Approximating Exact Probabilities by χ2 and Continuity-Corrected χ2 in 2×2 Tables

Computations have been performed to find an adequate definition of exact two-sided probabilities in 2times2 contingency tables. It turns out, that both uncorrected χ² and Yates' correction for continuity give only unsatisfactory approximations to the exact probabilities of the hypergeometric distribution. The latter are therefore recommended for general use.     

Jeffreys' Likelihood Ratio for the 2×2-Table — A Monte Carlo Study —

Jeffreys' approach for analyzing a 2×2-table is discussed via a Monte Carlo study. The main findings are reported.     

Alternatives to the Chi-Square Test of Homogeneity in 2×2 Tables and to Fisher's Exact Test

In comparing two independent binomial proportions by modified X² tests: Gart's modified likelihood-ratio, Overall and Starbuck's “tailored F”, Pearson's adjusted X²[=X² multiplied by (n - 1)/n] and its skewness-corrected version proposed by Berchtold, it was found that the last two have error probabilities that in the mean are close to the significance level.     

A new natural allotriploid,Lycoris × hubeiensis hybr. nov. (Amaryllidaceae), identified by morphological,karyological and molecular data

A new natural hybrid, Lycoris × hubeiensis K. Liu, is confirmed and described based on morphological, karyological and molecular data. The new natural hybrid displays remarkable morphological differences relative to the putative parents L. radiata (2n = 22 = 22A) and L. aurea (2n = 14 = 8m + 6T), and has a karyotype of 3n = 29 = 4m + 22A + 3T. Two chloroplast intergenic regions of ndhF‐rpl32R and rpl32F‐trnL were sequenced with three haplotypes found in the three taxa. The putative hybrid and L. radiata shared the same haplotype (H1), while L. aurea had two other haplotypes (H2 and H3). Combined with the morphological, karyological and molecular data, we conclude that the hybrid is an allotriploid with L. radiata being the maternal parent offering an unreduced gamete and L. aurea being the male parent.     

The effect of harvest date and harvest method on the combustion characteristics of Miscanthus × giganteus

Miscanthus × giganteus is an energy crop with many attributes that make it a potential biofuel feedstock. This study examined the chemical composition of M. × giganteus stems cut at different dates throughout the spring harvest window (January, February and March) and either left in a swath or left flat in a thin layer on the ground and compared the composition to that of the standing crop collected on the same date in April (control). The research then examined the effect of cutting date on the chemical composition of whole plant M. × giganteus biomass (leaf and stem). The parameters examined in both parts of this experiment were lower heating value on a wet basis (LHV_WB), ash, chlorine, potassium, nitrogen, sulphur, carbon and hydrogen content. The range of values recorded for the parameters from both aspects of this trial were LHV_WB 4.84–11.87 MJ kg^?1; ash 1.44–1.97%; Cl 0.07–0.23%; K 0.15–0.32%; N 0.28–0.39%; S 0.13–0.19%; C 46.75–50.00%; H 5.76–6.09%. The length of time that the M. × giganteus remained in the field after cutting affected the LHV_WB (increased with time) of the stem biomass material. Cutting the biomass and leaving it in the field lowered the ash, Cl and C content of the stem material compared to that of the control which was cut and collected on the same date. No differences were observed for the other parameters. Date of harvest affected the LHV_WB, Cl and C content which all improved with later cutting dates. Thus, combustion quality can be improved by delaying the harvest date or by cutting the crop and leaving it in the field for a period prior to collection. Choosing the correct combination of time and harvest method can therefore improve biomass fuel quality.     

The morphology and activity of the extrafloral nectaries in Reynoutria × bohemica (Polygonaceae)

• Reynoutria × bohemica is an invasive species causing significant damage to native ecosystems in North America and Europe.
• In this work, we performed an in‐depth micromorphological characterisation of the extrafloral nectaries (EFN), during their secretory and post‐secretory phases, in combination with field monitoring of nectary activity over time and the qualitative pool of insect visitors.
• EFN consist of secretory trichomes and vascularised parenchyma. Polysaccharides, lipids and proteins were histochemically detected in all trichome cells; phenolic substances were detected in parenchyma cells. Our data indicate that all nectary regions are involved in nectar production and release, constituting a functional unit. Moreover, the main compound classes of nectar and their transfer change over time: first, granulocrine secretion for sugars prevails, then eccrine secretion of the lipophilic fraction takes place. Active nectaries are mainly located in the apical portion of the stem during the growth phase (April–May), when we detected the highest number of individuals visited by ants; from mid‐August onwards, during flowering, the number of active nectaries declined then ceased production (September), with a concomitant decrease in visits by the ants. The spectrum of nectar‐foraging ants mainly included representatives of the genera Formica, Lasius and Camponotus.
• Reynoutria × bohemica produces an attractive secretion able to recruit local ants that may potentially act as ‘bodyguards’ for protecting young shoots, reducing secretions during the blooming stage. This defence mechanism against herbivores is the same as that displayed by the parental species in its native areas.

