gebhart/patrepeval huggingface dataset:
Yield tradeoffs and weed suppression in a winter annual oilseed relay‐cropping system (2020)

Abstract Midwest crop production is dominated by two summer annual crops grown in rotation, corn ( Zea mays L.) and soybean ( Glycine max [L.] Merr.). This rotation leaves a productivity gap during the spring and autumn. Winter oilseed crops, such as pennycress ( Thlaspi arvense L.), and winter camelina ( Camelina sativa [L.] Crantz), can fill this gap and provide ecosystem and economic benefits. The objectives of this study were to: (i) examine the tradeoffs between soybean and winter oilseed yields in the relay‐cropping system, (ii) determine legacy effects on corn 1 yr after oilseed–soybean relay‐cropping, and (iii) evaluate the weed suppression abilities of the winter oilseeds. Three sites were used across Minnesota to evaluate winter oilseeds and commodity crop yields in a relay‐cropping production system. Total seed production of the system (winter oilseed crop + soybean) was increased by 20% at one site, whereas at the other two sites, total yields were similar when compared to mono‐cropped soybean. Soybean yield was reduced at two of the three sites by 20 and 47% by the inclusion of winter oilseeds. Soybean yield was unaffected by inclusion of winter oilseeds at the third site. In the subsequent year, corn yield was unaffected by the winter oilseed treatments. Weeds were suppressed by the winter oilseeds crops. Pennycress reduced weed biomass by 97% to 100%, and camelina treatment reduced weed biomass by 85% to 87%. The inclusion of winter oilseeds in the corn–soybean cropping system can increase overall seed production and suppress early season weeds.
G‐PKDrep‐live, a genetically encoded FRET reporter to measure PKD activity at the trans‐Golgi‐network (2011)

The serine/threonine protein kinase D (PKD) is recruited to the trans-Golgi-network (TGN) by interaction with diacylglycerol (DAG) and Arf1 and promotes the fission of vesicles containing cargo destined for the plasma membrane. PKD activation is mediated by PKC(-induced phosphorylation. However, signaling pathways that activate PKD specifically at the TGN are only poorly characterized. Recently we created G-PKDrep, a genetically encoded fluorescent reporter for PKD activity at the TGN in fixed cells. To establish a reporter useful for monitoring Golgi-specific PKD activity in living cells we now refined G-PKDrep to generate G-PKDrep-live. Specifically, phosphorylation of G-PKDrep-live expressed in mammalian cells results in changes of fluorescence resonance energy transfer (FRET), and allows for indirect imaging of PKD activity. In a proof-of-principle experiment using phorbolester treatment, we demonstrate the reporter's capability to track rapid activation of PKD at the TGN. Furthermore, activation-induced FRET changes are reversed by treatment with PKD-specific pharmacological inhibitors. Thus, the newly developed reporter G-PKDrep-live is a suitable tool to visualize dynamic changes in PKD activity at the TGN in living cells. See accompanying commentary by Gautam DOI: 10.1002/biot.201100424.
A Molecular Switch between the Outer and the Inner Vestibules of the Voltage-gated Na+ Channel (2010)

Voltage-gated ion channels are transmembrane proteins that undergo complex conformational changes during their gating transitions. Both functional and structural data from K(+) channels suggest that extracellular and intracellular parts of the pore communicate with each other via a trajectory of interacting amino acids. No crystal structures are available for voltage-gated Na(+) channels, but functional data suggest a similar intramolecular communication involving the inner and outer vestibules. However, the mechanism of such communication is unknown. Here, we report that amino acid Ile-1575 in the middle of transmembrane segment 6 of domain IV (DIV-S6) in the adult rat skeletal muscle isoform of the voltage-gated sodium channel (rNa(V)1.4) may act as molecular switch allowing for interaction between outer and inner vestibules. Cysteine scanning mutagenesis of the internal part of DIV-S6 revealed that only mutations at site 1575 rescued the channel from a unique kinetic state ("ultra-slow inactivation," I(US)) produced by the mutation K1237E in the selectivity filter. A similar effect was seen with I1575A. Previously, we reported that conformational changes of both the internal and the external vestibule are involved in the generation of I(US). The fact that mutations at site 1575 modulate I(US) produced by K1237E strongly suggests an interaction between these sites. Our data confirm a previously published molecular model in which Ile-1575 of DIV-S6 is in close proximity to Lys-1237 of the selectivity filter. Furthermore, these functional data define the position of the selectivity filter relative to the adjacent DIV-S6 segment within the ionic permeation pathway.
Hot-boning enhances cook yield of boneless skinless chicken thighs (2014)

