Spandrels and a pervasive problem of evidence

Evolutionary biology, indeed any science that attempts to reconstruct prehistory, faces practical limitations on available data. These limitations create the problem of contrast failure: specific observations may fail to discriminate between rival evolutionary hypotheses. Assessing the risk of contrast failure provides a way to evaluate testing protocols in evolutionary science. Here I will argue that part of the methodological critique in the Spandrels paper involves diagnosing contrast failure problems. I then distinguish the problem of contrast failure from the more familiar philosophical problem of underdetermination, and demonstrate how contrast failure arises in scientific practice with an investigation into Lewontin and White’s (Evolution 14:116–129, 1960) estimation of an adaptive landscape.

Insecticide resistance and control failure likelihood of the whitefly Bemisia tabaci (MEAM1; B biotype): a Neotropical scenario

Insecticide resistance is a standing concern for arthropod pest species, which may result in insecticide control failure. Nonetheless, while insecticide resistance has remained a focus of attention for decades, the incurring risk of insecticide control failure has been neglected. The recognition of both problems is paramount for arthropod pest management and particularly so when invasive species notoriously difficult to control and exhibiting frequent cases of insecticide resistance are considered. Such is the case of the putative whitefly species Middle East‐Asia Minor I (MEAM1) (Bemisia tabaci B‐biotype), for which little information is available in the Neotropics. Thus, the likely occurrence and levels of resistance to seven insecticides were surveyed among Brazilian populations of this species. The likelihood of control failure to the five insecticides registered for this species was also determined. Resistance was detected to all insecticides assessed reaching instances of high (i.e. >100×) to very high levels (>1000×) in all of them. Overall efficacy was particularly low (<60%) and the control failure likelihood was high (>25%) and frequent (70%) for the bioinsecticide azadirachtin, followed by spiromesifen and lambda‐cyhalothrin. In contrast, the likelihood of control failure was low for diafenthiuron, and mainly imidacloprid. As cartap and chlorantraniliprole are not used against whiteflies, but are frequently applied on the same host plants, inadvertent selection probably took place leading to high levels of resistance, particularly for the latter. The resistance levels of cartap and chlorantraniliprole correlated with imidacloprid resistance (r > 0.65, P < 0.001), suggesting that the latter use may have somewhat favoured inadvertent selection for resistance to both compounds not used against the whitefly. A further concern is that chlorantraniliprole use in the reported scenario may allow cross selection to cyantraniliprole, a related diamide with recent registration against whiteflies demanding attention in designing resistance management programmes.     

基于FMEA的C形臂X线机的使用风险分析与控制

??????? 目的 基于失效模式与效应分析（FMEA）方法分析控制C形臂X线机的使用风险。方法 成立FMEA 5人小组,运用现场观察和访谈的方法,识别C形臂X线机使用的潜在失效模式,并对其发生的严重度、发生概率及检测的难易度进行评价打分,计算失效原因的风险优先指数。结果 FMEA小组找出了必须优先解决的C臂机使用的失效模式,制定并实施了改进措施,在不增加管理成本的基础上,取得了良好的管理效果。结论 FMEA可以评估医疗设备使用过程的失效,并能排序优先解决的问题,不增加管理成本就能预防问题的发生,是有效的过程管理工具。     

Preventing Overestimation of Pixels in Computed Tomography Assessment of Visceral Fat

Objective: Computed tomography (CT) is a common research procedure for measuring abdominal fat distribution, but little is written about the software used to analyze images. Our objective was to compare in‐house and commercially available software for quantitative measurement of abdominal fat distribution. In the process, we encountered some unexpected problems. Research Methods and Procedures: A total of 123 volunteers had single‐slice abdominal CT images taken that were used to evaluate various aspects of the commercial image analysis program. Results: The agreement between the commercial and in‐house programs was excellent (r = 0.996, p < 0.00, 001) for both total and intraabdominal fat, and we were able to reduce between‐observer variability in measured fat areas through the use of statistical handling of region of interest information. We also noted that intracolonic contents sometimes had the same Hounsfield units as adipose tissue. We analyzed single‐slice CT images from 50 volunteers to determine the potential impact of this effect on visceral fat area; the overestimate of visceral fat area was 19 ± 22% (maximum, 112% overestimate). The commercial program could prevent this error, whereas our in‐house program could not. Discussion: We concluded that a readily available commercial image analysis program compares well with a previously validated in‐house program and that it offers some advantages with respect to preventing overestimation of pixels as visceral fat.     