     

PtaRHE1, a Populus tremula × Populus alba RING‐H2 protein of the ATL family,has a regulatory role in secondary phloem fibre development

REALLY INTERESTING NEW GENE (RING) proteins play important roles in the regulation of many processes by recognizing target proteins for ubiquitination. Previously, we have shown that the expression of PtaRHE1, encoding a Populus tremula × Populus alba RING‐H2 protein with E3 ubiquitin ligase activity, is associated with tissues undergoing secondary growth. To further elucidate the role of PtaRHE1 in vascular tissues, we have undertaken a reverse genetic analysis in poplar. Within stem secondary vascular tissues, PtaRHE1 and its corresponding protein are expressed predominantly in the phloem. The downregulation of PtaRHE1 in poplar by artificial miRNA triggers alterations in phloem fibre patterning, characterized by an increased portion of secondary phloem fibres that have a reduced cell wall thickness and a change in lignin composition, with lower levels of syringyl units as compared with wild‐type plants. Following an RNA‐seq analysis, a biological network involving hormone stress signalling, as well as developmental processes, could be delineated. Several candidate genes possibly associated with the altered phloem fibre phenotype observed in amiRPtaRHE1 poplar were identified. Altogether, our data suggest a regulatory role for PtaRHE1 in secondary phloem fibre development.     

Assessing nitrate leaching during the three‐first years of Miscanthus × giganteus from on‐farm measurements and modeling

Miscanthus × giganteus is often regarded as one of the most promising crops to produce sustainable bioenergy. This perennial crop, renowned for its high productivity associated with low input requirements, in particular regarding fertilizers, is thought to have low environmental impacts, but few data are available to confirm this. Our study aimed at assessing nitrate leaching from Miscanthus × giganteus crops in farmers' fields, thus including a wide range of soil and cropping system conditions. We focused on the first years of growth after planting as experimental studies have suggested that Miscanthus × giganteus, once established, results in low nitrate leaching. We combined on‐farm measurements and modeling to estimate drainage, leached nitrogen, and nitrate concentration in drainage water in 38 fields located in Center‐East France during two winters (November 2010 to March 2011, November 2011 to March 2012). Nitrate leaching and nitrate concentration in drainage water were on average very low. Nitrate leaching averaged 6 kg N ha^?1 whereas nitrate concentration averaged 12 mg l^?1. These low values are attributable to the low estimates of drainage water (mean = 166 mm) but also to the low soil mineral nitrogen contents measured at the beginning of winter (mean = 37 kg N ha^?1). Our results were, however, very variable, mainly due to the crop age: nitrate leaching and nitrate concentration were critically higher during the winter following the first growth year of Miscanthus × giganteus, reflecting the low development of the crop. This variability was also explained by the range of soil and cropping conditions explored in the on‐farm design: shallow and/or sandy soils as well as fields where establishment failed had a higher risk of nitrate leaching.     

On analytical methods and inferences for 2×2 contingency table data using wildlife examples

The 2×2 contingency table is a common analytical method for wildlife studies, but inappropriate analyses and inferences are not uncommon. Issues of concern are presented for selecting the appropriate test for analyzing these data sets. These include the choice of test relative to experimental or sampling design and breadth of intended inferences, the careful statement of hypotheses, and analyses with small sample sizes. Examples from the wildlife literature are used to reinforce the statistical concepts.     

