Miracle-dz/UniFAR-FTUs huggingface dataset:
Agricultural Biomass Removal Rate Estimation for Real-time Optimization of Single Pass Crop Grain and Biomass Harvesting System

As the demand for biomass feedstocks grows, agricultural residue may be removed in a way that compromises soil sustainability due to increased soil erosion, depletion of organic matter and deterioration of soil physical characteristics. Since soil erosion from agricultural fields depends on several factors including soil type, field terrain and cropping practice, the amount of biomass that can be removed while maintaining soil tilth varies substantially over space and time. The RUSLE soil erosion model, which takes into account these spatio-temporal variations, was used to estimate sustainable agricultural biomass removal rates for single pass crop grain and biomass harvesting system. Soil type, field topography, climate data, management practices and conservation practices were stored in individual databases on a state and/or county basis. Geographic position of the field was used as a spatial key to access the databases to select site specific information such as soil, topography and management related parameters. These parameters along with the actual grain yield were provided as the inputs to the RUSLE model to calculate the yearly soil loss per unit area of the field. An iterative technique was then used to determine the site-specific biomass removal rate that keeps the soil loss below the soil loss threshold (T) of the field. The sustainable removal rate varied substantially with field terrain, crop management practices and soil type. At a location in a field in Winnebago county, Iowa with ~1% slope steepness and conventional tillage practice, up to 98% of 11 Mg/ha total corn stover was available for collection with negligible soil loss. The study, however, has considered only the soil erosion tolerance level and has neglected the potential effects in organic matter content and other biophysical properties of the soil due to excessive biomass removal. There was no biomass available to remove with conventional tillage practice in steep slopes such as a location in Crawford County, Iowa field with a 12.6% slope. If no-till crop practices were adopted, up to 70% of available biomass could be collected at the same location with 12.6% slope. In case of soybean-corn rotation with no-till practices, about 98% biomass was available for removal at the locations in Winnebago field with low slope steepness, whereas 77% biomass was available at a location in the Crawford field with 7.5% slope steepness. Sustainable removal rates varied substantial over an agricultural field, which showed the importance of site specific removal rate estimation. These sustainable removal rates will be provided as recommended rates for the producers to use during a single pass crop grain and biomass harvesting operation. This type of site-specific biomass removal rate estimation is necessary to achieve field level sustainability in agricultural biomass production and collection systems.
Preface to special section on Arctic Ocean Model Intercomparison Project (AOMIP) Studies and Results

] More than 130years ago,theAustrian Arctic explorer,Carl Weyprecht [Weyprecht and Ihne, 1913] (who discov-ered Franz Josef Land, an archipelago north of Russia, andwho advanced a successful scheme for international coop-eration in polar science—the International Polar Year con-cept) postulated that a number of fundamental problems ofmeteorology and geophysics could be solved near theEarth’spoles.Thishypothesisisstillvalidinthe21stcenturybecause the Arctic is recognized as a region where globalclimate change signals are amplified. The model-basedconclusion of Manabe and Stouffer [1994] that the firstsigns of climate change could be detected in the Arctic hasbeen corroborated by numerous other model results [e.g.,Holland and Bitz, 2003; Symon et al., 2005]. On the otherhand, it has been demonstrated that model conclusions maybe highly uncertain and that model estimates of futureclimate change differ significantly from model to model.In order to reduce these uncertainties, it is important tovalidate and to improve models. The latter is the first majorgoal of the Arctic Ocean Model Intercomparison Project(AOMIP). The second major AOMIP goal is to investigatevariability of the Arctic Ocean and sea ice at seasonal todecadal timescales, and identify mechanisms responsible forthe observed changes. Some of the latest AOMIP activitiesassociated with these project goals arereflected inthe papersof this special section. [
Pathology and classification of ovarian tumors

