Miracle-dz/UniFAR-FTUs huggingface dataset:
Environmental conditions and agronomic practices induce consistent global changes in DNA methylation patterns in grapevine (Vitis vinifera cv Shiraz)

Fruit attributes that affect wine quality are thought to be largely driven by the interaction of grapevine’s genetic characteristics with environmental factors (i.e. climate, soil and topography) and vineyard management. All these variables, in conjunction with the wine making process, give a wine its distinctive character. Understanding how grapevines perceive and adapt to a changing environment will provide us with an insight into how to better manage crop quality. Mounting evidence suggests that epigenetic mechanisms are a key interface between the environment and the genotype that ultimately affect the plant’s phenotype. Moreover, it is now widely accepted that epigenetic mechanisms are a source of useful variability during crop varietal selection that could affect crop performance. While the contribution of DNA methylation to plant performance has been extensively studied in other major crops, very little work has been done in grapevine. Here we used Methylation Sensitive Amplified Polymorphisms to obtain global patterns of DNA methylation, and to identify the main drivers of epigenetic diversity across 22 vineyards planted with the cultivar Shiraz in six distinctive wine areas of a major wine zone, The Barossa, South Australia. The observed epigenetic profiles showed a high level of differentiation that grouped vineyards by their area of provenance despite the low genetic differentiation between vineyards and sub-regions. Furthermore, pairwise epigenetic distances between vineyards with similar management systems showed a significant correlation with geographic distance. Finally, methylation sensitive Genotyping By Sequencing identified 3,598 differentially methylated genes that were assigned to 1,144 unique GO terms of which 8.6% were associated with response to environmental stimulus. Taken together, our results indicate that the intensity and directionality of DNA methylation differentiation between vineyards and wine sub-regions within The Barossa are driven by management and local growing conditions. Finally, we discuss how epigenetic variability can be used as a tool to understand and potentially modulate terroir in grapevine.
Portfolio optimization models for project valuation

This dissertation presents (i) a framework for selecting and managing a portfolio of risky multi-period projects, called Contingent Portfolio Programming (CPP), and (ii) an inverse optimization procedure that uses this framework to compute the value of a single project. The dissertation specifically examines a setting where the investor can invest both in private projects and securities in financial markets, but where the replication of project cash flows with securities is not necessarily possible. This setting is called a mixed asset portfolio selection (MAPS) setting. The valuation procedure is based on the concepts of breakeven selling and buying prices, which are obtained by first solving an optimization problem and then an inverse optimization problem. In the theoretical part of the dissertation, it is shown that breakeven prices are consistent valuation measures, exhibiting sequential consistency, consistency with contingent claims analysis (CCA), and sequential additivity. Due to consistency with CCA, the present approach can be regarded as a generalization of CCA to incomplete markets. It is also shown that, in some special cases, it is possible to derive simple calculation formulas for breakeven prices which do not require the use of inverse optimization. Further, it is proven that breakeven prices for a mean-variance investor converge towards the prices given by the Capital Asset Pricing Model (CAPM) as the investor's risk tolerance goes to infinity. The numerical experiments show that CPP is computationally feasible for relatively large portfolios both in terms of projects and states, and illustrate the basic phenomena that can be observed in a MAPS setting.
Protein kinase and protein phosphatase expression in the central nervous system of G93A mSOD over‐expressing mice

