Bootstrap Confidence Research Articles

First Report of False Rust caused by Synchytrium psophocarpi on Winged Bean (Psophocarpus tetragonolobus) in Taiwan.

From September 2020 to January 2021, an unknown disease of winged bean (Psophocarpus tetragonolobus) was reported by local growers in the Toucheng Town, Yilan County (N24.91, E121.85). The disease occurs in all age of winged bean, and the occurrence tended to be higher in humid environment, such as branches in lower canopy or branches in high density. The disease symptoms, which also appeared to be the sign of the pathogen, were spherical pustules in yellow to orange color on the stems, leaves, and pods of winged bean. Severely infected plants also exhibited growth reduction, malformation, and curling of the leaves and pods. According to the disease literature of winged bean, this unknown disease was likely to be the false rust caused by a chytrid pathogen, Synchytrium psophocarpi (UK, CAB International. 1993); and the uredinia-liked pustules could be the sori, which contain numerous ovoid to globose sporangia inside. In order to characterize the pathogen identity, the sori were manually ruptured to assess the size of individual sporangium, which had an average of 26.71 ± 4.25 μm x 26.61 ± 4.60 μm (n=42), similar to the size reported in literature (Drinkall and Price. 1979). To confirm the molecular identity, the full genomic sequences from the small subunit (SSU) to the internal transcribed spacer-1 (ITS-1), 5.8S unit, and ITS-2 were amplified using the primer sets NS3 and ITS4. The 2,263 bp amplicon was cloned and sequenced to reveal the identity (Smith et al. 2014). The BLASTN results matched the SSU of our isolate (MW649126.1) to the Synchytrium minutum (HQ324138.1) with 96% similarity (1,075 out of 1,121 bp in length), Synchytrium decipiens isolate DAOM_87618 (KF160868.1) with 92% similarity (1,215 out of 1,326 bp in length) and S. decipiens isolate AFTOL-ID 634 (DQ536475.1) with 92% similarity (1210 out of 1316 bp in length). Phylogenetic analysis using the SSU sequence revealed this unknown pathogen was the grouped within the clade of Synchytrium genus with 100% bootstrapping confidence (Smith et al. 2014). Accordingly, the pathogen was confirmed to be a Synchytrium chytrid fungus. To complete the Koch's postulates, the sori were collected from infected tissue. After vortexing washing in 1% bleach for surface sterilization, the sori were gently crashed by a plastic tube pestle to harvest sporangia. The sporangia were sprayed onto healthy winged beans cultivated in pots, and the inoculated plants were kept in a moisture bag in 25 °C. While leaf curling and malformation could be observed about 14 days post inoculation, the yellow to orange sori could be observed around 30 to 40 days post inoculation on the whole plants cultivated in pots. The sori were collected to confirm the sporangia and the sequences were identical to the original pathogen. Collectively, this study not only presents the first report for the false rust of winged bean in Taiwan, but also documents the first reference sequence of S. psophocarpi that will be useful for future molecular diagnosis. Since S. psophocarpi has been only reported in tropic regions including Indonesia, Malay Peninsula, Malaysia, Papua New Guinea, and Philippines, this report provides the first observation of S. psophocarpi moving in the subtropic region.

Estimating incidence of type 1 and type 2 diabetes using prevalence data: the SEARCH for Diabetes in Youth study

BackgroundIncidence is one of the most important epidemiologic indices in surveillance. However, determining incidence is complex and requires time-consuming cohort studies or registries with date of diagnosis. Estimating incidence from prevalence using mathematical relationships may facilitate surveillance efforts. The aim of this study was to examine whether a partial differential equation (PDE) can be used to estimate diabetes incidence from prevalence in youth.MethodsWe used age-, sex-, and race/ethnicity-specific estimates of prevalence in 2001 and 2009 as reported in the SEARCH for Diabetes in Youth study. Using these data, a PDE was applied to estimate the average incidence rates of type 1 and type 2 diabetes for the period between 2001 and 2009. Estimates were compared to annual incidence rates observed in SEARCH. Precision of the estimates was evaluated using 95% bootstrap confidence intervals.ResultsDespite the long period between prevalence measures, the estimated average incidence rates mirror the average of the observed annual incidence rates. Absolute values of the age-standardized sex- and type-specific mean relative errors are below 8%.ConclusionsIncidence of diabetes can be accurately estimated from prevalence. Since only cross-sectional prevalence data is required, employing this methodology in future studies may result in considerable cost savings.

