gebhart/patrepeval huggingface dataset:
Reach-through band bending in semiconductor thin films (2004)

We describe a phenomenon of reach-through band bending in thin film semiconductors. It occurs through generation of defects that change the semiconductor work function. This translates the effect of the metal presence through the semiconductor film and induces a Schottky barrier in another semiconductor tangent to the film on the opposite side (reach-through band bending). We have found experimental evidence of this effect in CdTe photovoltaics.
Farm Energy: Fuel efficiency factors for tractor selection (2011)

Considering fuel efficiency factors is important when adding new or used tractors to the farm equipment fleet. This publication provides pointers on what you should consider.
Status of Ablation in Patients with Atrial Tachycardia and Flutter (1994)

RF catheter ablation directed at the atrial substrate is a safe and effective means of treating patients with drug refractory atrial tachycardias and atrial flutter, avoiding the need for His-bundle ablation and permanent pacing. While further follow-up will be needed to evaluate the incidence of later recurrence or emergence of new arrhythmias, this is a promising technique for a growing cohort of patients.
HNRNPA1 promotes recognition of splice site decoys by U2AF2 <i>in vivo</i> (2017)

Abstract Alternative pre-mRNA splicing plays a major role in expanding the transcript output of human genes. This process is regulated, in part, by the interplay of trans -acting RNA binding proteins (RBPs) with myriad cis -regulatory elements scattered throughout pre-mRNAs. These molecular recognition events are critical for defining the protein coding sequences (exons) within pre-mRNAs and directing spliceosome assembly on non-coding regions (introns). One of the earliest events in this process is recognition of the 3’ splice site by U2 small nuclear RNA auxiliary factor 2 (U2AF2). Splicing regulators, such as the heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1), influence spliceosome assembly both in vitro and in vivo , but their mechanisms of action remain poorly described on a global scale. HNRNPA1 also promotes proof reading of 3’ss sequences though a direct interaction with the U2AF heterodimer. To determine how HNRNPA1 regulates U2AF-RNA interactions in vivo, we analyzed U2AF2 RNA binding specificity using individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) in control- and HNRNPA1 over-expression cells. We observed changes in the distribution of U2AF2 crosslinking sites relative to the 3’ splice sites of alternative cassette exons but not constitutive exons upon HNRNPA1 over-expression. A subset of these events shows a concomitant increase of U2AF2 crosslinking at distal intronic regions, suggesting a shift of U2AF2 to “decoy” binding sites. Of the many non-canonical U2AF2 binding sites, Alu-derived RNA sequences represented one of the most abundant classes of HNRNPA1-dependent decoys. Splicing reporter assays demonstrated that mutation of U2AF2 decoy sites inhibited HNRNPA1-dependent exon skipping in vivo . We propose that HNRNPA1 regulates exon definition by modulating the interaction of U2AF2 with decoy or bona fide 3’ splice sites.
Supplementary Methods from Single-Dose Anti–PD-L1/IL-15 Fusion Protein KD033 Generates Synergistic Antitumor Immunity with Robust Tumor-Immune Gene Signatures and Memory Responses (2023)

&lt;p&gt;Detailed Methods for in vitro and in vivo Studies&lt;/p&gt;
Improving the Morphological and Optical Properties of Sputtered Indium Tin Oxide Thin Films by Adopting Ultralow-Pressure Sputtering (2008)

The morphological and optical properties of indium tin oxide (ITO) thin films deposited by an ultralow-pressure dc magnetron sputtering (ULPS) method followed by postannealing treatment at are reported. The surface roughness of the film (: ) deposited using ULPS was about 5 times lower than that of the film (: ) sputtered using a pressure of . ITO thin films with a low resistivity of were also achieved using a continuous two-step deposition process, in which the initial layer was deposited using ULPS and then the final layer was deposited with a SP of , without the use of any other additional steps. Both the ULPS and continuous two-step deposition methods were found to be effective for producing ITO thin films with enhanced morphologies that make them suitable for use in display devices.
Predicting sediment and nutrient concentrations from high-frequency water-quality data (2019)

