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1.  Posterior fossa tuberculoma in a Huichol native Mexican child: a case report 
BMC Research Notes  2014;7(1):919.
Tuberculosis is a major health concern in Mexico, especially among the native population. Tuberculomas are a frequent and severe complication of pediatric tuberculosis, these are observed as tumors in neuroimaging studies but are often not diagnosed adequately.
Case presentation
We present a case of a 12-year-old native Mexican girl Huichol ethnicity diagnosed with a large posterior fossa tuberculoma found by imaging. This tuberculoma was surgically removed. Histopathologic examination and staining with hematoxylin and eosin, and Ziehl-Neelsen techniques of the surgical specimen were performed. Cerebrospinal fluid was analyzed by using the newly available Xpert® MTB/RIF assay (Cepheid, Sunnyvale CA, USA). Granulomatous inflammation with central caseous necrosis surrounded by edematous brain with reactive gliosis and acid-fast bacilli were revealed on histopathologic analysis. Mycobacterium tuberculosis DNA susceptible to rifampicin was detected in the patient’s cerebrospinal fluid and the patient was started on anti-tuberculosis treatment. The girl continued to show severe neurologic damage despite surgery and anti-tuberculosis treatment, and she eventually died of respiratory complications.
Our case highlights the need for early confirmation of tuberculoma diagnosis by molecular assay so that timely treatment can be initiated to prevent severe brain damage. Furthermore, it emphasizes the need to consider tuberculomas in the differential diagnosis of children with neurologic symptoms living in areas of high tuberculosis incidence and those belonging to native populations in developing countries.
PMCID: PMC4300823  PMID: 25515023
Tuberculoma; Tuberculosis; Molecular diagnosis; Huichol child; Mexico
2.  The lung cancer epidemic in Spanish women: an analysis of mortality rates over a 37-year period 
Journal of Thoracic Disease  2014;6(12):1668-1673.
Lung cancer continues to be the leading cause of cancer-related mortality in the European Union (EU) and deaths from lung cancer have been projected to escalate to epidemic proportions amongst females over the next years. We examined lung cancer mortality rates in men and women from Andalusia (Spain) over a 37-year period [1975-2012].
Longitudinal epidemiological study analyzing lung cancer mortality trends in males and females. Data on lung cancer mortality in Andalusia for the period 1975-2012 were obtained from the official cause-of-death publications of the Institute of Statistics of Andalusia. For each sex, age-standardized (European standard population) mortality rates (ASR) from lung cancer were calculated for all ages and truncated at 30-64, 65-74, and >75 years using the direct method. Standardized rate trends by age and sex were estimated by joinpoint regression analysis.
In men, the ASR steadily increased through the period 1993-1995, reaching a peak of 145.72 deaths/100,000 people. Subsequently, lung cancer deaths decreased to a rate of 125.47 in the 2011-2012 period. A moderate increase was seen in women until the late 1990s and early 2000s. Thereafter, a very notable rise was observed in females for all age groups, the only exception being older subjects. The sex differences decreased from 8.6:1 in the 1975-1977 period to 6.8:1 in the 2011-2012 period.
Lung cancer mortality rates decreased significantly in Andalusian men from 1975 to 2012. More importantly, we demonstrate for the first time the beginning of the lung cancer epidemics in Andalusian women as previously predicted for this area.
PMCID: PMC4283328  PMID: 25589958
Lung cancer; mortality; males; females; epidemics
3.  Conserving Tropical Tree Diversity and Forest Structure: The Value of Small Rainforest Patches in Moderately-Managed Landscapes 
PLoS ONE  2014;9(6):e98931.