Identification of HIV-1 subtype CRF18_cpx in a patient with multidrug resistance in KwaZulu-Natal, South Africa: An epidemiological worry?

The most common HIV-1 subtype in South Africa is subtype C, and detection of other subtypes is rare. We report the first known case of HIV-1 subtype CRF18_cpx identified in KwaZulu-Natal, South Africa, the epicenter of the HIV epidemic, through HIV drug resistance genotyping.The 31-year-old female patient was initiated on fixed dose combination (tenofovir, emtricitabine, efavirenz) in 2017, with failure to achieve virologic suppression. Change to second-line antiretroviral therapy (tenofovir, emtricitabine and ritonavir-boosted lopinavir) was made in 2018. Adherence was impacted by lopinavir-induced diarrhoea. In 2020, she was switched to zidovudine, lamivudine and ritonavir-boosted atazanavir. Virologic failure persisted, and HIV drug resistance genotyping in April 2021 showed multidrug resistance. Third-line regimen (tenofovir, lamivudine, dolutegravir and ritonavir-boosted darunavir) was commenced in May 2021 and virologic suppression was achieved.Co-incidentally we discovered from the HIV drug resistance sequence report that the patient was infected with HIV-1 subtype CRF18_cpx. Analysis of the HIV sequence using REGA HIV-1 Subtyping Tool confirmed sequence subtype assignment as HIV-1 CRF 18_cpx (bootstrap confidence = 90%). Subtyping was also confirmed with the COMET HIV-1 tool, HIV BLAST tool and phylogenetic analysis.Based on our incidental finding, CRF18_cpx may be circulating locally as the patient had no travel history. Introduction of non-subtype C and recombinant viruses are expected to have increased in South Africa due to increased travel. This highlights the need to characterize subtype diversity in South Africa, particularly in KwaZulu-Natal, as HIV subtype can influence pathogenesis, treatment response, drug resistance and efforts towards vaccine development.

Non-Bayesian and Bayesian estimation of stress-strength reliability from Topp-Leone distribution under progressive first-failure censoring

ABSTRACT In this paper, the Bayesian and non-Bayesian estimation of based on the progressively first-failure censored data is considered. The and are strength and stress random variables and follow the Topp-Leone distributions, respectively. The maximum likelihood and Bayes estimators of are derived. The Bayes estimators under generalized entropy loss function are computed using Lindley’s approximation and Gibbs sampling methods. Different interval estimates like asymptotic, bootstrap confidence, Bayesian credible, and highest posterior density credible intervals of are constructed. Furthermore, a Monte Carlo numerical study is conducted to check the performance of various estimators developed. Finally, an application of algorithm real data is considered for illustrative purposes.

Citrullus lanatus natural product library: A hoard of viable potential inhibitor candidates for diabetes mellitus type II therapeutic target enzymes

The ethnomedicinal function of several cucurbit species (cucumber, squash, melon, gourd, etc.) on diseases (i.e. diabetes, microbial infections, cancer, etc.), and as free radical scavengers have been reported. However, there remains infinitesimal record on citron watermelon broad use, which reflects the reason for wide oversight of underutilization, from lack of recognition for functional food crop development and commercialization. The objective of this study focus towards identifying the natural phytochemicals of C. lanatus on water melon molecules online database for insilico computational approach to screened for suitable antidiabetic lead, and construction of phylogenetic relatedness of target Type 2 Diabetes Mellitus proteins was conducted to predict reoccurrence of insilico analysis output with other homologous target proteins. The T2DM protein targets, phytochemical and standard inhibitory drugs are mined from different databases. Insilico docking analysis, and adme/toxicity profiling was virtually screened for the best fit. In additionally, phylogenetic relationship of the target proteins was aligned and construction with other homologous protein targets to predict the reoccurrence confidence of results on compounds. Seventeen phytochemicals out of the nineteen potential drug candidates substantially passed the profiling test. Also, homologous protein targets with > 90% bootstrap confidence are likely to produce a reoccurring insilico result. Thus, these phytochemicals fulfil all the enlisted criteria and it is suggestively determined to be suitable for the development of potent antidiabetic drugs. It is evident that phytochemicals from Citrullus lanatus produced satisfactory insilico output, and this reflect it to be a probable reservoir containing other potential therapeutic drug candidates for antidiabetic drug discovery and development. Additionally, derivatives can be developed for further effective screening result.

