gebhart/patrepeval huggingface dataset:
Intra‐ and inter‐annual variability of nitrification in the rhizosphere of field‐grown bioenergy sorghum (2022)

Abstract Biological nitrification inhibition (BNI) and plant–microbe competition for ammonium (NH 4 + ) by sorghum ( Sorghum bicolor (L.) Moench) have the potential to suppress nitrification, reducing nitrate (NO 3 − ) and nitrous oxide (N 2 O) production for more sustainable bioenergy feedstock production. However, it is unknown how variability in environmental factors, field management, and plant growth affect the suppression of nitrification. We conducted a field trial with four genotypes of energy sorghum and four fertilization rates in central Illinois, USA, and measured soil N pools, potential nitrification and denitrification rates, and microbial community composition in bulk and rhizosphere soils to assess nitrification suppression throughout the 2018 and 2019 growing seasons. Concentrations of NO 3 − and NH 4 + were very low in rhizosphere soil regardless of fertilization level, suggesting strong N demand by plants and microbes. Potential nitrification was lower in the rhizosphere soil than bulk soil, and this suppression was strongest mid‐season ~2 months after planting in both years (20% suppression in 2018 and 58% in 2019). Since precipitation was lower during the mid‐growing season of 2019 compared to 2018, we speculate that hydrophilic BNI root exudates accumulated in the rhizosphere and suppressed nitrification more than in 2018 when soil moisture was higher. Unfertilized plots had greater nitrification suppression than fertilized plots during the mid‐season in 2018, but otherwise nitrification suppression was insensitive to fertilizer treatment. Potential denitrification was stimulated in the rhizosphere compared to bulk soil in both study years, suggesting that heterotrophic activity was stimulated by plant carbon inputs, possibly further suppressing slower‐growing chemoautotrophic nitrifying microbes. Overall, we found inter‐ and intra‐annual variation in nitrification suppression in the rhizosphere of field‐grown biomass sorghum, suggesting that plant phenology and environmental conditions should be considered when devising strategies to improve the nitrogen sustainability of this annual bioenergy crop.
A 3D-printed transepidermal microprojection array for human skin microbiome sampling (2022)

Skin microbiome sampling is currently performed with tools such as swabs and tape strips to collect microbes from the skin surface. However, these conventional approaches may be unable to detect microbes deeper in the epidermis or in epidermal invaginations. We describe a sampling tool with a depth component, a transepidermal microprojection array (MPA), which captures microbial biomass from both the epidermal surface and deeper skin layers. We leveraged the rapid customizability of 3D printing to enable systematic optimization of MPA for human skin sampling. Evaluation of sampling efficacy on human scalp revealed the optimized MPA was comparable in sensitivity to swab and superior to tape strip, especially for nonstandard skin surfaces. We observed differences in species diversity, with the MPA detecting clinically relevant fungi more often than other approaches. This work delivers a tool in the complex field of skin microbiome sampling to potentially address gaps in our understanding of its role in health and disease.
ENVIRONMENTAL IMPACT ASSESSMENT OF LOCAL STRUCTURAL GLUED LAMINATED TIMBER BASED ON FIELD SURVEY(Environmental Engineering) (2006)

Sustainable buildings with low environmental impact have attracted great social concern. The purpose of this research is to evaluate the environmental impact of a sustainable building which utilizes local timbers quantitatively with Life Cycle Assessment (LCA) method. In addition, the comparison of the environmental impact of local timbers use with imported timbers use is tried in this research. This research describes the outline of the environmental impact assessment of local structural glued laminated timbers based on field survey and the effect of environmental load reduction by the local timbers use.
Introduction to Bayesian Models: Normal Models (2008)

This chapter contains sections titled: General modeling principles Model specification in normal regression models Using vectors and multivariate priors in normal regression models Analysis of variance models Problems
Self‐Sorting Effects in the Self‐Assembly of Metallosupramolecular Rhombi from Chiral BINOL‐Derived Bis(pyridine) Ligands (2013)

