gebhart/patrepeval huggingface dataset:
Amplified nanopatterning by self-organized shadow mask ion lithography (2010)

The self-organized formation of high aspect ratio dielectric nanostructures can be guided and sped-up recurring to a sacrificial metal film during ion beam sputtering. Following ion irradiation, the metal film evolves into a disconnected array of laterally ordered nanowires, which guide etching of the dielectric substrate. While the amplification rate of large scale features can be described simply in terms of the ratio of the sputtering yields of substrate and film, for small scale features the amplification rate depends on the interplay and lateral range of the smoothing and erosive mechanisms of the two materials.
Use of Thiazoles in the Halogen Dance Reaction:  Application to the Total Synthesis of WS75624 B (2004)

The total synthesis of the pyridine-thiazole-containing natural product WS75624 B (1) is described. This synthesis proceeds via the Stille coupling of appropriately functionalized pyridine and thiazole components, and this paper details our studies on the use of the halogen dance reaction to prepare the desired thiazole. Various halogen dance reactions on thizoles are described, including a novel one-pot multistep reaction in which 2-bromothiazole is treated with LDA in the presence of a silyl chloride at -78 degrees C and quenched with an electrophile to provide the highly functionalized thiazole derivatives 27.
Minimal requirements for inhibition of MraY by lysis protein E from bacteriophage ΦX174 (2012)

The DNA phage ΦX174 encodes the integral membrane protein E whose expression leads to host cell lysis by inhibition of the peptidoglycan synthesis enzyme MraY. Here we use mutagenesis to characterize the molecular details of the E lysis mechanism. We find that a minimal 18-residue region with the modified wild-type sequences of the conserved transmembrane helix of E is sufficient to lyse host cells and that specific residues within and at the boundaries of this helix are important for activity. This suggests that positioning of the helix in the membrane is critical for interactions with MraY. We further characterize the interaction site of the transmembrane helix with MraY demonstrating E forms a stable complex with MraY. Triggering cell lysis by peptidoglycan synthesis inhibition is a traditional route for antimicrobial strategies. Understanding the mechanism of bacterial cell lysis by E will provide insights into new antimicrobial strategies using re-engineered E peptides.
DELLA-Interacting SWI3C Core Subunit of Switch/Sucrose Nonfermenting Chromatin Remodeling Complex Modulates Gibberellin Responses and Hormonal Cross Talk in Arabidopsis (2013)

Switch (SWI)/Sucrose Nonfermenting (SNF)-type chromatin-remodeling complexes (CRCs) are involved in regulation of transcription, DNA replication and repair, and cell cycle. Mutations of conserved subunits of plant CRCs severely impair growth and development; however, the underlying causes of these phenotypes are largely unknown. Here, we show that inactivation of SWI3C, the core component of Arabidopsis (Arabidopsis thaliana) SWI/SNF CRCs, interferes with normal functioning of several plant hormone pathways and alters transcriptional regulation of key genes of gibberellin (GA) biosynthesis. The resulting reduction of GA4 causes severe inhibition of hypocotyl and root elongation, which can be rescued by exogenous GA treatment. In addition, the swi3c mutation inhibits DELLA-dependent transcriptional activation of GIBBERELLIN-INSENSITIVE DWARF1 (GID1) GA receptor genes. Down-regulation of GID1a in parallel with the DELLA repressor gene REPRESSOR OF GA1-3 1 in swi3c indicates that lack of SWI3C also leads to defects in GA signaling. Together with the recent demonstration of function of SWI/SNF ATPase BRAHMA in the GA pathway, these results reveal a critical role of SWI/SNF CRC in the regulation of GA biosynthesis and signaling. Moreover, we demonstrate that SWI3C is capable of in vitro binding to, and shows in vivo bimolecular fluorescence complementation interaction in cell nuclei with, the DELLA proteins RGA-LIKE2 and RGA-LIKE3, which affect transcriptional activation of GID1 and GA3ox (GIBBERELLIN 3-OXIDASE) genes controlling GA perception and biosynthesis, respectively. Furthermore, we show that SWI3C also interacts with the O-GlcNAc (O-linked N-acetylglucosamine) transferase SPINDLY required for proper functioning of DELLAs and acts hypostatically to (SPINDLY) in the GA response pathway. These findings suggest that DELLA-mediated effects in GA signaling as well as their role as a hub in hormonal cross talk may be, at least in part, dependent on their direct physical interaction with complexes responsible for modulation of chromatin structure.
Influence of Storage Conditions on the Structure, Thermal Behavior, and Formation of Enzyme-Resistant Starch in Extruded Starches (2007)