The expressions of 78 protein kinases, 24 protein phosphatases and 31 phosphoproteins were investigated by Kinetworks™ analysis in brain and spinal cord tissue of transgenic mice over‐expressing G93A mutant superoxide dismutase (mSOD), a murine model of amyotrophic lateral sclerosis (ALS). In the brains of affected mSOD mice, we observed increased expression of cAMP‐dependent protein kinase (PKA, 111% increase compared with control), and protein phosphatase 2B Aα‐catalytic subunit (calcineurin, 109% increase), and reductions in the levels of PAK3 (76% decrease) and protein phosphatase 2C Cβ‐subunit (32% decrease). Increased Ser259 phosphorylation of Raf1 (126% increase) in mSOD mice correlated with higher expression of p73 Raf1 (147% increase). There was also increased p73 Raf1 (69% increase) and Ser259 phosphorylation (45% increase) in the spinal cords of mSOD mice. While adducin underwent enhanced phosphorylation (αS724, 90% increase; γS662, 290% increase) in mSOD brain, its phosphorylation was lower in the mSOD spinal cord (αS724, 53% decrease; γS662, 46% decrease). In spinal cords of affected mSOD mice, we also observed elevated expression of casein kinase 1δ (CK1δ, 157% increase), JAK2 (84% increase), PKA (183% increase), protein kinase C (PKC) δ (123% increase), p124 PKCµ (142% increase), and RhoA kinase (221% increase), and enhanced phosphorylation of extracellular regulated kinases 1 (ERK1, T202/Y204, 90% increase), and 2 (ERK2, T185/Y187, 73% increase), p38 MAP kinase (T180/Y182, 1570% increase), and PKBα (T308, 154% increase; S473, 61% increase). There was also reduced phosphorylation of RB (S780, 45% decrease; S807/S811, 65% decrease), Src (Y418, 63% decrease) and p40 SAPK/JNKβ (T183/Y185, 43% decrease). Variability in the expression of kinases, phosphatases and phosphorylation of their substrates was observed even in mutant animals having a similar phenotype. The expression and phosphorylation differences between mSOD and control mice were dissimilar to those between ALS patients and controls. This finding indicates that the activation of protein kinases and phosphoproteins is different with neuron loss in the mSOD mouse compared with that seen in patients with the sporadic form of ALS.
The political economy of public organizations

The search for a theory of public administration often takes on aspects of a quest for the Hold Grail or a hunt for the mythical unicorn. Public administration theory has meant variously: a search for "scientific principles"; broad ruminations on what phenomena are included within "the field"; and general orientations of students of the subject, both professional and academic.1 Seldom has theory referred to systematic, empirically based explanations of a phenomenon; a system of related and proven propositions that answer the question "Why? " Though this article cannot begin to present such a theory, hopefully, it does more than issue another pious call for one. It is intended to set forth a framework with roots in organizational analysis that is simple but has enough heuristic power to make its application appealing to a wide range of students of public administration; that can pose questions for those areas still in need of exploration, and conceptually link them with those areas already well defined. A framework that can perform such an integrative role would represent a major step toward explanations of why individuals, groups, or organizations behave as they do in that part of the political system we have analytically abstracted and labeled public administration; and it would tell us something about how that behavior affects public policy. If we can better answer the "why" questions,
Handbook of Development Economics

Contents Volume IIIA: Preface. Analytical Tools. Introduction (J. Behrman, T.N. Srinivasan). Data and econometric tools for development analysis (A. Deaton). Human resources: Empirical modeling of household and family decisions (J. Strauss, D. Thomas). Applied general equilibrium models for policy analysis (J.W. Gunning, M. Keyzer). Resources, Technology, and Institutions. Introduction (J. Behrman, T.N. Srinivasan). Savings, credit and insurance (T. Besley). Technological change and technology strategy (R.E. Evenson, L.E. Westphal). Institutions and economic development (J.Y. Lin, J.B. Nugent). Poverty, institutions, and the environmental-resource base (P. Dasgupta, K.-G. Maler) Contents Volume IIIB: Policy Reform, Stabilization, Structural Adjustment and Growth. Introduction (J. Behrman, T.N. Srinivasan). Policy lessons from development experience since the second world war (A. Krueger). Poverty and policy (M. Lipton, M. Ravallion). Power, distortions, revolt and reform in agricultural land relations (H. Binswanger et al.). Human and physical infrastructure: investment and pricing policies in developing countries (E. Jiminez). Structural adjustment, stabilization and policy reform: domestic and international finance (V. Corbo, S. Fischer). Trade and industrial policy reform (D. Rodrik). The contributions of endogenous growth theory to the analysis of development problems: an assessment (P. Bardhan).
Pregnancy in patients with ankylosing spondylitis: do regulatory T cells play a role?

