gebhart/patrepeval huggingface dataset:
Cross‐resistance and redundant killing of Vip3Aa resistant populations of Helicoverpa zea on purified Bt proteins and pyramided Bt crops (2023)

Abstract BACKGROUND Pyramiding Bt proteins is a key strategy to delay insect resistance development. However, the durability of pyramided Bt crops for controlling insect pests is threatened by cross‐resistance among Bt proteins, which can ultimately contribute to resistance development. The corn earworm, Helicoverpa zea , is a major agricultural pest of pyramided Bt crops. Previous studies have examined cross‐resistance and redundant killing of Cry resistance in H. zea , but such information is lacking for Vip3Aa resistance in this pest. Here, we evaluated cross‐resistance and redundant killing of Vip3Aa‐resistant H. zea to purified Bt proteins, as well as Bt corn and Bt cotton. RESULTS Diet bioassays demonstrated high susceptibility of Vip3Aa‐resistant H. zea to Cry1Ac, Cry1A.105, and Cry2Ab2 purified proteins. No Vip3Aa‐susceptible, ‐heterozygous, or ‐resistant H. zea could survive on pyramided Bt corn containing Cry1 and/or Cry2 proteins. Complete redundant killing was observed in pyramided Bt corn containing Cry1 and/or Cry2 proteins against Vip3Aa resistance in H. zea . Vip3Aa‐susceptible, ‐heterozygous, and ‐resistant H. zea exhibited survival rates ranging from 0.0% to 22.5% on pyramided Bt cotton with Cry1 and/or Cry2 proteins. Incomplete to complete redundant killing was observed for Vip3Aa‐resistant H. zea on pyramided Bt cotton containing Cry1 and/or Cry2 proteins. CONCLUSION Our findings indicate that Vip3Aa‐resistant H. zea does not exhibit positive cross‐resistance to Cry1 or Cry2 proteins. In addition, most pyramided Bt crops showed complete or nearly complete redundant killing of Vip3Aa‐resistant H. zea . These results indicate that a pyramiding strategy would often be effective for managing Vip3Aa resistance in regions of the United States where H. zea has not evolved resistance to Cry1 and Cry2 toxins. © 2023 Society of Chemical Industry.
Conformational Preferences of Substrates for Human Prolyl 4-Hydroxylase (2008)

Prolyl 4-hydroxylase (P4H) catalyzes the posttranslational hydroxylation of (2 S)-proline (Pro) residues in procollagen strands. The resulting (2 S,4 R)-4-hydroxyproline (Hyp) residues are essential for the folding, secretion, and stability of the collagen triple helix. Even though its product (Hyp) differs from its substrate (Pro) by only a single oxygen atom, no product inhibition has been observed for P4H. Here, we examine the basis for the binding and turnover of substrates by human P4H. Synthetic peptides containing (2 S,4 R)-4-fluoroproline (Flp), (2 S,4 S)-4-fluoroproline (flp), (2 S)-4-ketoproline (Kep), (2 S)-4-thiaproline (Thp), and 3,5-methanoproline (Mtp) were evaluated as substrates for P4H. Peptides containing Pro, flp, and Thp were found to be excellent substrates for P4H, forming Hyp, Kep, and (2 S,4 R)-thiaoxoproline, respectively. Thus, P4H is tolerant to some substitutions on C-4 of the pyrrolidine ring. In contrast, peptides containing Flp, Kep, or Mtp did not even bind to the active site of P4H. Each proline analogue that does bind to P4H is also a substrate, indicating that discrimination occurs at the level of binding rather than turnover. As the iron(IV)-oxo species that forms in the active site of P4H is highly reactive, P4H has an imperative for forming a snug complex with its substrate and appears to do so. Most notably, those proline analogues with a greater preference for a C (gamma)- endo pucker and cis peptide bond were the ones recognized by P4H. As Hyp has a strong preference for C (gamma)- exo pucker and trans peptide bond, P4H appears to discriminate against the conformation of proline residues in a manner that diminishes product inhibition during collagen biosynthesis.
Defining Brugia malayi and Wolbachia symbiosis by stage-specific dual RNA-seq (2017)

This global transcriptional analysis has highlighted specific pathways to which both Wolbachia and B. malayi contribute concurrently over the life cycle of the parasite, paving the way for the development of novel intervention strategies.
Pre-α-pro-GDNF and Pre-β-pro-GDNF Isoforms Are Neuroprotective in the 6-hydroxydopamine Rat Model of Parkinson's Disease (2018)

