gebhart/patrepeval huggingface dataset:
In situ Raman spectroscopy of silicon surfaces during SF6plasma etching (1994)

In situ Raman scattering spectroscopy is performed in order to probe the chemical dynamics and structure modifications at Ar and SF6 low-pressure plasma-etched silicon surfaces. An Ar plasma induces relatively slight perturbation of the silicon surface, while a SF6 plasma creates highly disordered overlayers induced by the fluorine atoms reacting at ion-induced defects. The overlayer structure is a mixing of an amorphous phase and 10 AA microcrystallites expected to be close to porous silicon structure.
Photolysis and Thermolysis of Bis(imino)pyridine Cobalt Azides: C−H Activation from Putative Cobalt Nitrido Complexes (2010)

A series of planar aryl-substituted bis(imino)pyridine cobalt azide complexes were prepared and evaluated as synthetic precursors for the corresponding cobalt nitrido compounds. Thermolysis or photolysis of two examples resulted in intramolecular C-H activation of the benzylic positions of the aryl substituents. For the mesityl-substituted compound, C-H activation by the putative nitride resulted in formation of a neutral imine ligand and modification of the chelate by hydrogen transfer to the imine carbon.
A Novel Video Text Extraction Approach Based on Multiple Frames (2006)

This paper describes a novel approach to detect and segment static superimposed texts by utilizing multiple video frame information. For text detection, multiple frames are used to verify the appearance of the text regions which have been detected on a single frame. In order to refine the text regions, text detection is performed again on a synthesized image, which is produced by minimum/maximum pixel search on consecutive frames. In text segmentation, we exploit edge feature to further remove complex background in addition to traditional gray-value integration. Experimental results demonstrate the effectiveness of the proposed method
Comparison of Voluntary Feed Intake and Venom Production of Wild and Laboratory Bred Sand Vipers (2001)

The study was performed on vipers of the Vipera ammodytes ammodytes species and aimed to establish the differences in voluntary feed intake and venom production between a group of wild, recently captured vipers and a group of born and bred captive vipers. In addition, the influence of sex on both parameters was established. The research brought evidence of important differences concerning voluntary food ingestion and venom production between the two groups of animals. However, sex appeared not to significantly influence these parameters, both in wild, recently captured vipers and in born and bred captive vipers. Wild animals rapidly accommodated to the microclimate conditions in captivity and readily accepted food.
EPR characterization of the mononuclear Cu‐containing Aspergillus japonicus quercetin 2,3‐dioxygenase reveals dramatic changes upon anaerobic binding of substrates (2002)

Quercetin 2,3-dioxygenase (2,3QD) is a copper-containing dioxygenase that catalyses the oxidation of the flavonol quercetin to 2-protocatechuoylphloroglucinol carboxylic acid with concomitant production of carbon monoxide. In contrast to iron dioxygenases, very little is known about copper dioxygenases. We have characterized 2,3QD from the fungus Aspergillus japonicus by electron paramagnetic resonance spectroscopy (EPR). At pH 6.0, 2,3QD shows a mixture of two EPR species. The major form has parameters typical of type 2 Cu sites (g// = 2.330, A// = 13.7 mT), the minor one has a more distorted geometry (g// = 2.290, A// = 12.5 mT). Anaerobic addition of the substrate quercetin results in a different, single species EPR spectrum with g// = 2.336, A// = 11.4 mT, parameters, which are in-between those of the type 2 and type 1 Cu sites in the Peisach-Blumberg (g// vs. A//) plot. After turnover, a new EPR signal is observed, which is ascribed to the carboxylic acid ester product complex. This spectrum is similar to that of the native enzyme at pH 10.0 and has g-tensor parameters suggesting a trigonal bipyramidal site. Of a variety of flavonoids studied, only flavonols are able to bind to the copper centre of 2,3QD. Nine flavonols with different hydroxylation patterns at the A- and B-ring have been analysed. They cluster in two different regions of the Peisach-Blumberg plot and show that the presence of a 5-OH group has a large effect on the A// parameter. Several differences are noted between A. japonicus 2,3QD and the enzyme from A. niger German Collection of Microorganisms 821.
Kinematic analysis of low dimensional structure in walking and running (2015)

