ERRATUM: New Body Mass Estimates for Omomys carteri,a Middle Eocene Primate From North America. Am J Phys Anthropol 109:41–52.

Payseur BA, Covert HA, Vinyard CJ, Dagosto M. 1999. New Body Mass Estimates for Omomys carteri, a Middle Eocene Primate From North America. Am J Phys Anthropol 109:41–52. This article included an incomplete Table 2. The final two columns, showing “Intercept” and “SEE” data were omitted. The complete Table 2, with these two columns included, is provided below.     

Targeting Biocontrol with the Slug-Parasitic Nematode Phasmarhabditis hermaphrodita in Slug Feeding Areas: a Model Study

The nematode Phasmarhabditis hermaphrodita was applied to soil in an outdoor miniplot experiment to protect Chinese cabbage seedlings from damage by the field slug Deroceras reticulatum. The aim was to investigate the possibility of reducing the numbers of nematodes applied by only partially spraying soil in the area where slug control was needed. Nematodes sprayed as overall applications were compared with band applications along plant rows and spot applications around individual plants, in plots with nine or 18 plants. Band and spot applications were applied at two rates, designated the full rate (same number of nematodes per plot as in the overall application) and the area rate (same number of nematodes per unit area comprising 43% (band) and 18% (spot) of the overall application). In plots with 18 plants, where spot-treated plant alternated with untreated plants, no significant difference in damage was found between spot-treated plants and untreated plants. This indicates that slugs were not repelled from nematode-treated areas and that any effects in reducing slug damage were not due to repellency. All nematode treatments resulted in a significant reduction in the mean level of slug damage to seedlings from six or more days after treatment. However, there were significant interactions between nematode treatment, the number of plants per plot, the position of plants within plots (edge or middle) and time after treatment. The effect of time after treatment was modelled. The log time to 50% reduction in slug damage (t 50 ) was related to the area treated and the dose applied. In plots with band or spot treatments at the full dose, there was a relatively small increase in t 50 with declining area treated. In plots treated with band or spot treatments at the area dose, t 50 increased consistently with declining relative area treated. The final level of damage, expressed as a percentage of damage on untreated plots (P), was influenced by both the dose and area treated. Final damage was greatest on spoti treated plots where half the plants were untreated. We conclude that partial treatment of soil around all plants to be protected from slug damage is a potentially valuable method of reducing the overall nematode dose required for control of slug damage, provided that some damage can be tolerated.     

Overall Versus Band Application of the Nematode Phasmarhabditis hermaphrodita With and Without Incorporation into Soil, for Biological Control of Slugs in Winter Wheat

In two concurrent field experiments, the effects of three types of soil cultivation and two patterns of nematode application were studied in order to investigate their effects on damage to winter wheat by slugs (assessed at Zadoks Growth Stage 12). In experiment 1, infective juveniles (IJs) of the nematode Phasmarhabditis hermaphrodita were applied to soil as an overall spray or as a band spray (8-cm wide), centred on the drill rows (16.7-cm apart). Nematodes were either left undisturbed on the soil surface or harrowed into the soil immediately after application. The control provided by nematodes was compared with that provided by metaldehyde and methiocarb pellets broadcast at the recommended rate immediately after drilling. In this experiment, winter wheat on plots treated with IJs showed significantly less slug damage than on wheat plots treated with metaldehyde or methiocarb pellets or untreated plots. There was no significant difference in plant damage between plots treated with band and overall spray applications of IJs, nor was there any significant difference between plots with and without harrowing. There was also no significant difference between untreated plots and plots treated with metaldehyde or methiocarb pellets, probably because rainfall shortly after treatment rendered the pellets ineffective. In experiment 2, nematodes were applied as an overall spray or plots were not treated with nematodes before soil was cultivated with tines, Roterra or Dutzi cultivators. Nematode application before soil cultivation using tines or Roterra reduced the number of plants damaged significantly. However, nematodes applied before Dutzi cultivation appeared to be rendered ineffective. Damage to winter wheat was lowest in plots that had been sprayed with nematodes and subsequently cultivated with tines or Roterra.     

