Genetic Distance between Species Predicts Novel Trait Expression in Their Hybrids

Interspecific hybridization can generate transgressive hybrid phenotypes with extreme trait values exceeding the combined range of the parental species. Such variation can enlarge the working surface for natural selection, and may facilitate the evolution of novel adaptations where ecological opportunity exists. The number of quantitative trait loci fixed for different alleles in different species should increase with time since speciation. If transgression is caused by complementary gene action or epistasis, hybrids between more distant species should be more likely to display transgressive phenotypes. To test this prediction we collected data on transgression frequency from the literature, estimated genetic distances between the hybridizing species from gene sequences, and calculated the relationship between the two using phylogenetically controlled methods. We also tested if parental phenotypic divergence affected the occurrence of transgression. We found a highly significant positive correlation between transgression frequency and genetic distance in eudicot plants explaining 43% of the variance in transgression frequency. In total, 36% of the measured traits were transgressive. The predicted effect of time since speciation on transgressive segregation was unconfounded by the potentially conflicting effects of phenotypic differentiation between species. Our analysis demonstrates that the potential impact hybridization may have on phenotypic evolution is predictable from the genetic distance between species.

Aortic arch morphometry in living humans

Anatomical features of the aortic arch such as its steepness, the take-off angles and the distances between its supra-aortic branches can influence the feasibility and difficulty of interventional and/or surgical maneuvers. These anatomical characteristics were assessed by means of 3D multiplanar reconstruction of thoracic angio-computed tomography scans of 92 living patients (79 males, 13 females, mean age 69.4 ± 9.9 years) carried out for various indications (gross pathology of the thoracic aorta excluded). There was a significant variation of all measured parameters between the subjects - a standard aortic arch (i.e. with all measured parameters within 2 SD) does not seem to exist. There were no significant differences between genders but some of the parameters correlated significantly to age.

Geometric facial comparisons in speed-check photographs

In many cases, it is not possible to call the motorists to account for their considerable excess in speeding, because they deny being the driver on the speed-check photograph. An anthropological comparison of facial features using a photo-to-photo comparison can be very difficult depending on the quality of the photographs. One difficulty of that analysis method is that the comparison photographs of the presumed driver are taken with a different camera or camera lens and from a different angle than for the speed-check photo. To take a comparison photograph with exactly the same camera setup is almost impossible. Therefore, only an imprecise comparison of the individual facial features is possible. The geometry and position of each facial feature, for example the distances between the eyes or the positions of the ears, etc., cannot be taken into consideration. We applied a new method using 3D laser scanning, optical surface digitalization, and photogrammetric calculation of the speed-check photo, which enables a geometric comparison. Thus, the influence of the focal length and the distortion of the objective lens are eliminated and the precise position and the viewing direction of the speed-check camera are calculated. Even in cases of low-quality images or when the face of the driver is partly hidden, good results are delivered using this method. This new method, Geometric Comparison, is evaluated and validated in a prepared study which is described in this article.

Quantitative measurements in 3-dimensional datasets of mouse lymph nodes resolve organ-wide functional dependencies

Deep tissue imaging has become state of the art in biology, but now the problem is to quantify spatial information in a global, organ-wide context. Although access to the raw data is no longer a limitation, the computational tools to extract biologically useful information out of these large data sets is still catching up. In many cases, to understand the mechanism behind a biological process, where molecules or cells interact with each other, it is mandatory to know their mutual positions. We illustrate this principle here with the immune system. Although the general functions of lymph nodes as immune sentinels are well described, many cellular and molecular details governing the interactions of lymphocytes and dendritic cells remain unclear to date and prevent an in-depth mechanistic understanding of the immune system. We imaged ex vivo lymph nodes isolated from both wild-type and transgenic mice lacking key factors for dendritic cell positioning and used software written in MATLAB to determine the spatial distances between the dendritic cells and the internal high endothelial vascular network. This allowed us to quantify the spatial localization of the dendritic cells in the lymph node, which is a critical parameter determining the effectiveness of an adaptive immune response.