Abstract Water-quality monitoring in rivers often focuses on the concentrations of sediments and nutrients, constituents that can smother biota and cause eutrophication. However, the physical and economic constraints of manual sampling prohibit data collection at the frequency required to adequately capture the variation in concentrations through time. Here, we developed models to predict total suspended solids (TSS) and oxidized nitrogen (NOx) concentrations based on high-frequency time series of turbidity, conductivity and river level data from in situ sensors in rivers flowing into the Great Barrier Reef lagoon. We fit generalized-linear mixed-effects models with continuous first-order autoregressive correlation structures to water-quality data collected by manual sampling at two freshwater sites and one estuarine site and used the fitted models to predict TSS and NOx from the in situ sensor data. These models described the temporal autocorrelation in the data and handled observations collected at irregular frequencies, characteristics typical of water-quality monitoring data. Turbidity proved a useful and generalizable surrogate of TSS, with high predictive ability in the estuarine and fresh water sites. Turbidity, conductivity and river level served as combined surrogates of NOx. However, the relationship between NOx and the covariates was more complex than that between TSS and turbidity, and consequently the ability to predict NOx was lower and less generalizable across sites than for TSS. Furthermore, prediction intervals tended to increase during events, for both TSS and NOx models, highlighting the need to include measures of uncertainty routinely in water-quality reporting. Our study also highlights that surrogate-based models used to predict sediments and nutrients need to better incorporate temporal components if variance estimates are to be unbiased and model inference meaningful. The transferability of models across sites, and potentially regions, will become increasingly important as organizations move to automated sensing for water-quality monitoring throughout catchments.
[Screening and identification of the upregulators of ATP-binding cassette transporter A1]. (2012)

ATP-binding cassette transporter A1 (ABCA1) promotes cholesterol and phospholipid efflux from cells to lipid-poor apolipoprotein A-I (apoA-I), and plays a key role in the initial steps of the whole process of reverse cholesterol transport (RCT). Upregulation of ABCA1 is beneficial for atherosclerosis (AS) prevention and/or therapy, which indicated that ABCA1 was a target for anti-AS drug development. In the previous study, a high-throughput screening method was established using ABCA1p-LUC HepG2 cell line to find the upregulators of ABCA1. In the present study, compound 2030421B was found using this method, with EC50 of 0.50 microg x mL(-1). The compound was further identified as an upregulator of ABCA1 expression by real-time quantitative reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting analysis. Studies also showed that the 2030421B could induce apoA-I-mediated cholesterol efflux and inhibit lipids uptake into mouse peritoneal macrophages RAW264.7.
Plant Natural Products in Anti-Diabetic Drug Discovery (2010)

Plants and other natural sources have been useful in discovering drugs for treating patients with diabetes mellitus. Examples include the α-glucosidase inhibitor acarbose, and galegine, which contributed to the discovery and development of the biguanides. There are many traditionally used herbal medicines that lower blood glucose in experimental models, and, currently, there is considerable interest in exploring these plant extracts for compounds that might also be useful in the clinic or that might have novel effects, such as stimulation of β-cell proliferation. Often, neither their mechanism nor their active components have been defined, so it is possible that novel mechanisms of action and novel compounds will be discovered. In addition, there has been very little use of large collections of natural products in random screening campaigns against accepted therapeutic targets: there is great potential to find new chemical scaffolds for drugs with improved properties. This paper will provide an overview of recent activities relating to the use of natural products from plants as a source of compounds that might be beneficial in treating patients with diabetes.
Direct observation of the cell-wall remodeling in adhering Staphylococcus aureus 27217: An AFM study supported by SEM and TEM (2019)