*This article is a US Government work and, as such, is in the public domain of the United States of America. Knowledge of the embryology and microscopic anatomy of the ovary is fundamental to the understanding of the various cancer types that originate in this organ. A complete description of the embryology and anatomy of the ovary is beyond the scope of this monograph; however, comprehensive reviews are available for those who seek more detail. The current discussion focuses on key developmental events and anatomic features that shed light on the natural history of ovarian cancers. At approximately five weeks of gestation, thickenings of the lining of the posterior embryonic body cavity, the coelomic epithelium, form the genital ridges. Continued proliferation of the coelomic epithelium into the underlying primitive connective tissue, known as the mesenchyme, leads to the formation of the primordial indifferent gonads. Cells from adjacent transient embryonic structures, known as mesonephros, concurrently invade the mesenchyme, and the primordial germ cells arrive after a long journey that starts at their place of origin in the yolk sac and takes the cells along the distal embryonic intestine and the posterior wall of the embryonic body cavity. The different tumor types that arise in the ovary are linked to the different cell types that are present at this stage of development: coelomic epithelial, mesenchymal, mesonephric, and germ cells. Ovaries and testes develop in similar fashion until approximately the fourth month of embryonic life. This finding explains the origin of tumors that are commonly associated with testicular tissue but appear in the ovaries and vice versa. At two months gestation, the primitive gonad is recognized as an ovary because of the lack of development of the well-defined testicular sex cords. Instead, mesonephric cells and germ cells remain closely associated, forming illdefined ovarian sex cords embedded in the primitive mesenchyme. The coelomic epithelium remains at the periphery, enwrapping the developing ovary. In the adult, the ovaries are flat, nodular, oval structures that measure between 3 and 5 cm in their greatest dimension and weigh between 2 and 4 g. They are suspended by peritoneal folds and ligaments on either side of the uterus and attached to the back of the broad ligament of the uterus, behind and below the uterine tubes. A single layer of cells, the surface epithelium, which is derived from the coelomic epithelium, lines their external surface. A dense, fibrous tissue, the stroma, which is derived from the mesenchyme, makes up most of their internal substance. The germ cells, also known as oocytes, are located near the periphery of the stroma. The granulosa cells, specialized cells of probable mesonephric origin that are derived from the sex cords, surround the germinal cells that form the follicles. The stroma immediately surrounding the follicles differentiates into plum elongated cells known as theca cells. When stimulated, theca 2631
The Apnea Test: Rationale, Confounders, and Criticism

The apnea test is recommended for the diagnosis of brain death. There are several reasons this test should be reconsidered. Confounding factors for performing the test are vaguely and poorly specified. The following 2 confounders are usually present and not considered: potentially reversible high cervical spinal cord injury and central endocrine failure of adrenal and thyroid axes. There are case reports of breathing at a higher partial pressure of arterial carbon dioxide threshold and cases of recovery of breathing after brain death is diagnosed. The test is dangerous for an injured brain in the setting of high intracranial pressure. It can convert viable penumbral brain tissue to irreversibly nonfunctioning tissue via a transient increase in intracranial pressure and no-reflow phenomena. Hyperoxia during the apnea test can further suppress the function of medullary respiratory rhythm centers. Finally, the philosophical rationale for the need to show lack of spontaneous breathing in brain death is lacking.
Portfolio Symmetry and Momentum

This paper presents a theorical framework to model the evolution of a portfolio whose weights vary over time. Such a portfolio is called a dynamic portfolio. In a first step, considering a given investment policy, we define the set of the investable portfolios. Then, considering portfolio vicinity in terms of turnover, we represent the investment policy as a graph. It permits us to model the evolution of a dynamic portfolio as a stochastic process in the set of the investable portfolios. Our first model for the evolution of a dynamic portfolio is a random walk on the graph corresponding to the investment policy chosen. Next, using graph theory and quantum probability, we compute the probabilities for a dynamic portfolio to be in the different regions of the graph. The resulting distribution is called spectral distribution. It depends on the geometrical properties of the graph and thus in those of the investment policy. The framework is next applied to an investment policy similar to the Jeegadeesh and Titman's momentum strategy [JT1993]. We define the optimal dynamic portfolio as the sequence of portfolios, from the set of the investable portfolios, which gives the best returns over a respective sequence of time periods. Under the assumption that the optimal dynamic portfolio follows a random walk, we can compute its spectral distribution. We found then that the strategy symmetry is a source of momentum.
Immunohistochemistry of the Hfe protein in patients with hereditary hemochromatosis, iron deficiency anemia, and normal controls.

