gebhart/patrepeval huggingface dataset:
A Data-Driven Approach to Partitioning Net Ecosystem Exchange Using a Deep State Space Model (2021)

Describing ecosystem carbon fluxes is essential for deepening the understanding of the Earth system. However, partitioning net ecosystem exchange (NEE), i.e. the sum of ecosystem respiration (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eco</sub> ) and gross primary production (GPP), into these summands is ill-posed since there can be infinitely many mathematically-valid solutions. We propose a novel data-driven approach to NEE partitioning using a deep state space model which combines the interpretability and uncertainty analysis of state space models with the ability of recurrent neural networks to learn the complex functions governing the data. We validate our proposed approach on the FLUXNET dataset. We suggest using both the past and the future of R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eco</sub> 's predictors for training along with the nighttime NEE (NEE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">night</sub> ) to learn a dynamical model of R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eco</sub> . We evaluate our nighttime R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eco</sub> forecasts by comparing them to the ground truth NEE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">night</sub> and obtain the best accuracy with respect to other partitioning methods. The learned nighttime R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eco</sub> model is then used to forecast the daytime R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eco</sub> conditioning on the future observations of different predictors, i.e., global radiation, air temperature, precipitation, vapor pressure deficit, and daytime NEE (NEE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">day</sub> ). Subtracted from the NEE <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">day</sub> , these estimates yield the GPP, finalizing the partitioning. Our purely data-driven daytime R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eco</sub> forecasts are in line with the recent empirical partitioning studies reporting lower daytime R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eco</sub> than the Reichstein method, which can be attributed to the Kok effect, i.e., the plant respiration being higher at night. We conclude that our approach is a good alternative for data-driven NEE partitioning and complements other partitioning methods.
Disulfide-Linked Oligomerization of Basic Fibroblast Growth Factor (1994)

Heparin, sulfate ion, and a number of polysulfated saccharides enhance the stability of bFGF against thermal denaturation. To assess the potential enhancement of bFGF shelf life, solution formulations containing these excipients were incubated at 35°C and analyzed by heparin affinity HPLC for soluble protein content as well as monomer/multimer distribution. Loss of soluble protein due to precipitation was seen in all formulations. Fluorescence spectroscopy was used to show that the precipitates without added ligands were made up of unfolded protein, consistent with the requirement for chaotropes to solubilize them. In the presence of sulfated compounds, however, the precipitates dissociated by 1 MNaCl and were enriched in disulfide-linked multimers with native tertiary structure. Disulfide-linked multimers also appeared in solution, at ~2-fold greater amount in the presence than the absence of sulfated compounds. In buffer alone, multimers dissociated to unfolded monomers via spontaneous thiol-disulfide exchange, resulting in aggregation and precipitation. Heparin which increased structural stability of bFGF, prevented disulfide interchange and indirectly promoted multimerization; beyond a threshold multimer concentration in solution, the multimers precipitated with the sulfated compounds. Thus, despite stabilization of native bFGF structure by sulfated compounds, loss of soluble monomer was unabated.
Clustering rare diseases within an ontology-enriched knowledge graph (2023)

Our study lays out a method for clustering rare diseases using the graph node embeddings. We develop an easy to maintain pipeline that can be updated when new data on rare diseases emerges. The embeddings themselves can be paired with other representation learning methods for other data types, such as drugs, to address other predictive modeling problems. Detailed subnetwork analysis and in-depth review of individual clusters may lead to translatable findings. Future work will focus on incorporation of additional data sources, with a particular focus on common disease data.
Expression of surfactant protein D in airways of asthmatics and interleukin-13 modulation of surfactant protein D in human models of airway epithelium (2015)

SP-D is expressed differently in airways of asthmatics relative to that of non-asthmatics. This can have implications on the increased susceptibility to infections and altered inflammatory response in asthmatic patients. Future functional studies on the role of SP-D in asthma can provide better insight into defects in the structure and regulation of SP-D.
Performance evaluation of iterative reconstruction algorithms for achieving CT radiation dose reduction — a phantom study (2016)