Three experiments were conducted to evaluate the effects of postmortem deboning time on cook yield of boneless skinless chicken thighs. In experiment 1, chicken thigh meat was deboned at 0.75 (hot-bone), 2, and 24 h postmortem (PM) and trimmed to obtain mainly iliotibialis muscle. Samples were cooked directly from a frozen state. Cook yield of the muscle was significantly influenced by PM deboning time. Hot-boned thighs exhibited a 7% greater cook yield than the samples deboned at 24 h. In experiment 2, boneless skinless chicken thighs were deboned at 0.3, 2, and 24 h PM and cooked directly from a fresh, never-frozen state at 24 h PM. Cook yield of the hot-boned thighs was significantly higher than those of the 2 and 24 h deboned samples, which did not differ from each other. In experiment 3, whole legs (thigh + drumstick) were cut from the carcass backbone at 0.3 (hot-cut), 2, and 24 h PM. Thighs were separated from the legs (drumsticks) at either the same time the whole legs were removed from the carcasses or at 24 h PM. Intact thighs (bone in) were cooked fresh at 24 h PM. Color of fresh thigh muscles, cook yield, and Warner-Bratzler shear force of cooked samples were measured. Cook yield of the thighs cut from the backbone before chilling was significantly higher than those cut from the carcasses at 2 and 24 h PM, which did not differ from each other. The PM time at which intact thighs were separated from the leg (drumstick) did not influence cook yield. These results demonstrate that postmortem deboning time can significantly affect cook yield of boneless skinless chicken thigh products. Deboning chicken thighs after chilling reduces the cook yield. Differences in the cook yield of thighs may also result from the removal of whole chicken legs from the carcass backbone.
Novel Thymine-Functionalized Polystyrenes for Applications in Biotechnology. Polymer Synthesis and Characterization (2003)

Novel polystyrenes (PS) carrying thymine functional groups were synthesized by copolymerizing styrene (St) and 1-(vinylbenzyl)thymine (1-VBT) in the presence and absence of divinylbenzene (DVB) in batch free radical emulsion polymerization. Microsphere latexes were obtained with an average particle size of ≈60 nm (3.0 and 5.0 wt % [VBT]0) with ≈80% conversion and ≈38 nm (10 wt % [VBT]0) with 91% conversion. The final copolymer latexes were freeze-dried to obtain particles in the size range of 32−544 μm. Copolymer compositions were determined by FTIR-DRIFT, 1H NMR, and elemental analysis and were found to be close to the composition of the monomer charges. XPS analysis revealed that VBT concentration on the surface of the particles was much higher (17, 24, and 36 wt %) than in the bulk. Phenol was selected as a model compound to examine adsorption onto the thymine functional groups. Hydrogen bonding between the phenolic hydroxyl group and the thymine units of soluble polymers was evidenced by 1H NMR and FTIR spectroscopy. Adsorption isotherms obtained with all samples showed a good fit with Langmuir's model, supporting evidence for a monolayer chemisorption model in the heterogeneous adsorbent−phenol/hexane system investigated. 89.4% of the phenol was desorbed by adding Borax buffer solution of pH ≥ 10 to the adsorbent−phenol/hexane system. These novel copolymers have potential in biotechnology.
Theoretical study of the structure and specific capacity of an organic cathode based on poly(2,5-diaza-1,4-benzoquinone) in a lithiated state (2018)

A density functional theory computational study of poly(2,5-diaza-1,4-benzoquinone) as a potential organic cathode is presented. The lithium insertion in one-dimensional, two-dimensional and three-dimensional models was evaluated and yielded energies of 2.38, 3.12 and 3.59 eV per Li atom, respectively. These values taken together with the specific capacity of ∼500 mAh g−1 make poly(2,5-diaza-1,4-benzoquinone) a promising organic cathode material for Li-ion batteries.
Experimental Observation of Possible Pressure-Induced Phase Transformation in GdAlO3 Perovskite Using In Situ X-ray Diffraction (2023)