Temperature × light interaction and tolerance of high water temperature in the planktonic freshwater flagellates Cryptomonas (Cryptophyceae) and Dinobryon (Chrysophyceae)

Using microcosm experiments, we investigated the interactive effects of temperature and light on specific growth rates of three species each of the phytoplanktonic genera Cryptomonas and Dinobryon. Several species of these genera play important roles in the food web of lakes and seem to be sensitive to high water temperature. We measured growth rates at three to four photon flux densities ranging from 10 to 240 μmol photon · m^?2 · s^?1 and at 4–5 temperatures ranging from 10°C to 28°C. The temperature × light interaction was generally strong, species specific, and also genus specific. Five of the six species studied tolerated 25°C when light availability was high; however, low light reduced tolerance of high temperatures. Growth rates of all six species were unaffected by temperature in the 10°C–15°C range at light levels ≤50 μmol photon · m^?2 · s^?1. At high light, growth rates of Cryptomonas spp. increased with temperature until the temperature optimum was reached and then declined. The Dinobryon species were less sensitive than Cryptomonas spp. to photon flux densities of 40 μmol photon · m^?2 · s^?1 and 200 μmol photon · m^?2 · s^?1 over the entire temperature range but did not grow under a combination of very low light (10 μmol photon · m^?2 · s^?1) and high temperature (≥20°C). Among the three Cryptomonas species, cell volume declined with temperature and the maximum temperature tolerated was negatively related to cell size. Since Cryptomonas is important food for microzooplankton, these trends may affect the pelagic carbon flow if lake warming continues.     

Modeled spatial assessment of biomass productivity and technical potential of Miscanthus × giganteus,Panicum virgatum L., and Jatropha on marginal land in China

This article identifies marginal land technically available for the production of energy crops in China, compares three models of yield prediction for Miscanthus × giganteus, Panicum virgatum L. (switchgrass), and Jatropha, and estimates their spatially specific yields and technical potential for 2017. Geographic Information System (GIS) analysis of land use maps estimated that 185 Mha of marginal land was technically available for energy crops in China without using areas currently used for food production. Modeled yields were projected for Miscanthus × giganteus, a GIS‐based Environmental Policy Integrated Climate model for switchgrass and Global Agro‐Ecological Zone model for Jatropha. GIS analysis and MiscanFor estimated more than 120 Mha marginal land was technically available for Miscanthus with a total potential of 1,761 dry weight metric million tonne (DW Mt)/year. A total of 284 DW Mt/year of switchgrass could be obtained from 30 Mha marginal land, with an average yield of 9.5 DW t ha^?1 year^?1. More than 35 Mha marginal land was technically available for Jatropha, delivering 9.7 Mt/year of Jatropha seed. The total technical potential from available marginal land was calculated as 31.7 EJ/year for Miscanthus, 5.1 EJ/year for switchgrass, and 0.13 EJ/year for Jatropha. A total technical bioenergy potential of 34.4 EJ/year was calculated by identifying best suited crop for each 1 km² grid cell based on the highest energy value among the three crops. The results indicate that the technical potential per hectare of Jatropha is unable to compete with that of the other two crops in each grid cell. This modeling study provides planners with spatial overviews that demonstrate the potential of these crops and where biomass production could be potentially distributed in China which needs field trials to test model assumptions and build experience necessary to translate into practicality.     

On the Equivalence of the Information-Theoretic Transmission-Measure to the Common χ2 Statistic

The results of a simulation study are presented in which the χ²-and the information theoretic approach to association measurement were compared to one another. It could be shown that neither the maximal values nor the minimal values obtainable for a given sample size coincide in all cases. The underlying association concepts are defined; implications are discussed.     

Spatiotemporal assessment of farm‐gate production costs and economic potential of Miscanthus × giganteus,Panicum virgatum L., and Jatropha grown on marginal land in China

Spatially explicit farm‐gate production costs and the economic potential of three types of energy crops grown on available marginal land in China for 2017 and 2040 were investigated using a spatial accounting method and construction of cost–supply curves. The average farm‐gate cost from all available marginal land was calculated as 32.9 CNY/GJ for Miscanthus Mode, 27.5 CNY/GJ for Switchgrass Mode, 32.4 CNY/GJ for Miscanthus & Switchgrass Mode, and 909 CNY/GJ for Jatropha Mode in 2017. The costs of Miscanthus and switchgrass were predicted to decrease by approximately 11%‐15%, whereas the cost of Jatropha was expected to increase by 5% in 2040. The cost of Jatropha varies significantly from 193 to 9,477 CNY/GJ across regions because of the huge differences in yield across regions. The economic potential of the marginal land was calculated as 28.7 EJ/year at a cost of less than 25 CNY/GJ for Miscanthus Mode, 4.0 EJ/year at a cost of less than 30 CNY/GJ for Switchgrass Mode, 29.6 EJ/year at a cost of less than 25 CNY/GJ for Miscanthus & Switchgrass Mode, and 0.1 EJ/year at a cost of less than 500 CNY/GJ for Jatropha Mode in 2017. It is not feasible to develop Jatropha production on marginal land based on existing technologies, given its high production costs. Therefore, the Miscanthus & Switchgrass Mode is the most economical way, because it achieves the highest economic potential compared with other modes. The sensitivity analysis showed that the farm‐gate costs of Miscanthus and switchgrass are most sensitive to uncertainties associated with yield reduction and harvesting costs, while, for Jatropha, the unpredictable yield has the greatest impact on its farm‐gate cost. This study can help policymakers and industrial stakeholders make strategic and tactical bioenergy development plans in China (exchange rate in 2017: 1€ = 7.63￥; all the joules in this paper are higher heat value).     