The purpose of this study was to characterize image quality and dose performance with GE CT iterative reconstruction techniques, adaptive statistical iterative recontruction (ASiR), and model-based iterative reconstruction (MBIR), over a range of typical to low-dose intervals using the Catphan 600 and the anthropomorphic Kyoto Kagaku abdomen phantoms. The scope of the project was to quantitatively describe the advantages and limitations of these approaches. The Catphan 600 phantom, supplemented with a fat-equivalent oval ring, was scanned using a GE Discovery HD750 scanner at 120 kVp, 0.8 s rotation time, and pitch factors of 0.516, 0.984, and 1.375. The mA was selected for each pitch factor to achieve CTDIvol values of 24, 18, 12, 6, 3, 2, and 1 mGy. Images were reconstructed at 2.5 mm thickness with filtered back-projection (FBP); 20%, 40%, and 70% ASiR; and MBIR. The potential for dose reduction and low-contrast detectability were evaluated from noise and contrast-to-noise ratio (CNR) measurements in the CTP 404 module of the Catphan. Hounsfield units (HUs) of several materials were evaluated from the cylinder inserts in the CTP 404 module, and the modulation transfer function (MTF) was calculated from the air insert. The results were con-firmed in the anthropomorphic Kyoto Kagaku abdomen phantom at 6, 3, 2, and 1mGy. MBIR reduced noise levels five-fold and increased CNR by a factor of five compared to FBP below 6mGy CTDIvol, resulting in a substantial improvement in image quality. Compared to ASiR and FBP, HU in images reconstructed with MBIR were consistently lower, and this discrepancy was reversed by higher pitch factors in some materials. MBIR improved the conspicuity of the high-contrast spatial resolution bar pattern, and MTF quantification confirmed the superior spatial resolution performance of MBIR versus FBP and ASiR at higher dose levels. While ASiR and FBP were relatively insensitive to changes in dose and pitch, the spatial resolution for MBIR improved with increasing dose and pitch. Unlike FBP, MBIR and ASiR may have the potential for patient imaging at around 1 mGy CTDIvol. The improved low-contrast detectability observed with MBIR, especially at low-dose levels, indicate the potential for considerable dose reduction.
Stromal fibroblasts from basal cell carcinoma affect phenotype of normal keratinocytes (2007)

These observations indicate that BCCFs may differ from normal fibroblasts and may play a regulatory role in BCC biology.
Vanishing Quantum Discord is Necessary and Sufficient for Completely Positive Maps (2009)

Two long-standing open problems in quantum theory are to characterize the class of initial system-bath states for which quantum dynamics is equivalent to (i) a map between the initial and final system states, and (ii) a completely positive (CP) map. The CP map problem is especially important, due to the widespread use of such maps in quantum information processing and open quantum systems theory. Here we settle both these questions by showing that the answer to the first is "all", with the resulting map being Hermitian, and that the answer to the second is that CP maps arise exclusively from the class of separable states with vanishing quantum discord.
Osmoregulation as a selection criterion for drought tolerance in wheat (1983)

A method is described in which measurements of osmoregulation made on glasshouse-grown wheat plants may be used to select lines which yield higher under conditions of water deficit in the field. The procedure involved growing F4 breeding lines in pots in a semi-controlled glasshouse. When the plants reached booting stage, they were transferred to a controlled environment chamber and droughted by withholding water. During the water deficit cycle approximately 10 flag leaf samples from each line were taken, and measurements were made of relative water content, osmotic potential and water potential. The lines were evaluated using estimates of the relative water content at either osmotic or water potential values of -2.5 MPa, after relationships between these measurements and relative water content had been established. The distribution of data into two main groups with a smaller intermediate group indicated possible single gene control. Under drought conditions in the field, lines selected from the high osmoregulating group maintained turgor to lower water potentials and gave grain yields which were 1.6 and 1.5 times greater than those selected from the low group at the F4 and F6 stages respectively.
Java NIO (2002)