Sensitivity analysis for calibrated inverse probability-of-censoring weighted estimators under non-ignorable dropout.

Inverse probability of censoring weighting is a popular approach to handling dropout in longitudinal studies. However, inverse probability-of-censoring weighted estimators (IPCWEs) can be inefficient and unstable if the weights are estimated by maximum likelihood. To alleviate these problems, calibrated IPCWEs have been proposed, which use calibrated weights that directly optimize covariate balance in finite samples rather than the weights from maximum likelihood. However, the existing calibrated IPCWEs are all based on the unverifiable assumption of sequential ignorability and sensitivity analysis strategies under non-ignorable dropout are lacking. In this paper, we fill this gap by developing an approach to sensitivity analysis for calibrated IPCWEs under non-ignorable dropout. A simple technique is proposed to speed up the computation of bootstrap and jackknife confidence intervals and thus facilitate sensitivity analyses. We evaluate the finite-sample performance of the proposed methods using simulations and apply our methods to data from an international inception cohort study of systemic lupus erythematosus. An R Markdown tutorial to demonstrate the implementation of the proposed methods is provided.

First Report of Soybean Seedling Disease caused by Rhizoctonia solani AG-7 in Taiwan.

From August to November 2020, reduced emergence and damping-off of soybean seedlings were observed in two fields (Benzhou and Wandan) in Taiwan. Disease incidence was approximately 40% in Benzhou by field scouting. The roots of damping-off seedlings were brown. Affected seedlings could be easily pulled out from the soil and the lesions on the roots/stem were generally dry and sunken. These symptoms suggested the possibility of Rhizoctonia infection. Soil surrounding symptomatic seedlings were collected to bait the potential pathogen and symptomatic plants were used for pathogen isolation. The diseased tissues were washed with tap water and surface-disinfected with 1% bleach before placing on the Dexon selection medium at 26°C for 2 days (Ko and Hora 1971). Hyphae were transferred to potato dextrose agar (PDA), and a brown colony with brown and irregular-shaped sclerotia grew from 90 out of 99 isolates. The hyphae exhibited typical characteristics of Rhizoctonia solani, including a constriction and a septum near the end of branching hyphae (Ajayi-Oyetunde and Bradely, 2018). Two isolates from Benzhou and two isolates from Wandan were tested for their pathogenicity, and eight surface-disinfected seeds were distributed evenly on the water agar plates covered by 2-day-old mycelia at 25°C in dark for 7 days. All isolates caused cotyledon rot and reduced germination. To verify their pathogenicity in pots, double-sterilized sorghum seeds were inoculated with two strains and incubated at 25°C for 2 weeks to be used as fungal inoculum (Ajayi-Oyetunde and Bradely, 2017). A layer of 15 ml of fungal inoculum was placed 5 cm beneath the soil surface in pots. Four soybean seeds were planted approximately 3 cm above the inoculum in each pot. After two weeks, reddish lesions on the hypocotyls or taproots of all seedlings in the inoculated pots were observed, while seedlings in the control pots inoculated with sterile sorghum seeds remained healthy. The pathogen was re-isolated from lesions and had identical morphology to the original isolates. To characterize the fungal identity, the internal transcribed spacer (ITS) was sequenced using the primers ITS1/ITS4 (Sharon et al., 2006). Using BLASTN in the NCBI database, the sequence (GenBank no. MW410857 and MW410858) showed 100% (639/639 bp) similarity to KF907734 and 99.83% (635/636 bp) similarity to AF354099, both belong to R. solani anastomosis group 7 (AG-7) (Hua et al. 2014; Gonzalez et al. 2001). Phylogenetic analysis comparing sequences with different AGs (Ajayi-Oyetunde and Bradely, 2017) grouped our isolates within the AG-7 clade with a 100% bootstrap confidence. In the anastomosis test, an incompatible zonation and unequal mycelial growth rates were observed when AG-7 isolates were paired with an AG-1 IA isolate. On the other hand, the compatible tuft reaction was observed when two AG-7 isolates were paired, and the compatible merge reaction was observed in the self-pairing tests (Macnish et al. 1997). Accordingly, the molecular and morphological characterizations confirmed the causal pathogen as R. solani AG-7. R. solani AG-7 was first reported on radishes in Japan (Homma et al., 1983), first found on carnation in Taiwan (Lo et al., 1990), and in field soils of various crops but not soybean (Chuang, 1997). It was suggested that Rhizoctonia diseases of soybean may be present in Taiwan, but molecular confirmation was lacking (Anonymus, 1979). As R. solani AG-7 causes diseases of soybean in the US and Japan (Baird et al., 1996), the importance of AG-7 as an endemic pathogen of soybean in Taiwan should be recognized and its prevalence determined as a first step to managing this disease.