Glial cell line-derived neurotrophic factor (GDNF) is one of the most studied neurotrophic factors. GDNF has two splice isoforms, full-length pre-α-pro-GDNF (α-GDNF) and pre-β-pro-GDNF (β-GDNF), which has a 26 amino acid deletion in the pro-region. Thus far, studies have focused solely on the α-GDNF isoform, and nothing is known about the <i>in vivo</i> effects of the shorter β-GDNF variant. Here we compare for the first time the effects of overexpressed α-GDNF and β-GDNF in non-lesioned rat striatum and the partial 6-hydroxydopamine lesion model of Parkinson's disease. GDNF isoforms were overexpressed with their native pre-pro-sequences in the striatum using an adeno-associated virus (AAV) vector, and the effects on motor performance and dopaminergic phenotype of the nigrostriatal pathway were assessed. In the non-lesioned striatum, both isoforms increased the density of dopamine transporter-positive fibers at 3 weeks after viral vector delivery. Although both isoforms increased the activity of the animals in cylinder assay, only α-GDNF enhanced the use of contralateral paw. Four weeks later, the striatal tyrosine hydroxylase (TH)-immunoreactivity was decreased in both α-GDNF and β-GDNF treated animals. In the neuroprotection assay, both GDNF splice isoforms increased the number of TH-immunoreactive cells in the substantia nigra but did not promote behavioral recovery based on amphetamine-induced rotation or cylinder assays. Thus, the shorter GDNF isoform, β-GDNF, and the full-length α-isoform have comparable neuroprotective efficacy on dopamine neurons of the nigrostriatal circuitry.
Pushing the limits of silicon transistors (2016)

In this work we study Ge transistor structures grown on silicon substrate. We use photoluminescence to determine the band gap of Ge under tensile strain. The strain is induced by growing Ge on an InGaAs buffer layer with variable In content. The band energy levels are modeled using a 30 band k·p model based on first principles calculations. Photoluminescence measurements show a reasonable correspondence with calculated values of the band energies.
Nitrogen-enhanced negative bias temperature instability: An insight by experiment and first-principle calculations (2003)

The nitrogen-enhanced negative bias temperature instability (NBTI) effect has been studied experimentally and theoretically. It is observed that both the interface state and positive fixed charge generation increase linearly with interfacial nitrogen concentration. The experimental results can be understood in terms of the reaction energies of the hydrogen trapping reactions at the interface, which are obtained from first-principle calculations. These results improve our understanding of the mechanisms responsible for the nitrogen-enhanced NBTI effect.
[Gene cloning, expression of fusion protein TGF alpha-PE 40 and its inhibition activity on cancer cell growth]. (1993)

Recombinant plasmid pYX382 and pYX3825 were constructed by fusing the cDNA encoding transforming growth factor type alpha (TGF alpha) to Pseudomonas exotoxin gene (PE) in which the cell recognition domain was deleted. The chimeric proteins produced by host E. Coli cells BL21 transformed by plasmid pYX382 and pYX3825 are termed TGF alpha-PE 40 which reacts with antibody against TGF alpha or antibody against PE in immunoblotting to show a 46 kd protein band reflecting the fusion of 56 kD TGF alpha peptide and 40 kD truncated Pseudomonas exotoxin molecule. An additional signal sequence OmpA was inserted into upstream region of TGF alpha cDNA in plasmid pYX3825 resulting in the partly secreting of expression product into medium and periplasm of the cells. TGF alpha-PE 40 was purified from medium by MONO Q ion exchange column and TSK 250 gel filtration column attached to Pharmacia EPLC system. The TGF alpha-PE 40 molecules showed a very strong activities inhibiting the protein synthesis and killing the cancer cells overexpressing EGF receptor on the cell surface.
Modelica-Based Control of a Delta Robot (2020)