OBJECTIVE To investigate the numerical and functional changes of CD4+CD25(high) regulatory T (Treg) cells during pregnancy and postpartum in patients with ankylosing spondylitis (AS). METHODS The frequency of CD4+CD25(high) T cells was determined by flow cytometry in 10 pregnant and 5 nonpregnant patients with AS as well as in 14 pregnant and 4 nonpregnant healthy controls. Pregnant individuals were investigated at the third trimester and 8 weeks postpartum. Treg cells and CD4+CD25- effector T (Teff) cells separated by fluorescence-activated cell sorting were stimulated with anti-CD3 and anti-CD28 monoclonal antibodies, alone or in coculture, to investigate proliferation and cytokine secretion. RESULTS The frequency of CD4+CD25(high) Treg cells was significantly higher during pregnancy than postpartum in both healthy control subjects and patients with AS. In contrast to Treg cells in healthy pregnant women, Treg cells in pregnant women with AS secreted only small amounts of interleukin-10 and showed lower suppression of tumor necrosis factor alpha and interferon-gamma secretion by CD4+CD25- Teff cells. At the postpartum time point, proinflammatory cytokine levels in the Treg/Teff cell cocultures and Teff cell monocultures were significantly higher in patients with AS than in healthy controls. CONCLUSION Pregnancy influenced the expansion and cytokine secretion of Treg cells in both patients with AS and control subjects. However, the Treg cells of pregnant patients with AS failed to support an antiinflammatory cytokine milieu, thereby possibly contributing to the persistent disease activity of AS during pregnancy.
Validity of VO2max equations for aerobically trained males and females.

PURPOSE The purpose of this investigation was to cross-validate existing VO2max prediction equations on samples of aerobically trained males and females. METHODS A total of 142 aerobically trained males (mean +/- SD; 39.0 +/- 11.1 yr, N = 93) and females (39.7 +/- 10.1 yr, N = 49) performed a maximal incremental test to determine actual VO2max on a cycle ergometer. The predicted VO2max values from 18 equations (nine for each gender) were compared with actual VO2max by examining the constant error (CE), standard error of estimate (SEE), correlation coefficient (r), and total error (TE). RESULTS The results of this investigation indicated that all of the equations resulted in significant (P < 0.006) CE values ranging from -216 to 1415 mL x min(-1) for the males and 132 to 1037 mL x min(-1) for the females. In addition the SEE, r, and TE values ranged from 266 to 609 mL x min(-1), 0.36 to 0.88, and 317 to 1535 mL x min(-1), respectively. Furthermore, the lowest TE values for the males and females represented 10% and 12% of the mean actual VO2max values, respectively. CONCLUSIONS The results of the analysis indicated that the two equations using age, body weight, and the power output achieved at VO2 as predictor variables had the lowest SEE (7.7-9.8% of actual VO2max) and TE (10-12% of actual VO2max) values and are recommended for estimating VO2max in aerobically trained males and females. The magnitude of the TE values (>or= 20% of actual VO2max) associated with the remaining 16 equations, however, were too large to be of practical value for estimating VO2max.
Exploration of Anti-Hyperglycemic and Hypolipidemic Activities of Ethanolic Extract of Annona muricata Bark in Alloxan Induced Diabetic Rats

Natural remedies from medicinal plants are considered to be effective and safe alternative treatment for diabetes mellitus. The aim of present study was to demonstrate the hypoglycemic and anti-diabetic activity of the Ethanolic extract of Annona muricata stem bark in alloxan induced diabetic animals with a view to explore its use for the treatment of diabetes mellitus in humans. The Ethanolic extract of Annona muricata (Annonaceae) stem was investigated for its anti-hyperglycemic and anti-hyperlipidemic effects in male albino rats. Diabetes was induced in the albino rats by administration of a single dose of alloxan monohydrate (150 mg/kg, bwt, i.p) and the Ethanolic bark extract of A. muricata was administered daily at single doses of 150 and 300 mg/kg, p. o to diabetesinduced rats for a period of 14 days. The effect of Ethanolic extract of A. muricata bark on blood glucose level was measured in the diabetic rats. Serum lipid profiles [total cholesterol, triglycerides, phospholipids (low density, very low density and high density lipoprotein)] were also determined. The activities were also compared to the activity produced by a standard anti diabetic agent, Glibenclamide (500 μg/kg). The present investigation established pharmacological evidence to support the folklore claim that Ethanolic extract of Annona muricata stem bark is an anti-diabetic agent.
Low-cost, high-efficiency quasi-planar array of waveguide-fed circularly polarized microstrip antennas