Mortality Modeling of Skin Cancer Patients with Actuarial Applications

In this article, the Markovian aging process is used to model mortality of patients with skin cancer. The time until death is assumed to have a phase-type distribution (which is defined in a Markov chain environment) with interpretable parameters. The underlying continuous-time Markov chain has one absorbing state (death) and nx +1 (x is the age when the patient is diagnosed with cancer) transient states. Each transient state represents a physiological age, and aging is a transition from one physiological age to the next until the process reaches its end. The transition can occur from any other state to the absorbing state. For patients with skin cancer in the United States, we estimate unknown parameters related to the aging process that can be useful for comparing the physiological aging processes of patients with cancer and healthy people. For different age intervals, we estimate physiological age parameters for both males and females. The index of conditional expected physiological age of the patients with skin cancer at given ages is calculated and compared with the total U.S. population. By using bootstrap techniques, confidence bands and confidence intervals are constructed for the estimated survival curves and aging process parameters, respectively. The fitting results have been used for pricing substandard annuities.

Statistical Inference of Stress–Strength Reliability of a Parallel System with Mixed Standby Components

This paper presents the Bayesian analysis of the stress–strength reliability of a parallel system with active and mixed standby components. The Bayesian estimators of the parameters of exponential and Weibull stress–strength distributions are obtained by assuming informative and noninformative prior for the parameters of the respective distributions. The Gibbs sampling procedure is used to compute the Bayesian stress–strength reliability. The asymptotic distributions, of the maximum likelihood estimators of the parameters of the corresponding distributions, and of the respective system reliabilities are presented. The bootstrap estimate and confidence interval are also obtained. The procedures are illustrated based on certain datasets.

Reductions in emergency department presentations associated with opioid agonist treatment vary by geographic location: A retrospective study in New South Wales, Australia.

It is not known if the reduction in ED use during periods of OAT occurs across urgent and low acuity presentations. We aimed to compare the incidence and costs of urgent and low acuity ED presentations of people with opioid use disorder (OUD) in and out of opioid agonist treatment (OAT). This was a retrospective cohort study (N=24,875), using linked administrative health data from New South Wales (NSW), Australia. Urgent and low acuity ED incidence and associated costs were calculated for periods in and out of OAT. GEE models estimated the adjusted incidence rate ratio (IRR) for ED presentations. Average costs per person-day were calculated with bootstrap confidence intervals. Incidence of urgent presentations was lower in OAT compared to out of OAT [IRR (95%CI): 0.65 (0.61-0.69)]. In major cities, low acuity presentations were lower during OAT compared to timeout of OAT [IRR (95%CI): 0.82 (0.70-0.96)], in regional/remote areas, low acuity presentations were higher during OAT [IRR (95%CI): 2.65 (1.66-4.21)]. In major cities, average costs for low acuity presentations in OAT were 28% lower atA$0.50 (95%CI: A$0.48-A$0.52) and A$0.69 (95%CI: A$0.66-A$0.71) out of OAT, but 103% higher in regional/remote NSW, at A$2.12 (95%CI: A$1.91-A$2.34) in OAT and A$1.04 (95%CI: A$0.91-A$1.16) out of OAT. OAT was associated with reductions in urgent ED presentations and associated costs among people with OUD. Geographical variation was evident for low acuity ED presentations, highlighting the need to increase access to OAT in regional/remote areas.

Inference on $$P(X<Y)$$ for bivariate normal distribution based on ranked set sample

In this paper, we consider the problem of estimation of $$R=P(X<Y)$$, when X and Y are dependent, using bivariate ranked set sampling. The maximum likelihood estimates (MLEs) and Bayes estimates (BEs) of R are obtained based on ranked set sample when (X,Y) follows bivariate normal distribution. BEs are obtained based on both symmetric and asymmetric loss functions. The percentile bootstrap and HPD confidence intervals for R are also obtained. Simulation studies are carried out to find the accuracy of the proposed estimators. A real data is also used to illustrate the inferential procedures developed in this paper.

