gebhart/patrepeval huggingface dataset:
Environment Characterization in Sorghum (Sorghum bicolor L.) by Modeling Water-Deficit and Heat Patterns in the Great Plains Region, United States (2022)

Environmental characterization for defining the target population of environments (TPE) is critical to improve the efficiency of breeding programs in crops, such as sorghum ( Sorghum bicolor L.). The aim of this study was to characterize the spatial and temporal variation for a TPE for sorghum within the United States. APSIM-sorghum, included in the Agricultural Production Systems sIMulator software platform, was used to quantify water-deficit and heat patterns for 15 sites in the sorghum belt. Historical weather data (∼35 years) was used to identify water (WSP) and heat (HSP) stress patterns to develop water–heat clusters. Four WSPs were identified with large differences in the timing of onset, intensity, and duration of the stress. In the western region of Kansas, Oklahoma, and Texas, the most frequent WSP (∼35%) was stress during grain filling with late recovery. For northeast Kansas, WSP frequencies were more evenly distributed, suggesting large temporal variation. Three HSPs were defined, with the low HSP being most frequent (∼68%). Field data from Kansas State University sorghum hybrid yield performance trials (2006–2013 period, 6 hybrids, 10 sites, 46 site × year combinations) were classified into the previously defined WSP and HSP clusters. As the intensity of the environmental stress increased, there was a clear reduction on grain yield. Both simulated and observed yield data showed similar yield trends when the level of heat or water stressed increased. Field yield data clearly separated contrasting clusters for both water and heat patterns (with vs. without stress). Thus, the patterns were regrouped into four categories, which account for the observed genotype by environment interaction (GxE) and can be applied in a breeding program. A better definition of TPE to improve predictability of GxE could accelerate genetic gains and help bridge the gap between breeders, agronomists, and farmers.
Structural organization of apolipoprotein B-100 of human plasma low density lipoproteins. Comparison to B-48 of chylomicrons and very low density lipoproteins. (1986)

The present study characterizes the substructural organization of apolipoprotein B-100 (B-100) of human plasma low density lipoproteins (LDL) and its relation to B-74 and B-26 of LDL and B-48 of chylomicrons and very low density lipoproteins. LDL were digested with human kallikrein and thrombin to yield two major fragments: K1 (Mr 410,000) and K2 (Mr 145,000) and T1 (Mr 385,000) and T2 (Mr 170,000), respectively. The antigenic sequences, Mr, and amino acid compositions of K1 and K2 were identical to those of plasma B-74 and B-26; B-26 and K2 had identical NH2-terminal sequences and correspond to the NH2-terminal region of B-100. K1 was further degraded by kallikrein to give K3 (Mr 235,000) and K4 (Mr 170,000); these peptides correspond immunochemically to two newly discovered plasma LDL peptides B-44 and B-30 and are assigned as complementary fragments of B-74. The thrombin cleavage fragments, T1 and T2, did not correspond to B-74 and B-26. Neither kallikrein nor thrombin generated a fragment from B-100 corresponding to B-48 in chylomicrons. However, B-48 showed antigenic homology with B-26 and to the of B-74 adjoining B-26, indicating that its structure is represented in the NH2-terminal half of B-100. The structural studies further clarify the relatedness among the B-100, B-74, B-26, and B-48 polypeptides and should now make possible the delineation of the functional domains mediating the interactions of apolipoprotein B in the circulation and arterial wall.
Normalised frequency‐domain soft constraint satisfaction multimodulus blind algorithm (2015)

A frequency‐domain implementation of the soft constraint satisfaction multimodulus blind algorithm is proposed. This leads to a significant reduction in the computational complexity, thus making it suitable for broadband wireless systems. The convergence of the developed algorithm is then improved by normalising each of the frequency bins in the weight update. Simulation results support the superior performance of the proposed algorithm over its time domain counterpart in terms of faster convergence rate.
Nucleotide Analogues as Inhibitors of SARS-CoV Polymerase (2020)