Java NIO explores the new I/O capabilities of version 1.4 in detail and shows you how to put these features to work to greatly improve the efficiency of the Java code you write. This compact volume examines the typical challenges that Java programmers face with I/O and shows you how to take advantage of the capabilities of the new I/O features. You'll learn how to put these tools to work using examples of common, real-world I/O problems and see how the new features have a direct impact on responsiveness, scalability, and reliability. Because the NIO APIs supplement the I/O features of version 1.3, rather than replace them, you'll also learn when to use new APIs and when the older 1.3 I/O APIs are better suited to your particular application.
Measurements of Standard Gibbs Energies of Formation of Sb2O3, MgSb2O4and Ca4Sb2O7by an Emf Method (1996)

Magnesium and calcium antimonites, which can coexist with MgO and CaO, respectively, were synthesized by a phase-equilibration technique and identified by X-ray diffraction to be MgSb2O4 and Ca4Sb2O7. To determine the standard Gibbs energies of formation of those antimonites, emf values of the following galvanic cells have been measured:Pt, Re/Sb (s,l), Sb2O3 (Sl)/ZrO2 + CaO(or Y2O3)/air, Pt,Pt, Re/Sb (l), MgSb2O4(S), MgO/ZrO2 + CaO/air, Pt,Pt, Re/Sb (l), Ca4Sb2O7(S), CaO(s)/ZrO2 + CaO/air, Pt.The following free energies of formation were determined:∆G0/kJ mol−1 ± 0.4 = −687.7 + 0.2425 T (773–904 K), for 2 Sb(s) + 3/2 O2(g) = Sb2O3(S),∆G0/kJ mol−1 ± 0.3 = −730.2 + 0.2895 T (904–929 K), for 2 Sb(l) + 3/2 O2(g) = Sb2O3(S),∆G0/kJ mol−1 ± 0.2 = −683.1 + 0.2385 T (929–1095 K), for 2 Sb(l) + 3/2 O2(g) = Sb2O3(S),∆G0/kJ mol−1 ± 0.7 = −78.9 + 0.0495 T (929–1101 K), for Sb2O3 (l) + MgO(s) = MgSb2O4(S),∆G0/kJ mol−1 ± 0.7 = −134.7 + 0.0017 T (972–1101 K), for Sb2O3 (l) + 4CaO(s) = Ca4Sb2O7(S),Published by Elsevier Science Ltd Résumé Les antimonites de Mg et de Ca, qui peuvent coexister avec le MgO et le CaO, respectivement, ont été synthetisées par une technique d'equilibration de phase et identifiées par diffraction des rayons-x comme étant MgSb2O4 et Ca4Sb2O7. Pour déterminer les énergies de formation standards de Gibbs de ces antimonites, les ferns des cellules galvaniques suivantes ont été mesurées:Pt, Re/Sb (s,l), Sb2O3 (Sl)/ZrO2 + CaO(ou Y2O3)/air, Pt,Pt, Re/Sb (l), MgSb2O4(S), MgO/ZrO2 + CaO/air, Pt,Pt, Re/Sb (l), Ca4Sb2O7(S), CaO(s)/ZrO2 + CaO/air, Pt.Les énergies libres de formation qui suivent ont été déterminées:∆G0/kJ mol−1 ± 0.4 = −687.7 + 0.2425 T (773–904 K), pour 2 Sb(s) + 3/2 O2(g) = Sb2O3(S),∆G0/kJ mol−1 ± 0.3 = −730.2 + 0.2895 T (904–929 K), pour 2 Sb(l) + 3/2 O2(g) = Sb2O3(S),∆G0/kJ mol−1 ± 0.2 = −683.1 + 0.2385 T (929–1095 K), pour 2 Sb(l) + 3/2 O2(g) = Sb2O3(S),∆G0/kJ mol−1 ± 0.7 = −78.9 + 0.0495 T (929–1101 K), pour Sb2O3 (l) + MgO(s) = MgSb2O4(S),∆G0/kJ mol−1 ± 0.7 = −134.7 + 0.0017 T (972–1101 K), pour Sb2O3 (l) + 4CaO(s) = Ca4Sb2O7(S),
Infiltration of γδ T cells, IL-17+ T cells and FoxP3+ T cells in human breast cancer (2017)