Abstract Four BINOL‐based bis(4‐pyridyl) ligands were synthesised in enantiopure and racemic form. These ligands form metallosupramolecular [(dppp) 2 M 2 L 2 ] rhombi with cis ‐protected [(dppp)Pd] 2+ and [(dppp)Pt] 2+ ions. In principle, racemic ligands can self‐assemble into three stereoisomeric rhombi. The degree of self‐sorting in the self‐assembly process crucially depends on the substitution pattern and the resulting bend angle of the V‐shaped ligands as well as the degree of steric crowding within the assembly when racemic ligands are used. Thus, these processes either lead to homochiral assemblies in a narcissistic self‐recognition manner, to heterochiral assemblies in a social self‐discriminating manner, or proceed in a nonselective fashion as evidenced by NMR spectroscopy, mass spectrometry and single‐crystal X‐ray diffraction.
Interleukin 11 Reduces Apoptosis in UVB-Irradiated Mouse Skin (1999)

These findings suggest that IL-11 may play a role in the general homeostasis of the skin.
An experimental study on algorithms for drawing binary trees (2006)

In this paper we present the results of a comprehensive experimental study on the four most representative algorithms for drawing binary trees without distorting or occluding the information, one for each of the following distinct tree-drawing approaches: Separation-Based approach (Garg & Rusu 2003), Path-Based approach (Chan, Goodrich, Rao Kosaraju & Tamassia 2002), Level-Based approach (Reingold & Tilford 1981), and Ringed Circular Layout approach (Teoh & Ma 2002).Our study is conducted on randomly-generated, unbalanced, and AVL binary trees with up to 50,000 nodes, on Fibonacci trees with up to 46,367 nodes, on complete trees with up to 65,535 nodes, and on real-life molecular combinatory binary trees with up to 50,005 nodes. We compare the performance of the drawing algorithms with respect to five quality measures, namely Area, Aspect Ratio, Uniform Edge Length, Angular Resolution, and Farthest Leaf. None of the algorithms have been found to be the best in all categories.
Inner-Shell Photon-Ionized X-Ray Laser at 45(Angstrom) (2002)

This report summarizes the major accomplishments of this three-year Laboratory Directed Research and Development (LDRD) Lab Wide (LW) project entitled, ''An Inner-Shell Photo-Ionized X-Ray Laser at 45 {angstrom}'', tracking code 99-LW-042. The most significant accomplishments of this project include the design of a suitable x-ray laser target, the invention of a measurement technique for the determination of rise times of x-ray pulses on the order of 50 femtoseconds, and a novel setup for generating a traveling wave with an ultrashort optical laser pulse. The pump probe technique for rise time measurement will allow us to detect ultrashort x-ray pulses, whose generation by means of a variety of 4th generation light sources is currently under planning elsewhere.
Abstract 2450: Surface molecule CD229 represents a possible target for the treatment of multiple myeloma (2010)

Abstract BACKGROUND AND OBJECTIVES: The majority of patients with multiple myeloma (MM) will eventually relapse and succumb to their disease even after high dose chemotherapy and autologous stem cell transplantation, possibly due to the persistence of BM-residing myeloma stem cells. Therefore, new treatment strategies incorporating new therapeutic targets - ideally to be expressed by the bulk of end-stage myeloma cells and their dormant progenitors - are needed to improve the outcome of myeloma patients. DESIGN AND METHODS: We screened myeloma cell lines for the presence of a large number of immunoreceptors and verified expression of potential target molecules on cell lines and patient samples. The function of the respective proteins was evaluated using gene knockdown and their potential as targets for antibody therapies was investigated using in vitro cytotoxicity assays. RESULTS: Of all immunoreceptors analyzed, SLAM family member CD229 showed the strongest expression and was also found on myeloma precursors. Primary myeloma cells of myeloma patients uniformly evidenced CD229 surface expression while the molecule was absent from most healthy human tissues. Flow cytometric analysis of CD229 expression facilitated the detection of myeloma cells in the bone marrow. CD229 seemed to promote the survival of myeloma cells while CD229 silencing increased their susceptibility towards chemotherapy. Importantly, targeting CD229 with a monoclonal antibody resulted in specific lysis of the tumor cells. CONCLUSIONS: These results suggest that CD229 might represent an attractive diagnostic and therapeutic target for the treatment of MM. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2450.
Merging Electronics and Engineered Tissues (2012)