Gadolinium aluminate perovskite (GdAlO3) was studied at high pressures of up to 23 GPa in a diamond anvil cell (DAC) using monochromatic synchrotron X-ray powder diffraction. Evidence of a pressure-induced phase transformation from orthorhombic (Pbnm) to rhombohedral (R3¯c) structure was observed at 21 GPa and further proved by DFT calculations. Before phase transition, the volumetric ratio of polyhedron A and B (i.e., VA/VB for ABX3 general notation) in the Pbnm phase continuously increased towards the ideal value of five at the transition, indicating a pressure-induced decrease in the structural distortion as opposed to the trend in many other orthorhombic perovskites (e.g., CaSnO3, CaGeO3, MgSiO3 and NaMgF3). Pressure–volume data of the Pbnm phase were fitted to the third-order Birch–Murnaghan equation of state yielding a bulk modulus (Ko) of 216 ± 7 GPa with a pressure derivative of the bulk modulus (Ko′) of 5.8 GPa (fixed). This work confirms the pressure-induced phase transformation from orthorhombic to a higher symmetry structure previously predicted in GdAlO3 perovskite.
Generation of broadband THz transients via metallic spintronic emitters driven by 20-fs pulses at 1030 nm (2020)

We explore power and bandwidth scaling for the generation of highly-temporally-confined THz transients from spintronic emitters, driven by the 250-fs and 20-fs pulses of a high-power 28-MHz Yb-based laser, spectrally centered at 1030 nm.
Table S8 from Parallel analysis of Arabidopsis circadian clock mutants reveals different scales of transcriptome and proteome regulation (2017)

The circadian clock regulates physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have integrated RNA-sequencing and protein mass spectrometry data to comparatively analyse the <i>lhycca1</i>, <i>prr7prr9</i>, <i>gi</i> and <i>toc1</i> circadian clock mutant rosette at the end of day and end of night. Each mutant affects specific sets of genes and proteins, suggesting that the circadian clock regulation is modular. Furthermore, each circadian clock mutant maintains its own dynamically fluctuating transcriptome and proteome profile specific to subcellular compartments. Most of the measured protein levels do not correlate with changes in their corresponding transcripts. Transcripts and proteins that have coordinated changes in abundance are enriched for carbohydrate- and cold-responsive genes. Transcriptome changes in all four circadian clock mutants also affect genes encoding starch degradation enzymes, transcription factors and protein kinases. The comprehensive transcriptome and proteome datasets demonstrate that future system-driven research of the circadian clock requires multi-level experimental approaches. Our work also shows that further work is needed to elucidate the roles of post-translational modifications and protein degradation in the regulation of clock-related processes.
Atypical<scp>TDP</scp>‐43 protein expression in an<scp>ALS</scp>pedigree carrying a p.<scp>Y374X</scp>truncation mutation in<i>TARDBP</i> (2022)

We describe an autosomal dominant, multi-generational, amyotrophic lateral sclerosis (ALS) pedigree in which disease co-segregates with a heterozygous p.Y374X nonsense mutation within TDP-43. Mislocalization of TDP-43 and formation of insoluble TDP-43-positive neuronal cytoplasmic inclusions is the hallmark pathology in >95% of ALS patients. Neuropathological examination of the single case for which CNS tissue was available indicated typical TDP-43 pathology within lower motor neurons, but classical TDP-43-positive inclusions were absent from motor cortex. The mutated allele is transcribed and translated in patient fibroblasts and motor cortex tissue, but overall TDP-43 protein expression is reduced compared to wild-type controls. Despite absence of TDP-43-positive inclusions we confirmed deficient TDP-43 splicing function within motor cortex tissue. Furthermore, urea fractionation and mass spectrometry of motor cortex tissue carrying the mutation revealed atypical TDP-43 protein species but not typical C-terminal fragments. We conclude that the p.Y374X mutation underpins a monogenic, fully penetrant form of ALS. Reduced expression of TDP-43 combined with atypical TDP-43 protein species and absent C-terminal fragments extends the molecular phenotypes associated with TDP-43 mutations and with ALS more broadly. Future work will need to include the findings from this pedigree in dissecting the mechanisms of TDP-43-mediated toxicity.
Differential Distribution of Major Brain Gangliosides in the Adult Mouse Central Nervous System (2013)