We took benefit from Atomic Force Microscopy (AFM) in the force spectroscopy mode to describe the time evolution - over 24 h - of the surface nanotopography and mechanical properties of the strain <i>Staphylococcus aureus 27217</i> from bacterial adhesion to the first stage of biofilm genesis. In addition, Transmission Electron Microscopy (TEM) and Scanning Electron Microscopy (SEM) experiments allowed identifying two types of self-adhering subpopulations (the so-called "bald" and "hairy" cells) and revealed changes in their relative populations with the bacterial culture age and the protocol of preparation. We indeed observed a dramatic evanescing of the "hairy" subpopulation for samples that underwent centrifugation and resuspension processes. When examined by AFM, the "hairy" cell surface resembled to a herringbone structure characterized by upper structural units with lateral dimensions of ∼70 nm and a high Young modulus value (∼2.3 MPa), a mean depth of the trough between them of ∼15 nm and a resulting roughness of ∼5 nm. By contrast, the "bald" cells appeared much softer (∼0.35 MPa) with a roughness one order of magnitude lower. We observed too the gradual detachment of the herringbone patterns from the "hairy" bacterial envelope of cell harvested from a 16 h old culture and their progressive accumulation between the bacteria in the form of globular clusters. The secretion of a soft extracellular polymeric substance was also identified that, in addition to the globular clusters, may contribute to the initiation of the biofilm spatial organization.
Resonant Tunneling Through Discrete Electronic Levels of a C<sub>60</sub>Molecule in the Presence of Charging Effects (1998)

We have conducted tunneling spectroscopy studies for isolated C60 molecules in the double barrier tunnel junction configuration. The tunneling current-voltage (I-V) and dI/dV vs. V spectra of these molecules exhibit rich structures resulting from both resonant tunneling through the discrete levels and single electron charging effects. In particular, we observe degeneracy lifting within the molecular orbitals, probably due to the Jahn-Teller effect and local electric fields. Theoretical fits, performed using the "orthodox" model for single-electron tunneling modified to account for the discrete level spectrum of C60, agree well with our data.
Dynamics of antifolate transport via the reduced folate carrier and the membrane folate receptor in murine leukaemia cells in vitro and in vivo (2008)

Murine L1210 leukaemia cells expressing either the reduced folate carrier (RFC) or the membrane folate receptor (MFR) were studied in vitro and in vivo to assess the dynamics of membrane transport of two categories antifolates; folate-based inhibitors of dihydrofolate reductase (methotrexate, edatrexate, aminopterin, PT523, and PT644) and thymidylate synthase (TS) [CB3717, raltitrexed, plevitrexed (BGC9331), pemetrexed and GW1843]. The potency of in situ inhibition of TS was used as an endpoint to analyze the in vitro dynamics of RFC/MFR-membrane transport of these antifolates. Both for L1210-RFC and L1210-MFR cells, the potency of in situ TS inhibition was closely correlated with increasing affinities of these transporters for the antifolates (r = 0.64, P < 0.05 and r = -0.65, P < 0.05, respectively). Within the group of antifolates for which MFR had a low binding affinity, those that had the ability to become polyglutamylated, were more potent inhibitors of TS in situ activity than non-polyglutamatable antifolates. In vivo activity of methotrexate, edatrexate, raltitrexed and pemetrexed was assessed in L1210-RFC and L1210-MFR bearing mice that were fed either a standard or a folate-deficient chow. Dietary folate depletion significantly reduced the MTD for methotrexate (sevenfold), edatrexate (sevenfold), raltitrexed (50-fold) and pemetrexed (150-fold). Based on increased life spans, antitumor effects of methotrexate and edatrexate were markedly better in L1210-RFC bearing mice on the folate-deficient chow (ILS: 455 and 544%, respectively) than on standard chow (ILS: 213 and 263%, respectively). No therapeutic effects of methotrexate and edatrexate were observed for L1210-MFR bearing mice on either chow condition, which may be consistent with the low binding affinity for MFR. Irrespective of the folate diet status, pemetrexed and raltitrexed were inactive against both L1210-RFC and L1210-MFR bearing mice, which may be due to high circulating plasma thymidine levels. Collectively, this study underscores that modulation of dietary folate status can provide a basis within which the therapeutic effect of antifolates may be further improved.
The 2020 photovoltaic technologies roadmap (2020)