This study sheds further light on the prognostic impact of various T cell subtypes in breast cancer.
Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function (2018)

Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50-400 nm) and their ability to physically pass through <0.45 μm pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., <i>Nanoarchaeum equitans</i> and "<i>Candidatus</i> Pelagibacter ubique"). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their 'hosts.' This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.
Tailoring the Spray Conditions for Suspension Plasma Spraying (2014)

Abstract In this study, a wide range of suspension plasma spraying conditions are used to produce YSZ coatings for intended use in liquid gas engines. To meet specifications, the coatings must exhibit a homogeneous microstructure with no vertical cracks or columns, low surface roughness, and low thermal conductivity. The properties of the plasma jet (velocity, enthalpy, stability), droplets (trajectory, number, size), and particles (velocity) were measured during spray trials and are correlated with coating microstructure. Suspension plasma spraying conditions necessary for depositing disk-shaped splats and achieving finely structured coatings with no stacking defects are described along with substrate cooling requirements.
Biochemical Logic of Antibiotic Inactivation and Modification (2009)

Bacterial resistance to antibiotics manifests itself in both general and specifi c protection mechanisms. Consequently, the characteristics of resistance can be paralleled to those of the mammalian immune response. Antibiotic resistance can be differentiated into: (1) nonspecifi c mechanisms that confer general innate immunity to a class of antibiotics (e.g., broad spectrum effl ux mechanisms, target modifi cation), and (2) highly precise responses that include selective enzymebased mechanisms that mirror the acquired immune response with respect to target specifi city and potency. Bacteria deploy both types of mechanisms in response to the presence of cytotoxic antibiotics.
Contrôle des échangeurs de chaleur : application au circuit de refroidissement d'un système pile à combustible (2010)

6 pages
DNA Structures and Transitions: X-Ray Diffraction Studies of Solvated Fibers (1983)

The distinctive X-ray diffraction patterns of fibers provide a rich source of data. They are the basis for the original definitions of the conformations of DNA, except for the Z form, and can readily serve as “fingerprints” for their presence. Furthermore, simple measurements of layer line spacings in fiber patterns can often supply both of the individual helical parameters (pitch and rise per residue) needed to give the number of residues per turn (Zimmerman 1982).
Unified power control, error correction coding and scheduling for a CDMA downlink system (2002)

Transmitting multimedia data over a CDMA channel presents a new set of challenges. Sometimes, data demands will exceed the system capacity, in which case the system must make the most efficient use of its limited resources. The resources we consider are: fixed bandwidth available for each user and the transmit power budget for each cell. We present our approach for unifying power control, variable forward error correction (VFEC), and scheduling for allocating the system resources. Our objective is to maximize the overall system satisfaction, which we call "system utility". This objective is achieved by applying a distributed algorithm which divides the overall optimization problem into a hierarchy of three levels (system, cell and user). At each level, the system performs independent and parallel optimizations; the critical information is then passed to the higher level for further optimization. Finally, an iterative and distributed algorithm is applied at the system level to achieve the overall system optimization.
Affine invariant salient patch descriptors for image retrieval (2013)

Image description constitutes a major part of matching-based tasks in computer vision. The size of descriptors becomes more important for retrieval tasks in large datasets. In this paper, we propose a compact and robust image description algorithm for image retrieval, which consists of three main stages: salient patch extraction, affine invariant feature computation over concentric elliptical tracks on the patch, and global feature incorporation. We evaluate the performance of our algorithm for region-based image retrieval and image reuse detection, a special case of image retrieval. We present a novel synthetic image reuse dataset, which is generated by superimposing objects on different background images with systematic transformations. Our results show that the proposed descriptor is effective for this problem.
Characterization of Vadose Zone Sediment: RCRA Borehole 299-E33-338 Located Near the B-BX-BY Waste Management Area (2003)