Humans walk and run at various speeds by coordinating their whole-body movements skillfully, where they regulate the movements in accordance with the speed. However, it remains unclear what kinds of locomotion parameters they regulate and how to regulate the parameters. In the present study, to clarify the human strategy for regulating the whole-body movements in accordance with the speed, we measured human joint angles on sagittal plane during walking and running and analyzed the measured data by extracting low dimensional structure of the joint movements using singular value decomposition. Our results suggest a formation mechanism of human gaits, which contributes to elucidating the adaptation mechanism of human locomotion.
A large-Travel vertical planar actuator with improved stability (2004)

We report achieving 3.9 microns of planar analog vertical travel in a robust electrostatically actuated polysilicon mid-infrared programmable diffraction grating. Typically, achieving such large travel would require prohibitively large gaps and actuation voltages. In order to reduce the actuation voltage and achieve greater travel before pull-in, we use thin beams and exploit stress-stiffening. Thin beams create stress management hazards because tensile stress in one layer can induce buckling in a lower layer. The problem with induced buckling has been solved with detailed attention to supports and their compliance. To make the device more robust against pull-in, the design incorporates a multi-layer nonlinear spring.
Drivers for performance improvement originating from the Dutch drinking water benchmark (2016)

The Dutch drinking water sector has been benchmarked every 3 years since 1997, and the sector has significantly improved performance since then. Based on interviews with CEOs and financial managers of drinking water companies five drivers for improvement as a result of this benchmark are identified: ‘learning effect’, ‘enhanced transparency’, ‘managed competition’, ‘avoidance of negative consequences' and ‘personal honour of director’. Different developments have caused stagnation of further improvement: the variation on the benchmarked performance indicators has decreased, participation in the benchmark became mandatory for all Dutch drinking water supply organizations, it lacks a focus on the future, and participating organizations experience high financial pressure. These developments decrease the influence of the drivers. Four possible new impulses for the benchmark are identified and their influence on the effect of the drivers is analysed. The two most promising new impulses are to make the benchmark adaptive and to involve consumers in the process of benchmarking, both have a positive influence on the effect of almost all drivers. This study contributes to the understanding of how benchmarking leads to improvement and to the analysis of the impact of design choices, leading to well-founded decisions for re-design of the Dutch drinking water benchmark.
TaN metal gate MOSFETs with aggressively scaled HfO2 gate dielectrics (2003)

We have developed a robust and simple approach for integrating new materials in aggressively scaled MOSFETs. This incorporates the most important aspects of a commercially viable process and has been used to integrate both poly-Si and TaN metal gates together with HfO 2 gate dielectrics in an etched gate process. This has yielded sub-lOOnm gate length nMOSFETs with sub-1.2nm effective oxide thickness that appears to be stable even for junction activation anneals up to 1000 °C/ls. These results are compared with equivalent poly-Si HfO 2 nMOSFETs and it is shown that the replacement of poly-Si with metal not only eliminates the gate depletion effect but also improves the channel mobility, yields thinner EOTs, and appears to stabilize the dielectric-electrode interface.
Comparing Data Collection Alternatives: Amazon Mturk, College Students, And Secondary Data Analysis (2013)

An abstract of a study which compared the effectiveness of Amazon Mechanical Turk (mTurk), college students and secondary data sources in terms of demographic variables distribution, psychometric properties and testing relationships among variables is presented.
Basic principles of electrolyte chemistry for microfluidic electrokinetics. Part I: Acid–base equilibria and pH buffers (2009)

We review fundamental and applied acid-base equilibrium chemistry useful to microfluidic electrokinetics. We present elements of acid-base equilibrium reactions and derive rules for pH calculation for simple buffers. We also present a general formulation to calculate pH of more complex, arbitrary mixtures of electrolytes, and discuss the effects of ionic strength and temperature on pH calculation. More practically, we offer advice on buffer preparation and on buffer reporting. We also discuss "real world" buffers and likely contamination sources. In particular, we discuss the effects of atmospheric carbon dioxide on buffer systems, namely, the increase in ionic strength and acidification of typical electrokinetic device buffers. In Part II of this two-paper series, we discuss the coupling of acid-base equilibria with electrolyte dynamics and electrochemistry in typical microfluidic electrokinetic systems.
Bioaccumulation of metals by Hyalella azteca exposed to contaminated sediments from the upper clark fork river, montana (1994)