Starch structures from an extrusion process were stored at different temperatures to allow for molecular rearrangement (retrogradation); their thermal characteristics (DSC) and resistance to amylase digestion were measured and compared. The structure of four native and processed starches containing different amylose/amylopectin compositions (3.5, 30.8, 32, and 80% amylose content, respectively) before and after digestion was studied with small-angle X-ray scattering (SAXS) and X-ray diffraction (XRD). Rearrangement of the amylose molecules was observed for each storage condition as measured by the DSC endotherm at around 145 degrees C. The crystalline organization of the starches after processing and storage was qualitatively different to that of the native starches. However, there was no direct correlation between the initial crystallinity and the amount of enzyme-resistant starch (ERS) measured after in vitro digestion, and only in the case of high-amylose starch did the postprocess conditioning used lead to a small increase in the amount of starch remaining after the enzymatic treatment. From the results obtained, it can be concluded that retrograded amylose is not directly correlated with ERS and alternative mechanisms must be responsible for ERS formation.
Sweet Spot Interpretation from Multiple Attributes: Machine Learning and Neural Networks Technologies (2018)

During the exploration and development of shale gas, the key is to find the “sweet spot” where shows good characteristics of natural fracture and hydrocarbon enrichment. There have been efforts to distill numerous seismic attributes into volumes that are easily evaluated for improved seismic interpretation. Aiming at the multi-attributes comprehensive evaluation of the unconventional reservoirs, the research work has been carried out on neural network technology including self-organizing map (SOM) and K-means clustering algorithm (Kohonen, 2001). According to the fusion evaluation target with various attribute parameters, such as the total organic carbon content (TOC), brittleness and pore pressure, principal component analysis (PCA) technology, two-dimensional HSV coloring technology (Roy and Marfurt, 2015) and human-computer interaction monitoring clustering technology are further applied for flexibly explaining the characteristics of “sweet spot” . Through the attribute clusters and patterns, the ultimate goal is to enable the geoscientist to produce a more accurate interpretation and reduce exploration and development risk.
Renal allograft thrombosis (2009)

Early graft thrombosis Renal allograft thrombosis may be responsible for 2–7% of early allograft losses in adults [1] and up to 35% in children [2]. The North American Pediatric Renal Transplant Cooperative Study (NAPRTCS) reported that graft thrombosis represented the main cause of graft failure in the first year. Most cases of renal allograft thrombosis occur early in the postoperative period with a peak incidence of 48 h. However, thrombus formation may be delayed until after the first week [3]. Thrombosis may initially involve the renal artery or more frequently the renal vein, but in some cases it is difficult to ascertain where the thrombosis originated. Several factors may be involved in the pathogenesis of graft thrombosis. Thrombosis may be caused by technical errors, by vascular clamp injury or perfusion cannulation injury. Although vascular abnormalities in the donor kidney may be responsible for graft thrombosis [4] (thrombosis is reported in up to 36% of allografts with multiple renal arteries), however, in a multivariate analysis, the presence of atheroma was the only independent factor associated with the risk of arterial renal thrombosis [5]. Paediatric transplant recipients of kidneys from cadaver donors <5 years of age had a significantly higher thrombosis rate than did recipients from older donors [6]. This increased risk is attributable to the discrepancy in the size between the vessels of the donor and the recipient. In the past, cases of arterial thrombosis have been reported with cadaveric paediatric ‘en bloc’ transplantation. Recent results with this technique are excellent with no vascular thrombosis [7,8].
Supplementary Tables 1-5 from Activation of the JAK/STAT Pathway Leads to BRAF Inhibitor Resistance in BRAF<sup>V600E</sup> Positive Thyroid Carcinoma (2023)

&lt;p&gt;Supplementary Table 1. Gene expression changes in 8505C after vemurafenib treatment.Supplementary Table 2. Gene expression changes in WRO after vemurafenib treatment.Supplementary Table 3. Gene expression changes in 8505C -Vem-Res 1 relative to parental 8505C.Supplementary Table 4. Gene expression changes in WRO -Vem-Res 6 relative to parental WRO.Supplementary Table 5. Clinical features of thyroid tumors used in Fig. 5.&lt;/p&gt;
Mobilities of Mass-IdentifiedH3+andH+Ions in Hydrogen (1968)