Three-dimensional tissue cultures embedded with flexible networks of transistors enable the spatially resolved sensing of cellular microenvironments.
On the separability of two mechanisms involved in the detection of grating patterns in humans. (1979)

1. The detectability of contrast modulation (M) of sinusoidal gratings was explored at the rate of 8 Hz. The luminance profile of a contrast modulated sinusoidal grating is L = L(1 + C cos 2 pi F chi). This stimulus may also be regarded as the sum of a steady grating pattern and counter phase flicker of the same spatial frequency. 2. Contrast modulation sensitivity (1/M) was established in five observers at several levels of constract and over a range of spatial frequencies, where M = delta C/C of delta C is the just detectable contrast change and C is the mean contrast of the grating. The slope of a modulation sensitivity function (C/delta C vs. C) is 1 (i.e. delta C = constant) near threshold contrast at each spatial frequency, but in the suprathreshold contrast range the slope flattens from close to 1 at 1.5 c/deg to almost 0 (delta C/C = constant) at 12 c/deg. 3. Adaptation to a high contrast steady grating of the same spatial frequency as the contrast modulated test gratings shifts each modulation sensitivity function to the right at low contrasts, but not at high. As a result the adapted curves cross their corresponding unadapted ones. At each spatial frequency the modulation sensitivity function is now fitted by a straight line of slope 1. While delta C needs to be higher than half the detection threshold of the same grating at spatial frequencies above 3 c/deg, in the adapted condition the values are nearly equal at each frequency. Thus pattern adaptation unmasks the threshold of the counterphase component of the contrast modulated grating near threshold contrast as well as above it. The phase of the steady adapting grating, relative to the steady component of the test grating, does not make any difference. 4. Apparently contrast modulation reveals differences beyond threshold sensitivity between spatial frequencies adjacent to the peak of the contrast sensitivity curve. For each spatial frequency channel there must be different neural coupling between steady and modulated inputs. Electrophysiological studies using contrast modulated gratings would be useful in the exploration of individual and ensemble properties of neurones of the visual cortex.
Analysis and Design of 3.3 kV IGBT Based Three-Level DC/DC Converter with High-Frequency Isolation and Current Doubler Rectifier (2009)

Analysis and Design of 3.3 kV IGBT Based Three-Level DC/DC Converter with High-Frequency Isolation and Current Doubler Rectifier The paper presents the findings of a R&amp;D project connected to the development of auxiliary power supply (APS) for the high-voltage DC-fed rolling stock applications. The aim was to design a new-generation power converter utilizing high-voltage IGBT modules, which can outpace the predecessors in terms of power density, i.e. to provide more power for smaller volumetric space. The topology proposed is 3.3 kV IGBT-based three-level neutral point clamped (NPC) half-bridge with high-frequency isolation transformer and current doubler rectifier that fulfils all the targets imposed by the designers. Despite an increased component count the proposed converter is very simple in design and operation. The paper provides an overview of the design with several recommendations and guidelines. Moreover, the simulation and experimental results are discussed and the performance evaluation of the proposed converter is presented.
“Write/Read/Erase” with Laser Irradiation of Dicyanoargentate(I) Doped and Pure Crystals (2003)

Laser irradiation of single crystals of doped Ag(CN)2-/KCl and pure KAg(CN)2 at 77 K results in dramatic changes in their emission spectra. Higher-energy bands that were either absent or weak start appearing concomitant with a quenching of the original major lower-energy bands as samples are exposed to 266 nm laser light. These changes are progressive with increased irradiation time and they are also reversible. Thus, when a given crystal is heated from 77 K to ambient temperature and then re-cooled to 77 K, hysteresis occurs as the original luminescence spectra before irradiation are obtained. Two doped Ag(CN)2-/KCl single crystals with Ag content of 1.21 and 2.23% (wt) as well as pure single crystals of KAg(CN)2 show this “write/read/erase” effect to various extents. By analyzing the luminescence profile versus exposure time to 266 nm laser irradiation at cryogenic temperatures, it was possible to calculate the rate constants for the forward (k1) and reverse (k2) reactions of the writing process. The fastest changes are for the 1.21% doped crystals (k1 = 0.04493 min-1), followed by the 2.23% doped crystals (k1 = 0.01245 min-1) while the slowest changes were for pure KAg(CN)2 (k1 = 0.00178 min-1). The results were explained in terms of a change in the distribution of *[Ag(CN)2-]n excitons with different geometries following laser irradiation.
Design and fabrication of polymer-based photonic crystals (2006)