Abstract Macroinvertebrates contaminated with metals in the Clark Fork River of Montana have been demonstrated to be a potentially toxic component in the diet of trout Because sediment was the suspected source of metals to these invertebrates, bioaccumulation of As, Cd, Cu, Pb, and Zn from sediment was evaluated by exposing the amphipod Hyalella azteca for 28 d in the laboratory to samples of sediment collected from depositional areas of the Clark Fork River Benthic invertebrates collected from riffles adjacent to the depositional areas were also analyzed for metals The pattern of metal accumulation between laboratory-exposed and field-collected animals was similar, however, the concentrations of metals in laboratory exposed amphipods were often 50 to 75% less than were the concentrations of metals in the field collected invertebrates These findings indicate that sediment is a significant source of metals to invertebrates in the Clark Fork River Additional studies should be conducted to determine threshold concentrations for effects of dietary metals on fish Long-term monitoring of the river should include sampling benthic invertebrates for metal accumulation
Human and Bacterial Toll-Interleukin Receptor Domains Exhibit Distinct Dynamic Features and Functions (2022)

Toll-interleukin receptor (TIR) domains have emerged as critical players involved in innate immune signaling in humans but are also expressed as potential virulence factors within multiple pathogenic bacteria. However, there has been a shortage of structural studies aimed at elucidating atomic resolution details with respect to their interactions, potentially owing to their dynamic nature. Here, we used a combination of biophysical and biochemical studies to reveal the dynamic behavior and functional interactions of a panel of both bacterial TIR-containing proteins and mammalian receptor TIR domains. Regarding dynamics, all three bacterial TIR domains studied here exhibited an inherent exchange that led to severe resonance line-broadening, revealing their intrinsic dynamic nature on the intermediate NMR timescale. In contrast, the three mammalian TIR domains studied here exhibited a range in terms of their dynamic exchange that spans multiple timescales. Functionally, only the bacterial TIR domains were catalytic towards the cleavage of NAD<sup>+</sup>, despite the conservation of the catalytic nucleophile on human TIR domains. Our development of NMR-based catalytic assays allowed us to further identify differences in product formation for gram-positive versus gram-negative bacterial TIR domains. Differences in oligomeric interactions were also revealed, whereby bacterial TIR domains self-associated solely through their attached coil-coil domains, in contrast to the mammalian TIR domains that formed homodimers and heterodimers through reactive cysteines. Finally, we provide the first atomic-resolution studies of a bacterial coil-coil domain and provide the first atomic model of the TIR domain from a human anti-inflammatory IL-1R8 protein that undergoes a slow inherent exchange.
A Tactile Sensor Based on Computer Tomograph (2004)

In order to obtain a creative design solution, which is not obtained only with existing design knowledge, it is required to unify different knowledge groups, which exist independently, and to perform gradual extension of knowledge. Authors have proposed some knowledge representations and algorithms of knowledge integration for realizing knowledge extension with the aim of development of "Universal Abduction Studio", which supports creative design synthetically. In this paper, the fundamental framework for dealing with information as knowledge is proposed. And the representation and the knowledge integration based on it are proposed.
Transcription of Two Long Noncoding RNAs Mediates Mating-Type Control of Gametogenesis in Budding Yeast (2012)

The cell-fate decision leading to gametogenesis is essential for sexual reproduction. In S. cerevisiae, only diploid MATa/a but not haploid MATa orMATa cells undergo gametogenesis, known as sporulation. We find that transcription of two long noncoding RNAs (lncRNAs) mediates mating-type control of sporulation. In MATa orMATa haploids, expression of IME1, the central inducer of gametogenesis, is inhibited in cis by transcription of the lncRNA IRT1, located in the IME1 promoter. IRT1 transcription recruits the Set2 histone methyltransferase and the Set3 histone deacetylase complex to establish repressive chromatin at the IME1 promoter. Inhibiting expression of IRT1 and an antisense transcript that antagonizes the expression of the meiotic regulator IME4 allows cells expressing the haploid mating type to sporulate with kinetics that are indistinguishable from that of MATa/a diploids. Conversely, expression of the two lncRNAs abolishes sporulation in MATa/a diploids. Thus, transcription of two lncRNAs governs mating-type control of gametogenesis in yeast.
Novel SiGe Coherent Island Coarsening: Ostwald Ripening, Elastic Interactions, and Coalescence (1999)