Abstract Over the past decade, the global cumulative installed photovoltaic (PV) capacity has grown exponentially, reaching 591 GW in 2019. Rapid progress was driven in large part by improvements in solar cell and module efficiencies, reduction in manufacturing costs and the realization of levelized costs of electricity that are now generally less than other energy sources and approaching similar costs with storage included. Given this success, it is a particularly fitting time to assess the state of the photovoltaics field and the technology milestones that must be achieved to maximize future impact and forward momentum. This roadmap outlines the critical areas of development in all of the major PV conversion technologies, advances needed to enable terawatt-scale PV installation, and cross-cutting topics on reliability, characterization, and applications. Each perspective provides a status update, summarizes the limiting immediate and long-term technical challenges and highlights breakthroughs that are needed to address them. In total, this roadmap is intended to guide researchers, funding agencies and industry in identifying the areas of development that will have the most impact on PV technology in the upcoming years.
Spatial Variations in Vitreous Oxygen Consumption (2016)

We investigated the spatial variation of vitreous oxygen consumption in enucleated porcine eyes. A custom made oxygen source was fabricated that could be localized to either the mid or posterior vitreous cavity and steady state vitreous oxygen tension was measured as a function of distance from the source using a commercially available probe. The reaction rate constant of ascorbate oxidation was estimated ex vivo by measuring the change in oxygen tension over time using vitreous harvested from porcine eyes. Vitreous ascorbate from mid and posterior vitreous was measured spectrophotometrically. When the oxygen source was placed in either the mid-vitreous (N = 6) or the posterior vitreous (N = 6), we measured a statistically significant decrease in vitreous oxygen tension as a function of distance from the oxygen source when compared to control experiments without an oxygen source; (p<0.005 for mid-vitreous and p<0.018 for posterior vitreous at all distances). The mid-vitreous oxygen tension change was significantly different from the posterior vitreous oxygen tension change at 2 and 3mm distances from the respective oxygen source (p<0.001). We also found a statistically significant lower concentration of ascorbate in the mid-vitreous as compared to posterior vitreous (p = 0.02). We determined the reaction rate constant, k = 1.61 M(-1) s(-1) ± 0.708 M(-1) s(-1) (SE), of the oxidation of ascorbate which was modeled following a second order rate equation. Our data demonstrates that vitreous oxygen consumption is higher in the posterior vitreous compared to the mid-vitreous. We also show spatial variations in vitreous ascorbate concentration.
Iron-Based Layered Superconductor La[O<sub>1-</sub><i><sub>x</sub></i>F<i><sub>x</sub></i>]FeAs (<i>x</i> = 0.05−0.12) with <i>T</i><sub>c</sub> = 26 K (2008)

We report that a layered iron-based compound LaOFeAs undergoes superconducting transition under doping with F- ions at the O2- site. The transition temperature (Tc) exhibits a trapezoid shape dependence on the F- content, with the highest Tc of ∼26 K at ∼11 atom %.
Single Nucleotide Polymorphisms Associated with Increased Risk for Statin Myopathy (2009)

Approximately 2% to 7% of statin users develop myalgias. Elevated serum creatine kinase (CK) levels occur in 0.1% to 1.0% of users, whereas the
Ordered subsets linkage analysis of antisocial behavior in substance use disorder among participants in the collaborative study on the genetics of alcoholism (2008)

Heterogeneity in complex diseases such as Substance Use Disorder (SUD) reduces the power to detect linkage and makes replication of findings in other populations unlikely. It is therefore critical to refine the phenotype and use methods that account for genetic heterogeneity between families. SUD was operationalized as diagnosis of abuse or dependence to alcohol and/or any one of five illicit substances. Whole-genome linkage analysis of 241 extended pedigree families from the Collaborative Study on the Genetics of Alcoholism was performed in Merlin using an affected sibship design. An Ordered Subsets Analysis (OSA) using FLOSS sought to increase the homogeneity of the sample by ranking families by their density of childhood and adult antisocial behaviors, producing new maximum Nonparametric Lod (NPL) scores on each chromosome for each subset of families. Prior to OSA, modest evidence for linkage was found on chromosomes 8 and 17. Although changes in NPL scores were not statistically significant, OSA revealed possible evidence of linkages on chromosome 7, near markers D7S1795 and D7S821. NPL scores >3.0 were also observed on chromosomes 2, 3, 5, 9, and 14. However, the number of families used in these latter subsets for linkage may be too small to be meaningful. Results provide some evidence for the ability of OSA to reduce genetic heterogeneity, and add further support to chromosome 7 as a possible location to search for genes related to various SUD related processes. Nonetheless, replication of these results in other samples is essential.
A new framework for computational protein design through cost function network optimization (2013)