Abstract In this paper we derive a dynamic model of the delta robot and two formulations of the manipulator Jacobian that comprise a system of singularity-free, index-one differential algebraic equations that is well-suited for model-based control design and computer simulation. One of the Jacobians is intended for time-domain simulation, while the other is for use in discrete-time control algorithms. The model is well-posed and numerically well-conditioned throughout the workspace, including at kinematic singularities. We use the model to derive an approximate feedback linearizing control algorithm that can be used for both trajectory tracking and impedance control, enabling some assembly tasks involving contact and collisions. The model and control algorithms are realized in the open-source Modelica language, and a Modelica-based software architecture is described that allows for a seamless development process from mathematical derivation of control algorithms, to desktop simulation, and finally to laboratory-scale experimental testing without the need to recode any aspect of the control algorithm. Simulation and experimental results are provided.
Limited differential expression of miRNAs and other small RNAs in LPS-stimulated human monocytes (2019)

Monocytes are a distinct subset of myeloid cells with diverse functions in early inflammatory immune modulation. While previous studies have surveyed the role of miRNA regulation on different myeloid cell lines and primary cultures, the time-dependent kinetics of inflammatory stimulation on miRNA expression and the relationship between miRNA-to-target RNA expression have not been comprehensively profiled in monocytes. In this study, we use next-generation sequencing and RT-PCR assays to analyze the non-coding small RNA transcriptome of unstimulated and lipopolysaccharide (LPS)-stimulated monocytes at 6 and 24 hours. We identified a miRNA signature consisting of five mature miRNAs (hsa-mir-146a, hsa-mir-155, hsa-mir-9, hsa-mir-147b, and hsa-mir-193a) upregulated by LPS-stimulated monocytes after 6 hours and found that most miRNAs were also upregulated after 24 hours of stimulation. Only one miRNA gene was down-regulated and no other small RNAs were found dysregulated in monocytes after LPS treatment. In addition, novel tRNA-derived fragments were also discovered in monocytes although none showed significant changes upon LPS stimulation. Interrogation of validated miRNA targets by transcriptomic analysis revealed that absolute expression of most miRNA targets implicating in innate immune response decreased over time in LPS-stimulated monocytes although their expression patterns along the treatment were heterogeneous. Our findings reveal a potential role by which selective miRNA upregulation and stable expression of other small RNAs enable monocytes to develop finely tuned cellular responses during acute inflammation.
GBS type III oligosaccharides containing a minimal protective epitope can be turned into effective vaccines by multivalent presentation (2019)

Recent structural studies demonstrated that the epitope recognized by a monoclonal antibody representative of the protective response against the type III group B Streptococcus polysaccharide was comprised within 2 of the repeating units that constitute the full-length native structure. In the current study, we took advantage of this discovery to design a novel vaccine based on multivalent presentation of the identified minimal epitope on a carrier protein. We show that highly glycosylated short oligosaccharide conjugates elicit functional immune responses comparable to those of the full-length native polysaccharide. The obtained results pave the way to the design of well-defined glycoconjugate vaccines based on short synthetic oligosaccharides.
Graph Learning from Data under Laplacian and Structural Constraints (2016)

Graphs are fundamental mathematical structures used in various fields to represent data, signals and processes. In this paper, we propose a novel framework for learning/estimating graphs from data. The proposed framework includes (i) formulation of various graph learning problems, (ii) their probabilistic interpretations and (iii) associated algorithms. Specifically, graph learning problems are posed as estimation of graph Laplacian matrices from some observed data under given structural constraints (e.g., graph connectivity and sparsity level). From a probabilistic perspective, the problems of interest correspond to maximum a posteriori (MAP) parameter estimation of Gaussian-Markov random field (GMRF) models, whose precision (inverse covariance) is a graph Laplacian matrix. For the proposed graph learning problems, specialized algorithms are developed by incorporating the graph Laplacian and structural constraints. The experimental results demonstrate that the proposed algorithms outperform the current state-of-the-art methods in terms of accuracy and computational efficiency.
HEAR: Fog-Enabled Energy-Aware Online Human Eating Activity Recognition (2020)

