gebhart/patrepeval huggingface dataset:
Enhanced mass sensitivity of stress-free, silicon nanowire-grown microcantilever sensors (2007)

A thin catalytic layer of nickel was evaporated onto one side of silicon microcantilevers and amorphous silicon nanowires were synthesized on the nickel surface. When nanowire-grown cantilevers were exposed to mercaptohexanol vapor, their mass sensitivity was almost two orders of magnitude greater than that of the corresponding plain cantilever due to the increase in surface area afforded by the nanowires, whereas adsorption of mercaptohexanol induced negligible deflection of the nanowire-grown cantilevers. This indicates that the gold-coated nanowire-grown cantilever can be used as a sensitive, stress-free sensor whose spring constant is not affected by the adsorption of alkanethiols.
Correlation of polymorphic variation in the promoter region of the interleukin‐1β gene with secretion of interleukin‐1β protein (2004)

These data suggest that polymorphisms within the promoter region of the IL1B gene contribute to observed differences in LPS-induced IL-1 beta protein secretion.
Malonyl-CoA Signaling, Lipid Partitioning, and Glucolipotoxicity (2002)

Beta-cells possess inherent mechanisms to adapt to overnutrition and the prevailing concentrations of glucose, fatty acids, and other fuels to maintain glucose homeostasis. However, this is balanced by potentially harmful actions of the same nutrients. Both glucose and fatty acids may cause good/adaptive or evil/toxic actions on the beta-cell, depending on their concentrations and the time during which they are elevated. Chronic high glucose dramatically influences beta-cell lipid metabolism via substrate availability, changes in the activity and expression of enzymes of glucose and lipid metabolism, and modifications in the expression level of key transcription factors. We discuss here the emerging view that beta-cell "glucotoxicity" is in part indirectly caused by "lipotoxicity," and that beta-cell abnormalities will become particularly apparent when both glucose and circulating fatty acids are high. We support the concept that elevated glucose and fatty acids synergize in causing toxicity in islets and other organs, a process that may be instrumental in the pleiotropic defects associated with the metabolic syndrome and type 1 and type 2 diabetes. The mechanisms by which hyperglycemia and hyperlipidemia alter insulin secretion are discussed and a model of beta-cell "glucolipotoxicity" that implicates alterations in beta-cell malonyl-CoA concentrations; peroxisome proliferator-activated receptor-alpha and -gamma and sterol regulatory element binding protein-1c expression; and lipid partitioning is proposed.
Development of Novel G-Protein-Coupled Receptor 54 Agonists with Resistance to Degradation by Matrix Metalloproteinase (2008)

Kisspeptin-GPR54 signaling is involved in the suppression of cancer metastasis and regulation of hormonal secretion. Recently, matrix metalloproteinase mediated deactivation of kisspeptins through hydrolysis of the Gly-Leu peptide bond has been reported. In the present report, GPR54 agonistic peptides having several nonhydrolyzable Gly-Leu dipeptide isosteres were designed and synthesized. (E)-Alkene- and hydroxyethylene-type isostere-containing analogues maintained the original activity with higher stability in murine serum and resistance to MMP-9-mediated cleavage.
Chiral 3D Photonic Crystals as Compact Optical Isolators (2007)

We present a novel photonic heterostructure based on chiral 3D photonic crystals allowing for non-reciprocal transmission of light. We fabricate various corresponding structures by means of direct laser writing.
Enhancement of pomalidomide anti-tumor response with ACY-241, a selective HDAC6 inhibitor (2017)

Thalidomide-based Immunomodulatory Drugs (IMiDs®), including lenalidomide and pomalidomide, are effective therapeutics for multiple myeloma. These agents have been approved with, or are under clinical development with, other targeted therapies including proteasome inhibitors, αCD38 monoclonal antibodies, as well as histone deacetylase (HDAC) inhibitors for combination therapy. HDAC inhibitors broadly targeting Class I and IIb HDACs have shown potent preclinical efficacy but have frequently demonstrated an undesirable safety profile in combination therapy approaches in clinical studies. Therefore, development of more selective HDAC inhibitors could provide enhanced efficacy with reduced side effects in combination with IMiDs® for the treatment of B-cell malignancies, including multiple myeloma. Here, the second generation selective HDAC6 inhibitor citarinostat (ACY-241), with a more favorable safety profile than non-selective pan-HDAC inhibitors, is shown to synergize with pomalidomide in in vitro assays through promoting greater apoptosis and cell cycle arrest. Furthermore, utilizing a multiple myeloma in vivo murine xenograft model, combination treatment with pomalidomide and ACY-241 leads to increased tumor growth inhibition. At the molecular level, combination treatment with ACY-241 and pomalidomide leads to greater suppression of the pro-survival factors survivin, Myc, and IRF4. The results presented here demonstrate synergy between pomalidomide and ACY-241 in both in vitro and in vivo preclinical models, providing further impetus for clinical development of ACY-241 for use in combination with IMiDs for patients with multiple myeloma and potentially other B-cell malignancies.
Value of neonicotinoid seed treatments to <scp>US</scp> soybean farmers (2016)