Bayesian parameter estimation of beta log Weibull distribution under Type II progressive censoring

In this article we discuss classical and Bayesian estimation procedures for estimating the unknown parameters as well as the reliability and hazard functions of the Beta Log Weibull distribution under Type II progressive censoring scheme. Conjugate and non-informative priors under squared error and entropy loss function are considered for Bayesian analysis. Complex and intractable integral functions are numerically approximated through Lindley approximation method and Markov Chain Monte Carlo techniques. Asymptotic confidence, Bootstrap confidence, Bayesian credible and highest posterior density intervals along with their coverage probability are also evaluated. A comprehensive simulation study to compare the performances of the maximum likelihood and Bayes estimates in terms of their mean squared errors is carried out. A real data set illustrates theoretical results.

Bootstrap Confidence Interval for Model Based Sampling

The bootstrap approach to statistical inference in sample surveys is an area which has seen considerable development in the recent past. In model based approach to sample survey theory the main interest has been to overcome the problem of robustness under misspecifications. The bootstrap method under restrictive model specifications has been suggested by some authors as a way of achieving this. In this study, bootstrap and conventional confidence intervals for the population total in model based surveys using the simple random sampling without replacement are constructed. This is to provide a better measure of uncertainty associated with estimates of population total as compared to the corresponding rival confidence intervals under restrictive model. In order to achieve this, generated bootstrap simulations for the population of interest in assumed general model are used. The bootstrap method is less cumbersome to apply and in terms of coverage performance in 95% confidence interval, the bootstrap method is better compared to corresponding one under conventional methods. In terms of length, the confidences generated by the bootstrap method are much smaller as compared to the conventional counterparts. It is noted that the best performing confidence interval is one whose coverage rate is close to the true population total and its length small. The study research results provides great insight in constructing better confidence interval for the finite population total estimators.

Abstract TMP88: Male Gender Predicts Ultrafast Administration of Intravenous Tissue Plasminogen Activator in a Twenty-Six Hospital Network

Background: The benefits of intravenous tissue-type plasminogen activator (IV-Alteplase) in acute ischemic stroke (AIS) are time dependent. Current guidelines recommend a 60-minute door-to-needle (DTN) time for IV-Alteplase. Moreover, for every 15-minute reduction in treatment time, clinical outcomes are improved by an estimated 4%. In this study, we identified characteristics of patients with DTN times less than 30 minutes (i.e. “ultrafast DTN”). Methods: Data obtained from the 26-hospital Providence Health and Services Get With the Guidelines stroke registry were used to identify patients with ultrafast DTN. IV-Alteplase-treated AIS patients over age 18 who were discharged from the hospital between 2009 and 2015 were included. A mixed effects logistic regression model with backwards elimination was used to identify which of the following variables were significant in predicting ultrafast DTN: year of discharge, age, gender, NIHSS score, weekend or evening admission, telestroke usage, hospital arrival time, mode of arrival (EMS vs private car), medical history of dyslipidemia, diabetes, atrial fibrillation, or hypertension, consult with a stroke neurologist, and the certification of the hospital. Parametric bootstrapped p-values, mean estimates and percentile confidence intervals were calculated. Results: We identified 2,695 AIS patients who received IV-Alteplase between 2009 and 2015. Of those, only 108 (3.9%) had ultrafast DTN times. In the final bootstrap analysis, ultrafast DTN patients were more likely to be male (adjusted odds ratio (AOR) = 2.23; p&lt;.001), ambulance arrivals (AOR = 4.76; p&lt;.001), weekday arrivals (AOR = 1.89; p&lt;.001), more severe cases (AOR per NIHSS point = 1.03; p=0.04), and more recently discharged (AOR per year = 1.34; p&lt;.001). Conclusion: In our large hospital network, we found that only a small proportion of AIS patients received ultrafast Alteplase administration, with males twice as likely as females to receive treatment in less than 30 minutes. This study highlights the necessity to further understand the role gender plays in treatment-related decisions.

