8mm) coronary arteries, were undertaken to determine the functional state of alpha- and beta-adrenergic receptors and their role in regulation of coronary arterial tone. Both large and small coronary arteries of the dog possess alpha and beta adrenergic receptors. Alpha-adrenergic receptors are more numerous on the circumflex vessel than elsewhere. Functionally, beta-adrenergic receptors appear to be dominant under physiological conditions in most types of coronary arteries. In canine coronary arteries, beta-adrenergic receptors have a greater affinity for noradrenaline than adrenaline. Alpha-adrenergic receptors have a greater affinity for adrenaline than noradrenaline. It is concluded that after beta-adrenergic blockade, in both large and small coronary arteries, alpha-adrenergic receptors play an important role in regulation of coronary arterial tone.
Hippocampal episode fields develop with learning (2010)

Several recent studies have shown that hippocampal neurons fire during the delay period in between trials and that these firing patterns differ when different behaviors are required, suggesting that the neuronal responses may be involved in maintaining the memories needed for the upcoming trial. In particular, one study found that hippocampal neurons reliably fired at particular times, referred to as "episode fields" (EFs), during the delay period of a spatial alternation task (Pastalkova et al. (2008) Science 321:1322-1327). The firing of these neurons resulted in distinct sequential firing patterns on left and right turn trials, and these firing patterns could be used to predict the upcoming behavioral response. In this study, we examined neuronal firing during the delay period of a hippocampus-dependent plus maze task, which involved learning to approach two different reward locations (east and west), and we examined the development of these firing patterns with learning. As in the previous study, hippocampal neurons exhibited discrete periods of elevated firing during the delay (EFs) and the firing patterns were distinct on the east and west trials. Moreover, these firing patterns emerged and began to differentiate the east and west conditions during the first training session and continued to develop as the rats learned the task. The finding of similar firing patterns in different tasks suggests that the EFs are a robust phenomenon, which may occur whenever subjects must maintain distinct memory representations during a delay period. Additionally, in the previous study (Pastalkova et al. (2008) Science 321:1322-1327), the distinct firing patterns could have been due to the differing goal locations, behavioral responses (left or right turns), or trajectories. In this study, neuronal firing varied with the goal location regardless of the trajectories or responses, suggesting that the firing patterns encode the behavioral context rather than specific behaviors.
Corrigendum: Safe and Facile Access to Nonstabilized Diazoalkanes Using Continuous Flow Technology (2020)

In the Supporting Information of this Communication, the structure of the compound 3k obtained after the [3þ2] cycloaddition of compound 2k with dimethyl acetylenedicarboxylate is incorrect.Whereas the pyrazolenine was initially drawn, the pyrazole 3k was obtained in this example.The structure was corrected accordingly in the revised