Pericentromeric regions of soybean (Glycine max L. Merr.) chromosomes consist of retroelements and tandemly repeated DNA and are structurally and evolutionarily labile

Little is known about the physical makeup of heterochromatin in the soybean (Glycine max L. Merr.) genome. Using DNA sequencing and molecular cytogenetics, an initial analysis of the repetitive fraction of the soybean genome is presented. BAC 076J21, derived from linkage group L, has sequences conserved in the pericentromeric heterochromatin of all 20 chromosomes. FISH analysis of this BAC and three subclones on pachytene chromosomes revealed relatively strict partitioning of the heterochromatic and euchromatic regions. Sequence analysis showed that this BAC consists primarily of repetitive sequences such as a 102-bp tandem repeat with sequence identity to a previously characterized approximately 120-bp repeat (STR120). Fragments of Calypso-like retroelements, a recently inserted SIRE1 element, and a SIRE1 solo LTR were present within this BAC. Some of these sequences are methylated and are not conserved outside of G. max and G. soja, a close relative of soybean, except for STR102, which hybridized to a restriction fragment from G. latifolia. These data present a picture of the repetitive fraction of the soybean genome that is highly concentrated in the pericentromeric regions, consisting of rapidly evolving tandem repeats with interspersed retroelements.     

High definition bronchoscopy: a randomized exploratory study of diagnostic value compared to standard white light bronchoscopy and autofluorescence bronchoscopy

Background

Videobronchoscopy is an essential diagnostic procedure for evaluation of the central airways and pivotal for the diagnosis and staging of lung cancer. Technological improvements have resulted in high definition (HD) images with advanced real time image enhancement techniques (i-scan).

Objectives

In this study we aimed to explore the sensitivity of HD+ i-scan bronchoscopy for detection of epithelial changes like vascular abnormalities and suspicious preinvasive lesions, and tumors.

Methods

In patients scheduled for a therapeutic or diagnostic procedure under general anesthesia videos of the bronchial tree were made using 5 videobronchoscopy modes in random order: normal white light videobronchoscopy (WLB), HD-bronchoscopy (HD), HD bronchoscopy with surface enhancement technique (i-scan1), HD with surface- and tone enhancement technique (i-scan2) and dual mode autofluorescence videobronchoscopy (AFB). The videos were scored in random order by two independent and blinded expert bronchoscopists.

Results

In 29 patients all videos were available for analysis. Vascular abnormalities were scored most frequently in HD + i-scan2 bronchoscopy (1.33 ± 0.29 abnormal or suspicious sites per patient) as compared to 0.12 ± 0.05 site for AFB (P = 0.003). Sites suspicious for preinvasive lesions were most frequently reported using AFB (0.74 ± 0.12 sites per patient) as compared to 0.17 ± 0.06 for both WLB and HD bronchoscopy (P = 0.003). Tumors were detected equally by all modalities. The preferred modality was HD bronchoscopy with i-scan (tone- plus surface and surface enhancement in respectively 38% and 35% of cases P = 0.006).

Conclusions

This study shows that high definition bronchoscopy with image enhancement technique may result in better detection of subtle vascular abnormalities in the airways. Since these abnormalities may be related to preneoplastic lesions and tumors this is of clinical relevance. Further investigations using this technique relating imaging to histology are warranted.     

Comparative chromosome maps of neotropical rodents Necromys lasiurus and Thaptomys nigrita (Cricetidae) established by ZOO-FISH

This work presents chromosome homology maps between Mus musculus (MMU) and 2 South American rodent species from the Cricetidae group: Necromys lasiurus (NLA, 2n = 34) and Thaptomys nigrita (TNI, 2n = 52), established by ZOO-FISH using mouse chromosome-specific painting probes. Extending previous molecular cytogenetic studies in Neotropical rodents, the purpose of this work was to delineate evolutionary chromosomal rearrangements in Cricetidae rodents and to reconstruct the phylogenetic relationships among the Akodontini species. Our phylogenetic reconstruction by maximum parsimony analysis of chromosomal characters confirmed one consistent clade of all Neotropical rodents studied so far. In both species analyzed here, we observed the syntenic association of chromosome segments homologous to MMU 8/13, suggesting that this chromosome form is a synapomorphic trait exclusive to Neotropical rodents. Further, the previously described Akodontini-specific syntenic associations MMU 3/18 and MMU 6/12 were observed in N.lasiurus but not in T. nigrita, although the latter species is considered a member of the Akodontini tribe by some authors. Finally, and in agreement with this finding, N.lasiurus and Akodon serrensis share the derived fission of MMU 13, which places them as basal sister clades within Akodontini.     

The BioLexicon: a large-scale terminological resource for biomedical text mining

Background

Due to the rapidly expanding body of biomedical literature, biologists require increasingly sophisticated and efficient systems to help them to search for relevant information. Such systems should account for the multiple written variants used to represent biomedical concepts, and allow the user to search for specific pieces of knowledge (or events) involving these concepts, e.g., protein-protein interactions. Such functionality requires access to detailed information about words used in the biomedical literature. Existing databases and ontologies often have a specific focus and are oriented towards human use. Consequently, biological knowledge is dispersed amongst many resources, which often do not attempt to account for the large and frequently changing set of variants that appear in the literature. Additionally, such resources typically do not provide information about how terms relate to each other in texts to describe events.