Agrowastes as Feedstock for the Production of Endo-β-Xylanase from Cohnella sp. Strain AR92

Members of Cohnella sp. isolated from a variety of environments have been shown to be glycoside hydrolase producers. Nevertheless, most evaluations of members of this genus are limited to their taxonomic description. The strain AR92, previously identified as belonging to the genus Cohnella, formed a well-supported cluster with C. thailandensis and C. formosensis (>80% bootstrap confidence). Its growth and xylanase production were approached by using a mineral-based medium containing alkali-pretreated sugarcane bagasse as the main carbon source, which was assayed as a convenient source to produce biocatalysts potentially fitting its degradation. By means of a two-step statistical approach, the production of endoxylanase was moderately improved (20%). However, a far more significant improvement was observed (145%), by increasing the inoculum size and lowering the fermentation temperature to 25°C, which is below the optimal growth temperature of the strain AR92 (37°C). The xylanolytic preparation produced by Cohnella sp. AR92 contained mild temperature-active endoxylanase (identified as redundant GH10 family) for the main activity which resulted in xylobiose and xylo-oligosaccharides as the main products from birchwood xylan.

Application of hidden semi-Markov models for the seismic hazard assessment of the North and South Aegean Sea, Greece

ABSTRACTThe real stress field in an area associated with earthquake generation cannot be directly observed. For that purpose we apply hidden semi-Markov models (HSMMs) for strong earthquake occurrence in the areas of North and South Aegean Sea considering that the stress field constitutes the hidden process. The advantage of HSMMs compared to hidden Markov models (HMMs) is that they allow any arbitrary distribution for the sojourn times. Poisson, Logarithmic and Negative Binomial distributions as well as different model dimensions are tested. The parameter estimation is achieved via the EM algorithm. For the decoding procedure, a new Viterbi algorithm with a simple form is applied detecting precursory phases (hidden stress variations) and warning for anticipated earthquake occurrences. The optimal HSMM provides an alarm period for 70 out of 88 events. HMMs are also studied presenting poor results compared to these obtained via HSMMs. Bootstrap standard errors and confidence intervals for the parameters are evaluated and the forecasting ability of the Poisson models is examined.

Validación de escala de apoyo en duelo en atención de salud para población hispanoparlante

The death of a child, who is attended by professionals, can be conceived by them as a loss, sometimes resulting in a traumatic expe­rience. Social support becomes an important mediator of the grieving process, helping to relieve the stress and to cope better. Objec­tive: Translation and validation into Spanish of «Grief Support in Health Care Scale (GS­HCS)» . Method: Through the translation and validation of cross-cultural equivalence of GS­HCS in its Spanish version: «Apoyo en Duelo en Atencion de Salud (EADAS)», we procee­ded to auto-apply this instrument to 215 pro­fessionals working in oncology units and cri­tical pediatric care. With this data there was an internal analysis of the tendencies using Cronbach’s Alpha, Bootstrap Confidence In­tervals and an exploratory analysis was perfor­med to test the psychometric properties of the scale divided into three dimensions; recogni­tion of the relationship, recognition of the loss and incorporation of belief rituals, performing a comparison of means using the t test for independent samples. Results: The «Grief Sup­port in Health Care Scale» (GSHCS) obtained a validation and reliability with a coefficient Cronbach’s Alpha score of 0.81. By analyzing the variables, it was found that oncology unit professionals and both units women perceive themselves to be more socially supported in their mourning. Conclusion: The «Grief Sup­port in Health Care Scale» (GSHCS) is a valid and reliable instrument, which allows to iden­tify the perception of support in the mourning process.

Age and gender related neuromuscular changes in trunk flexion-extension.