Real-time measurements of island coarsening during SiGe/Si (001) deposition reveal unusual kinetics. In particular, the mean island volume increases superlinearly with time, while the areal density of islands decreases at a faster-than-linear rate. Neither observation is consistent with standard considerations of Ostvvald ripening. We attribute our observed kinetics to the effect of elastic interactions in the densely growing island array. Island coalescence likely plays an important role as well.
Irreversible Demagnetization Reduced Order Modeling in MnBi Interior Permanent Magnet Synchronous Motor Multi-Objective Optimization (2023)

Permanent magnet synchronous machines (PMSM) with neodymium iron boron (NdFeB) permanent magnets (PM) are typically used in applications, such as electric transportation, that require high power/torque density and efficiency. NdFeB is popular because of its exceptionally high remanent flux density ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$B_{r}$</tex> ) and high coercivity ( <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$H_{c}$</tex> ) at room temperature, but supply chain limitations of rare-earth elements (REE), such as neodymium (N d) and dysprosium (Dy), have recently caused significant REE price fluctuations. As a result, researchers are searching for ways to reduce or eliminate using NdFeB in PMSM designs. In the past, ferrite PMs were the next best option, but recently, manganese bismuth (MnBi) has emerged as another possible alternative to ferrites, with magnetic properties superior to ferrites but inferior to NdFeB at room temperature. MnBi is relatively new compared to commercial PMs and shows a unique trend of significantly increasing coercivity with increasing temperature. This makes rotor PMs significantly more susceptible to irreversible demagnetization at low temperatures. Reduced order models (ROMs), or meta-models, can estimate nonlinear machine phenomenon well enough for multi-objective optimization, but no literature has used this tool to characterize MnBi low temperature demagnetization. Furthermore, few sources explain how to work through the challenges of multi-objective optimization when using ROMs. Therefore, this paper presents a case study for limiting low temperature irreversible demagnetization in MnBi IPMSMs using ROMs and multi-objective optimization. The choices made and the tools available to produce a sufficiently accurate demagnetization ROM can be applied to a wide variety of nonlinear multiphysics phenomena.
Mycobacterial Membrane Vesicles Administered Systemically in Mice Induce a Protective Immune Response to Surface Compartments of Mycobacterium tuberculosis (2014)

This work offers a new vaccine approach against tuberculosis using mycobacterial MV. Mycobacterium MV are a naturally released product combining immunogenic antigens in the context of a lipid structure. The fact that MV do not need adjuvants and elicit protection comparable to that elicited by the BCG vaccine encourages vaccine approaches that combine protein antigens and lipids. Consequently, mycobacterium MV establish a new type of vaccine formulation.
CD103+ tumor-resident CD8+ T cell numbers underlie improved patient survival in oropharyngeal squamous cell carcinoma (2020)

Our results show that CD103+ tumor-resident CD8+ T cells are critical for protective immunity in both types of OPSCCs. Our data further suggest that the enhanced local protective immunity provided by tumor-resident T cell responses is the underlying factor driving favorable clinical outcomes in HPV+ OPSCCs over HPV- OPSCCs.
Mouse Adapted SARS-CoV-2 (MA10) Viral Infection Induces Neuroinflammation in Standard Laboratory Mice (2023)