Eating activity recognition (EAR) plays an important role in ensuring healthy eating habits. Recent advancements of the Internet of Things (IoT) have bolstered automated EAR through various wearable edge devices. State-of-the-art work uses some offline trained classifiers at the fog device to recognize eating activities. However, the eating habits of a person change quite frequently and vary from person to person. Therefore, the classifiers should be updated continuously with new data to adapt to these changes and be personalized over time through online learning. To the best of our knowledge, no state-of-the-art work has addressed this issue so far. In this article, we propose an online learning methodology called human eating activity recognition (HEAR) by introducing an online update phase. We also design an algorithm to be used in the online update phase that provides approximate true labels for the new data. Moreover, we also design a wearable neckband as the edge device to capture eating activity data (Chewing, Swallowing, Talking, and Idle) in a lab environment. Through a detailed experimental evaluation on 12 users, we show that an online learned neural network (OLNN) classifier using our HEAR methodology performs better than any state-of-the-art offline trained classifier. We also demonstrate that our OLNN classifier is energy efficient compared to the competitive offline trained classifiers.
LIF instrument development, in situ measurement at South Pole and 1D air-snowpack modeling of atmospheric nitrous acid (HONO) (2008)

Atmospheric nitrous acid (HONO) is a significant and sometimes dominant OH source at polar region. An improved method of detecting HONO is developed using photo-fragmentation and laser-induced fluorescence (LIF). The detection limit of this method is 2-3 pptv for ten-minute integration time with 35% uncertainty. The abundance of laser-induced fluorescence (LIF) HONO measurements during ANTCI (Antarctic troposphere chemistry investigation) 2003 exceeds the pure gas phase model predictions by a factor of 1.92±0.67, which implies snow emission of HONO. A 1D air-snowpack model of HONO was developed and constrained by observed chemistry and meteology data. The 1D model includes pure gas phase chemical mechanisms, molecular diffusion and mechanical dispersion, windpumping in snow, gas phase to quasi-liquid layer phase HONO transfer and quasi-liquid layer nitrate photolysis. Based on the air-snowpack model, snow emission of HONO is highly likely and will be transported to place of the measurements. The pH, thickness of quasi liquid layer and contineous nitrite measurement are key factors to calibrate and validate the air snowpack model.
Generation of Microcellular Biodegradable Polymers Using Supercritical Carbon Dioxide (1999)

In this study, a pressure quench method employing supercritical carbon dioxide was utilized to produce microcellular poly(lactic -co-glycolic acid) (PLGA). Saturation temperatures and pressures were varied to determine effects on average cell size, foam bulk density, and cell number density. PLGA foams were produced having average cell sizes ranging from 11 to 70 μm and cell number densities from 106 to 109 cells/cm3. Reductions in bulk density from 82 to 89 percent were achieved. Average cell size exhibited a minimum with increasing pressure (or CO2 density), and cell number density and foam bulk density exhibited corresponding maxima with increasing pressure (or CO2 density). Possible reasons for this behavior include cell coagulation due to low melt strength and low interfacial tension at high pressure, or a situation where the phase diagram of the polymer-CO2 mixture exhibits a maximum in swelling with increasing pressure.
Activation of the mitochondrial permeability transition pore modulates Ca2+ responses to physiological stimuli in adult neurons (2011)

The participation of mitochondria in cellular and neuronal Ca(2+) homeostatic networks is now well accepted. Yet, critical tests of specific mitochondrial pathways in neuronal Ca(2+) responses have been hampered because the identity of mitochondrial proteins that must be integrated within this dynamic system remain uncertain. One putative pathway for Ca(2+) efflux from mitochondria exists through the formation of the permeability transition pore (PTP) that is often associated with cellular and neuronal death. Here, we have evaluated neuronal Ca(2+) dynamics and the PTP in single adult neurons in wild-type mice and those missing cyclophilin D (CyPD), a key regulator of the PTP. Using high-resolution time-lapse imaging, we demonstrate that PTP opening only follows simultaneous activation with two physiological stimuli that generate critical threshold levels of cytosolic and mitochondrial Ca(2+) . Our results are the first to demonstrate CyPD-dependent PTP opening in normal neuronal Ca(2+) homeostatic mechanisms not leading to activation of cell death pathways. As neurons in mice lacking CyPD are protected in a number of neurodegenerative disease models, the results suggest that improved viability of CyPD-knockout animals in these pathological states may be due to the transient, rather than persistent, activation of the PTP in mutant mitochondria, thereby shielding neurons from cytoplasmic Ca(2+) overload.
A New Approach for the Failure Detection and the Self-healing Process in A Solar-based Tap Changing Transformer (2022)