Quantitative analysis of OCT characteristics in patients with achromatopsia and blue-cone monochromatism

PURPOSE: To quantify optical coherence tomography (OCT) images of the central retina in patients with blue-cone monochromatism (BCM) and achromatopsia (ACH) compared with healthy control individuals. METHODS: The study included 15 patients with ACH, 6 with BCM, and 20 control subjects. Diagnosis of BCM and ACH was established by visual acuity testing, morphologic examination, color vision testing, and Ganzfeld ERG recording. OCT images were acquired with the Stratus OCT 3 (Carl Zeiss Meditec AG, Oberkochen, Germany). Foveal OCT images were analyzed by calculating longitudinal reflectivity profiles (LRPs) from scan lines. Profiles were analyzed quantitatively to determine foveal thickness and distances between reflectivity layers. RESULTS: Patients with ACH and BCM had a mean visual acuity of 20/200 and 20/60, respectively. Color vision testing results were characteristic of the diseases. The LRPs of control subjects yielded four peaks (P1-P4), presumably representing the RPE (P1), the ovoid region of the photoreceptors (P2), the external limiting membrane (ELM) (P3), and the internal limiting membrane (P4). In patients with ACH, P2 was absent, but foveal thickness (P1-P4) did not differ significantly from that in the control subjects (187 +/- 20 vs. 192 +/- 14 microm, respectively). The distance from P1 to P3 did not differ significantly (78 +/- 10 vs. 82 +/- 5 microm) between ACH and controls subjects. In patients with BCM, P3 was lacking, and P2 advanced toward P1 compared with the control subjects (32 +/- 6 vs. 48 +/- 4 microm). Foveal thickness (153 +/- 16 microm) was significantly reduced compared with that in control subjects and patients with ACH. CONCLUSIONS: Quantitative OCT image analysis reveals distinct patterns for controls subjects and patients with ACH and BCM, respectively. Quantitative analysis of OCT imaging can be useful in differentiating retinal diseases affecting photoreceptors. Foveal thickness is similar in both normal subjects and patients with ACH but is decreased in patients with BCM.

Electroanatomic reconstruction of the left atrium, pulmonary veins, and esophagus compared with the "true anatomy" on multislice computed tomography in patients undergoing catheter ablation of atrial fibrillation

BACKGROUND: Current concepts of catheter ablation for atrial fibrillation (AF) commonly use three-dimensional (3D) reconstructions of the left atrium (LA) for orientation, catheter navigation, and ablation line placement. OBJECTIVES: The purpose of this study was to compare the 3D electroanatomic reconstruction (Carto) of the LA, pulmonary veins (PVs), and esophagus with the true anatomy displayed on multislice computed tomography (CT). METHODS: In this prospective study, 100 patients undergoing AF catheter ablation underwent contrast-enhanced spiral CT scan with barium swallow and subsequent multiplanar and 3D reconstructions. Using Carto, circumferential plus linear LA lesions were placed. The esophagus was tagged and integrated into the Carto map. RESULTS: Compared with the true anatomy on CT, the electroanatomic reconstruction accurately displayed the true distance between the lower PVs; the distances between left upper PV, left lower PV, right lower PV, and center of the esophagus; the longitudinal diameter of the encircling line around the funnel of the left PVs; and the length of the mitral isthmus line. Only the distances between the upper PVs, the distance between the right upper PV and esophagus, and the diameter of the right encircling line were significantly shorter on the electroanatomic reconstructions. Furthermore, electroanatomic tagging of the esophagus reliably visualized the true anatomic relationship to the LA. On multiple tagging and repeated CT scans, the LA and esophagus showed a stable anatomic relationship, without relevant sideward shifting of the esophagus. CONCLUSION: Electroanatomic reconstruction can display with high accuracy the true 3D anatomy of the LA and PVs in most of the regions of interest for AF catheter ablation. In addition, Carto was able to visualize the true anatomic relationship between the esophagus and LA. Both structures showed a stable anatomic relationship on Carto and CT without relevant sideward shifting of the esophagus.