Further crystallographic evidence of NH· · ·π (system) and CO· · ·π (system) interactions: The structures of bis(diarylhydrazonecarbonyl)methylene derivatives [{ArPhCNNH—C(O)}2CH2] (Ar = Ph, 2‐C5H4N, 2‐C4H3S)

In this study are reported the syntheses of three bis(diarylhydrazonecarbonyl)methylene derivatives [{ArPhCNNH C(O)}₂CH₂] [Ar = 2 C₅H₄N (5), C₆H₅ (6), and 2‐C₄H₃S (7)], obtained by condensation of corresponding hydrazones with carbon suboxide, C₃O₂. The solid‐state self‐assembly of these carbonyl derivatives, giving rise to polymeric and dimeric networks, is described. In the formation of these structural features, in addition to N—H· · ·OC intermolecular hydrogen bonds, stabilizing intramolecular NH· · · π (systems) and intermolecular CO· · ·π (systems) interactions also seem to play an important role. Solution ¹H‐nmr data of compounds 5–7 indicate that the polymeric and dimeric structures are not maintained in solution and show the occurrence of keto‐enolic equilibria. © 1999 John Wiley & Sons, Inc. Biopoly 49: 541–549, 1999     

Development and validation of a high-performance liquid chromatography assay for the quantitative determination of 7-oxo-dehydroepiandrosterone-3β-sulfate in human plasma

A new, simple, reproducible and reliable high-performance liquid chromatography method with ultraviolet absorbance detection at 240 nm was developed and validated for the determination of 7-oxo-dehydroepiandrosterone-3β-sulfate in human plasma. The method was based upon solid-phase (C₁₈) extraction of plasma after addition of 17β-hydroxy-3β-methoxyandrost-5-en-7-one as internal standard. Using 1 ml of plasma for extraction, the detection limit of the assay was 3 ng/ml. The standard curve was linear over the concentration range 10–1000 ng/ml. Stored at −20°C for about 4 months at various concentrations in plasma, 7-oxo-dehydroepiandrosterone-3β-sulfate did not reveal any appreciable degradation. Also included herein is a method for the simultaneous detection and determination of 7-oxo-dehydroepiandrosterone and 7-oxo-dehydroepiandrosterone-3β-acetate in plasma.     

Cryptic association of B7‐2 molecules and its implication for clustering

T‐cell co‐stimulation through CD28/CTLA4:B7‐1/B7‐2 axis is one of the extensively studied pathways that resulted in the discovery of several FDA‐approved drugs for autoimmunity and cancer. However, many aspects of the signaling mechanism remain elusive, including oligomeric association and clustering of B7‐2 on the cell surface. Here, we describe the structure of the IgV domain of B7‐2 and its cryptic association into 1D arrays that appear to represent the pre‐signaling state of B7‐2 on the cell membrane. Super‐resolution microscopy experiments on heterologous cells expressing B7‐2 and B7‐1 suggest, B7‐2 form relatively elongated and larger clusters compared to B7‐1. The sequence and structural comparison of other B7 family members, B7‐1:CTLA4 and B7‐2:CTLA‐4 complex structures, support our view that the observed B7‐2 1D zipper array is physiologically important. This observed 1D zipper‐like array also provides an explanation for its clustering, and upright orientation on the cell surface, and avoidance of spurious signaling.     