Subspecies of the Eeuropean beaver<Emphasis Type="Italic">Castor fiber</Emphasis> Linnaeus, 1758

Subspecific relationships of the European beaverCastor fiber have been obscured by failure to follow the rules of the International Code of Zoological Nomenclature and remain an open issue. Inconsequence in the use of subspecies names caused a nomenclatural as well as a taxonomic confusion. We discuss these controversial and incorrect nomenclatural decisions, and recognize 9 nominal subspecies of European beaver, bearing 9 available names:C. f. fiber Linnaeus, 1758,C. f. galliae Geoffroy, 1803, C. f. albicus Matschie, 1907,C. f. vistulanus Matschie, 1907,C. f. pohlei Serebrennikov, 1929,C. f. birulai Serebrennikov, 1929,C. f. tuvinicus Lavrov, 1969,C. f. belorussicus Lavrov, 1981, andC. f. orientoeuropaeus Lavrov, 1981.     

Assessment of changes in oral health‐related quality of life among patients with complete denture before and 1 month post‐insertion using Geriatric Oral Health Assessment Index

doi:10.1111/j.1741‐2358.2009.00323.x
Assessment of changes in oral health‐related quality of life among patients with complete denture before and 1 month post‐insertion using Geriatric Oral Health Assessment Index Objective: Geriatric Oral Health Assessment Index (GOHAI) is a 12‐item measure of “patient‐reported oral functional problems” intended for use in the assessment of the effectiveness of dental treatment. Design and Setting: As there is scanty literature available on GOHAI in the Indian population, the present study was undertaken to assess the changes in GOHAI before and 1 month after placement of dentures in completely edentulous patients reporting to a dental hospital at Indore, India. Measurements: The GOHAI questionnaire was completed by the examiner who interviewed the patients (n = 35) before placement of complete dentures and 1 month later. Mean, median values were calculated and the data were analysed using Wilcoxon signed‐rank test. Results: When overall mean was considered, the GOHAI scores increased from 27.48 to 30.19 (p = 0.002; highly significant). Conclusion: Patients reported improvement in functional changes after placement of complete dentures.     

Immunocontraception of captive exotic species

The biological efficacy of porcine zona pellucida (PZP) immunocontraception and the timing of booster inoculations were determined in 24 species of ungulates and five species of non‐ungulates across 10 years of treatment and for which no technical problems were identified. The collective contraceptive efficacy for 265 ungulates, 25 bears, and 11 sea lions, across 517 contraceptive intervals was 93.3%, and contraceptive efficacy ranged from a low of 60% in nyala (Taurotragus angasi) to 100% in 16 other species. The timing of annual booster inoculations was adjusted, between 6 months and 12 months, depending on the length of the breeding season and the species‐specific immune responses. The high degree of efficacy in bears and sea lions suggests that the PZP vaccine has some application in certain non‐ungulate species. Technical problems in the timing and delivery of the vaccine can cause non‐biological failures and were identified in an additional 20 animals, not included above, and included inoculating pregnant animals, the use of needles too short for effective intramuscular injections, failure to complete the initial inoculation series, and failure to give booster inoculations at the prescribed time. Zoo Biol 0:1–10, 2005. © 2005 Wiley‐Liss, Inc.     

Assessing group differences in biodiversity by simultaneously testing a user‐defined selection of diversity indices

Comparing diversities between groups is a task biologists are frequently faced with, for example in ecological field trials or when dealing with metagenomics data. However, researchers often waver about which measure of diversity to choose as there is a multitude of approaches available. As Jost (2008, Molecular Ecology, 17 , 4015) has pointed out, widely used measures such as the Shannon or Simpson index have undesirable properties which make them hard to compare and interpret. Many of the problems associated with the use of these ‘raw’ indices can be corrected by transforming them into ‘true’ diversity measures. We introduce a technique that allows the comparison of two or more groups of observations and simultaneously tests a user‐defined selection of a number of ‘true’ diversity measures. This procedure yields multiplicity‐adjusted P‐values according to the method of Westfall and Young (1993, Resampling‐Based Multiple Testing: Examples and Methods for p‐Value Adjustment, 49, 941), which ensures that the rate of false positives (type I error) does not rise when the number of groups and/or diversity indices is extended. Software is available in the R package ‘simboot’.     