In 1996 two mutations in Hfe, the gene affected in hereditary hemochromatosis, were identified as C282Y (c.845G. A) and H63D (c.187C. G). Immunohistochemical studies have localized the protein product of Hfe to the deep crypts of the duodenum, the maximum site of iron absorption. To date, there are no published data on the cellular location and regulation of Hfe in patients with hemochromatosis who are homozygous for C282Y. The aim of this study was to identify the cellular localization of Hfe in genotyped individuals and to study possible regulation of this protein by the mutations described in the Hfe gene locus and iron deficiency. Duodenal biopsy specimens and serum for iron, ferritin, and transferrin saturation were taken from controls (n = 10) and patients with hereditary hemochromatosis (n = 10) and iron deficiency anemia (n = 10). All participants were genotyped for C282Y and H63D mutations. Expression of Hfe in the duodenum was demonstrated by immunohistochemistry. Hfe was expressed in the deep crypts of the duodenum in all three groups in a perinuclear fashion. Hfe staining was weaker in the hemochromatosis and iron deficiency patients (mean transferrin saturation 69.6%, SD 23% and 15%, SD 11%, respectively) when compared to controls (mean transferrin saturation 33.1%, SD 15%). There was no difference in the intensity of Hfe staining within the hemochromatosis group who were iron overloaded when compared to their iron-depleted counterparts. In summary, Hfe is expressed strongly in the deep crypts of the small intestine of normal subjects. Homozygosity for C282Y and conditions of iron deficiency result in a downregulation of Hfe. Furthermore, Hfe is not regulated by therapeutic iron depletion in patients with hemochromatosis who are homozygous for the C282Y mutation.
The relationship between job satisfaction and contingent-employment

This paper analyses job satisfaction as an aggregate of satisfaction with several job aspects, with special focus on the influence of contingent-employment contracts. Fixed-effect analysis is applied on a longitudinal sample of Dutch employees in four work arrangements: regular, fixed-term, on-call and temporary agency work. Our results indicate that temporary agency work is the only contingent employment relation that is associated with lower job satisfaction compared to regular workers. Decomposition of this gap indicates that the major part is due to the low satisfaction experienced by agency workers regarding the content of their jobs. A lack of job security is also responsible for part of the gap. For fixed-term and on-call workers the negative satisfaction effect originating from the lack of job security and lower wages is compensated by other job aspects and a variant relationship between total job satisfaction and its components. JEL codes: J28, J40, C23
Relationship between sleep parameters and cognitive performance in HIV-positive individuals.

disoproxil fumarate versus efavirenz/emtricitabine/tenofovir disoproxil fumarate for initial treatment of HIV-1 infection: analysis of week 96 results. J Acquir Immune Defic Syndr. 2013; 63:96–100. 3. DeJesus E, Rockstroh J, Henry K, et al. Coformulated elvitegravir, cobicistat, emtricitabine, and tenofovir disoproxil fumarate versus ritonavir-boosted atazanavir plus co-formulated emtricitabine and tenofovir disoproxil fumarate for initial treatment of HIV-1 infection: a randomised, double-blind, phase 3, non-inferiority trial. Lancet. 2012;379:2429–2438. 4. Cohen CJ, Andrade-Villanueva J, Clotet B, et al. Rilpivirine versus efavirenz with two background nucleoside or nucleotide reverse transcriptase inhibitors in treatment-naive adults infected with HIV-1 (THRIVE): a phase 3, randomised, non-inferiority trial. Lancet. 2011; 378:229–237. 5. Molina JM, Cahn P, Grinsztejn B, et al. Rilpivirine versus efavirenz with tenofovir and emtricitabine in treatment-naive adults infected with HIV-1 (ECHO): a phase 3 randomised double-blind active-controlled trial. Lancet. 2011;378:238–246. 6. Daar ES, Tierney C, Fischl M, et al. ACTG 5202: final results of abacavir/lamivudine (ABC/3TC) or tenofovir DF/emtricitabine (TDF/FTC) with either efavirenz (EFV) or atazanavir/ritonavir (ATV/r) in treatmentnaive HIV-infected patients [Abstract]. In: 17th Conference on Retroviruses and Opportunistic Infections (CROI). San Francisco, CA; 2010. 7. Lennox JL, DeJesus E, Lazzarin A, et al. Safety and efficacy of raltegravir-based versus efavirenz-based combination therapy in treatment-naive patients with HIV-1 infection: a multicentre, double-blind randomised controlled trial. Lancet. 2009;374: 796–806. 8. Lennox JL, Dejesus E, Berger DS, et al. Raltegravir versus Efavirenz regimens in treatmentnaive HIV-1-infected patients: 96-week efficacy, durability, subgroup, safety, and metabolic analyses. J Acquir Immune Defic Syndr. 2010;55:39–48.
Effect of Cyclical Mechanical Stretch and Exogenous Transforming Growth Factor-β1 on Matrix Metalloproteinase-2 Activity in Lamina Cribrosa Cells from the Human Optic Nerve Head