A low-cost quasiplanar Ku-band array of circularly polarized microstrip antennas benefiting from a low-loss waveguide feed network is demonstrated (patent pending). The 32 elements of the array which are arranged in a 2-by-16 configuration are subdivided into four two-by-four subarrays. To maintain feed losses and thus the overall noise temperature at a minimum, the subarrays are excited using a one-by-four corporate feed network of hollow metallic waveguides. This network is composed of E-plane components such as Tee-junctions and bends and is manufactured out of only two metallic pieces that accommodate the feed network in the form of milled grooves. Because of insensitivity of the exploited E-plane components to air gaps or slight misalignments, the pieces are secured together with only four screws without welding, braising, or conducting adhesives. Owing to a low-loss foam substrate, the array elements show high circular polarization gain of 9 dBic and wide relative bandwidth of 4%. To achieve circular polarization, use is made of circular patches with two nearly perpendicular perturbations. Using sequential rotation of the elements along with quadrature phase shifting, the axial ratio of the array is reduced to 1 dB over 4% of bandwidth. The measured circular polarization gain of the array amounts to 23 dBic with an aperture efficiency of 63% in the Ku-band of frequencies. The achieved efficiency, which is higher than the reported efficiency for comparable planar arrays with microstrip feed networks, can be credited to the low losses of only 0.2 dB in its waveguide corporate feed. The paper also presents measurement results for an arrangement of two inclined single arrays mounted in parallel. This configuration which has a measured circular polarization gain of 25.7 dBic with an axial ratio of 1 dB is desirable for mobile low-profile antenna systems.
Interleukin 6 is associated with subclinical atherosclerosis: a link with soluble intercellular adhesion molecule 1

Background Among the markers of inflammation, a cytokine, interleukin (IL)-6, promotes the expression of intercellular adhesion molecule 1 (ICAM-1), C-reactive protein (CRP) synthesis, and leads to a series of procoagulant actions with potential major implications on the progression of atherosclerosis. Aim of the study To analyse in a population-based study, the relationship between IL-6 and atherosclerotic lesions and the role of serum ICAM-1 and CRP on this relationship. Population Among 1015 individuals randomly recruited between 1995 and 1997 in Haute-Garonne, a French region with a low cardiovascular risk, 953 subjects with complete data for all measurements were analysed. Common carotid intima–media thickness (IMT) and the presence of plaques in the carotid and femoral arteries were assessed by ultrasonography. Results Quartiles of IL-6, serum ICAM-1 and CRP were positively associated with plaques and IMT. After adjustment for traditional risk factors, IL-6 (P < 0.001) and serum ICAM-1 (P < 0.002) remained positively associated with plaques but not CRP (P = 0.20). Neither IL-6, nor serum ICAM-1, nor CRP were independently associated with IMT. When serum ICAM-1 was entered into the model in addition to traditional risk factors and IL-6, the percentage of variance in the number of plaques explained by the model did not increase significantly. Conclusion IL-6 levels are associated with subclinical atherosclerotic lesions independently of traditional risk factors; the influence of IL-6 on ICAM-1 secretion may play a role in this association. These results argue the interest of IL-6 in the stratification of cardiovascular risk.
Current understanding of the epidemiology and clinical implications of BRCA1 and BRCA2 mutations for ovarian cancer

Genetic testing for susceptibility to ovarian cancer is rapidly becoming integrated into the clinical practice of oncology. Genetic testing for BRCA1 and BRCA2 is now recommended to most women with invasive ovarian cancer. Approximately 10% of these women will have a positive test, including 4% of women without a family history of cancer. Currently, the treatment of hereditary ovarian cancer is the same as for non-hereditary ovarian cancer. It appears that women with ovarian cancer and a BRCA mutation experience better survival than women without a mutation, possibly due to enhanced susceptibility to chemotherapy. Strategies for prevention of ovarian cancer among carriers include oral contraceptives, tubal ligation and prophylactic oophorectomy.
Clinicopathologic Features of Gastric Cancers Producing Alpha-Fetoprotein