These estimates using different data and methods are consistent and suggest the value of insecticide seed treatments to the US soybean farmers who used them in 2013 was around $US 28-42 ha<sup>-1</sup> treated, net of seed treatment costs. © 2016 Society of Chemical Industry.
Review of optical tweezers in vacuum (2019)

As a versatile tool for trapping and manipulating neutral particles, optical tweezers have been studied in a broad range of fields such as molecular biology, nanotechnology, and experimentally physics since Arthur Ashkin pioneered the field in the early 1970s. By levitating the “sensor” with a laser beam instead of adhering it to solid components, excellent environmental decoupling is achieved. Furthermore, unlike levitating particles in liquid or air, optical tweezers operating in vacuum are isolated from environmental thermal noise, thus eliminating the primary source of dissipation present for most inertial sensors. This attracted great attention in both fundamental and applied physics. In this paper we review the history and the basic concepts of optical tweezers in vacuum and provide an overall understanding of the field.
Reevaluation of the growth-permissive substrate properties of goldfish optic nerve myelin and myelin proteins (1995)

To determine whether optic nerve myelin of goldfish carries mammalian-like neurite growth inhibitory proteins which can be neutralized by the antibody IN-1, myelin fractions of fish optic nerves were used as substrates for fish retinal ganglion cell axons and rat dorsal root ganglia (DRG). Axonal growth was monitored and compared with that of IN-1 treated preparations. Growth of fish retinal axons and rat DRG neurites was substantial on goldfish optic nerve myelin and no improvement was observed with IN-1. In contrast, rat CNS myelin allowed only poor growth, and number of axons and length of DRG neurites increased significantly with IN-1. In addition, proteins of fish optic nerve myelin and bovine CNS myelin were extracted, reconstituted in liposomes and applied to growth cones. When goldfish myelin proteins in liposomes were seeded onto growth cones, 77% of fish and 89% of rat DRG growth cones continued to elongate, and the proportion of elongating fish growth cones (80%) did not significantly change when liposomes were pretreated with IN-1. But 73% of fish and 93% of rat growth cones collapsed with liposomes containing proteins from bovine CNS myelin. Upon IN-1 treatment, only 24% of fish growth cones collapsed. Thus, axon growth in vitro indicates that goldfish optic nerves, which permit successful axon regeneration in vivo, lack mammalian-like neurite growth inhibitors which are neutralized by IN-1.
ChemInform Abstract: Oxidative Conversion of N,N‐Dimethylhydrazones Derived from Aliphatic and Heteroaromatic Aldehydes into Nitriles with Hydrogen Peroxide or 3‐ Chloroperoxybenzoic Acid. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Venous-arterial PCO2 and pH gradients in acutely ill postsurgical patients. (1995)

This study suggests that in acutely ill postoperative patients increased venous-arterial PCO2 and pH gradients are directly and principally related to the reduction in blood flow and are both suggestive of low-flow state.
Central pyrogenic activity of muramyl dipeptide. (1980)

Fever can be elicited in the rabbit by the intravenous administration of relatively large doses of a synthetic immunoadjuvant, N-acetylmuramyl-L-alanyl-D-isoglutamine, or muramyl dipeptide (MDP). This response could be mediated by endogenous pyrogen because MDP has been shown to induce their production both in vivo and in vitro. The results reported here show that intracisternal injection of minute amounts of MDP could elevate fever without activating the release of endogenous pyrogen in the plasma or in the cerebrospinal fluid. Moreover, indomethacin inhibited hyperthermia produced by intracerebroventricular administration of MDP. Therefore, our findings argue in favor of a direct effect of the glycopeptide on the thermoregulatory centers besides its indirect effect through the production of leukocytic pyrogen. This molecule apparently represents the minimal requirement for the pyrogenicity of bacterial peptidoglycan because administration, even by the intracerebral route, of a mixture of muramic acid and of its dipeptide moiety did not elicit fever.
Numerical Modeling of a Deep, Fixed Bed Combustor (1996)