BackgroundThe root mean square surface electromyographic activity of lumbar extensor muscles during dynamic trunk flexion and extension from a standing position and task specific spine ranges of motion objectively assess muscle function in healthy young and middle age individuals. However, literature on neuromuscular activation and associated spine and hip kinematics in older individuals is sparse. This cross sectional study sought to examine the sex and age (<40 versus >60 years) related differences in the neuromuscular activation profiles of the lumbar extensors and the related spine and hip kinematics from healthy individuals during a standardized trunk flexion-extension task.MethodsTwenty five older (13 females, 60–90 years) and 24 younger (12 females, 18–40 years) healthy individuals performed trunk flexion-extension testing by holding static positions at half-flexion way and full range of motion between standing and maximum trunk flexion. The associated lumbar extensor muscle activity was derived from measurements at standing, half, and maximum flexion positions. The range of motion at the hip and lumbar spine was recorded using 3d accelerometers attached to the skin overlying the multifidus and semispinalis thoracis muscles lateral to the L5 and T4 spinous processes, respectively. Statistical calculations were performed using a permutation ANOVA with bootstrap confidence intervals.ResultsThe muscle activity in the half related to the maximum flexion position (half flexion relaxation ratio) was significantly smaller in older males when compared with younger males. Moreover, measurements revealed smaller activity changes from standing to the half and from half to the maximum flexion position in older compared to younger individuals. Older males displayed smaller gross trunk range of motion from standing to maximum flexion than any other group.ConclusionsGender and normal aging significantly affect both the activation patterns of the lumbar extensor muscles and the kinematics of the trunk during a standardized trunk flexion-extension task. Measurement results from healthy young and middle age individuals should not be used for the assessment of individuals older than 60 years of age.Electronic supplementary materialThe online version of this article (doi:10.1186/1743-0003-12-3) contains supplementary material, which is available to authorized users.

Fungal diversity in permafrost and tallgrass prairie soils under experimental warming conditions.

Soil fungi play a major role in terrestrial ecosystem functioning through interactions with soil structure, plants, micro- and mesofauna, and nutrient cycling through predation, pathogenesis, mutualistic, and saprotrophic roles. The diversity of soil fungi was assessed by sequencing their 28S rRNA gene in Alaskan permafrost and Oklahoma tallgrass prairie soils at experimental sites where the effect of climate warming is under investigation. A total of 226,695 reads were classified into 1,063 genera, covering 62% of the reference data set. Using the Bayesian Classifier offered by the Ribosomal Database Project (RDP) with 50% bootstrapping classification confidence, approximately 70% of sequences were returned as "unclassified" at the genus level, although the majority (∼65%) were classified at the class level, which provided insight into these lesser-known fungal lineages. Those unclassified at the genus level were subjected to BLAST analysis against the ARB-SILVA database, where ∼50% most closely matched nonfungal taxa. Compared to the more abundant sequences, a higher proportion of rare operational taxonomic units (OTU) were successfully classified to genera at 50% bootstrap confidence, indicating that the fungal rare biosphere in these sites is not composed of sequencing artifacts. There was no significant effect after 1 year of warming on the fungal community structure at both sites, except perhaps for a few minor members, but there was a significant effect of sample depth in the permafrost soils. Despite overall significant community structure differences driven by variations in OTU dominance, the prairie and permafrost soils shared 90% and 63% of all fungal sequences, respectively, indicating a fungal "seed bank" common between both sites.

Genetic structure of Eurasian and North American Leymus (Triticeae) wildryes assessed by chloroplast DNA sequences and AFLP profiles

Leymus is a genomically defined allopolyploid of genus Triticeae with two distinct subgenomes. Chloroplast DNA sequences of Eurasian and North American species are distinct and polyphyletic. However, phylogenies derived from chloroplast and nuclear DNA sequences are confounded by polyploidy and lack of polymorphism among many taxa. The AFLP technique can resolve phylogenetic relationships between closely related species, with a curvilinear relationship expected between the proportion of shared bands and nucleotide substitution rate (D), up to about 0.100 D. The objective of this study was to compare D and phylogenetic relationships among 16 Leymus taxa, based on chloroplast DNA sequences and multi-locus AFLP genotypes. Estimates of chloroplast D between taxa were 0.002 and 0.013 within and among continental regions, respectively. Estimates of AFLP D between taxa were 0.076 and 0.093 compared within and between continental regions, respectively, versus 0.024 within taxa. Bayesian and neighbor-joining cluster analyses effectively separated all AFLP genotypes by species, but showed that North American L. ambiguus is a hybrid species with nearly equal contributions from sympatric L. cinereus and L. salinus taxa. Two hierarchical AFLP clades, containing six North American taxa and four Eurasian taxa, had more than 98% bootstrap confidence with 0.071 and 0.055 D among taxa. Three other Eurasian taxa clustered with 79% and 89% confidence, with up to 0.79 D between taxa. These estimates provide benchmarks for phylogenetic comparisons of AFLP profiles, but three taxa could not be reliably grouped, which may reflect concurrent radiation of multiple lineages or lack of homologous AFLP characters caused by a high D.