Photonic have crystals shown promise in a variety of applications. Recently, there has been a great interest in designing and building three-dimensional (3D) photonic crystals whose fabrication can be integrated with standard CMOS processes. In this paper, we explore both of these areas in more detail. We first present techniques for modeling 3D photonic crystals and the analysis of practical lattice configurations. We then discuss our process for fabricating such structures built on standard lithography methods. We conclude by showing how these techniques have been used to design and build practical photonic crystal structures capable integration with CMOS circuitry.
Mg(OH)2@reduced graphene oxide composite for removal of dyes from water (2011)

The Mg(OH)2@reduced graphene oxide (rGO) composite (MGC) was synthesized via a chemical deposition method. Its mesoporous structures and application as an adsorbent for the removal of methylene blue (MB) from water were investigated. The Mg(OH)2 nanosheets were formed and dispersed homogeneously onto the surface of rGO sheets, which provided high surface area, pore volume, and uniform pore width distribution. MGC exhibited excellent adsorption behavior for MB.
A pilot study assessing the brain gauge as an indicator of cognitive recovery in alcohol dependence (2021)

We conclude it is possible that the prefrontal cortex (PFC) recovers more slowly compared to other brain areas, and there are compounding effects of improvements in anxiety and depression, and metacognitive deficits on subjective EF assessments. Future research should seek to validate the clinical utility of the BG by comparing against established neuroimaging methods.
Wireless Sensor Networks for Intelligent Transportation Systems (2009)

This paper presents a traffic monitoring system implemented through Wireless Sensor Network (WSN) technology within SAFESPOT Project funded by the European Community. The aim of this project is to provide a flexible, robust, low-cost and low-maintenance wireless solution for obtaining traffic-related data that can be used for automatically generating safety warnings at black spots along the road network. The WSN consists of one Gateway Node (GN) and n Sensor Nodes (SNs) deployed along the roadside according to an approximately linear topology. Each SN is able to monitor a section of road, collecting parameters such as vehicle count, speed and direction. Data from the SNs is collected by the GN and delivered to a Road Side Unit (RSU) responsible for fusing it with traffic-related data generated by alternative sources. The system has been tested and performance evaluated under a number of real use-case scenarios.
Near‐surface circulation and tidal currents of the Okhotsk Sea observed with satellite‐tracked drifters (2002)

Near‐surface circulation of the Okhotsk Sea was observed with ARGOS drifters from August 1999 to February 2000. The drifters clearly revealed the existence of the southward boundary current (the East Sakhalin Current) off the east Sakhalin. This current is strongly controlled by bottom topography and confined to the region shallower than 1000 m. The volume transport of this current is estimated to be in the range of 4–9 Sv (1 Sv = 10 6 m 3 s −1 ), with the increase from summer to winter. The current appears to consist of two cores: one exists near the coast (50–150 m depths) with typical speeds of 0.3–0.4 m s −1 and the other exists over the shelf slope (300–900 m depths) with typical speeds of 0.2–0.3 m s −1 . A part of this southward current continues as far as the southern tip of Sakhalin Island, while another part turns to the east around Terpeniya Bay (∼48°N) flowing eastward as far as Bussol' Strait. Most of the drifters that survived in the Okhotsk Sea went out to the Pacific through Bussol' Strait by less than a half year, suggesting that Bussol' Strait is the main pathway for the surface water to flow out from the Okhotsk Sea. Mesoscale anticyclonic eddies with diameters of 100–200 km are dominant in the Kuril Basin. Diurnal shelf waves were identified over the shelf in the northern part of the east Sakhalin shelf. Large amplification of diurnal tidal currents (order of 1.0 m s −1 ) was observed over Kashevarov Bank along with the residual anticyclonic circulation. Both diurnal and semidiurnal tidal currents were found to be enhanced in and around Bussol' Strait.
Optical metrology of micro- and nanostructures at PTB: status and future developments (2008)