Rainforests are undergoing severe deforestation and fragmentation worldwide. A huge amount of small forest patches are being created, but their value in conserving biodiversity and forest structure is still controversial. Here, we demonstrate that in a species-rich and moderately-managed Mexican tropical landscape small rainforest patches (<100 ha) can be highly valuable for the conservation of tree diversity and forest structure. These patches showed diverse communities of native plants, including endangered species, and a new record for the country. Although the number of logged trees increased in smaller patches, patch size was a poor indicator of basal area, stem density, number of species, genera and families, and community evenness. Cumulative species-area curves indicated that all patches had a similar contribution to the regional species diversity. This idea also was supported by the fact that patches strongly differed in floristic composition (high β-diversity), independently of patch size. Thus, in agreement with the land-sharing approach, our findings support that small forest patches in moderately-managed landscapes should be included in conservation initiatives to maintain landscape heterogeneity, species diversity, and ecosystem services.
PMCID: PMC4047051  PMID: 24901954
4.  Restoration Enhances Wetland Biodiversity and Ecosystem Service Supply, but Results Are Context-Dependent: A Meta-Analysis 
PLoS ONE  2014;9(4):e93507.
Wetlands are valuable ecosystems because they harbor a huge biodiversity and provide key services to societies. When natural or human factors degrade wetlands, ecological restoration is often carried out to recover biodiversity and ecosystem services (ES). Although such restorations are routinely performed, we lack systematic, evidence-based assessments of their effectiveness on the recovery of biodiversity and ES. Here we performed a meta-analysis of 70 experimental studies in order to assess the effectiveness of ecological restoration and identify what factors affect it. We compared selected ecosystem performance variables between degraded and restored wetlands and between restored and natural wetlands using response ratios and random-effects categorical modeling. We assessed how context factors such as ecosystem type, main agent of degradation, restoration action, experimental design, and restoration age influenced post-restoration biodiversity and ES. Biodiversity showed excellent recovery, though the precise recovery depended strongly on the type of organisms involved. Restored wetlands showed 36% higher levels of provisioning, regulating and supporting ES than did degraded wetlands. In fact, wetlands showed levels of provisioning and cultural ES similar to those of natural wetlands; however, their levels of supporting and regulating ES were, respectively, 16% and 22% lower than in natural wetlands. Recovery of biodiversity and of ES were positively correlated, indicating a win-win restoration outcome. The extent to which restoration increased biodiversity and ES in degraded wetlands depended primarily on the main agent of degradation, restoration actions, experimental design, and ecosystem type. In contrast, the choice of specific restoration actions alone explained most differences between restored and natural wetlands. These results highlight the importance of comprehensive, multi-factorial assessment to determine the ecological status of degraded, restored and natural wetlands and thereby evaluate the effectiveness of ecological restorations. Future research on wetland restoration should also seek to identify which restoration actions work best for specific habitats.
PMCID: PMC3990551  PMID: 24743348
5.  5-Chloro-2-methyl­sulfanyl-6-(naphtha­len-1-yl­oxy)-1H-benzimidazole methanol monosolvate 
In the title compound, C18H13ClN2OS·CH3OH, the dihedral angle between the benzimidazole group and the naphth­yloxy moiety [82.89 (5)°] very near to orthogonality. The H atom in the five-membered ring is disordered with equal occupancies at the two N atoms and the H atom of the methano­lic hy­droxy group is disordered with equal occupancies over two sites at the O atom. The methanol mol­ecule acts as a hydrogen-bond acceptor for the amino H atom and donates a hydrogen bond to the nonprotonated ring N atom. As a result, chains are formed running along the a axis.
PMCID: PMC3914104  PMID: 24527009
6.  Effects of ENSO and Temporal Rainfall Variation on the Dynamics of Successional Communities in Old-Field Succession of a Tropical Dry Forest 
PLoS ONE  2013;8(12):e82040.