Summary SARS-CoV-2, a member of the coronavirus family, has caused a global public health emergency. 1 Based on our analysis of hepatitis C virus and coronavirus replication, and the molecular structures and activities of viral inhibitors, we previously reasoned that the FDA-approved heptatitis C drug EPCLUSA (Sofosbuvir/Velpatasvir) should inhibit coronaviruses, including SARS-CoV-2. 2 Here, using model polymerase extension experiments, we demonstrate that the activated triphosphate form of Sofosbuvir is incorporated by low-fidelity polymerases and SARS-CoV RNA-dependent RNA polymerase (RdRp), and blocks further incorporation by these polymerases; the activated triphosphate form of Sofosbuvir is not incorporated by a host-like high-fidelity DNA polymerase. Using the same molecular insight, we selected two other anti-viral agents, Alovudine and AZT (an FDA approved HIV/AIDS drug) for evaluation as inhibitors of SARS-CoV RdRp. We demonstrate the ability of two HIV reverse transcriptase inhibitors, 3’-fluoro-3’-deoxythymidine triphosphate and 3’-azido-3’-deoxythymidine triphosphate (the active triphosphate forms of Alovudine and AZT), to be incorporated by SARS-CoV RdRp where they also terminate further polymerase extension. Given the 98% amino acid similarity of the SARS-CoV and SARS-CoV-2 RdRps, we expect these nucleotide analogues would also inhibit the SARS-CoV-2 polymerase. These results offer guidance to further modify these nucleotide analogues to generate more potent broad-spectrum anti-coronavirus agents.
Translational molecular imaging for cancer (2005)

Although most clinical diagnostic imaging studies employ anatomic techniques such as computed tomography (CT) and magnetic resonance (MR) imaging, much of radiology research currently focuses on adapting these conventional methods to physiologic imaging as well as on introducing new techniques and probes for studying processes at the cellular and molecular levels in vivo, i.e. molecular imaging. Molecular imaging promises to provide new methods for the early detection of cancer and support for personalized cancer therapy. Although molecular imaging has been practiced in various incarnations for over 20 years in the context of nuclear medicine, other imaging modalities have only recently been applied to the noninvasive assessment of physiology and molecular events. Nevertheless, there has been sufficient experience with specifically targeted contrast agents and high-resolution techniques for MR imaging and other modalities that we must begin moving these new technologies from the laboratory to the clinic. This brief review outlines several of the more promising areas of pursuit in molecular imaging for oncology with an emphasis on those that show the most immediate likelihood for clinical translation.
N-Phenylphenylglycines as Novel Corticotropin Releasing Factor Receptor Antagonists (2004)

Screening of a computationally designed synthetic library led to the discovery of the N-phenylphenylglycines (NPPGs) as a novel class of human corticotropin releasing factor (h-CRF(1)) antagonists. Several NPPGs with greater potency than the original hit 1 were rapidly identified, and resolution of the racemate demonstrated that only the R-enantiomer displays activity. This structural class represents the first example of a non-peptide CRF(1) antagonist with a stereochemically distinct receptor binding affinity.
Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders (2017)

Abstract Hundreds of penetrant risk loci have been identified across different neurodevelopmental disorders (NDDs), and these often involve rare (&lt;1% frequency) copy number variations (CNVs), which can involve one or more genes. Monozygotic (MZ) twin pairs are long thought to share 100% of their genomic information. However, genetic differences in the form of postzygotic somatic variants have been reported recently both in typically developing (TD) and in clinically discordant MZ pairs. Here, we sought to investigate the contribution of CNVs in 100 twin pairs enriched for NDD phenotypes with a particular focus on MZ pairs discordant for autism spectrum disorder (ASD) using the PsychChip array. In our collection, no postzygotic de novo CNVs were found in 55 MZ twin pairs, including the 13 pairs discordant for ASD. When analyzing the burden of rare CNVs among pairs concordant and discordant for ASD/NDD in comparison with typically developed (TD) pairs, no differences were found. However, we did detect a higher rate of CNVs overlapping genes involved in disorders of the nervous system in MZ pairs discordant and concordant for ASD in comparison with TD pairs (p=0.02). Our results are in concordance with earlier findings that postzygotic de novo CNV events are typically rare in genomic DNA derived from saliva or blood and, in the majority of MZ twins, do not explain the discordance of NDDs. Still, studies investigating postzygotic variation in MZ discordant twins using DNA from different tissues and single cells and higher resolution genomics are needed in the future.
Prevalence of respiratory pathogens detected in dogs with kennel cough in Poland (2016)