Location and dimensions of the mental foramen: a radiographic analysis by using cone-beam computed tomography

INTRODUCTION The mental foramen (MF) is an important landmark in dentistry. Knowledge of its position is central to perform block anesthesia of the mental nerve or to avoid nerve damage during surgical procedures in the premolar area of the mandible. The present radiographic study aimed at evaluating the location and dimension of the MF and measuring distances to neighboring structures by using limited cone-beam computed tomography (CBCT). METHODS Sagittal, axial, and coronal CBCT images of 142 patients (26 bilateral and 116 unilateral cases) were retrospectively screened to determine the location of the MF with respect to adjacent teeth and to take linear measurements of the size of the MF and its distances to the upper and lower borders of the mandible. In addition, the course and angulation of the mental canal exiting the MF were assessed. RESULTS The majority of MF (56%) were located apically between the 2 premolars, and another 35.7% of MF were positioned below the second premolar. On average, the MF was localized 5.0 mm from the closest root of the adjacent tooth (range, 0.3-9.8 mm). The mean size of the MF showed a height of 3.0 mm and a length of 3.2 mm; however, individual cases showed large differences in height (1.8-5.1 mm) and in length (1.8-5.5 mm). All mental canals exiting the MF demonstrated an upward course in the coronal plane, with 70.1% of the mental canal presenting an anterior loop (AL) in the axial view. The mean extension of AL in cases with an AL was 2.3 mm. CONCLUSIONS This study is consistent with previous radiographic studies regarding size and location of MF and distances between MF and adjacent anatomic structures. The assessed bilateral cases showed a high intraindividual concordance for certain features when comparing right and left sides.

Electrode location and clinical outcome in hippocampal electrical stimulation for mesial temporal lobe epilepsy

PURPOSE To study the clinical outcome in hippocampal deep brain stimulation (DBS) for the treatment of patients with refractory mesial temporal lobe epilepsy (MTLE) according to the electrode location. METHODS Eight MTLE patients implanted in the hippocampus and stimulated with high-frequency DBS were included in this study. Five underwent invasive recordings with depth electrodes to localize ictal onset zone prior to chronic DBS. Position of the active contacts of the electrode was calculated on postoperative imaging. The distances to the ictal onset zone were measured as well as atlas-based hippocampus structures impacted by stimulation were identified. Both were correlated with seizure frequency reduction. RESULTS The distances between active electrode location and estimated ictal onset zone were 11±4.3 or 9.1±2.3mm for patients with a >50% or <50% reduction in seizure frequency. In patients (N=6) showing a >50% seizure frequency reduction, 100% had the active contacts located <3mm from the subiculum (p<0.05). The 2 non-responders patients were stimulated on contacts located >3mm to the subiculum. CONCLUSION Decrease of epileptogenic activity induced by hippocampal DBS in refractory MTLE: (1) seems not directly associated with the vicinity of active electrode to the ictal focus determined by invasive recordings; (2) might be obtained through the neuromodulation of the subiculum.

Topographic bone thickness maps for Bonebridge implantations.

Bonebridge™ (BB) implantation relies on optimal anchoring of the bone-conduction implant in the temporal bone. Preoperative position planning has to account for the available bone thickness minimizing unwanted interference with underlying anatomical structures. This study describes the first clinical experience with a planning method based on topographic bone thickness maps (TBTM) for presigmoid BB implantations. The temporal bone was segmented enabling three-dimensional surface generation. Distances between the external and internal surface were color encoded and mapped to a TBTM. Suitable implant positions were planned with reference to the TBTM. Surgery was performed according to the standard procedure (n = 7). Computation of the TBTM and consecutive implant position planning took 70 min on average for a trained technician. Surgical time for implantations under passive TBTM image guidance was 60 min, on average. The sigmoid sinus (n = 5) and dura mater (n = 1) were exposed, as predicted with the TBTM. Feasibility of the TBTM method was shown for standard presigmoid BB implantations. The projection of three-dimensional bone thickness information into a single topographic map provides the surgeon with an intuitive display of the anatomical situation prior to implantation. Nevertheless, TBTM generation time has to be significantly reduced to simplify integration in clinical routine.

