Mesoscale transect sampling of trees in the lomako–yekokora interfluvium, democratic republic of the Congo

We conducted a mesoscale transect sampling of trees 10cm DBH in the Lomako–Yekokora interfluvial forest, Democratic Republic of the Congo. Our objective was to characterize the forest landscape contained between the Lomako and Yekokora rivers in terms of its floristic composition and to investigate how representative the Lomako study site, the location of a long-term study of primates, was of the entire forest block. Fifteen transects were laid out at seven sample stations placed approximately 10km apart and alongside a 70km trail running from the Lomako study site to the margins of the Yekokora river. Three transects totaling 3.65ha were laid out at the Lomako study site and two transects totaling 2ha at each of the remaining six sample stations, amounting to 15.65ha in total. Average DBH, tree density, tree species richness and floristic composition were determined for each transect. There were 5353 trees 10cm DBH in the total sample, representing 150 species in 35 families. Caesalpinoideae trees dominated the sample followed by Olacaceae and Annonaceae. Four forest types were identified: mixed primary (57% of the sampled plots), secondary forest (9%), Gilbertiodendron (22%), and swamp (12%). The seven sample stations differed from each other in average DBH, tree density, tree species richness and floristic composition. Most of the difference, however, was due to the fact that the four forest types were not equally represented at each sample station. When forest types were contrasted independently, a marked difference in average DBH, tree density, tree species richness and floristic composition was recorded. Conversely, when only mixed primary forest was analyzed across the sample stations, no significant difference was detected except for average DBH. Thus the Lomako study site is representative of the forest landscape contained between the Lomako and Yekokora rivers only when the different forest types are treated separately. The sample stations (including Lomako) differ from each other, however, in the proportional contribution of each forest type.     

A re-evaluation of the ‘mid-Cretaceous sauropod hiatus’ and the impact of uneven sampling of the fossil record on patterns of regional dinosaur extinction

The mid-Cretaceous of North America and Europe has long been noted for the absence of sauropod dinosaurs, leading several authors to suggest that this depauperate interval is a consequence of an end-Albian sauropod extinction. This time period has become known as the ‘mid-Cretaceous sauropod hiatus’, with the subsequent presence of titanosaurian sauropods in the latest Cretaceous of North America and Europe interpreted as the result of dispersal of taxa from South America and Africa, respectively. However, several lines of evidence indicate that this hiatus is probably a sampling artefact. New fossil and trackway discoveries have considerably shortened the hiatus, reducing it to the Turonian–early Campanian in North America, and to just two short intervals in the late Cenomanian–early Turonian and late Coniacian–Santonian of Europe. Palaeoenvironmental analyses of sauropods demonstrate an inland terrestrial preference for titanosaurs, the dominant Late Cretaceous sauropods; however, during the hiatus there was a decline in inland deposits and increase in coastal sediments in Europe and North America, which would have greatly reduced the probability of preserving titanosaurs. Neither the decline in inland deposits, nor the ‘sauropod hiatus’, occurred elsewhere in the world. Statistical comparisons also demonstrate a significant positive correlation between fluctuations in inland deposits and sauropod occurrences during the mid–Late Cretaceous in Europe and North and South America. Lastly, cladistic analyses do not place latest Cretaceous North American and European titanosaurs within South American and African clades, contradicting the predictions of the ‘austral immigrant’ hypothesis. The latter hypothesis also receives little support from biogeographical analysis of dispersal among titanosaurs. Thus, the ‘sauropod hiatus’ of North America and Europe is most plausibly interpreted as the product of a sampling bias pertaining to the rarity of inland sediments and dominance of coastal deposits preserved in these two regions during the mid-Cretaceous. The presence of titanosaurs in these areas during the latest Cretaceous can be explained by dispersal from Southern Hemisphere continents, but this is no more probable than descent from Early Cretaceous incumbent faunas or dispersal from Asia.     

Wang–Landau sampling of the interplay between surface adsorption and folding of HP lattice proteins

Generic features associated with the adsorption of proteins on solid surfaces are reviewed within the framework of the hydrophobic-polar (HP) lattice protein model. The thermodynamic behaviour and structural properties of various HP protein sequences interacting with attractive surfaces have been studied using extensive Wang–Landau sampling with different types of surfaces, each of which attracts either: all monomers, only hydrophobic (H) monomers or only polar (P) monomers, respectively. Consequently, different types of folding behaviour occur for varied surface strengths. Analysis of the combined patterns of various structural observables, e.g. the derivatives of the number of interaction contacts, together with the specific heat, leads to the identification of fundamental categories of folding and transition hierarchies. We also inferred a connection between the transition categories and the relative surface strengths, i.e. the ratios of the surface attractive strengths to the intra-chain attraction among H monomers. Thus, we believe that the folding hierarchies and identification scheme are generic for different HP sequences interacting with attractive surfaces, regardless of the chain length, sequence or surface attraction.     