Gangliosides - sialic acid-bearing glycolipids - are major cell surface determinants on neurons and axons. The same four closely related structures, GM1, GD1a, GD1b and GT1b, comprise the majority of total brain gangliosides in mammals and birds. Gangliosides regulate the activities of proteins in the membranes in which they reside, and also act as cell-cell recognition receptors. Understanding the functions of major brain gangliosides requires knowledge of their tissue distribution, which has been accomplished in the past using biochemical and immunohistochemical methods. Armed with new knowledge about the stability and accessibility of gangliosides in tissues and new IgG-class specific monoclonal antibodies, we investigated the detailed tissue distribution of gangliosides in the adult mouse brain. Gangliosides GD1b and GT1b are widely expressed in gray and white matter. In contrast, GM1 is predominately found in white matter and GD1a is specifically expressed in certain brain nuclei/tracts. These findings are considered in relationship to the hypothesis that gangliosides GD1a and GT1b act as receptors for an important axon-myelin recognition protein, myelin-associated glycoprotein (MAG). Mediating axon-myelin interactions is but one potential function of the major brain gangliosides, and more detailed knowledge of their distribution may help direct future functional studies.
The Polycomb protein <scp>LHP</scp>1 regulates <i>Arabidopsis thaliana</i> stress responses through the repression of the <scp>MYC</scp>2‐dependent branch of immunity (2019)

Polycomb repressive complexes (PRCs) have been traditionally associated with the regulation of developmental processes in various organisms, including higher plants. However, similar to other epigenetic regulators, there is accumulating evidence for their role in the regulation of stress and immune-related pathways. In the current study we show that the PRC1 protein LHP1 is required for the repression of the MYC2 branch of jasmonic acid (JA)/ethylene (ET) pathway of immunity. Loss of LHP1 induces the reduction in H3K27me3 levels in the gene bodies of ANAC019 and ANAC055, as well as some of their targets, leading to their transcriptional upregulation. Consistently, increased expression of these two transcription factors leads to the misregulation of several of their genomic targets. The lhp1 mutant mimics the MYC2, ANAC019, and ANAC055 overexpressers in several of their phenotypes, including increased aphid resistance, abscisic acid (ABA) sensitivity and drought tolerance. In addition, like the MYC2 and ANAC overexpressers, lhp1 displays reduced salicylic acid (SA) content caused by a deregulation of ICS1 and BSMT1, as well as increased susceptibility to the hemibiotrophic pathogen Pseudomonas syringae pv. tomato DC3000. Together, our results indicate that LHP1 regulates the expression of stress-responsive genes as well as the homeostasis and responses to the stress hormones SA and ABA. This protein emerges as a key chromatin player fine tuning the complex balance between developmental and stress-responsive processes.
Limits on communications in a cognitive radio channel (2006)

In this article we review FCC secondary markets initiatives and how smart wireless devices could be used to increase spectral efficiency. We survey the current proposals for cognitive radio deployment, and present a new, potentially more spectrally efficient model for a wireless channel employing cognitive radios; the cognitive radio channel. This channel models the simplest scenario in which a cognitive radio could be used and consists of a 2 Tx, 2 Rx wireless channel in which one transmitter knows the message of the other. We obtain fundamental limits on the communication possible over such a channel, and discuss future engineering and regulatory issues
Erfolgsadaptierte Therapie mit Lamivudin – eine Option auf langfristige Virussuppression im ausgesuchten HBV-Patientenkollektiv? (2010)

Einleitung: Die Therapie der chronischen Hepatitis B (CHB) mit Lamivudin wird sehr gut vertragen, bietet hierbei jedoch nur eine mittlere antivirale Potenz und eine geringe Resistenzschwelle. Daher wird Lamivudin meist zur Prophylaxe einer CHB Reaktivierung unter Immunsuppression oder Chemotherapie eingesetzt. Allerdings zeigen viele Patienten in Europa eine CHB mit geringer entzündlicher Aktivität und allenfalls mittelgradiger Viruslast, bei denen mit Lamivudin möglicherweise eine zuverlässige HBV-DNS Suppression erreicht werden könnte.
Auditing SNOMED relationships using a converse abstraction network. (2009)