A computational model to evaluate the anticipated performance characteristics of a deep, fixed bed combustor/gasifier utilizing whole trees as the source of fuel is presented. This combustor/gasifier is the heat source for a proposed steam-driven electric power plant utilizing whole trees as the source of fuel. In the simulation model presented, hardwood logs 20 cm in diameter are burned in a 3.7 m deep fuel bed. Solid and gas velocity and CO, CO2, H2O, hydrocarbon, and O2 profiles are calculated. This deep bed combustor obtains high energy release rates per unit area due to the high inlet air velocity and extended reaction zone. The lowest portion of the overall bed is an oxidizing region and the remainder of the bed acts as a gasification and drying region. The overfire air region completes the combustion. Approximately 40% of the energy is released in the lower oxidizing region. The wood consumption rate obtained from the computational model is compared with test results obtained from full scale testing. The wood consumption rate predicted by the model is 2630 kg/(m2 h) which matches well the consumption rate of 2670 kg/(m2 h) observed during the 2 h test period of the field test. This corresponds to a heat release rate of 9.6 MW/m2. The model is used to investigate the performance of the combustor under a variety of load conditions, fuel sizes, and moisture conditions.
The Wolfe cycle comes full circle (2012)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Stabilization of metastable phases in hafnia owing to surface energy effects (2016)

The recent empirical observation of ferroelectricity in hafnia is rather surprising since all of its known ground-state phases are nonpolar. In this letter, we show that finite size effects, relevant under experimental conditions, may themselves lead to this unexpected phenomenon due to stabilization of metastable polar phase(s). Using surface energies computed from first principles, we determine the thermodynamic stability of a parallelepiped shaped particle constructed from various low energy nonpolar and polar phases of hafnia. We find that at small dimensions, surface effects may stabilize either one of the polar phases or the nonpolar tetragonal phase (the parent phase of the polar phases), suggesting a possible explanation of the ferroelectric behavior observed in pure hafnia films. These results also explain the stabilization of the metastable tetragonal phase in nanoparticles of zirconia, the twin oxide of hafnia. While a comprehensive understanding of the origins of ferroelectricity in hafnia will require inclusion of other relevant factors (such as strain and dopants), this work highlights the importance of finite size effects as a possible key factor.
Genome-wide discovery of human splicing branchpoints (2015)

During the splicing reaction, the 5' intron end is joined to the branchpoint nucleotide, selecting the next exon to incorporate into the mature RNA and forming an intron lariat, which is excised. Despite a critical role in gene splicing, the locations and features of human splicing branchpoints are largely unknown. We use exoribonuclease digestion and targeted RNA-sequencing to enrich for sequences that traverse the lariat junction and, by split and inverted alignment, reveal the branchpoint. We identify 59,359 high-confidence human branchpoints in >10,000 genes, providing a first map of splicing branchpoints in the human genome. Branchpoints are predominantly adenosine, highly conserved, and closely distributed to the 3' splice site. Analysis of human branchpoints reveals numerous novel features, including distinct features of branchpoints for alternatively spliced exons and a family of conserved sequence motifs overlapping branchpoints we term B-boxes, which exhibit maximal nucleotide diversity while maintaining interactions with the keto-rich U2 snRNA. Different B-box motifs exhibit divergent usage in vertebrate lineages and associate with other splicing elements and distinct intron-exon architectures, suggesting integration within a broader regulatory splicing code. Lastly, although branchpoints are refractory to common mutational processes and genetic variation, mutations occurring at branchpoint nucleotides are enriched for disease associations.
The feasibility of analysing food consumption combinations from overweight and obese participants of weight loss clinical trials (2016)

Overweight and obesity is a global epidemic. Investigating food consumption combinations (FCCs) may offer useful insights into addressing eating behaviours to manage overweight and obesity. Using food intake data generated from a detailed dietary assessment method allows advanced analytical methods to be employed. Food intake data collected by a diet history interview appears to be more precise in terms of capturing the usual food intakes of individuals. Exploration of FCCs can be conducted using the Apriori algorithm, but this method is dependent on correct data preparation. Given the uncertainties related to collecting food intake data via diet history interviews, the aim of this study was to explore the feasibility of using food intake data derived from diet history interviews from three weight-loss clinical trials to investigate FCCs. A 10% random sample (n=62) of baseline paper-based diet history records, reflecting usual food intake by meal, from three registered clinical trials (n=617) were extracted. FCCs were assessed by considering the sum of single food items consumed at the same time or in the same occasion using the United States Department of Agriculture Food Combination Codes and the nested hierarchical food groups of the 2011-13 Australian Health Survey food classification system. FCCs were identified in all diet history data records at the major food group level. A proportion of FCCs for the dinner meal (n=13) were unable to be assessed at the specific food level due to limited detail for meat-containing FCCs. FCCs for the dinner meal created more challenges for accurately distinguishing and naming FCCs. Given the complexity of beverage reporting, combinations of foods and beverages were not revealed in the selected data set. In conclusion, despite a lack of meat-containing FCCs at dinner and food-beverage combinations, the food intake data collected using the diet history interview method can feasibly be used to investigate FCCs.
DNA-Damage-Induced Type I Interferon Promotes Senescence and Inhibits Stem Cell Function (2015)