Increasing evidence suggests that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection impacts neurological function both acutely and chronically, even in the absence of pronounced respiratory distress. Developing clinically relevant laboratory mouse models of the neuropathogenesis of SARS-CoV-2 infection is an important step toward elucidating the underlying mechanisms of SARS-CoV-2-induced neurological dysfunction. Although various transgenic models and viral delivery methods have been used to study the infection potential of SARS-CoV-2 in mice, the use of commonly available laboratory mice would facilitate the study of SARS-CoV-2 neuropathology. Herein we show neuroinflammatory profiles of immunologically intact mice, C57BL/6J and BALB/c, as well as immunodeficient (Rag2−/−) mice, to a mouse-adapted strain of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2 (MA10)). Our findings indicate that brain IL-6 levels are significantly higher in BALB/c male mice infected with SARS-CoV-2 MA10. Additionally, blood-brain barrier integrity, as measured by the vascular tight junction protein claudin-5, was reduced by SARS-CoV-2 MA10 infection in all three strains. Brain glial fibrillary acidic protein (GFAP) mRNA was also elevated in male C57BL/6J infected mice compared with the mock group. Lastly, immune-vascular effects of SARS-CoV-2 (MA10), as measured by H&E scores, demonstrate an increase in perivascular lymphocyte cuffing (PLC) at 30 days post-infection among infected female BALB/c mice with a significant increase in PLC over time only in SARS-CoV-2 MA10) infected mice. Our study is the first to demonstrate that SARS-CoV-2 (MA10) infection induces neuroinflammation in laboratory mice and could be used as a novel model to study SARS-CoV-2-mediated cerebrovascular pathology.
Amplification of the androgen receptor gene in bone metastases from hormone‐refractory prostate cancer (2002)

The aim of this study was to examine the prevalence of androgen receptor (AR) amplification in metastases to bone and other sites in patients with hormone-refractory prostate cancer (HRPC) and to compare these findings with those in pretreatment primary tumour samples from the same patients. Tissue from 24 patients with HRPC was available for study, together with 13 primary tumour specimens. AR gene amplification and copy number for X-chromosome were assessed by fluorescence in situ hybridization (FISH) using a SpectrumOrange-labelled probe at locus Xq11-13 for the AR gene and a SpectrumGreen-labelled alpha-satellite probe for the X-chromosome (Vysis, UK, Ltd.). A minimum of 20 nuclei were scored in each of three tumour areas by two independent observers. Samples from 18/24 patients with HRPC (12 bone marrow biopsies, three local tumour recurrences, and three lymph nodes) and nine primary tumour specimens were adequate for FISH analysis. Results were expressed as a mean ratio of AR gene copy number : mean X-chromosome number, with a ratio of greater than 1.5 defined as amplification. AR gene amplification was seen in 9/18 (50%) cases of HRPC and in none of the primary (untreated) tumour specimens (p = 0.0048, Fisher's exact test). For the 12 bone marrow samples, AR gene amplification occurred in 5/12 (38%) cases. Elevated copy number for chromosome X occurred in 3/18 (17%) HRPC and 4/9 (44%) matched primary tumours. This study shows for the first time that AR gene amplification can be demonstrated by FISH in bone metastases from HRPC patients. Because bone marrow biopsies can be obtained from most patients with HRPC, the findings provide a rational basis for the routine selection of patients who may respond more favourably to second-line anti-androgen therapy.
Layer-by-layer biofunctionalization of nanostructured porous silicon for high-sensitivity and high-selectivity label-free affinity biosensing (2018)

Nanostructured materials premise to revolutionize the label-free biosensing of analytes for clinical applications, leveraging the deeper interaction between materials and analytes with comparable size. However, when the characteristic dimension of the materials reduces to the nanoscale, the surface functionalization for the binding of bioreceptors becomes a complex issue that can affect the performance of label-free biosensors. Here we report on an effective and robust route for surface biofunctionalization of nanostructured materials based on the layer-by-layer (LbL) electrostatic nano-assembly of oppositely-charged polyelectrolytes, which are engineered with bioreceptors to enable label-free detection of target analytes. LbL biofunctionalization is demonstrated using nanostructured porous silicon (PSi) interferometers for affinity detection of streptavidin in saliva, through LbL nano-assembly of a bi-layer of positively-charged poly(allylamine hydrochloride) (PAH) and negatively-charged biotinylated poly(methacrylic acid) (b-PMAA). High sensitivity in streptavidin detection is achieved, with high selectivity and stability, down to a detection limit of 600 fM.