In SNOMED CT, a given kind of attribute relationship is defined between two hierarchies, a source and a target. Certain hierarchies (or subhierarchies) serve only as targets, with no outgoing relationships of their own. However, converse relationships-those pointing in a direction opposite to the defined relationships-while not explicitly represented in SNOMED's inferred view, can be utilized in forming an alternative view of a source. In particular, they can help shed light on a source hierarchy's overall relationship structure. Toward this end, an abstraction network, called the converse abstraction network (CAN), derived automatically from a given SNOMED hierarchy is presented. An auditing methodology based on the CAN is formulated. The methodology is applied to SNOMED's Device subhierarchy and the related device relationships of the Procedure hierarchy. The results indicate that the CAN is useful in finding opportunities for refining and improving SNOMED.
Distribution of air temperature in the greenhouses with different ridge-roof inclinations (2017)

We developed a greenhouse with an inclined-ridge roof designed to accelerate the movement of rising air across the roof slope, and to enhance greenhouse ventilation. In this study, distributions of air temperatures of 3 m wide and 10.8 m long plastic greenhouses with different ridge-roof inclinations (horizontal ridges, inclined-ridge of 2.7°, 5.3° or 7.9°) were investigated. The upper parts of the two gable-ends on each greenhouse were opened for ventilation. The average air temperature was the highest in the greenhouses with horizontal ridges, and gradually decreased as the ridge inclination increased. An air temperature gradient was clearly observed along the long axis in the inclined-ridge greenhouses; the air temperature was lower on the lower roof side. This temperature gradient is probably due to air movement from the lower to the higher-roof side caused by natural ventilation, which can be enhanced by the ridge inclination.
Phase I Trial of Topotecan in Combination with Gemcitabine in Refractory Solid Tumor Patients (2004)

The MTD was observed at a T dose of 1 mg/m2 administered on days 1 through 15, and a G dose of 1250 mg/m2 administered on days 1 and 15 via 30 minute intravenous (IV) infusion.
Effects of Bulk Photoconductivity on Photocurrent Action Spectra of Molecular p-n Heterojunction Solar Cells (2005)

We have investigated how bulk photoconductivity influences the photovoltaic parameters of zincphthalocyanine-fullerene p-n heterojunction solar cells. The results indicate that the photocurrent action spectrum of a cell depends strongly on the photoconductivity and spectral characteristics of each component material. We therefore propose a model that simulates the action spectra of the short-circuit photocurrent in the molecular organic solar cells, and our model is based on the assumption that the photocurrent action spectrum depends on the bulk layer photoconductivity.
New processes for homojunction silicon solar cells doping: From beam line to plasma immersion ion implantation (2016)

The doping of n-type silicon solar cells was investigated using two ion implantation techniques: beam line and plasma immersion. Initially, we evaluated the benefits of beamline ion implantation in replacement of diffusion anneal doping process. Two different annealing routines were studied. The first one using a single annealing to activate both B implanted emitter and P implanted BSF, while the second one used two different annealing to separately activate each dopant. Good yield was reached with a record cell of 20.33% efficiency. Secondly, we investigated the doping by plasma immersion ion implantation where the final objective was the fabrication of a solar cell fully doped by plasma. BF3 and B2H6 were compared as precursor gases for the boron emitter doping, while PH3 was used for the BSF doping. Hybrid cells were fabricated using both implantation techniques and a maximum efficiency of 19.8% was obtained. First cells fully doped by plasma shown promising results with a yield of 18.8%.
Glycerophosphocholine and Glycerophosphoethanolamine Are Not the Main Sources of the In Vivo31P MRS Phosphodiester Signals from Healthy Fibroglandular Breast Tissue at 7 T (2016)

The available experimental evidence suggests that GPC and GPE are not the main source of the PDE signals measured in fibroglandular breast tissue at 7 T. These signals may predominantly originate from mobile phospholipids.
The Laplacian Spectral Classifier (2006)

We develop a novel classifier in a kernel feature space defined by the eigenspectrum of the Laplacian data matrix. The classification cost function is derived from a distance measure between probability densities. The Laplacian data matrix is obtained based on a training set, while test data is mapped to the kernel space using the Nystrom routine. In that space, the test data is classified based on the angle between the test point and the training data class means. We illustrate the performance of the new classifier on synthetic and real data.