Purpose:Extensive remodeling of the lamina cribrosa extracellular matrix occurs in primary open angle glaucoma. The transforming growth factor-β (TGF-β) and matrix metalloproteinase (MMP) protein families are implicated in this process. The authors investigated (a) the effect of cyclical mechanical stretch on TGF-β1 mRNA synthesis, TGF-β1 protein secretion, MMP-2 protein activity and (b) the effect of exogenous TGF-β1 on MMP-2 protein activity in human lamina cribrosa cells in vitro. Methods:Primary human lamina cribrosa cells grown on flexible and rigid plates were exposed to cyclical stretch (1Hz, 15%) or static conditions for 12 and 24 hours. Cells grown on 100-mm plates were exposed to human TGF-β1 (10 ng/ml) or vehicle (4 mM HCl/1% BSA) for 24 hours. TGF-β1 mRNA synthesis in stretched and static cells was measured using real-time polymerase chain reaction. TGF-β1 protein secretion in stretched and static cell media was measured using enzyme linked immunosorbent assay. Gelatin zymography measured MMP-2 activity in stretched, static, TGF-β1- treated and vehicle-treated cell media. Results:Cyclical stretch induced significant increases in TGF-β1 mRNA synthesis after 12 hours (**P < 0.01) and TGF-β1 protein secretion after 24 hours (*P < 0.05). Cyclical stretch significantly (*P < 0.05) increased MMP-2 activity in cell media after 24 hours. Exogenous TGF-β1 induced a significant (**P < 0.01) increase in cell media MMP-2 activity after 24 hours. Conclusions:These results suggest that cyclical stretch and TGF-β1 modulate MMP-2 activity in human lamina cribrosa cells. TGF-β1 and MMP-2 release from lamina cribrosa cells may facilitate matrix remodeling of the optic nerve head in primary open angle glaucoma.
The Human NK Cell Response to Yellow Fever Virus 17D Is Primarily Governed by NK Cell Differentiation Independently of NK Cell Education

NK cells play an important role in the defense against viral infections. However, little is known about the regulation of NK cell responses during the first days of acute viral infections in humans. In this study, we used the live attenuated yellow fever virus (YFV) vaccine 17D as a human in vivo model to study the temporal dynamics and regulation of NK cell responses in an acute viral infection. YFV induced a robust NK cell response in vivo, with an early activation and peak in NK cell function at day 6, followed by a delayed peak in Ki67 expression, which was indicative of proliferation, at day 10. The in vivo NK cell response correlated positively with plasma type I/III IFN levels at day 6, as well as with the viral load. YFV induced an increased functional responsiveness to IL-12 and IL-18, as well as to K562 cells, indicating that the NK cells were primed in vivo. The NK cell responses were associated primarily with the stage of differentiation, because the magnitude of induced Ki67 and CD69 expression was distinctly higher in CD57− NK cells. In contrast, NK cells expressing self- and nonself-HLA class I–binding inhibitory killer cell Ig-like receptors contributed, to a similar degree, to the response. Taken together, our results indicate that NK cells are primed by type I/III IFN in vivo early after YFV infection and that their response is governed primarily by the differentiation stage, independently of killer cell Ig-like receptor/HLA class I–mediated inhibition or education.
A structure of the COPI coat and the role of coat proteins in membrane vesicle assembly