Improved Localization of Implanted Subdural Electrode Contacts on MRI Using an Elastic Image Fusion Algorithm in Invasive EEG Recording

BACKGROUND: Accurate projection of implanted subdural electrode contacts in presurgical evaluation of pharmacoresistant epilepsy cases by invasive EEG is highly relevant. Linear fusion of CT and MRI images may display the contacts in the wrong position due to brain shift effects. OBJECTIVE: A retrospective study in five patients with pharmacoresistant epilepsy was performed to evaluate whether an elastic image fusion algorithm can provide a more accurate projection of the electrode contacts on the pre-implantation MRI as compared to linear fusion. METHODS: An automated elastic image fusion algorithm (AEF), a guided elastic image fusion algorithm (GEF), and a standard linear fusion algorithm (LF) were used on preoperative MRI and post-implantation CT scans. Vertical correction of virtual contact positions, total virtual contact shift, corrections of midline shift and brain shifts due to pneumencephalus were measured. RESULTS: Both AEF and GEF worked well with all 5 cases. An average midline shift of 1.7mm (SD 1.25) was corrected to 0.4mm (SD 0.8) after AEF and to 0.0mm (SD 0) after GEF. Median virtual distances between contacts and cortical surface were corrected by a significant amount, from 2.3mm after LF to 0.0mm after AEF and GEF (p<.001). Mean total relative corrections of 3.1 mm (SD 1.85) after AEF and 3.0mm (SD 1.77) after GEF were achieved. The tested version of GEF did not achieve a satisfying virtual correction of pneumencephalus. CONCLUSION: The technique provided a clear improvement in fusion of pre- and post-implantation scans, although the accuracy is difficult to evaluate.

Proximity of premolar roots to maxillary sinus: a radiographic survey using cone-beam computed tomography.

INTRODUCTION The proximity of the roots of the posterior maxillary teeth to the maxillary sinus is a constant challenge to the dental practitioner. Because the majority of studies have assessed the relationship regarding molars, the present study focused on premolars. METHODS Cone-beam computed tomographic images of 192 patients were reconstructed in sagittal, coronal, and axial planes to quantify the distances between the root apices of the maxillary premolars and the adjacent maxillary sinus. Measurements were taken for each root, and data were correlated with age, sex, side, and presence of both or absence of 1 of the 2 premolars. RESULTS A total of 296 teeth (177 first and 119 second premolars) were evaluated. The mean distances from buccal roots of the first premolars to the border of the maxillary sinus in the sagittal, coronal, and axial planes ranged from 5.15 ± 2.99 to 8.28 ± 6.27 mm. From palatal roots, the mean distances ranged from 4.20 ± 3.69 to 7.17 ± 6.14 mm. The mean distances of second premolars were markedly shorter in buccal roots between 2.32 ± 2.19 and 3.28 ± 3.17 mm and in palatal roots between 2.68 ± 3.58 and 3.80 ± 3.71 mm, respectively. The frequency of a premolar root protrusion into the maxillary sinus was very low in first premolars (0%-7.2%) but higher in second premolars (2.5%-13.6%). Sex, age, side, and presence/absence of premolars failed to significantly influence the mean distances between premolar roots and the maxillary sinus. CONCLUSIONS Based on the calculated mean distances of the present study, only few premolars (and if so second premolars) would present a risk of violating the border of the maxillary sinus during conventional or surgical endodontic treatment or in case of tooth extraction.

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

Background Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Results Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. Conclusions 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch webcite and should provide useful assistance to drug discovery projects.

Evaluation of 3-dimensional superimposition techniques on various skeletal structures of the head using surface models.