The drift velocities of mass-identified $\mathrm{H}_{3}^{+}$ and ${\mathrm{H}}^{+}$ ions in hydrogen gas at room temperature were measured. The $\mathrm{H}_{3}^{+}$ ions were found to be in thermal equilibrium with the gas at $\frac{E}{{p}_{0}}$ less than about 10 V/cm Torr; the ${\mathrm{H}}^{+}$ ions, at $\frac{E}{{p}_{0}}$ less than about 5 V/cm Torr. From these measurements, the reduced zero-field mobilities were deduced: $\mathrm{H}_{3}^{+}$, 11.1\ifmmode\pm\else\textpm\fi{}0.6 ${\mathrm{cm}}^{2}$/V sec; ${\mathrm{H}}^{+}$, 16.0\ifmmode\pm\else\textpm\fi{}0.8 ${\mathrm{cm}}^{2}$/V sec. This investigation was performed with a long, low-pressure drift tube using a pulsed time-of-flight technique. The arrival-time histograms presented evidence of hydrogen ion-molecule reactions. It is shown that these reactions introduce no ambiguity in ascribing the above zero-field mobilities to single ionic species. Only a negligible fraction of the detected $\mathrm{H}_{3}^{+}$ ions were formed by the three-body conversion of ${\mathrm{H}}^{+}$ into $\mathrm{H}_{3}^{+}$. Above an $\frac{E}{{p}_{0}}$ of about 54 V/cm Torr, the disruption of $\mathrm{H}_{3}^{+}$ ions contributes substantially to the ${\mathrm{H}}^{+}$ signal. The reactive formation of $\mathrm{H}_{5}^{+}$ from $\mathrm{H}_{3}^{+}$ was evident in the $\mathrm{H}_{5}^{+}$ arrival-time histograms. The zero-field mobility of potassium ions in hydrogen was also determined, and the close agreement with the data of other investigators demonstrates that the apparatus is relatively free of unknown systematic uncertainties.
Amino-steroids. Part IV. 16β-Morpholino-17-oxo- and 17β-morpholino-16-oxo-5α-androstanes (1969)

Condensation of a 17β-acetoxy-16α,17α-epoxy-5α-androstane with morpholine yields a 17β-morpholino-16-ketone as the major product, contaminated with some isomeric 16β-morpholino-17-ketone; in the presence of water the condensation yields the latter isomer as the major product. An intermediate in these reactions was shown to be a 16α-hydroxy-17-ketone. The mechanisms of these reactions are discussed and also those of the condensations of 16α-acetoxy-17-ketone, 17β-acetoxy-16-ketone, and 17β-hydroxy-16-ketone systems with morpholine to give 16β-morpholino-17-ketones.
THE EXPERIMENTAL PRODUCTION IN DOGS OF EMPHYSEMA WITH ASSOCIATED ASTHMATIC SYNDROME BY MEANS OF AN INTRATRACHEAL BALL VALVE (1919)

1. Experimental emphysema can be produced in dogs by impeding expiration by means of a properly constructed ball valve introduced into the trachea. 2. This method affords a practical means of study of various physiological, pathological, and clinical aspects of emphysema. 3. The experiments demonstrate that any lesion or factor capable of interfering sufficiently with proper air expulsion yet permitting of sufficient air intake will occasion emphysema. 4. Attacks simulating those of asthma are occasioned in experimental emphysematous animals after exercise as well as during and following inhalation of mildly irritant gases.
Identifying Toxicologically Significant Compounds in Urban Wildfire Ash Using In Vitro Bioassays and High-Resolution Mass Spectrometry (2021)