Influence of orthosteric ligand binding on the conformational dynamics of the β-2-adrenergic receptor via essential dynamics sampling simulation

The influence of the binding of orthosteric ligands on the conformational dynamics of the β-2-adrenoreceptor was identified using the molecular dynamics method. It was found that there was a small fraction of active states of the receptor in its apo (ligand free) ensemble. An analysis of the MD trajectories indicated that this spontaneous activation of the receptor was accompanied by the motion of its VI helix. Thus, the receptor’s constitutive activity is a direct result of its conformational dynamics. On the other hand, the binding of the full agonist resulted in a significant shift in the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized receptor in its inactive state. It is likely that the binding of the inverse agonists might be a universal method of the constitutive activity inhibition. Our results indicate that ligand binding redistributes preexisting conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux Model), rather than causes an induced fit. Therefore, the ensemble of the biologically relevant receptors conformations has been encoded in its spatial structure and individual conformations from that ensemble and might be used by the cell according to the physiological behavior.     

Altered low-γ sampling in auditory cortex accounts for the three main facets of dyslexia

It has recently been conjectured that dyslexia arises from abnormal auditory sampling. What sampling rate is altered and how it affects reading remains unclear. We hypothesized that by impairing phonemic parsing abnormal low-gamma sampling could yield phonemic representations of unusual format and disrupt phonological processing and verbal memory. Using magnetoencephalography and behavioral tests, we show in dyslexic subjects a reduced left-hemisphere bias for phonemic processing, reflected in less entrainment to ≈30?Hz acoustic modulations in left auditory cortex. This deficit correlates with measures of phonological processing and rapid naming. We further observed enhanced cortical entrainment at rates beyond 40?Hz in dyslexics and show that this particularity is associated with a verbal memory deficit. These data suggest that a single auditory anomaly, i.e., phonemic oversampling in left auditory cortex, accounts for three main facets of the linguistic deficit in dyslexia.     

Evaluation of the Salivette as sampling device for monitoring β-adrenoceptor blocking drugs in saliva

The Salivette® was evaluated with a range of racemic β-adrenoceptor blocking drugs with different lipophilicity. Recovery from the Salivette appeared to be independent of the stereochemical configuration of the drugs but a significant loss of drug due to the Salivette was observed for all tested drugs. The performance of the method, in terms of accuracy and precision, fitted well within the generally accepted criteria for validation, except near the limit of quantification. The Salivette is successfully used for quantitating salivary β-blocking drugs.     

How does sampling strategy influence detection of morphological variation in orchids? A case-study of the epiphyte Oberonia hosseusii

Effects of sampling strategy on detection of morphological variation were studied in the epiphytic orchid Oberonia hosseusii in Thailand. We compared the different effects of local versus regional sampling on the one hand and the size of local samples on the other. A local data set was collected by sampling a natural population on Doi Inthanon, during which process a preservation experiment was made. A regional data set was established by measurement of 18 preserved specimens from 12 different localities. Based on the preservation experiment, data from the regional sampling were calibrated (whenever needed) to make the two data sets more directly comparable. Heat drying and spirit preservation significantly influenced measurements for two mutually exclusive sets of characters. Increasing the local sample size from 18 to 52 individuals had no statistically significant effect on the mean value of any character. In contrast, local versus regional sampling significantly influenced the mean value of every character, virtually irrespective of local sample size. In the regional data set only, a difference was found in overall variability in vegetative versus floral characters. Three cluster analyses with equal representation of individuals from the local and regional samples were performed using different clustering techniques. Only in the analysis using neighbour-joining did pure “local clusters” prove to be significantly larger than pure “regional clusters”, suggesting that this clustering technique is particularly sensitive to effects from sampling strategy.     

Iwao’s patchiness regression through the origin: biological importance and efficiency of sampling applications

Iwao’s mean crowding-mean density relation can be treated both as a linear function describing the biological characteristics of a species at a population level, or a regression model fitted to empirical data (Iwao’s patchiness regression). In this latter form its parameters are commonly used to construct sampling plans for insect pests, which are characteristically patchily distributed or overdispersed. It is shown in this paper that modifying both the linear function and statistical model to force the intercept or lower functional limit through the origin results in more intuitive biological interpretation of parameters and better sampling economy. Firstly, forcing the function through the origin has the effect of ensuring that zero crowding occurs when zero individuals occupy a patch. Secondly, it ensures that negative values of the intercept, which do not yield an intuitive biological interpretation, will not arise. It is shown analytically that sequential sampling plans based on regression through the origin should be more efficient compared to plans based on conventional regression. For two overdispersed data sets, through-origin based plans collected a significantly lower sample size during validation than plans based on conventional regression, but the improvement in sampling efficiency was not large enough to be of practical benefit. No difference in sample size was observed when through-origin and conventional regression based plans were validated using underdispersed data. A field researcher wishing to adopt a through-origin form of Iwao’s regression for the biological reasons outlined above can therefore be confident that their sampling strategies will not be affected by doing so.     