In this paper, a new approach for the self-healing process of the on-load tap-changer (OLTC) is proposed. The proposed circuit detects the failed power switch and enables the system to continue operation by using a series relay to disconnect the failed switch from the circuit. When the tap is moving from one level to the other, during this time the failure detection approach checks all power switches. The detection process is based on the tap voltage measurement while all gate signals of power switches are off. If the tap voltage during this time is not less than a certain voltage value, it means one switch fails. Then, the failed switch removes from the circuit via a series relay, and the substitute TRIAC replace the failed one. This removes any possible interruption in the voltage of the load. Also, the presented method is easy to implement, cost-effective and utilizes fewer components. An EMT simulation is performed to examine the effectiveness and robustness of the proposed circuit and methods.
Staining Doppler Audio (2006)

Carotid stenoses are responsible for many of the strokes occurring each year. We have developed a low-cost-of-use instrument for use in primary-care physicians' offices that can detect these stenoses before they produce a stroke. Non- specialists are to use the instrument with only limited training, so it is desirable to make the Doppler audio it produces as easy to interpret as possible. We present two techniques for doing so by processing or staining the original audio signal to make it easier for neophyte operators to recognize the information present in the signal. In a small user study, a technique based on adaptive filtering did not result in an improvement, but another technique based on adding a sine tone of varying frequency to the signal produced a significant improvement in accuracy over the unstained Doppler audio. The study also showed that untrained subjects were capable of performing quite well even on unstained audio.
Neutral and stereospecific Tc-99m complexes: [99mTc]N-benzyl-3,4-di-(N-2-mercaptoethyl)-amino- pyrrolidines (P-BAT) (1999)

Technetium-99m-labeled radiopharmaceuticals are currently the most commonly used agents in nuclear medicine. To prepare binding site-specific small molecules containing a Tc-99m complexing core, it is important to consider a ligand system, which selectively forms only one stereoisomer. A novel series of bisaminoethanethiol (BAT) derivatives as a model system were prepared. Stereoisomers of N-benzyl-3,4-di(N-2-mercaptoethyl)-amino pyrrolidines (P-BAT): (3R,4R)-P-BAT (R,R-4) and (3,4)meso-P-BAT (8), the trans and meso isomer, respectively, as a chelating group were prepared successfully. The desired Tc-99m P-BAT complexes were obtained by using Sn(II)/glucoheptonate as the reducing agent for [99mTc]pertechnetate. As predicted, after complexation with [99mTc]Tc'O, the trans isomer, (3R,4R)-P-BAT (R,R-4), showed only one isomer; whereas the corresponding meso isomer, (3,4)meso-P-BAT (8), produced two distinctive complexes isolated readily by high performance liquid chromatography (HPLC). The [99mTc](R,S) meso-P-BAT (8) isomers showed a different lipophilicity (partition coefficient [P.C.] = 54.3 and 55.4 for peak A and peak B, respectively), as compared with that of the corresponding [99mTc](3R,4R)-P-BAT (R,R-4), trans isomer (P.C. = 163). Results of the biodistribution study in rats of these isomers show different heart and brain uptake, suggesting that the intrinsic differences in biodistribution are due to structural and stereospecific factors. Examples in this report confirm that it is possible to design stereospecific Tc-99m complexes based on the bisaminoethanethiol (N2S2, BAT) ligand system. Consideration on stereoselectivity of site-specific agents labeled with Tc-99m is likely an essential requirement on developing binding-site specific radiopharmaceuticals.
Synthesis and substance P antagonist activity of naphthimidazolium derivatives (1992)

The synthesis of unsymmetrical naphth[2,3-d]imidazolium and bridged naphth[2,3-d]imidazolium derivatives and their substance P (SP) antagonist activity are described. All compounds were evaluated for their ability to displace SP from neurokinin-1 (NK-1) receptor sites using standard receptor binding methodology (rat forebrain membrane). 1,3-Diethyl-2-[3-(1,3-dihydro-1,3,3-timethyl-2H-indol-2-ylidene) -1-propenyl]-1H-naphth[2,3-d]imidazolium chloride (7a), a representative compound in this series, was further evaluated for SP antagonist activity in a guinea pig ileum contractility assay. In vivo SP antagonist activity of 7a was demonstrated using SP-induced salivation and paw edema models performed in rats.
Diagnosis and Outcomes of Enterovirus Infections in Young Infants (2005)

EV infections are common in febrile infants younger than 90 days. Blood and CSF are equally likely to yield positive results by PCR, but the combination of both specimens improved the diagnostic yield.