Today, various types of high resolution dimensional metrology instrumentation are in use for a quantitative characterisation of micro- and nanostructures. Although sophisticated ultra high resolution microscopic techniques like SEM and AFM are available, optical methods like microscopy and scatterometry are still of interest and are important because they are non-destructive, fast and have a good in-line capability. At PTB different optical tools are used for high-resolution metrology. Our standard instrument for CD metrology is a special UV transmission microscope. A new 193nm microscope is currently under development which will meet future requirements at least for the 32nm node as specified in the ITRS roadmap. A special alternating grazing incidence dark field microscope is used to measure the width of single features down to 100nm. For grating structures, we developed an optical diffractometer for pitch calibrations with an uncertainty down to 10 pm. Recently we realised a DUV scatterometer and ellipsometer capable to measure accurately CD, edge profile, layer thickness, and optical parameters. A versatile EUV scatterometer can be used to characterise absorber structures e. g. on EUV photomasks. For accurate measurements a thorough modelling on the basis of rigorous diffraction calculation is essential, which accounts for both polarisation effects and the 3D geometry of the structures. We use the rigorous coupled wave analysis (RCWA) method and the finite elements (FEM) method. We present an overview of PTB's current and future activities in optical high-resolution metrology and how these systems compare to ultra-high resolution microscopy like SEM or AFM.
Impact of H216 on the DNA Binding and Catalytic Activities of the HIV Restriction Factor APOBEC3G (2013)

APOBEC3G has an important role in human defense against retroviral pathogens, including HIV-1. Its single-stranded DNA cytosine deaminase activity, located in its C-terminal domain (A3Gctd), can mutate viral cDNA and restrict infectivity. We used time-resolved nuclear magnetic resonance (NMR) spectroscopy to determine kinetic parameters of A3Gctd's deamination reactions within a 5'-CCC hot spot sequence. A3Gctd exhibited a 45-fold preference for 5'-CCC substrate over 5'-CCU substrate, which explains why A3G displays almost no processivity within a 5'-CCC motif. In addition, A3Gctd's shortest substrate sequence was found to be a pentanucleotide containing 5'-CCC flanked on both sides by a single nucleotide. A3Gctd as well as full-length A3G showed peak deamination velocities at pH 5.5. We found that H216 is responsible for this pH dependence, suggesting that protonation of H216 could play a key role in substrate binding. Protonation of H216 appeared important for HIV-1 restriction activity as well, since substitutions of H216 resulted in lower restriction in vivo.
Rapid Assessment of Viability and Function of Human Hepatocytes for Possible Transplantation (2012)

Hepatocyte transplantation is an alternative to liver transplantation in the management of some liver-based diseases. Regulatory authorities require testing of quality and function of cells prior to transplantation. However, traditional functional assays can take several days to perform and analyze so that the data from these assays may not be available to assess hepatic function prior to the transplant procedure. We have adapted 10 assays that can be completed within 2 hours of isolation that test a wide range of hepatic functions. Long-term survival and function of the hepatocytes in culture was assessed by analyzing the same metabolic functions after 5 days of in vitro culture. Hepatocytes from up to 75 isolations, from 33 organ donors and 42 liver resection specimens were evaluated for viability (trypan blue exclusion), mitochondrial function and apoptosis, plating efficiency, ammonia metabolism and the phase I and II drug metabolism. Cytochromes P450 (CYP) 1A, 2C9, and 3A activities were also analyzed after a 3 day exposures to prototypical inducing agents with luminescent/fluorescent assays. The initial viability, plating efficiency and metabolic activities measured in the short-term assays is highly predictive of long-term viability and function. The results of these 75 cases have established a normal range for each of the assays. While no single assay should be used to identify or eliminate a cell preparation from being considered for a possible transplant, cells that showed activities 20% of the average value on more than 2 assays were found to have the lowest viability, plating efficiencies and over all long-term function. A panel of assays has been adapted to analyze several distinct hepatic functions. The assays are simple, reproducible and can be completed within 2 hours of cell isolation with common laboratory equipment. The results of these assays demonstrate hepatic function and can be obtained in real-time, to provide data with which to accept or eliminate a particular cell isolation for consideration for transplantation.