Expression of type I interferons (IFNs) can be induced by DNA-damaging agents, but the mechanisms and significance of this regulation are not completely understood. We found that the transcription factor IRF3, activated in an ATM-IKKα/β-dependent manner, stimulates cell-autonomous IFN-β expression in response to double-stranded DNA breaks. Cells and tissues with accumulating DNA damage produce endogenous IFN-β and stimulate IFN signaling in vitro and in vivo. In turn, IFN acts to amplify DNA-damage responses, activate the p53 pathway, promote senescence, and inhibit stem cell function in response to telomere shortening. Inactivation of the IFN pathway abrogates the development of diverse progeric phenotypes and extends the lifespan of Terc knockout mice. These data identify DNA-damage-response-induced IFN signaling as a critical mechanism that links accumulating DNA damage with senescence and premature aging.
Terrestrial laser scanning - a supplementary approach for 3D documentation and animation (2005)

While aerial methods undesputedly form the backbone of modern photogrammetry, we have seen an increased use of terrestrial methods in the past years to supplement aerial data especially in the field of 3D city modelling and the animation thereof. This article describes an approach to use terrestrial laser scanning in order to increase detail and realism of datasets derived from arial methods. When devising a new strategy for the integration of data from multiple sources two aspects come to focus. For one methods for the registration of the datasets are needed. Secondly a suitable data model has to be introduced to hold multiple aspects of the data. Consequently we present our methods for the automatted georeferencing of terrestrial laser data and we introduce the concept of LASERMAPs, which are extracted from terrestrial laser data and mapped onto the 3D building model.
Degradation of plastics and plastic-degrading bacteria in cold marine habitats (2018)

Synthetic plastics present in everyday materials constitute the main anthropogenic debris entering the Earth’s oceans. The oceans provide important and valuable resources such as food, energy, and water. They are also the main way of international trade and the main stabilizer of the climate. Hence, changes in the marine ecosystem caused by anthropogenic influences such as plastic pollution can have a dramatic impact on a global scale. Although the problem of plastics still remains unsolved, different ways are being considered to reduce their impact on the environment. One of them is to use microorganisms capable of degradation of plastic. A particularly interesting area is the application of microorganisms isolated from cold regions in view of their unique characteristics. Nevertheless, the interactions between plastic and microorganisms are still poorly known. Here, we present a review of current knowledge on plastic degradation and plastic-microorganism interactions in cold marine habitats. Moreover, we highlight the advantages of microorganisms isolated from this environment for eliminating plastic waste from ecosystems.
Polymorphisms in drug-resistant-related genes shared among drug-resistant and pan-susceptible strains of sequence type 10, Beijing family of Mycobacterium tuberculosis (2015)

Mutations in genes involved in drug metabolism have been well-associated with drug resistance. Sequence analysis of known antimycobacterial drug-resistant genes is often used to predict resistance to antibiotics. However, some polymorphisms in such genes may serve a phylogenetic purpose rather than resistance to drugs. The Beijing family of Mycobacterium tuberculosis (MTB) is prevalent worldwide and has been associated with the emergence of multidrug resistance. Sequence type (ST) 10 of the Beijing family is the most predominant in countries like Peru, Taiwan and Thailand. A sequence analysis was performed of 81 previously reported drug-resistant associated genes in multidrug-resistant and pan-susceptible strains of the Beijing family sequence type 10 of MTB. This analysis revealed 10 synonymous and 12 nonsynonymous single nucleotide polymorphisms (SNPs) that are shared by all strains under study. One frameshift mutation was also observed to be common to all. These data might be useful in excluding some observed SNPs in drug-resistant-associated genes of MTB Beijing ST 10 when performing genotypic drug susceptibility assay.
Optimization of partial-state feedback for vibratory energy harvesters subjected to broadband stochastic disturbances (2011)

In many applications of vibratory energy harvesting, the external disturbance is most appropriately modeled as a broadband stochastic process. Optimization of the average power generated from such disturbances is a feedback control problem, and solvable via LQG (linear–quadratic–Gaussian) control theory. Implementing the optimal feedback controller requires a power electronic drive capable of two-way power flow, which can impose dynamic relationships between the voltage and current of the transducer. Determining the optimal energy harvesting current control is accomplished by solving a nonstandard Riccati equation. In this paper we show that appropriate tuning of the passive parameters in the harvesting system results in a decoupled solution to the Riccati equation and a corresponding controller that only requires half of the states for feedback. However, even when such tuning methods are not used and the solution to the Riccati equation does not decouple, it is possible to determine the states in the feedback law that contribute the most to the average power generated by the harvester. As such, partial-state feedback gains can be optimized using a gradient descent method. Two energy harvesting examples are presented, including a single-degree-of-freedom oscillator with an electromagnetic actuator and a piezoelectric bimorph cantilever beam, to demonstrate these concepts.