The effects of temporal variation of rainfall on secondary succession of tropical dry ecosystems are poorly understood. We studied effects of inter-seasonal and inter-year rainfall variation on the dynamics of regenerative successional communities of a tropical dry forest in Mexico. We emphasized the effects caused by the severe El Niño Southern Oscillation (ENSO) occurred in 2005. We established permanent plots in sites representing a chronosequence of Pasture (abandoned pastures, 0–1 years fallow age), Early (3–5), Intermediate (8–12), and Old-Growth Forest categories (n = 3 per category). In total, 8210 shrubs and trees 10 to 100-cm height were identified, measured, and monitored over four years. Rates of plant recruitment, growth and mortality, and gain and loss of species were quantified per season (dry vs. rainy), year, and successional category, considering whole communities and separating seedlings from sprouts and shrubs from trees. Community rates changed with rainfall variation without almost any effect of successional stage. Mortality and species loss rates peaked during the ENSO year and the following year; however, after two rainy years mortality peaked in the rainy season. Such changes could result from the severe drought in the ENSO year, and of the outbreak of biotic agents during the following rainy years. Growth, recruitment and species gain rates were higher in the rainy season but they were significantly reduced after the ENSO year. Seedlings exhibited higher recruitment and mortality rate than sprouts, and shrubs showed higher recruitment than trees. ENSO strongly impacted both the dynamics and trajectory of succession, creating transient fluctuations in the abundance and species richness of the communities. Overall, there was a net decline in plant and species density in most successional stages along the years. Therefore, strong drought events have critical consequences for regeneration dynamics, delaying the successional process and modifying the resilience of these systems.
PMCID: PMC3861369  PMID: 24349179
7.  Urinary ATP May Be a Dynamic Biomarker of Detrusor Overactivity in Women with Overactive Bladder Syndrome 
PLoS ONE  2013;8(5):e64696.
Nowadays, there is a considerable bulk of evidence showing that ATP has a prominent role in the regulation of human urinary bladder function and in the pathophysiology of detrusor overactivity. ATP mediates nonadrenergic-noncholinergic detrusor contractions in overactive bladders. In vitro studies have demonstrated that uroepithelial cells and cholinergic nerves from overactive human bladder samples (OAB) release more ATP than controls. Here, we compared the urinary ATP concentration in samples collected non-invasively from OAB women with detrusor overactivity and age-matched controls.
Patients with neurologic diseases, history of malignancy, urinary tract infections or renal impairment (creatinine clearance <70 ml/min) were excluded. All patients completed a 3-day voiding diary, a 24 h urine collection and blood sampling to evaluate creatinine clearance. Urine samples collected during voluntary voids were immediately freeze-preserved for ATP determination by the luciferin-luciferase bioluminescence assay; for comparison purposes, samples were also tested for urinary nerve growth factor (NGF) by ELISA.
The urinary content of ATP, but not of NGF, normalized to patients’ urine creatinine levels (ATP/Cr) or urinary volume (ATP.Vol) were significantly (P<0.05) higher in OAB women with detrusor overactivity (n = 34) than in healthy controls (n = 30). Significant differences between the two groups were still observed by boosting urinary ATP/Cr content after water intake, but these were not detected for NGF/Cr. In OAB patients, urinary ATP/Cr levels correlated inversely with mean voided volumes determined in a 3-day voiding diary.
A high area under the receiver operator characteristics (ROC) curve (0.741; 95% CI 0.62–0.86; P<0.001) is consistent with urinary ATP/Cr being a highly sensitive dynamic biomarker for assessing detrusor overactivity in women with OAB syndrome.
PMCID: PMC3669404  PMID: 23741373
8.  Auditory selective attention and processing in children with attention-deficit/hyperactivity disorder 
Clinical Neurophysiology  2011;123(2):293-302.
This study sought to better characterize the contributions of deficits in attention allocation and distracter inhibition to the poor performance on attention tasks often seen in children with ADHD.
Electrophysiological (Nd, P3b) and behavioral measures (speed and accuracy) were examined during an auditory selective attention task in children with ADHD, children with typical development (TD), and adults. Thirty children (15 ADHD; 13 females) between the ages of 7 and 13 and 16 adults (8 females) participated.
Nd waveforms were elicited from adults and children with TD, but not from children with ADHD. Further, those with ADHD exhibited significantly smaller auditory responses at 100ms (Ta). P3bs were elicited in all three groups by targets but not by unattended deviants. Performance was significantly poorer in children with ADHD than TD and RTs were more variable.
Children with ADHD evidenced poorer attention allocation, as measured by Nd and hits, but were not more distracted by unattended deviants, as measured by P3b and false alarms, than children with TD.