Assessment of the efficiency of a hand-held suction device for sampling spiders: improved density estimation or oversampling?

In the study a comparison is made between the results of two sampling procedures, both based on the application of the same hand-held suction apparatus. Sampling was aimed at spiders, and was carried out on two alfalfa fields. In the first method suction sampling was applied to an enclosure of 0.48 m². The enclosed area was sampled intensively, which was facilitated by the removal of the vegetation. The second method was a transect sampling procedure during which the suction apparatus with a 0.01 m² nozzle was applied to single unenclosed sampling points 1 m apart. A linear series of 48 such subsamples comprised a transect, thus the total area covered in a transect equalled the area of the enclosure. In the transect samples three times more spiders were caught than in the enclosures. This result was consistent on different occasions and at both fields. This basic trend was found in all spider families that were present in significant numbers in the samples. Species composition in the samples collected by the two methods was similar, and species abundance ranks were highly correlated across dates. We propose that an “edge effect” can explain higher catches in transect samples. This edge effect is caused by lateral suction at the edges, which inflated the number of animals caught in the transect application.     

A survey of ciliates at the long-term sampling station “Helgoland Roads”, North Sea

This study presents a new checklist of ciliates at the long-term sampling station Helgoland Roads. The work is based on a microzooplankton monitoring programme from January 2007 to June 2009 and a ciliate monitoring programme from June 2010 to May 2012. The checklist includes 89 ciliate taxa from 46 different genera. The total abundance of the ciliate community at Helgoland Roads ranged between 0.14 and 67.7 × 10³ cells L^?1 with a distinct peak in June. The total carbon biomass ranged between 0.2 and 234.6 μg C L^?1. The ciliate community showed a clear temporal succession pattern during the monitoring periods. The present study is not only the first detailed and updated list of ciliates at Helgoland Roads, but also provides information on seasonality, i.e. the temporal variation of species composition, abundance and carbon biomass as well as information on the biogeographic distribution of dominant ciliates in comparison with other relevant studies.     

Multicenter fresh frozen tissue sampling in colorectal cancer: does the quality meet the standards for state of the art biomarker research?

The growing interest in the molecular subclassification of colorectal cancers is increasingly facilitated by large multicenter biobanking initiatives. The quality of tissue sampling is pivotal for successful translational research. This study shows the quality of fresh frozen tissue sampling within a multicenter cohort study for colorectal cancer (CRC) patients. Each of the seven participating hospitals randomly contributed ten tissue samples, which were collected following Standard Operating Procedures (SOP) using established techniques. To indicate if the amount of intact RNA is sufficient for molecular discovery research and prove SOP compliance, the RNA integrity number (RIN) was determined. Samples with a RIN < 6 were measured a second time and when consistently low a third time. The highest RIN was used for further analysis. 91% of the tissue samples had a RIN ≥ 6 (91%). The remaining six samples had a RIN between 5 and 6 (4.5%) or lower than 5 (4.5%). The median overall RIN was 7.3 (range 2.9–9.0). The median RIN of samples in the university hospital homing the biobank was 7.7 and the median RIN for the teaching hospitals was 7.3, ranging from 6.5 to 7.8. No differences were found in the outcome of different hospitals (p = 0.39). This study shows that the collection of high quality fresh frozen samples of colorectal cancers is feasible in a multicenter design with complete SOP adherence. Thus, using basic sampling techniques large patient cohorts can be organized for predictive and prognostic (bio)marker research for CRC.     

Phylogeographic sampling guided by species distribution modeling reveals the Quaternary history of the Mediterranean–Canarian Cistus monspeliensis (Cistaceae)

Accurate inference in phylogeography requires appropriate sampling strategies. Complex questions demand a large sample size at both the population and genetic levels to obtain precise reconstructions. This is the case of the phylogeographic history of Cistus monspeliensis, a plant that displays low plastid (cpDNA) diversity in the Mediterranean Basin but high diversity in the Canary Islands. Here, we aimed to identify Mediterranean refugial areas and to accurately quantify inter‐island colonization events in the Canaries. Using a previous study as starting point, we increased sample size in two ways: (i) additional sampling of plastid genetic markers (from 1041 to 1899 bp); and (ii) additional sampling of populations (from 47 to 69) in long‐term persistence areas suggested by species distribution modeling (SDM). The synergy between SDM and extended population sampling helped find higher genetic diversity. Our deeper phylogeographic sampling of C. monspeliensis revealed the following: (i) potential refugia in long‐term persistence areas with high cpDNA diversity in western Europe and the Canary Islands; and (ii) a significant increase (from 7 to 12) in the number of inferred inter‐island colonization events across the archipelago. Our results stress the usefulness of SDM to identify the genetic signature associated with potential refugial areas. We herein propose a field sampling approach based on SDM that, in combination with a larger cpDNA sampling, can help answer a wide array of phylogeographic questions, such as the location of Quaternary refugia and number of colonizations across archipelagos.     