A coat of many components The formation of coated trafficking vesicles is among the most fundamental of cellular processes. COP1 transport vesicles are involved in retrograde membrane trafficking in the Golgi apparatus and endoplasmic reticulum. Dodonova et al. applied cryo–electron tomography to determine the structure of the COPI coat in its fully assembled form on budded vesicles (see the Perspective by Noble and Stagg). They combined structural data with cross-linking mass spectrometry to generate a complete molecular model. The model suggests a mechanism of coat assembly in which coat proteins cluster via flexible interactions instead of forming a protein cage on the membrane. Science, this issue p. 195; see also p. 142 The structure of the assembled COPI intracellular vesicle transport coat differs from clathrin and COPII. [Also see Perspective by Noble and Stagg] Transport of material within cells is mediated by trafficking vesicles that bud from one cellular compartment and fuse with another. Formation of a trafficking vesicle is driven by membrane coats that localize cargo and polymerize into cages to bend the membrane. Although extensive structural information is available for components of these coats, the heterogeneity of trafficking vesicles has prevented an understanding of how complete membrane coats assemble on the membrane. We combined cryo–electron tomography, subtomogram averaging, and cross-linking mass spectrometry to derive a complete model of the assembled coat protein complex I (COPI) coat involved in traffic between the Golgi and the endoplasmic reticulum. The highly interconnected COPI coat structure contradicted the current “adaptor-and-cage” understanding of coated vesicle formation.
Mean field games for multiagent systems in a Markov environment

In this paper, distributed games for large population multiagent systems in a Markov environment are investigated. To reduce the computational complexity, the mean field approach is adopted to construct distributed strategies. The population aggregate effect is provided by analyzing the consistency equation system which is obtained by the parameterized method. A set of distributed strategies is given from the population aggregate effect and the solution of a Markov jump tracking problem. It is shown that the closed-loop system is uniformly stable, and the distributed strategies are asymptotically optimal in the sense of Nash equilibrium, as the number of agents grows to infinity.
Expression of the transforming growth factor beta isoforms in inflammatory cells of nasal polyps.

OBJECTIVE To determine the expression and the potential role of transforming growth factor beta (TGF-beta) in nasal polyposis. DESIGN Comparison of TGF-beta expression between normal and inflammatory nasal mucosa and polyps; in inflammatory nasal polyps, characterization of the TGF-beta isoforms expression and their potential location in macrophages and eosinophils. SETTING Patients and samples were selected at the Hôpital Intercommunal, Créteil, France, and immunohistochemistry and immunoblots were performed at the Institut National de la Sante et de la Recherche Medicale U296 (Universite Paris XII, France). SUBJECTS Nasal polyps and nasal mucosa were sampled in 21 patients during ethmoidectomy, and muscosa was sampled in 6 healthy patients during rhinoplasty. METHODS Immunohistochemistry and Western blot analysis were performed using specific antibodies to TGF-beta1-3, TGF-beta1, TGF-beta2, and TGF-beta3 isoforms. Double labeling was also performed using anti-TGF-beta1 antibody together with macrophages or eosinophil-specific antibodies. RESULTS The expression of TGF-beta(1-3) was significantly higher in inflammatory nasal polyps than in inflammatory nasal mucosa and higher in inflammatory nasal mucosa than in nasal mucosa from healthy patients. Transforming growth factor beta1 was the main isoform detected in inflammatory nasal polyps, and it was present in numerous macrophages and in some eosinophils. CONCLUSIONS Transforming growth factor beta, mainly TGF-beta1, is strongly expressed in inflammatory nasal mucosa, where it could be produced by macrophages and eosinophils. Transforming growth factor beta could induce epithelium and connective tissue modifications and therefore be involved in the pathogenesis of nasal polyposis.