Urban wildfires may generate numerous unidentified chemicals of toxicity concern. Ash samples were collected from burned residences and from an undeveloped upwind reference site, following the Tubbs fire in Sonoma County, California. The solvent extracts of ash samples were analyzed using GC- and LC-high-resolution mass spectrometry (HRMS) and using a suite of <i>in vitro</i> bioassays for their bioactivity toward nuclear receptors [aryl hydrocarbon receptor (AhR), estrogen receptor (ER), and androgen receptor (AR)], their influence on the expression of genetic markers of stress and inflammation [interleukin-8 (IL-8) and cyclooxygenase-2 (COX-2)], and xenobiotic metabolism [cytochrome P4501A1 (CYP1A1)]. Genetic markers (CYP1A1, IL-8, and COX-2) and AhR activity were significantly higher with wildfire samples than in solvent controls, whereas AR and ER activities generally were unaffected or reduced. The bioassay responses of samples from residential areas were not significantly different from the samples from the reference site despite differing chemical compositions. Suspect and nontarget screening was conducted to identify the chemicals responsible for elevated bioactivity using the multiple streams of HRMS data and open-source data analysis workflows. For the bioassay endpoint with the largest available database of pure compound results (AhR), nontarget features statistically related to whole sample bioassay response using Spearman's rank-order correlation coefficients or elastic net regression were significantly more likely (by 10 and 15 times, respectively) to be known AhR agonists than the overall population of compounds tentatively identified by nontarget analysis. The findings suggest that a combination of nontarget analysis, <i>in vitro</i> bioassays, and statistical analysis can identify bioactive compounds in complex mixtures.
Development of a novel system for isolating genes involved in predator-prey interactions using host independent derivatives of Bdellovibrio bacteriovorus 109J (2008)

In this study we describe a new method for isolating genes that are required for Bdellovibrio biofilm predation. Focusing on mechanisms that were previously attributed to be involved in predation, we demonstrate that motility systems are required for predation of bacterial biofilms. Furthermore, genes identified in this study suggest that surface gliding motility may also play a role in predation of biofilms consistent with Bdellovibrios occupying a biofilm niche. We believe that the methodology presented here will open the way for future studies on the mechanisms involved in Bdellovibrio host-prey interaction and a greater insight of the biology of this unique organism.
THE PARATHYROID HORMONE-RELATED PROTEIN STIMULATES HUMAN OSTEOBLAST-LIKE CELLS TO SECRETE A 9,000 DALTON BONERESORBING PROTEIN (1990)

The mechanism by which parathyroid hormone-related protein (PTH-RP) stimulates bone resorption is not known. Like certain other resorbing agents it may act to release bone-resorbing cytokines from the osteoblast. To examine this hypothesis, we used serum-free conditioned media (CM) from SAOS II cells incubated with 10(-8) M h(1-74) PTH-RP for 48 h. Treated CM contained substantially more bone-resorbing activity (BRA) in the fetal-rat long-bone assay than CM from untreated cells (2.17 +/- 0.21 vs 1.38 +/- 0.16 fold stimulation over basal [f]; p less than 0.05]. After centrifugation and dialysis, 1 liter of treated CM contained a total BRA of 7102 ngeq b(1-34) PTH with a specific activity (SA) of 447 ngeq b(1-34) PTH/mg protein. Treated CM did not stimulate the ROS assay and the cytokines PGE2, TGF-alpha, EGF, GM-CSF and IL-1 were present in low concentrations. The BRA was heat sensitive. Ultrafiltration revealed that 97% of the BRA was in a 3-30 kD fraction. Further purification was achieved by sequential reverse phase HPLC and size exclusion-HPLC (SE-HPLC). A single fraction containing BRA from SE-HPLC was purified 277-fold to a SA of 123,810 ngeq b(1-34) PTH/mg protein and had an apparent MW of 9 kD. SDS-PAGE revealed 4 bands in this SE-HPLC fraction with 1 band at 9 kD unique to that fraction. PTH-RP may cause bone resorption in part by stimulating the release of a 9 kD protein from osteoblasts which is responsible for activating osteoclasts.
Adhesion of Two Lactobacillus Strains, One Lactococcus and One Propionibacterium Strain to Cultured Human Intestinal Caco-2 Cell Line (1997)

Adhesion to intestinal surfaces is considered a prerequisite for effective probiotic bacterial strains. In this study, the in vitro adhesion properties of dairy strains Lactobacillus rhamnosus LC-705, Lactococcus lactis ssp. cremoris ARH 74 and Propionibacterium freudenreichii ssp. shermanii JS were investigated using human intestinal Caco-2 cell cultures. Lactobacillus strain GG (ATCC 53103) was used as a positive probiotic control, because the strain is known to adhere to Caco-2 cell cultures. Enterotoxigenic human E. coli (H 10407) and bovine E. coli (B 44) strains were used as positive and negative control, respectively. Bacteria were radioactively labeled, and the adhesion to Caco-2 cell cultures was assessed using liquid scintillation. The tested strains adhered to Caco-2 cell cultures and the adherence was similar to that of Lactobacillus strain GG. The adhesion was significantly higher when compared to the negative E. coli control. Adhesion was concentration dependent and no saturation level was achieved with bacterial concentrations used in this study. The Caco-2 cell cultures were also pretreated with nonlabeled bacteria of one strain prior to adhesion of radiolabeled bacteria. The nonlabeled adhered bacteria influenced the adhesion of radiolabeled bacteria in only one case: the adhesion of P. freudenreichii was significantly reduced by previously adhered L. rhamnosus LC-705. This result may indicate competition for adhesion sites between these strains. The adhesion properties of Lc. lactis and P. freudenreichii to intestinal cells make the strains interesting as potential new probiotic strains.
Electron Transfer Limitation in Carbon Dioxide Reduction Revealed by Data-Driven Tafel Analysis (2020)