Biological nitrogen fixation for sustainable agriculture: A perspective

The economic and environmental costs of the heavy use of chemical N fertilizers in agriculture are a global concern. Sustainability considerations mandate that alternatives to N fertilizers must be urgently sought. Biological nitrogen fixation (BNF), a microbiological process which converts atmospheric nitrogen into a plant-usable form, offers this alternative. Nitrogen-fixing systems offer an economically attractive and ecologically sound means of reducing external inputs and improving internal resources. Symbiotic systems such as that of legumes and Rhizobium can be a major source of N in most cropping systems and that of Azolla and Anabaena can be of particular value to flooded rice crop. Nitrogen fixation by associative and free-living microorganisms can also be important. However, scientific and socio-cultural constraints limit the utilization of BNF systems in agriculture. While several environmental factors that affect BNF have been studied, uncertainties still remain on how organisms respond to a given situation. In the case of legumes, ecological models that predict the likelihood and the magnitude of response to rhizobial inoculation are now becoming available. Molecular biology has made it possible to introduce choice attributes into nitrogen-fixing organisms but limited knowledge on how they interact with the environment makes it difficult to tailor organisms to order. The difficulty in detecting introduced organisms in the field is still a major obstacle to assessing the success or failure of inoculation. Production-level problems and socio-cultural factors also limit the integration of BNF systems into actual farming situations. Maximum benefit can be realized only through analysis and resolution of major constraints to BNF performance in the field and adoption and use of the technology by farmers.     

Mycobacteria: Bugs and bugbears (Two steps forward and one step back)

The use of molecular techniques to study the mycobacteria has advanced greatly since the first genomic libraries of Mycobacterium tuberculosis and M. leprae were constructed in 1985. However, there are still pitfalls for the unwary. Most of the problems associated with the use of molecular techniques to study mycobacteria can be related to one of the following problems: slow growth rate causing problems with contamination; the formation of macroscopic clumps when grown in culture; resistance to standard chemical lysis procedures; the requirement for containment facilities for pathogenic species; the lack of suitable genetic vectors; and the problems of spontaneous antibiotic resistance. Despite these problems, considerable progress has been made and standard techniques have been developed for the preparation of protein, nucleic acids (DNA and RNA) and cell wall components, chemical and transposon mutagenesis and gene replacement methods, the use of reporter genes and expression vectors, and improved detection and drug sensitivity testing.     

塔克拉玛干沙漠南缘荒漠绿洲过渡带不同土地利用影响下土壤化学计量特征

荒漠绿洲过渡带在维护绿洲生态安全和绿洲稳定上具有重要作用。垦荒等土地利用的增强使得荒漠绿洲过渡带的健康稳定受到了巨大的挑战。以塔克拉玛干沙漠南缘典型荒漠绿洲过渡带为研究对象,系统分析了不同土地利用方式(桑田、半自然柽柳林、瓜地、棉花-玉米地)对土壤养分化学计量特征的影响。土壤取样沿农田到荒漠方向进行,分5层进行。研究发现,土壤各养分指标均受土地利用方式(4种)、土层(5层)和与农田边缘垂直距离(4梯度)的显著影响,且存在一定的交互作用。土地利用方式显著影响土壤各养分元素含量。随土层由浅到深,有机碳(C)、有效氮(N)和有效磷(P)基本呈下降趋势,全N具有波动变化,而全P变化不显著。随与农田边缘垂直距离的增加,各养分含量基本呈递减趋势。对同一土层(共选择三层)不同土地利用方式下土壤养分具体分析表明,棉花-玉米地这一利用方式在农田内部具有最高的土壤有机C和全N含量,其次为桑田。随着与农田边缘垂直距离的增加,土壤C、N含量优势减弱。除农田内部样地(0 m)外,三层土壤全P含量基本呈桑田柽柳林棉花-玉米地趋势。表层有效N含量在农田内部样地(0 m)瓜地最高,其他距离处(大于等于20 m)棉花-玉米地高,下层土壤有效氮含量在农田内部各土地利用方式间无差异。在各距离样点处不同土地利用类型间土壤有效P含量的变化无明显规律,在农田内部以瓜地有效P含量最高。棉花-玉米地土壤全量N/P在农田内部和与农田边缘垂直距离20 m处含量最高。三土层土壤有效N/P在农田内部以柽柳林最高,随着与农田边缘垂直距离增加,土壤有效N/P显著改变。综合来看,土地利用对荒漠绿洲过渡带土壤营养含量的增加具有正向作用,由土壤养分变化带来的生态效应值得关注。     