OBJECTIVES To test the applicability, accuracy, precision, and reproducibility of various 3D superimposition techniques for radiographic data, transformed to triangulated surface data. METHODS Five superimposition techniques (3P: three-point registration; AC: anterior cranial base; AC + F: anterior cranial base + foramen magnum; BZ: both zygomatic arches; 1Z: one zygomatic arch) were tested using eight pairs of pre-existing CT data (pre- and post-treatment). These were obtained from non-growing orthodontic patients treated with rapid maxillary expansion. All datasets were superimposed by three operators independently, who repeated the whole procedure one month later. Accuracy was assessed by the distance (D) between superimposed datasets on three form-stable anatomical areas, located on the anterior cranial base and the foramen magnum. Precision and reproducibility were assessed using the distances between models at four specific landmarks. Non parametric multivariate models and Bland-Altman difference plots were used for analyses. RESULTS There was no difference among operators or between time points on the accuracy of each superimposition technique (p>0.05). The AC + F technique was the most accurate (D<0.17 mm), as expected, followed by AC and BZ superimpositions that presented similar level of accuracy (D<0.5 mm). 3P and 1Z were the least accurate superimpositions (0.79between time points on the precision of each superimposition technique (p>0.05), the detected structural changes differed significantly between different techniques (p<0.05). Bland-Altman difference plots showed that BZ superimposition was comparable to AC, though it presented slightly higher random error. CONCLUSIONS Superimposition of 3D datasets using surface models created from voxel data can provide accurate, precise, and reproducible results, offering also high efficiency and increased post-processing capabilities. In the present study population, the BZ superimposition was comparable to AC, with the added advantage of being applicable to scans with a smaller field of view.

A comparison between 2D and 3D cephalometry on CBCT scans of human skulls

The purpose of this study was to evaluate whether measurements on conventional cephalometric radiographs are comparable with 3D measurements on 3D models of human skulls, derived from cone beam CT (CBCT) data. A CBCT scan and a conventional cephalometric radiograph were made of 40 dry skulls. Standard cephalometric software was used to identify landmarks on both the 2D images and the 3D models. The same operator identified 17 landmarks on the cephalometric radiographs and on the 3D models. All images and 3D models were traced five times with a time-interval of 1 week and the mean value of repeated measurements was used for further statistical analysis. Distances and angles were calculated. Intra-observer reliability was good for all measurements. The reproducibility of the measurements on the conventional cephalometric radiographs was higher compared with the reproducibility of measurements on the 3D models. For a few measurements a clinically relevant difference between measurements on conventional cephalometric radiographs and 3D models was found. Measurements on conventional cephalometric radiographs can differ significantly from measurements on 3D models of the same skull. The authors recommend that 3D tracings for longitudinal research are not used in cases were there are only 2D records from the past.

Phenotypic novelty in experimental hybrids is predicted by the genetic distance between species of cichlid fish

Background: Transgressive segregation describes the occurrence of novel phenotypes in hybrids with extreme trait values not observed in either parental species. A previously experimentally untested prediction is that the amount of transgression increases with the genetic distance between hybridizing species. This follows from QTL studies suggesting that transgression is most commonly due to complementary gene action or epistasis, which become more frequent at larger genetic distances. This is because the number of QTLs fixed for alleles with opposing signs in different species should increase with time since speciation provided that speciation is not driven by disruptive selection. We measured the amount of transgression occurring in hybrids of cichlid fish bred from species pairs with gradually increasing genetic distances and varying phenotypic similarity. Transgression in multi-trait shape phenotypes was quantified using landmark-based geometric morphometric methods. Results: We found that genetic distance explained 52% and 78% of the variation in transgression frequency in F1 and F2 hybrids, respectively. Confirming theoretical predictions, transgression when measured in F2 hybrids, increased linearly with genetic distance between hybridizing species. Phenotypic similarity of species on the other hand was not related to the amount of transgression. Conclusion: The commonness and ease with which novel phenotypes are produced in cichlid hybrids between unrelated species has important implications for the interaction of hybridization with adaptation and speciation. Hybridization may generate new genotypes with adaptive potential that did not reside as standing genetic variation in either parental population, potentially enhancing a population's responsiveness to selection. Our results make it conceivable that hybridization contributed to the rapid rates of phenotypic evolution in the large and rapid adaptive radiations of haplochromine cichlids.