Findings for Nd, P3b, and Ta considered together suggest that deficits in auditory selective attention in children with ADHD may be attributable to reduced information early in the processing stream.
PMCID: PMC3232335  PMID: 21839675
selective attention; Nd; ADHD; ERP; auditory; Ta
9.  Lack of association of the HMGA1 IVS5-13insC variant with type 2 diabetes in an ethnically diverse hypertensive case control cohort 
Recently, the high-mobility group A1 gene (HMGA1) variant IVS5-13insC has been associated with type 2 diabetes, but reported associations are inconsistent and data are lacking in Hispanic and African American populations. We sought to investigate the HMGA1-diabetes association and to characterize IVS5-13insC allele frequencies and linkage disequilibrium (LD) in 3,070 Caucasian, Hispanic, and African American patients from the INternational VErapamil SR-Trandolapril STudy (INVEST).
INVEST was a randomized, multicenter trial comparing two antihypertensive treatment strategies in an ethnically diverse cohort of hypertensive, coronary artery disease patients. Controls, who were diabetes-free throughout the study, and type 2 diabetes cases, either prevalent or incident, were genotyped for IVS5-13insC using Taqman®, confirmed with Pyrosequencing and Sanger sequencing. For LD analysis, genotyping for eight additional HMGA1 single nucleotide polymorphisms (SNPs) was performed using the Illumina® HumanCVD BeadChip. We used logistic regression to test association of the HMGA1 IVS5-13insC and diabetes, adjusted for age, gender, body mass index, and percentage European, African, and Native American ancestry.
We observed IVS5-13insC minor allele frequencies consistent with previous literature in Caucasians and African Americans (0.03 in cases and 0.04 in controls for both race/ethnic groups), and higher frequencies in Hispanics (0.07 in cases and 0.07 in controls). The IVS5-13insC was not associated with type 2 diabetes overall (odds ratio 0.98 [0.76-1.26], p=0.88) or in any race/ethnic group. Pairwise LD (r2) of IVS5-13insC and rs9394200, a SNP previously used as a tag SNP for IVS5-13insC, was low (r2=0.47 in Caucasians, r2=0.25 in Hispanics, and r2=0.06 in African Americans). Furthermore, in silico analysis suggested a lack of functional consequences for the IVS5-13insC variant.
Our results suggest that IVS5-13insC is not a functional variant and not associated with type 2 diabetes in an ethnically diverse, hypertensive, coronary artery disease population. Larger, more adequately powered studies need to be performed to confirm our findings.
Trial registration (NCT00133692)
PMCID: PMC3558451  PMID: 23302499
HMGA1; Type 2 diabetes; Genetics
10.  The effect of magnetic field on the impurity binding energy of shallow donor impurities in a Ga1−xInxNyAs1−y/GaAs quantum well 
Nanoscale Research Letters  2012;7(1):586.
Using a variational approach, we have investigated the effects of the magnetic field, the impurity position, and the nitrogen and indium concentrations on impurity binding energy in a Ga1−xInxNyAs1−y/GaAs quantum well. Our calculations have revealed the dependence of impurity binding on the applied magnetic field, the impurity position, and the nitrogen and indium concentrations.
PMCID: PMC3519723  PMID: 23095253
Impurities; Quantum well; Dilute nitride
11.  Donor impurity-related linear and nonlinear intraband optical absorption coefficients in quantum ring: effects of applied electric field and hydrostatic pressure 
Nanoscale Research Letters  2012;7(1):538.
The linear and nonlinear intraband optical absorption coefficients in GaAs three-dimensional single quantum rings are investigated. Taking into account the combined effects of hydrostatic pressure and electric field, applied along the growth direction of the heterostructure, the energies of the ground and first excited states of a donor impurity have been found using the effective mass approximation and a variational method. The energies of these states are examined as functions of the dimensions of the structure, electric field, and hydrostatic pressure. We have also investigated the dependencies of the linear, nonlinear, and total optical absorption coefficients as a function of incident photon energy for several configurations of the system. It is found that the variation of distinct sizes of the structure leads to either a redshift and/or a blueshift of the resonant peaks of the intraband optical spectrum. In addition, we have found that the application of an electric field leads to a redshift, whereas the influence of hydrostatic pressure leads to a blueshift (in the case of on-ring-center donor impurity position) of the resonant peaks of the intraband optical spectrum.