Significance of lytic enzymes from Trichoderma spp. in the biocontrol of fungal plant pathogens

The use of specific mycolytic soil microorganisms to control plant pathogens is an ecological approach to overcome the problems caused by standard chemical methods of plant protection. The ability to produce lytic enzymes is a widely distributed property of rhizosphere-competent fungi and bacteria. Due to the higher activity of Trichoderma spp. lytic enzymes as compared to the same class of enzymes from other microorganisms and plants, effort is being aimed at improving biocontrol agents and plants by introducing Trichoderma genes via genetic manipulations. An overview is presented of the data currently available on lytic enzymes from the mycoparasitic fungus Trichoderma. This revised version was published online in August 2006 with corrections to the Cover Date.     

Evidence that impaired citrate transport into the cell is a contributory factor to extracellular citrate accumulation by a strain of Candida guilliermondii

Candida guilliermondii IMK 1 is a mutant strain that accumulates concentrations of citric acid approximately seven times higher than does its parent strain, NRRL Y-448. In contrast to its parent, strain IMK 1 cannot use citrate as the sole carbon source, or assimilate citrate in the presence of glucose. Measurements of membrane ATPase activity show consistently lower values in the mutant strain than in its parent. It is suggested that failure to re-assimilate the excreted citrate is a major contributory factor in the extracellular accumulation of high citrate concentrations, and that this failure is related to a defect in the membrane structure. Correspondence to: N. A. Gutierrez     

Behaviour of interleukin-2 serum levels in advanced non-small-cell lung cancer patients: relationship with response to therapy and survival

 Interleukin(IL)-2 is a T helper (Th) 1 type cytokine that has been shown to play an important role in antitumour immune responses. In this study, the prognostic significance of serum IL-2 levels was investigated in 60 advanced non-small-cell lung cancer (NSCLC) patients. IL-2 serum levels were determined before chemotherapy, at the end of chemotherapy and during follow-up, using a commercially available enzyme-linked immunoadsorbent assay kit. The results were analysed according to the response to therapy and were used to generate a model predicting overall survival and time to treatment failure. All 60 patients were shown to have higher IL-2 serum levels than controls (P < 0.0001). Stage IV patients had significantly lower IL-2 levels than stage III patients (P < 0.0001), although they were still significantly higher than controls (P < 0.0001). It is interesting that, when patients were divided into responders and non-responders according to the response to therapy, the former were shown to have significantly higher pre-chemotherapy levels than the latter (P < 0.0001). Moreover, a further significant increase in IL-2 serum levels (P=0.004) and a significant decrease (P < 0.0001) were shown in responders and non-responders, respectively at the end of the therapy. Using univariate and multivariate analyses, both overall survival and time to treatment failure were shown to be affected by the mean pathological levels of IL-2. Furthermore, the prognostic significance of the serum level of IL-2 was confirmed by the stepwise regression analysis. In conclusion, determination of pre-treatment IL-2 serum levels was shown to be of independent prognostic utility in patients with advanced NSCLC; therefore, its possible use for prediction of outcome is proposed. Received: 16 March 2000 / Accepted: 27 July 2000     

High yield expression of an AHL-lactonase from <Emphasis Type="Italic">Bacillus</Emphasis> sp. B546 in <Emphasis Type="Italic">Pichia pastoris</Emphasis> and its application to reduce <Emphasis Type="Italic">Aeromonas hydrophila</Emphasis> mortality in aquaculture

Background  

Aeromonas hydrophila is a serious pathogen and can cause hemorrhagic septicemia in fish. To control this disease, antibiotics and chemicals are widely used which can consequently result in "superbugs" and chemical accumulation in the food chain. Though vaccine against A. hydrophila is available, its use is limited due to multiple serotypes of this pathogen and problems of safety and efficacy. Another problem with vaccination is the ability to apply it to small fish especially in high numbers. In this study, we tried a new way to attenuate the A. hydrophila infection by using a quorum quenching strategy with a recombinant AHL-lactonase expressed in Pichia pastoris.     