Does random blood glucose sampling outdate testing for glycosuria in the detection of diabetes during pregnancy?

A random blood glucose concentration was determined in 2403 pregnant women attending an antenatal clinic at between 28 and 32 weeks'' gestation. The calculated 99% cut off values were 6.1 mmol/l (110 mg/100 ml) within two hours after a meal and 5.6 mmol/l (101 mg/100 ml) more than two hours after a meal. Patients with a blood glucose concentration in excess of these values were referred for a 75 g oral glucose tolerance test. Of 59 referred, four were found to have previously unsuspected but unequivocal diabetes mellitus and another four to have impaired glucose tolerance on the basis of the World Health Organisation''s criteria. Screening all antenatal patients by randomly measuring blood glucose concentrations is not only cheap and efficient but also does not interfere with the routine of busy antenatal clinics.     

The Index of Biological Integrity and the bootstrap: Can random sampling error affect stream impairment decisions?

Multimetric indices, such as the Index of Biological Integrity (IBI), are increasingly used by management agencies to determine whether surface water quality is impaired. However, important questions about the variability of these indices have not been thoroughly addressed in the scientific literature. In this study, we used a bootstrap approach to quantify variability associated with fish IBIs developed for streams in two Minnesota river basins. We further placed this variability into a management context by comparing it to impairment thresholds currently used in water quality determinations for Minnesota streams. We found that 95% confidence intervals ranged as high as 40 points for IBIs scored on a 0–100 point scale. However, on average, 90% of IBI scores calculated from bootstrap replicate samples for a given stream site yielded the same impairment status as the original IBI score. We suggest that sampling variability in IBI scores is related to both the number of fish and the number of rare taxa in a field collection. A comparison of the effects of different scoring methods on IBI variability indicates that a continuous scoring method may reduce the amount of bias in IBI scores.     

Where to sample? Ecological implications of sampling strata in determining abundance and impact of natural enemies of the coffee berry borer,Hypothenemus hampei

Several parasitoids of African origin have been introduced to coffee producing areas of the Americas and Asia as biological control agents of the coffee berry borer (CBB) Hypothenemus hampei (Coleoptera: Curculionidae). These parasitoids have become established in the field but their effect on the CBB has been limited. A two-year field study in Western Kenya has found Prorops nasuta (Hymenoptera: Bethylidae) to be the predominant parasitoid emerging from CBB-infested coffee berries collected on coffee trees or from the ground. P. nasuta comprises more than 75% of the total natural enemies collected. The density of P. nasuta was 90% higher in the berries collected from the ground than from the trees. Its hyperparasitoid, Aphanogmus sp. (Hymenoptera: Ceraphronidae), also emerged from both type of berries. Across the two seasons, the average P. nasuta density per berry was 18–35 times higher than that of Aphanogmus sp. Throughout the two years sampled, significantly higher numbers of P. nasuta and Aphanogmus sp. occurred between February and March, which coincides with the beginning of the rainy season. Higher numbers of live CBB females were recorded in berries collected from the trees. Nevertheless, mortality of adult CBB was considerably higher from January to March and started to decrease from April onwards. The possibly negative effects of cultural control practices in Latin America which include the removal of berries fallen to the ground on biological control of CBB are discussed, and the use of screened collection devices for these berries which would permit the release of parasitoids but prevent escape of the pest is proposed.     

In situ sampling of small volumes of soil solution using modified micro-suction cups

Two modified designs of micro-pore-water samplers were tested for their capacity to collect unbiased soil solution samples containing zinc and citrate. The samplers had either ceramic or polyethersulfone (PES) suction cups. Laboratory tests of the micro-samplers were conducted using (a) standard solutions with zinc and citrate concentrations that can be found in the rhizosphere and (b) two soils with contrasting texture. The results showed that both suction cups were inert with respect to citrate and zinc: they did not affect the concentrations of the two ions in freshly prepared and directly sampled standard solutions. Both micro-suction cups removed most microorganisms by filtration, though the PES cups were more effective in this respect. This filtering by the suction cups allowed for relatively accurate analysis of citrate in solutions containing microorganisms. These capacities, together with their small size and small dead volume, make the two micro-pore-water samplers highly suitable for sampling of rhizosphere soil solutions although further testing with other organic acids and trace metals may be needed.