PMCID: PMC3534551  PMID: 23021497
GaAs; Quantum ring; Optical absorption; 78.67.De; 71.55.Eq; 32.10.Dk
12.  Exciton-related nonlinear optical properties in cylindrical quantum dots with asymmetric axial potential: combined effects of hydrostatic pressure, intense laser field, and applied electric field 
Nanoscale Research Letters  2012;7(1):508.
The exciton binding energy of an asymmetrical GaAs-Ga1−xAlxAs cylindrical quantum dot is studied with the use of the effective mass approximation and a variational calculation procedure. The influence on this quantity of the application of a direct-current electric field along the growth direction of the cylinder, together with that of an intense laser field, is particularly considered. The resulting states are used to calculate the exciton-related nonlinear optical absorption and optical rectification, whose corresponding resonant peaks are reported as functions of the external probes, the quantum dot dimensions, and the aluminum molar fraction in the potential barrier regions.
PMCID: PMC3515405  PMID: 22971418
Exciton binding energy; GaAs-Ga1−xAlxAs cylindrical quantum dot; Effective mass approximation; 78.67.De; 71.55.Eq; 32.10.Dk
13.  Exciton properties in zincblende InGaN-GaN quantum wells under the effects of intense laser fields 
Nanoscale Research Letters  2012;7(1):492.
In this work, we study the exciton states in a zincblende InGaN/GaN quantum well using a variational technique. The system is considered under the action of intense laser fields with the incorporation of a direct current electric field as an additional external probe. The effects of these external influences as well as of the changes in the geometry of the heterostructure on the exciton binding energy are discussed in detail.
PMCID: PMC3499168  PMID: 22937963
Nitrides; Excitons; Intense laser field; Quantum wells
14.  Tunable resonance transmission modes in hybrid heterostructures based on porous silicon 
Nanoscale Research Letters  2012;7(1):392.
In this work, we report the experimental results and theoretical analysis of strong localization of resonance transmission modes generated by hybrid periodic/quasiperiodic heterostructures (HHs) based on porous silicon. The HHs are formed by stacking a quasiperiodic Fibonacci (FN) substructure between two distributed Bragg reflectors (DBRs). FN substructure defines the number of strong localized modes that can be tunable at any given wavelength and be unfolded when a partial periodicity condition is imposed. These structures show interesting properties for biomaterials research, biosensor applications and basic studies of adsorption of organic molecules. We also demonstrate the sensitivity of HHs to material infiltration.
PMCID: PMC3466137  PMID: 22793498
Fibonacci substructure; Porous silicon; Heterostructures
15.  Does 3D Ultrasound Enhance the Diagnosis of Bladder Tumours in Patients with Haematuria? 
ISRN Urology  2012;2012:158437.
Purpose. Bladder cancer is a frequent cause of haematuria in elderly patients, and bladder ultrasound (US) is a valuable tool in diagnosing these malignancies. We examined the accuracy of 3D bladder US in diagnosing bladder tumors in patients with haematuria. Patients and Methods. Twenty-one patients observed in the emergency department for haematuria underwent a kidney and bladder US. Patients with normal or uncertain bladder US findings underwent a 3D US and a cystoscopy. Results. In 5 (23.8%) patients, the 3D US detected bladder tumours not seen in 2D US. All these patients were found to have bladder tumours on cystoscopy. Another 5 (23.8%) patients with uncertain findings on 2D US had normal 3D US and cystoscopy. 3D US showed a sensitivity of 83.3% and a specificity of 100% with a positive predicted value and negative predictive values of 100% and 93.8%, respectively. Conclusion. 3D US was more sensitive than 2D US in diagnosing bladder tumours in patients with haematuria.