Results

This article provides an overview of the design, construction and evaluation of a large-scale lexical and conceptual resource for the biomedical domain, the BioLexicon. The resource can be exploited by text mining tools at several levels, e.g., part-of-speech tagging, recognition of biomedical entities, and the extraction of events in which they are involved. As such, the BioLexicon must account for real usage of words in biomedical texts. In particular, the BioLexicon gathers together different types of terms from several existing data resources into a single, unified repository, and augments them with new term variants automatically extracted from biomedical literature. Extraction of events is facilitated through the inclusion of biologically pertinent verbs (around which events are typically organized) together with information about typical patterns of grammatical and semantic behaviour, which are acquired from domain-specific texts. In order to foster interoperability, the BioLexicon is modelled using the Lexical Markup Framework, an ISO standard.

Conclusions

The BioLexicon contains over 2.2 M lexical entries and over 1.8 M terminological variants, as well as over 3.3 M semantic relations, including over 2 M synonymy relations. Its exploitation can benefit both application developers and users. We demonstrate some such benefits by describing integration of the resource into a number of different tools, and evaluating improvements in performance that this can bring.     

The Structure of the Cytochrome P450cam–Putidaredoxin Complex Determined by Paramagnetic NMR Spectroscopy and Crystallography

Cytochrome P450cam catalyzes the hydroxylation of camphor in a complex process involving two electron transfers (ETs) from the iron-sulfur protein putidaredoxin. The enzymatic control of the successive steps of catalysis is critical for a highly efficient reaction. The injection of the successive electrons is part of the control system. To understand the molecular interactions between putidaredoxin and cytochrome P450cam, we determined the structure of the complex both in solution and in the crystal state. Paramagnetic NMR spectroscopy using lanthanide tags yielded 446 structural restraints that were used to determine the solution structure. An ensemble of 10 structures with an RMSD of 1.3 Å was obtained. The crystal structure of the complex was solved, showing a position of putidaredoxin that is identical with the one in the solution structure. The NMR data further demonstrate the presence of a minor state or set of states of the complex in solution, which is attributed to the presence of an encounter complex. The structure of the major state shows a small binding interface and a metal-to-metal distance of 16 Å, with two pathways that provide strong electronic coupling of the redox centers. The interpretation of these results is discussed in the context of ET. The structure indicates that the ET rate can be much faster than the reported value, suggesting that the process may be gated.     

Application of Artificial Intelligence/Machine Vision & Learning for the Development of a Live Single-cell Phenotypic Biomarker Test to Predict Prostate Cancer Tumor Aggressiveness

To assess the usefulness and applications of machine vision (MV) and machine learning (ML) techniques that have been used to develop a single cell-based phenotypic (live and fixed biomarkers) platform that correlates with tumor biological aggressiveness and risk stratification, 100 fresh prostate samples were acquired, and areas of prostate cancer were determined by post-surgery pathology reports logged by an independent pathologist. The prostate samples were dissociated into single-cell suspensions in the presence of an extracellular matrix formulation. These samples were analyzed via live-cell microscopy. Dynamic and fixed phenotypic biomarkers per cell were quantified using objective MV software and ML algorithms. The predictive nature of the ML algorithms was developed in two stages. First, random forest (RF) algorithms were developed using 70% of the samples. The developed algorithms were then tested for their predictive performance using the blinded test dataset that contained 30% of the samples in the second stage. Based on the ROC (receiver operating characteristic) curve analysis, thresholds were set to maximize both sensitivity and specificity. We determined the sensitivity and specificity of the assay by comparing the algorithm-generated predictions with adverse pathologic features in the radical prostatectomy (RP) specimens. Using MV and ML algorithms, the biomarkers predictive of adverse pathology at RP were ranked and a prostate cancer patient risk stratification test was developed that distinguishes patients based on surgical adverse pathology features. The ability to identify and track large numbers of individual cells over the length of the microscopy experimental monitoring cycles, in an automated way, created a large biomarker dataset of primary biomarkers. This biomarker dataset was then interrogated with ML algorithms used to correlate with post-surgical adverse pathology findings. Algorithms were generated that predicted adverse pathology with >0.85 sensitivity and specificity and an AUC (area under the curve) of >0.85. Phenotypic biomarkers provide cellular and molecular details that are informative for predicting post-surgical adverse pathologies when considering tumor biopsy samples. Artificial intelligence ML-based approaches for cancer risk stratification are emerging as important and powerful tools to compliment current measures of risk stratification. These techniques have capabilities to address tumor heterogeneity and the molecular complexity of prostate cancer. Specifically, the phenotypic test is a novel example of leveraging biomarkers and advances in MV and ML for developing a powerful prognostic and risk-stratification tool for prostate cancer patients.