Kennel cough is a multifactorial disease occurring all over the world; however, its epidemiology is still not fully understood. To the authors’ knowledge, no studies monitoring the occurrence of infectious agents responsible for kennel cough have been carried out in Poland. Therefore, the objective of our study was to determine which of the four pathogens most frequently isolated in other countries are predominant in north-eastern Poland. Swabs from the upper respiratory tract and tracheal lavage fluids from dogs (n = 40) exhibiting symptoms of this disease were analysed. Canine herpesvirus, canine parainfluenza virus, canine adenovirus type 2 and Bordetella bronchiseptica were identified by polymerase chain reaction. At least one of the above-listed infectious agents was found in all dogs. The predominant pathogen within the area under our study, both in mono- and co-infections, was canine herpesvirus (32/40), whereas canine adenovirus type 2 occurred least frequently (4/40). The effectiveness of detection of selected pathogens from both types of study material was also compared. Tracheal lavage fluid was more suitable for the isolation of canine herpes virus, canine parainfluenza virus, and Bordetella bronchiseptica . Swabs from the upper respiratory tract were more suitable for the isolation of canine adenovirus type 2.
A rapid single flux quantum 1 bit arithmetic logic unit constructed with a half-adder cell (2004)

We have designed, fabricated, and tested a rapid single flux quantum (RSFQ) 1 bit arithmetic logic unit (ALU) block. The circuit consists of three DC current driven SFQ switches and a half-adder. We successfully tested the half-adder cell at clock frequency up to 20 GHz. The switches were commutating output ports of the half-adder to produce AND, OR, XOR, or ADD functions. For a high-speed test, we attached two switches at the input ports of the half-adder to control the high-speed input data by low-frequency pattern generators. The output in this measurement was an eye-diagram. Using this set-up, the circuit was successfully tested up to 20 GHz. The chip was fabricated using a standard HYPRES 1 kA cm−2 Nb Josephson junction fabrication process.
Understanding the Molecular Basis of Toxin Promiscuity: The Analgesic Sea Anemone Peptide APETx2 Interacts with Acid-Sensing Ion Channel 3 and hERG Channels via Overlapping Pharmacophores (2014)

The sea anemone peptide APETx2 is a potent and selective blocker of acid-sensing ion channel 3 (ASIC3). APETx2 is analgesic in a variety of rodent pain models, but the lack of knowledge of its pharmacophore and binding site on ASIC3 has impeded development of improved analogues. Here we present a detailed structure–activity relationship study of APETx2. Determination of a high-resolution structure of APETx2 combined with scanning mutagenesis revealed a cluster of aromatic and basic residues that mediate its interaction with ASIC3. We show that APETx2 also inhibits the off-target hERG channel by reducing the maximal current amplitude and shifting the voltage dependence of activation to more positive potentials. Electrophysiological screening of selected APETx2 mutants revealed partial overlap between the surfaces on APETx2 that mediate its interaction with ASIC3 and hERG. Characterization of the molecular basis of these interactions is an important first step toward the rational design of more selective APETx2 analogues.
Relaxation Filtered Hyperfine (REFINE) Spectroscopy:  A Novel Tool for Studying Overlapping Biological Electron Paramagnetic Resonance Signals Applied to Mitochondrial Complex I (2004)