PMCID: PMC3329719  PMID: 22550603
17.  The Rover Environmental Monitoring Station Ground Temperature Sensor: A Pyrometer for Measuring Ground Temperature on Mars 
Sensors (Basel, Switzerland)  2010;10(10):9211-9231.
We describe the parameters that drive the design and modeling of the Rover Environmental Monitoring Station (REMS) Ground Temperature Sensor (GTS), an instrument aboard NASA’s Mars Science Laboratory, and report preliminary test results. REMS GTS is a lightweight, low-power, and low cost pyrometer for measuring the Martian surface kinematic temperature. The sensor’s main feature is its innovative design, based on a simple mechanical structure with no moving parts. It includes an in-flight calibration system that permits sensor recalibration when sensor sensitivity has been degraded by deposition of dust over the optics. This paper provides the first results of a GTS engineering model working in a Martian-like, extreme environment.
PMCID: PMC3230958  PMID: 22163405
IR ground temperature sensor; sensor thermal model; spacecraft instrumentation; in-flight calibration
18.  Attaining the canopy in dry and moist tropical forests: strong differences in tree growth trajectories reflect variation in growing conditions 
Oecologia  2009;163(2):485-496.
Availability of light and water differs between tropical moist and dry forests, with typically higher understorey light levels and lower water availability in the latter. Therefore, growth trajectories of juvenile trees—those that have not attained the canopy—are likely governed by temporal fluctuations in light availability in moist forests (suppressions and releases), and by spatial heterogeneity in water availability in dry forests. In this study, we compared juvenile growth trajectories of Cedrela odorata in a dry (Mexico) and a moist forest (Bolivia) using tree rings. We tested the following specific hypotheses: (1) moist forest juveniles show more and longer suppressions, and more and stronger releases; (2) moist forest juveniles exhibit wider variation in canopy accession pattern, i.e. the typical growth trajectory to the canopy; (3) growth variation among dry forest juveniles persists over longer time due to spatial heterogeneity in water availability. As expected, the proportion of suppressed juveniles was higher in moist than in dry forest (72 vs. 17%). Moist forest suppressions also lasted longer (9 vs. 5 years). The proportion of juveniles that experienced releases in moist forest (76%) was higher than in dry forest (41%), and releases in moist forests were much stronger. Trees in the moist forest also had a wider variation in canopy accession patterns compared to the dry forest. Our results also showed that growth variation among juvenile trees persisted over substantially longer periods of time in dry forest (>64 years) compared to moist forest (12 years), most probably because of larger persistent spatial variation in water availability. Our results suggest that periodic increases in light availability are more important for attaining the canopy in moist forests, and that spatial heterogeneity in water availability governs long-term tree growth in dry forests.
Electronic supplementary material
The online version of this article (doi:10.1007/s00442-009-1540-5) contains supplementary material, which is available to authorized users.
PMCID: PMC2871094  PMID: 20033820
Canopy accession; Cedrela odorata; Gap dynamics; Growth suppression; Tree rings
19.  Relationships Among Ecologically Important Dimensions of Plant Trait Variation in Seven Neotropical Forests 
Annals of Botany  2006;99(5):1003-1015.
Background and Aims
When ecologically important plant traits are correlated they may be said to constitute an ecological ‘strategy’ dimension. Through identifying these dimensions and understanding their inter-relationships we gain insight into why particular trait combinations are favoured over others and into the implications of trait differences among species. Here we investigated relationships among several traits, and thus the strategy dimensions they represented, across 2134 woody species from seven Neotropical forests.
Six traits were studied: specific leaf area (SLA), the average size of leaves, seed and fruit, typical maximum plant height, and wood density (WD). Trait relationships were quantified across species at each individual forest as well as across the dataset as a whole. ‘Phylogenetic’ analyses were used to test for correlations among evolutionary trait-divergences and to ascertain whether interspecific relationships were biased by strong taxonomic patterning in the traits.