Background: Patients with gastric cancers producing alpha-fetoprotein (AFP) were reported to have a poor prognosis with high rates of liver metastasis. The purpose of the present study was to clarify the clinicopathological features of AFP-producing gastric cancers, in particular characteristics of liver metastasis, and to evaluate treatment of these cancers. Methods: In 27 of the 29 cases with elevated preoperative serum AFP levels among a total of 974 primary gastric cancers, AFP production was confirmed in gastric cancer cells by immunohistochemistry. These cases were included in the AFP-positive gastric cancer group (AFP(+), 2.7%). The remaining 945 cases with normal serum AFP levels were designated the AFP-negative gastric cancer group (AFP(–)). Results: There was a higher incidence of lymph node metastasis, a deeper invasion of the gastric wall, a higher frequency of advanced stage, a more marked lymphatic invasion and a higher rate of liver metastasis in the AFP(+) group than in the AFP(–) group. The patients received curative resection in AFP(+) group had a significantly worse survival rates in comparison to that in AFP(–) group. With respect to liver metastasis (n = 17) in AFP(+) group, of 3 cases who received curative hepatic resection, 1 patient survived more than 3 years, while the remaining 2 died in less than 3 years due to multiple liver recurrence. The patients (n = 5) who received palliative resection for liver metastasis followed by transarterial continuous infusion chemotherapy all died in less than 1 year. Conclusion: AFP-producing gastric cancers had aggressive behavior and their clinical or biological features were quite different from the common AFP-negative gastric cancers. Surgical resection of liver metastasis from AFP-producing gastric cancers was unsatisfactory. The development of a novel multimodal therapy against AFP-producing gastric cancers is needed.
Examination of alpha 1 adrenoceptor subtypes in the human ureter

Aim: Urinary stone disease is a common condition affecting up to 12% of the population. Speedy elimination of ureterolithiasis in the lower part of ureters is reported with the alpha 1‐blocker. This study was carried out to characterize the alpha 1 adrenoceptors (AR) subtype gene and protein expression in the proximal, medial, and distal regions of the human ureter with the aim of facilitating stone expulsion.
Activity‐dependent properties of synaptic transmission at two classes of connections made by rat neocortical pyramidal axons in vitro

1 To compare the dynamics of synaptic transmission at different types of connection, dual intracellular recordings were made from pairs of neurones in slices of adult rat neocortex. Excitatory postsynaptic potentials (EPSPs) were elicited by single spikes, spike pairs and brief spike trains in presynaptic pyramidal cells and responses recorded in postsynaptic pyramidal cells and in inter neurones. 2 Pyramid–pyramid EPSPs were strongly voltage dependent and this resulted in a range of paired pulse effects. At thirty‐two of sixty‐nine pyramid–pyramid connections, the 2nd EPSP was the same shape as the 1st, indicating minimal interaction between active synapses. In these thirty‐two connections, paired pulse depression (PPD) was apparent (2nd EPSP integral 46 ± 21% of the 1st, at 5–20 ms), which recovered within 60–70 ms. 3 In eleven additional pyramid–pyramid pairs, the 2nd EPSP was also the same shape as the 1st, but paired pulse facilitation (PPF, 149 ± 32%) decaying within 50–60 ms was apparent. Even these connections displayed frequency‐dependent depression, however, as 3rd EPSPs were smaller than 1st EPSPs at intervals < 100 ms. 4 At twenty‐five pyramid–pyramid connections, 2nd EPSPs were broader than 1st EPSPs and in sixteen of these, voltage‐ and NMDA receptor‐dependent enhancement was large enough to obscure the underlying PPD. PPD was revealed by postsynaptic hyperpolarization (4 pairs), N‐methyl‐D‐aspartate (NMDA) receptor blockade (3 pairs), or if Mg2+ was removed (in the one case studied). If synapse location allowed significant depolarization of one active site by another, voltage‐dependent enhancement could produce supralinear EPSP summation and overcome PPD. Third EPSPs were, however, consistently smaller than 1st EPSPs. 5 In striking contrast, profound frequency‐dependent facilitation, independent of voltage or NMDA receptors was seen at fifteen connections involving two classes of postsynaptic inter neurones. 6 At these pyramid–interneurone connections, facilitation of the 2nd EPSP (655 ± 380% at 5–20 ms) decayed rapidly, within 50–60 ms. Third and fourth EPSPs showed additional facilitation which decayed more slowly, within 90 ms and 2 s, respectively. Facilitation due to five to six spike trains was still apparent at 3 s. Therefore, once initiated by a brief high frequency spike train, facilitation was maintained at lower frequencies.