The role of calcium in apoptosis induced by 7β‐hydroxycholesterol and cholesterol‐5β,6β‐epoxide

Oxysterols, such as 7β‐hydroxy‐cholesterol (7β‐OH) and cholesterol‐5β,6β‐epoxide (β‐epoxide), may have a central role in promoting atherogenesis. This is thought to be predominantly due to their ability to induce apoptosis in cells of the vascular wall and in monocytes/macrophages. Although there has been extensive research regarding the mechanisms through which oxysterols induce apoptosis, much remains to be clarified. Given that experimental evidence has long associated alterations of calcium (Ca²⁺) homeostasis to apoptotic cell death, the aim of the present study was to determine the influence of intracellular Ca²⁺ changes on apoptosis induced by 7β‐OH and β‐epoxide. Ca²⁺ responses in differentiated U937 cells were assessed by epifluorescence video microscopy, using the ratiometric dye fura‐2. Over 15‐min exposure of differentiated U937 cells to 30 μM of 7β‐OH induced a slow but significant rise in fura‐2 ratio. The Ca²⁺ channel blocker nifedipine and the chelating agent EGTA blocked the increase in cytoplasmic Ca²⁺. Moreover, dihydropyridine (DHP) binding sites identified with BODIPY‐FLX‐DHP were blocked following pretreatment with nifedipine, indicating that the influx of Ca²⁺ occurred through L‐type channels. However, following long‐term incubation with 7β‐OH, elevated levels of cytoplasmic Ca²⁺ were not maintained and nifedipine did not provide protection against apoptotic cell death. Our results indicate that the increase in Ca²⁺ may be an initial trigger of 7β‐OH–induced apoptosis, but following chronic exposure to the oxysterol, the influence of Ca²⁺ on apoptotic cell death appears to be less significant. In contrast, Ca²⁺ did not appear to be involved in β‐epoxide–induced apoptosis. © 2009 Wiley Periodicals, Inc. J Biochem Mol Toxicol 23:324–332, 2009; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20295     

Selection and optimization of MCF‐7 cell line for screening selective inhibitors of 11β‐hydroxysteroid dehydrogenase 2

An 11β‐hydroxysteroid dehydrogenase type 1 (11β‐HSD1) produces glucocorticoid (GC) from 11‐keto metabolite, and its modulation has been suggested as a novel approach to treat metabolic diseases. In contrast, type 2 isozyme 11β‐HSD2 is involved in the inactivation of glucocorticoids (GCs), protecting the non‐selective mineralocorticoid receptor (MR) from GCs in kidney. Therefore, when 11β‐HSD1 inhibitors are pursued to treat the metabolic syndrome, preferential selectivity of inhibitors for type 1 over type 2 isozyme is rather important than inhibitory potency. Primarily, to search for cell lines with 11β‐HSD2 activity, we investigated the expression profiles of enzymes or receptors relevant to GC metabolism in breast, colon, and bone‐derived cell lines. We demonstrated that MCF‐7 cells had high expression for 11β‐HSD2, but not for 11β‐HSD1 with its cognate receptor. Next, for the determination of enzyme activity indirectly, we adopted homogeneous time resolved fluorescence (HTRF) cortisol assay. Obviously, the feasibility of HTRF to cellular 11β‐HSD2 was corroborated by constructing inhibitory response to an 11b‐HSD2 inhibitor glycyrrhetinic acid (GA). Taken together, MCF‐7 that overexpresses type 2 but not type 1 enzyme is chosen for cellular 11β‐HSD2 assay, and our results show that a nonradioactive HTRF assay is applicable for type 2 as well as type 1 isozyme. Copyright © 2010 John Wiley & Sons, Ltd.     

A method for rapid and sensitive negative staining of proteins in SDS‐PAGE using 2′,7′‐dichlorofluorescein

We report here a rapid and sensitive technique for negative visualization of protein in 1D and 2D SDS‐PAGE by using 2′, 7′‐dichlorofluorescein (DCF), which appeared as transparent and colorless bands in an opaque gel matrix background. For DCF stain, down to 0.1–0.2 ng protein could be easily visualized within 7 min by only two steps, and the staining is fourfold more sensitive than that of Eosin Y (EY) negative stain and glutaraldehyde (GA) silver stain, and eightfold more sensitive than that of the commonly used imidazole‐zinc (IZ) negative stain. Furthermore, DCF stain provided good reproducibility, linearity, and MS compatibility compared with those of IZ stain. In addition, the potential staining mechanism was investigated by colorimetric experiment and molecular docking, and the results demonstrated that the interaction between DCF and protein occurs mainly via van der waals force, electrostatic interaction, and hydrogen bonding.