A simple strategy to separate overlapping electron paramagnetic resonance (EPR) signals in biological systems is presented. Pulsed EPR methods (inversion- and saturation-recovery) allow the determination of the T(1) spin-lattice relaxation times of paramagnetic centers. T(1) may vary by several orders of magnitude depending on the species under investigation. These variations can be employed to study selectively individual species from a spectrum that results from an overlap of two species using an inversion-recovery filtered (IRf) pulsed EPR technique. The feasibility of such an IRf field-swept technique is demonstrated on model compounds (alpha,gamma-bisphenylene-beta-phenylallyl-benzolate, BDPA, and 2,2,6,6-tetramethyl-piperidine-1-oxyl, TEMPO) and a simple strategy for the successful analysis of such mixtures is presented. Complex I is a multisubunit membrane protein of the respiratory chain containing several iron-sulfur (FeS) centers, which are observable with EPR spectroscopy. It is not possible to investigate the functionally important FeS cluster N2 separately because this EPR signal always overlaps with the other FeS signals. This cluster can be studied selectively using the IRf field-swept technique and its EPR spectrum is in excellent agreement with previous cw-EPR data from the literature. In addition, the possibility to separate the hyperfine spectra of two spectrally overlapping paramagnetic species is demonstrated by applying this relaxation filter together with hyperfine spectroscopy (REFINE). For the first time, the application of this filter to a three-pulse electron spin-echo envelope modulation (ESEEM) pulse sequence is demonstrated to selectively observe hyperfine spectra on a system containing two paramagnetic species. Finally, REFINE is used to assign the observed nitrogen modulation in complex I to an individual iron-sulfur cluster.
LTV controller design for vehicle lateral control under fault in rear sensors (2005)

This work focuses on vehicle lateral control for automated highway systems (AHSs) studied as a part of the California Partners for Advanced Transit and Highways (PATH) Program. In the PATH lateral control system, magnetometers are installed under both front and rear bumpers of the vehicle; these magnetometers measure the lateral deviation of the vehicle relative to the magnets buried along the centerline of each automated lane. Lateral controllers have been designed and tested successfully provided that there is no fault in magnetometers. It has been argued that these controllers are NOT tolerant to the fault in magnetometers. The focus of This work is the degraded-mode lateral control under fault in rear magnetometers. The aim of the controller design is to accomplish adequate performance with the remaining set of magnetometers, the front magnetometers. The effects of the fault are examined, and the significance of the linear time-varying (LTV) property of the front-magnetometer-based vehicle lateral dynamics is recognized. Popular control methods for LTV systems generally involve gain scheduling by switching between several linear time-invariant (LTI) controllers. Such methods are complicated and it is difficult to prove the stability of the switching mechanism. To derive a simple effective LTV controller, feedback linearization is applied to approximately cancel out the time-varying terms in the plant and to function as a gain scheduler. However, due to the weakly damped zeroes of the plant, feedback linearization with state feedback or matched observer state feedback results in weakly damped internal dynamics. In order to tune the internal dynamics, a mismatched observer is designed based on H-infinity optimal control techniques. Experimental results are presented to show the effectiveness of the controller design.
Optical nanotrapping using cloaking metamaterial (2009)

We study the electromagnetic behavior of spherical semishell structures that have cloaking material properties proposed by Pendry, Schurig, and Smith [Science 312, 1780 (2006)]. We use three-dimensional full-wave time-harmonic field analysis to evaluate the field and dipolar force distribution produced by these structures in free-space under plane wave illumination. We show that the optical force in proximity to these structures is suitable for active and size-selective manipulation and trapping of neutral nanoscale particles.
Designing Oxide Aerogels With Enhanced Sorptive and Degradative Activity for Acute Chemical Threats (2021)

Oxide aerogels are pore–solid networks notable for their low density, large pore volume, and high surface area. This three-dimensional arrangement of pore and solid provides critical properties: the high surface area required to maximize the number of active sites and a through-connected porosity that plumbs reactants to the active interior. In decontamination applications where reactivity beyond adsorption is desired to degrade deleterious molecules, oxide aerogels offer multiple avenues to add oxidative power to this unique arrangement of pore and solid. For protection against chemical warfare agents or toxic industrial chemicals, metal-oxide aerogels with their oxide/hydroxide surfaces afford stability under ambient conditions against competing sorbents such as water and oxygen. In this review, strategies to maximize sorptive capacity and degradation rate by modifying surface functionality, compositing with dissimilar oxides, or adding metallic nanoparticles and the subsequent impact on decontamination performance will be summarized and expected directions for future research will be discussed based on the observed trends.
Discrimination between noise and gamma-background in scintillation neutron detectors containing ZnS(Ag) (1975)