Key Results
The interspecific and phylogenetic analyses yielded congruent results. Seed and fruit size were expected, and confirmed, to be tightly related. As expected, plant height was correlated with each of seed and fruit size, albeit weakly. Weak support was found for an expected positive relationship between leaf and fruit size. The prediction that SLA and WD would be negatively correlated was not supported. Otherwise the traits were predicted to be largely unrelated, being representatives of putatively independent strategy dimensions. This was indeed the case, although WD was consistently, negatively related to leaf size.
The dimensions represented by SLA, seed/fruit size and leaf size were essentially independent and thus conveyed largely independent information about plant strategies. To a lesser extent the same was true for plant height and WD. Our tentative explanation for negative WD–leaf size relationships, now also known from other habitats, is that the traits are indirectly linked via plant hydraulics.
PMCID: PMC2802905  PMID: 16595553
Fruit size; leaf size; phylogenetically independent contrasts; plant height; plant strategies; seed size; specific leaf area; tropical rainforest ecology; wood density
20.  Rates of change in tree communities of secondary Neotropical forests following major disturbances 
Rates of change in tree communities following major disturbances are determined by a complex set of interactions between local site factors, landscape history and structure, regional species pools and species life histories. Our analysis focuses on vegetation change following abandonment of agricultural fields or pastures, as this is the most extensive form of major disturbance in Neotropical forests. We consider five tree community attributes: stem density, basal area, species density, species richness and species composition. We describe two case studies, in northeastern Costa Rica and Chiapas, Mexico, where both chronosequence and annual tree dynamics studies are being applied. These case studies show that the rates of change in tree communities often deviate from chronosequence trends. With respect to tree species composition, sites of different ages differ more than a single site followed over time through the same age range. Dynamic changes in basal area within stands, on the other hand, generally followed chronosequence trends. Basal area accumulation was more linked with tree growth rates than with net changes in tree density due to recruitment and mortality. Stem turnover rates were poor predictors of species turnover rates, particularly at longer time-intervals. Effects of the surrounding landscape on tree community dynamics within individual plots are poorly understood, but are likely to be important determinants of species accumulation rates and relative abundance patterns.
PMCID: PMC2311434  PMID: 17255036
forest succession; vegetation dynamics; chronosequence; species turnover; Netropics
21.  Usefulness of Spoligotyping in Molecular Epidemiology of Mycobacterium bovis-Related Infections in South America 
Journal of Clinical Microbiology  1999;37(2):296-303.
Two hundred twenty-four Mycobacterium bovis isolates, mainly from South American countries, were typed by spoligotyping, and 41 different spoligotypes were identified. A total of 202 M. bovis isolates (90%) were grouped into 19 different clusters. The largest cluster contained 96 isolates (42.8%) on the basis of the most frequently observed spoligotype, spoligotype 34. Nineteen M. bovis isolates from humans in Argentina had spoligotypes and polymorphic GC-rich repetitive sequence (PGRS) types that represented the most common types found among isolates from cattle. All five isolates from Uruguay and three of the six isolates from Paraguay had spoligotypes that were also detected for isolates from Argentina. The spoligotypes of isolates from Brazil, Costa Rica, and Mexico and of some of the isolates from Paraguay could not be found in Argentina. A total of 154 M. bovis isolates were selected in order to compare the discriminative power of spoligotyping and restriction fragment length polymorphism (RFLP) analysis with direct repeat (DR) and PGRS probes. By spoligotyping, 31 different types were found, while AluI-digested DR probe-associated RFLP analysis identified 42 types, and RFLP analysis with the PGRS probe also detected 42 types; these were partly independent of the DR types. By combining the results obtained by spoligotyping and by RFLP analysis with the DR and PGRS probes, 88 different types were obtained. Although the differentiation of M. bovis by spoligotyping was less discriminatory than differentiation by RFLP analysis with the DR and PGRS probes, spoligotyping is easier to perform and its results are easier to interpret. Therefore, for the purpose of typing of M. bovis isolates, spoligotyping could be performed first and the isolates could be grouped into clusters and then analyzed by RFLP analysis with the DR and PGRS probes.
PMCID: PMC84290  PMID: 9889207

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