The combined pipeline used to generate energetic models (based on a patched version of the open source solver Osprey 2.0), the conversion to CFN models (based on Perl scripts) and CFN solving (based on the open source solver toulbar2) are all available at http://genoweb.toulouse.inra.fr/~tschiex/CPD
Isolation and characterization of 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole-resistant mutants of the Chinese hamster ovary cell line. (1982)

Mutants resistant to the RNA synthesis inhibitor 5,6-dichloro-1-beta-D-ribofurano-sylbenzimidazole (DRB) have been isolated in the Chinese hamster ovary cell line CHO-K1. Three independently isolated mutants, DRB6 DRB10, and DRB13, were 3-, 5-, and 3.5-fold, respectively, more resistant to DRB than the parental cell line WTCHO. The DRB-resistant mutations were expressed codominantly in somatic cell hybrids of DRB-resistant and DRB-sensitive cell lines. In vivo treatment of CHO-K1 cells with DRB resulted in specific inhibition of endogenous RNA polymerase II activity in cell lysates. Whereas DRB inhibited RNA polymerase II activity in WTCHO cells by a maximum of 60% at concentrations as low as 60 microM, 300 microM DRB was required to inhibit 60% of the RNA polymerase II activity in DRB10 cells. However, the inhibition of the DRB-sensitive RNA polymerase II activity in DRB10 was biphasic. About half (53 to 56%) of this activity was inhibited by 90 microM DRB and thus showed a DRB sensitivity similar to the wild-type RNA polymerase II activity; the remaining DRB-sensitive RNA polymerase II activity was maximally inhibited by 300 microM DRB. These results indicated that there were two copies of the drbR locus (drb+ and drbR-10) in DRB10 and confirmed that the drbR-10 mutation was expressed codominantly. Somatic cell hybrids of DRB-resistant and alpha-amanitin-resistant cell lines grew in medium containing both DRB and alpha-amanitin, demonstrating that the drbR and amaR mutations were not in the same gene. Thus, the drbR mutations may define an additional component of the RNA polymerase II transcriptional complex in mammalian cells.
ChemInform Abstract: SYNTHESIS OF SODIUM AND TETRA‐N‐BUTYLAMMONIUM DICYANODIHYDROBORATE (1985)

Abstract Durch Cyanidaustausch der schwachen Base Anilin in (I) wird das stark hygroskopische (II) dargestellt.
ChemInform Abstract: ISOTHIAZOLO(5,4‐B)PYRIDINE ANALOGS OF NALIDIXIC ACID (1980)

Abstract Aus den Imino‐nitrilen (I) erhält man mit Schwefelwasserstoff die Thioamide (II), die zu den 5‐Amino‐isothiazolen (III) oxidativ cyclisiert werden.
Theoretical analysis of the microwave-drill near-field localized heating effect (2005)

The microwave-drill principle [Jerby et al., Science 298, 587 (2002)] is based on a localized hot-spot effect induced by a near-field coaxial applicator. The microwave drill melts the nonmetallic material locally and penetrates mechanically into it to shape the hole. This paper presents a theoretical analysis of the thermal-runaway effect induced in front of the microwave drill. The model couples the Maxwell’s and heat equations including the material’s temperature-dependent properties. A finite-difference time-domain algorithm is applied in a two-time-scale numerical model. The simulation is demonstrated for mullite, and benchmarked in simplified cases. The results show a temperature rise of ∼103K∕s up to 1300K within a hot spot confined to a ∼4-mm width (∼0.1 wavelength). The input-port response to this near-field effect is modeled by equivalent time-varying lumped-circuit elements. Besides the physical insight, this theoretical study provides computational tools for design and analysis of microwave drills and for their real-time monitoring and adaptive impedance matching.