Carbon dioxide (CO&lt;sub&gt;2&lt;/sub&gt;) recycling holds promise to mitigate anthropogenic emissions and to increase the sustainability of many chemical and fuel production processes. Despite marked advances in catalyst activity and selectivity at laboratory scale, fundamental understanding of the electrocatalytic reduction of CO&lt;sub&gt;2&lt;/sub&gt; remains limited, resulting in great uncertainty when extrapolating data to industrially relevant reaction rates. Importantly, the predominant models apply linear Tafel extrapolation, which drastically overpredicts the current density at large overpotentials. Researchers have posited several models to explain the curvature in Tafel behavior for CO&lt;sub&gt;2&lt;/sub&gt; reduction catalysis. Here we compare the ability of select models using Bayesian inference to explain curvature in Tafel behavior within the context of CO&lt;sub&gt;2&lt;/sub&gt; reduction to CO catalyzed by gold surfaces. By harvesting Tafel data on gold surfaces from multiple literature sources in a variety of reactor configurations, we identify three important features common to the aggregate data on Au-mediated CO&lt;sub&gt;2&lt;/sub&gt; reduction: (1) curvature in the Tafel plot at high overpotentials is only partly caused by mass transfer limitations; (2) the Marcus-Hush-Chidsey model for rate-limiting single-electron transfer kinetics provides the best fit to the data of the models tested; and finally, (3) the highly varied data collapse onto a single curve governed by the maximum predicted current in the electron-transfer-limited model. This analysis sets a foundation for determining more accurate activity-driving force relationships for CO&lt;sub&gt;2&lt;/sub&gt; reduction on electrocatalytic surfaces, both improving the quality of system-level analyses and motivating further research into the underlying mechanisms of CO&lt;sub&gt;2&lt;/sub&gt; reduction catalysis.
Outage Probability and Power Allocation for Collaborative Relaying of Multiple-Access Primary Users by Secondary User With Partial/Full Channel Knowledge (2016)

This paper investigates collaborative spectrum sharing (CSS) for which a cognitive secondary transmitter acts as a decode-and-forward (DF) relay for two primary users (PUs) occupying an interfering multiple-access channel. PUs are assumed to send their signals simultaneously; hence, interference between the primary signals exists due to the multiple-access nature. The secondary user (SU) selects and forwards one of the PU's signals to a desired destination, and at the same time, the SU also transmits its own signal only if it is not harmful to PUs. The selection of a primary signal to relay is investigated, depending on SU's knowledge of two primary source-destination channels, for which closed-form outage probabilities for PUs and SU are provided accordingly. With the help of the closed-form PU's outage probability, an optimal selection strategy between the primary signals and an optimal power allocation between the primary and secondary signals are also obtained in closed form, which minimizes SU's outage probability while keeping the PU's outage performance at an SU-free level. Numerical investigation is used to verify and illustrate the analysis given in this paper. Numerical results also show that the SU's performance can vary significantly according to the amount of channel knowledge that the SU can have.
Klumpke’s Birth Palsy (1995)

Erb's palsy is the most common obstetric brachial plexus injury followed by total plexus palsy. The distribution of Klumpke's birth palsy with modern obstetric practice is unknown. In this paper, we studied the distribution of Klumpke's birth palsy in our series of 235 consecutive cases of obstetrical brachial plexus injury and determined the incidence of this type of palsy to be 0.6% as cited in the English literature over the last decade.
Prevalence of asymptomatic vasogenic edema in pretreatment Alzheimer's disease study cohorts from phase 3 trials of semagacestat and solanezumab (2011)

VE seems to be rare at baseline in patients with AD in clinical trials, 2 of 2,762 associated with AD. Additional cohorts should be evaluated to support these findings.