First report of amitraz and cypermethrin resistance in Rhipicephalus sanguineus sensu lato infesting dogs in Mexico

Engorged female Rhipicephalus sanguineus sensu lato (Ixodida: Ixodidae) were collected from dogs in the state of Yucatán, Mexico. Fourteen tick populations were collected from dogs at seven veterinary clinics, four residential homes and three cattle farms. The larval immersion test was used in the progeny of collected adult females to test susceptibility to amitraz and cypermethrin. Dose–mortality regressions, 50% lethal concentrations (LC₅₀), confidence intervals and slope were estimated by probit analysis. For amitraz, 12 tick populations (85.7%) were classified as resistant and low inter‐population variation in the phenotypic level of resistance was evident [resistance ratios (RRs) at LC₅₀: 1.0–13.0]. For cypermethrin, 12 tick populations (85.7%) were classified as resistant and substantial inter‐population variation in the phenotypic level of resistance was evident (RRs at LC₅₀: 1.0–104.0). Thus, amitraz resistance in R. sanguineus s.l. is common, but generally occurs at low levels; however, alarmingly high levels of cypermethrin resistance are present in R. sanguineus s.l. populations in dogs in Yucatán, Mexico. The intensive use of both acaricides to control ectoparasites on dogs is likely to lead to more serious resistance problems that may cause high levels of control failure in the future.     

AM1* parameters for bromine and iodine

Our extension of the AM1 semiempirical molecular orbital technique, AM1*, has been parameterized for the elements Br and I. The basis sets for both halogens contain a set of d-orbitals as polarization functions. AM1* performs as well as other MNDO-like methods that use d-orbitals in the basis, and better than those that rely on an sp-basis. Thus, AM1* parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, Cu, Zn, Br, Zr, Mo and I. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

English names for a world list of mammals, exemplified by species of Indochina

1. The lack of a globally accepted list of English‐language names for mammal species leads to various problems stemming from the reduced ability to communicate unambiguously. This impacts directly on their conservation. We use the larger mammals of Indochina to exemplify the use of an explicit set of principles designed to provide each species with a unique and non‐misleading (or at least minimally so) English name. 2. For most species, a suitable name is already in use, sometimes generally so. For species for which multiple names are in use, standardization would consist of adopting the most suitable name. Only for a very few species are all extant names so unsuitable that a neologism should be coined. One species, Panthera pardus, presents potentially insoluble problems. 3. Name standardization among the world's birds has generated some controversy, but this has not led to abandonment of the process. Much can be learned by those developing a similar process for mammals, through studying the bird‐naming process. Progress can be advanced by detractors indicating whether they oppose standardization per se, the principles used or the names resulting from application of the principles. Also, proponents of standardization should always emphasize that the purpose of the process is to produce a list available for those who want to use it, not to produce a binding selection that must be used in all circumstances.     

Tables and Procedures for the Determination of Power and Sample Sizes in Univariate and Multivariate Analyses of Variance and Regression

The available power tables for use in experimental design only serve for limited practical purposes, since they are restricted to very few levels of significance such as .01, .05, and .10. With these values, however, usually no correction for cumulating error probabilities, for example, by the Dunn-Bonferroni method, can be achieved, because (very) low values of a and sometimes even of α are necessary. Therefore, power tables are presented that encompass a wide range of different values for a (.0005 to .40), for power (.50 to .9995), and for 45 different values of the degrees of freedom for the numerator of the F ratio (u = 1 to 150). Four of the 16 tables are printed. Their use is demonstrated for some paradigmatic problems in univariate and multivariate analyses of variance and regression.     

How do trees die? A test of the hydraulic failure and carbon starvation hypotheses

Despite decades of research on plant drought tolerance, the physiological mechanisms by which trees succumb to drought are still under debate. We report results from an experiment designed to separate and test the current leading hypotheses of tree mortality. We show that piñon pine (Pinus edulis) trees can die of both hydraulic failure and carbon starvation, and that during drought, the loss of conductivity and carbohydrate reserves can also co‐occur. Hydraulic constraints on plant carbohydrate use determined survival time: turgor loss in the phloem limited access to carbohydrate reserves, but hydraulic control of respiration prolonged survival. Our data also demonstrate that hydraulic failure may be associated with loss of adequate tissue carbohydrate content required for osmoregulation, which then promotes failure to maintain hydraulic integrity.