The possibilities of isolating signals produced by neutrons against the background for intense ..gamma.. radiation in detectors containing ZnS(Ag) by selecting current pulses according to their duration at a fixed level are investigated. Using a simple identification system, the improvement in the effect-to-background ratio amounts to 1-2 orders of magnitude in comparison to that achieved for amplitude selection of the signals under conditions of high background intensity.
Solution structures of proteins from NMR data and modeling: alternative folds for neutrophil peptide 5 (1989)

The structure of neutrophil peptide 5 in solution has recently been reported (Pardi et al., 1988). The structure determination was accomplished by using a distance geometry algorithm and 107 interproton distance constraints obtained from 2D NMR data. In each of the eight independent solutions to the distance geometry equations, the overall fold of the polypeptide backbone was identical and the root mean square (rms) deviation between backbone atoms of the superimposed structures was small (approximately 2.4 A). In this paper we report additional NP-5 structures obtained by using a new structure generation algorithm: a Monte Carlo search in torsion angle space. These structures have a large rms backbone deviation from the distance geometry structures (approximately 5.0 A). The backbone topologies differ in significant respects from the distance geometry structures and from each other. Structures are found that are pseudo mirror images of part or all of the fold corresponding to that first obtained with the distance geometry procedure. For small proteins, the problem of distinguishing the correct structure among pseudo mirror images is likely to be greater than previously recognized. When a set of test distance constraints constructed from a novel Monte Carlo structure is used as input in the distance geometry algorithm, the fold of the resulting structure does not correspond to that of the target. The results also demonstrate that the previously accepted criteria (the magnitude of the rms deviation between multiple solutions of the distance geometry equations) for defining the accuracy and precision of a peptide structure generated from NMR data are inadequate. An energetic analysis of structures corresponding to the different folding topologies has been carried out. The molecular mechanics energies obtained by minimization and molecular dynamics refinement provide sufficient information to eliminate certain alternative structures. On the basis of a careful comparison of the different trial structures with the experimental data, it is concluded that the NP-5 peptide fold which was originally reported is most consistent with the data. An alternative fold corresponding to structures with low energies and small total distance violations is ruled out because for this fold predicted NOEs are not observed experimentally.
Isolation of the Heterofullerene C 59 N as Its Dimer (C 59 N) 2 (1995)

The heterofullerene ion C(59)N(+) is formed efficiently in the gas phase during fast atom bombardment mass spectroscopy of a cluster-opened N-MEM (N-methoxyethoxy methyl) ketolactam. This transformation is shown to occur also in solution in the presence of strong acid, affording biazafullerenyl (C(59)N)(2) in good yield. It is proposed that the azafullerene dimer is formed upon in situ reduction of the highly reactive azafulleronium ion. The isolation and characterization of biazafullerenyl opens a viable route for the preparation of other heterofullerenes in solution.
Total Synthesis of the Marine Ladder Polyether Gymnocin B (2019)

Herein, we report the first total synthesis of marine ladder polyether gymnocin B (<b>1</b>) based on a two-phase strategy. In Phase I, inspired by the proposed biosynthesis, epoxide-opening cascades assemble 10 out of 15 cyclic ether rings making up the molecular core. In the subsequent Phase II, coalescence elevates the molecular complexity further by coupling of these subunits. Our two-phase synthetic approach significantly improved the step efficiency of the synthesis of this class of natural products.
Field results for a distribution circuit state estimator implementation (2002)

Summary form only given as follows. Distribution automation encompasses functions that rely on knowledge of the state of the distribution circuit in real-time. This paper presents field results for a distribution circuit state estimator that was implemented on an electric utility distribution circuit. The state estimation algorithm is based on a probabilistic radial power flow approach that incorporates real-time measurements as solution constraints. A load modeling technique based on using customer billing information and daily load profiles is used to provide needed load estimates. This paper provides an assessment of how accurately the developed state estimation algorithm is able to predict circuit states. The improvement in circuit estimates as a function of available feeder measurements is illustrated as well. Finally, difficulties encountered with implementing an actual distribution state estimator are discussed.