This report summarizes data collected from samples in borehole 299-E33-338 (C3391). Borehole 299-E33-338 was drilled for two purposes. One purpose was for installation of a RCRA ground-water monitoring well and the other was to characterize the in situ soils and background porewater chemistry near WMA B-BX-BY that have been largely uncontaminated by tank farm and crib and trench discharge operations. This borehole was drilled just outside the southeast fence line of the B tank farm. The borehole was drilled between July 23 and August 8, 2001 to a total depth of 80.05 m (275.75 ft) bgs using the cable-tool method (Horton 2002). The water table was contacted at 77.5 m (254.2 ft) bgs and the top of basalt at 82.6 m (271 ft) bgs. Samples to the top of basalt were collected via a drive barrel/splitspoon, before switching to a hard tool to drill 5 feet into the basalt. Nearly continuous core was obtained down to a depth of ~78.6 m (258 ft) bgs. Two hundred and two 2-ft long by 4-in diameter cores were retrieved, which accounts for ~75% the total length of the borehole. Each 2-ft splitspoon contained two 1-ft lexan-lined core segments. The lithology of this borehole was summarized onto a field geologist's log by a CH2M HILL Hanford Group, Inc. geologist (L. D. Walker); subsequently visual inspection of the cores was performed in the laboratory by K. A. Lindsey (Kennedy/Jenks), K. D. Reynolds (Duratek), and B. N. Bjornstad (Pacific Northwest National Laboratory), who also collected 24 samples for paleomagnetic analysis. Subsamples were taken from all 102 cores for moisture content (Table B.1). In addition, 21 core subsamples were collected from a depth of geological interest for mineralogical and geochemical analysis. Data from these samples allow for comparison of uncontaminated versus contaminated soils to better understand the contributions of tank wastes and other wastewaters on the vadose zone in and around WMA B-BX-BY.
Improved Moisture Management Technology for Eco-N-Control Fertilizer (2022)

Three fertilizer technologies to manage nitrogen (N) release rates in soil dominate the market today: 1) bulk controlled-release technologies, which use the intrinsic solubility properties of a N-organic co-polymer to control N release; 2) barrier-based controlled-release technologies, which use porous polymer or sulfur coatings as a physical barrier to control N release from encapsulated N nutrients; and 3) slow-release technologies, which use enzyme inhibitors to chemically slow down the transformation of N nutrients into ammonia (NH<sub>3</sub>) or to temporarily reduce populations of bacteria in the soil that are responsible for converting ammonium (NH<sub>4</sub><sup>+</sup>) to highly soluble nitrates. These technologies are expensive and provide only limited control of N-release rates. Also, from another environmental perspective, synthetic polymer coatings do not decompose easily and will accumulate over time with continuous application of fertilizer. For most of the past two decades we have been developing the Eco-N-Control solid-nitride fertilizer technology, a type of bulk controlled-release technology. With Eco-N-Control, solid-nitride compounds weather like a mineral, slowly releasing N at a rate determined by their composition. Testing by an industrial collaborator, however, showed that earlier versions of Eco-N-Control released at 25% of the desired rate when deployed in unsaturated soils. The overall goal of the current project, therefore, was to strengthen our IP position and the potential for licensing of Eco-N-Control solid-nitride fertilizer technology by developing new ways to manage the level of moisture in contact with the fertilizer when applied to soil thereby ensuring the desired N-release rate. We achieved this goal by developing a biodegradable polymer cross-linking approach that substantially improved performance of our patented solid-nitride fertilizer. We found that cross-linking an environmentally friendly and biodegradable polymer with a mixture of solid nitrides, other N-nutrient compounds and other additives offers several advantages: 1) mechanical robustness of fertilizer beads, 2) chemical stability during storage, 3) maintenance of sufficient water content in the vicinity of the nitride, and 4) control of N-release rates. We also updated our N-release testing protocol to more realistically simulate the conditions found in soil. Finally, we filed an invention disclosure record to protect these new aspects of Eco-N-Control technology, which offers a potential way to lower both agricultural and industrial pollution by providing an efficient N-delivery mechanism to plants.