Human L3L4 intervertebral disc mean 3D shape,modes of variation,and their relationship to degeneration

Intervertebral disc mechanics are affected by both disc shape and disc degeneration, which in turn each affect the other; disc mechanics additionally have a role in the etiology of disc degeneration. Finite element analysis (FEA) is a favored tool to investigate these relationships, but limited data for intervertebral disc 3D shape has forced the use of simplified or single-subject geometries, with the effect of inter-individual shape variation investigated only in specialized studies. Similarly, most data on disc shape variation with degeneration is based on 2D mid-sagittal images, which incompletely define 3D shape changes. Therefore, the objective of this study was to quantify inter-individual disc shape variation in 3D, classify this variation into independently-occurring modes using a statistical shape model, and identify correlations between disc shape and degeneration. Three-dimensional disc shapes were obtained from MRI of 13 human male cadaver L3L4 discs. An average disc shape and four major modes of shape variation (representing 90% of the variance) were identified. The first mode represented disc axial area and was significantly correlated to degeneration (R²=0.44), indicating larger axial area in degenerate discs. Disc height variation occurred in three distinct modes, each also involving non-height variation. The statistical shape model provides an average L3L4 disc shape for FEA that is fully defined in 3D, and makes it convenient to generate a set of shapes with which to represent aggregate inter-individual variation. Degeneration grade-specific shapes can also be generated. To facilitate application, the model is included in this paper?s supplemental content.     

Development and validation of a generic 3D model of the distal femur

The development and validation of a virtual generic 3D model of the distal femur using computer graphical methods is presented. The synthesis of the generic model requires the following steps: acquisition of bony 3D morphology using standard computed tomography (CT) imaging; alignment of 3D models reconstructed from CT images with a common coordinate system; computer graphical sectioning of the models; extraction of bone contours from the image sections; combining and averaging of extracted contours; and 3D reconstruction of the averaged contours.

The generic models reconstructed from the averaged contours of six cadaver femora were validated by comparing their surface geometry on a point to point basis with that of the CT reconstructed reference models. The mean errors ranged from 0.99 to 2.5 mm and were in agreement with the qualitative assessment of the models.     

Statistical shape and appearance models for fast and automated estimation of proximal femur fracture load using 2D finite element models

Estimating the risk of osteoporotic fractures is an important diagnostic step that needs to be taken before medicinal treatment. Densitometry-based criteria are normally used in clinical practice for this purpose. However, densitometry-based techniques could not explain all low-energy fractures. As patient-specific finite element (FE) models allow for consideration of other parameters (e.g. load conditions) that are known to be associated with fracture, they are considered promising candidates for more accurate fracture risk estimation. Nevertheless, they are often time consuming, expensive, and complex to build and may need the type of expertise that is not normally available in clinical settings. In this study, we report the development of an automated platform for estimating proximal femur fracture loads using patient-specific 2D FE models generated using dual-energy x-ray absorptiometry (DXA) scans. First, a statistical shape and appearance model (SSAM) is built using DXA scans of patients screened for osteoporosis following a low energy fracture. SSAM is then used together with Active Appearance Models (AAM) for automated segmentation of the proximal femur from new unseen DXA scans. The mean point-to-curve error of the automated procedure, i.e. 1.2–1.4 mm, is shown to be only slightly larger than the intra-observer variability of manual segmentation, i.e. 1.0 mm. Moreover, the developed platform automatically meshes the segmented shape, assigns density-based mechanical properties, assigns loads and boundary conditions, submits the 2D FE model for solution, and performs post-processing of the 2D FE simulation data to determine fracture loads. The fracture loads predicted using the manually generated and automatically generated 2D FE models are shown to be very close with a mean difference of around 8.8%. Repeated measures ANOVA showed no significant differences between the fracture loads calculated using FE models manually generated by three independent observers and those calculated using the automatically generated FE models (p>0.05).     

Statistical shape modelling versus linear scaling: Effects on predictions of hip joint centre location and muscle moment arms in people with hip osteoarthritis

Marker-based dynamic functional or regression methods are used to compute joint centre locations that can be used to improve linear scaling of the pelvis in musculoskeletal models, although large errors have been reported using these methods. This study aimed to investigate if statistical shape models could improve prediction of the hip joint centre (HJC) location. The inclusion of complete pelvis imaging data from computed tomography (CT) was also explored to determine if free-form deformation techniques could further improve HJC estimates. Mean Euclidean distance errors were calculated between HJC from CT and estimates from shape modelling methods, and functional- and regression-based linear scaling approaches. The HJC of a generic musculoskeletal model was also perturbed to compute the root-mean squared error (RMSE) of the hip muscle moment arms between the reference HJC obtained from CT and the different scaling methods. Shape modelling without medical imaging data significantly reduced HJC location error estimates (11.4 ± 3.3 mm) compared to functional (36.9 ± 17.5 mm, p = <0.001) and regression (31.2 ± 15 mm, p = <0.001) methods. The addition of complete pelvis imaging data to the shape modelling workflow further reduced HJC error estimates compared to no imaging (6.6 ± 3.1 mm, p = 0.002). Average RMSE were greatest for the hip flexor and extensor muscle groups using the functional (16.71 mm and 8.87 mm respectively) and regression methods (16.15 mm and 9.97 mm respectively). The effects on moment-arms were less substantial for the shape modelling methods, ranging from 0.05 to 3.2 mm. Shape modelling methods improved HJC location and muscle moment-arm estimates compared to linear scaling of musculoskeletal models in patients with hip osteoarthritis.     

Estimation of 3D shape, internal density and mechanics of proximal femur by combining bone mineral density images with shape and density templates

Measurement of bone mineral density (BMD) by dual-energy X-ray absorptiometry (DXA) alone is only a moderate predictor of fracture risk. Finite element analysis (FEA) of bone mechanics, based on DXA images, may improve the prediction of fracture risk. We developed a method to estimate the 3D shape and density distribution of the proximal femur, using a 2D BMD image and a femur shape template. Proximal femurs of eighteen human cadavers were imaged using computed tomography and divided into two sets (N = 9 + 9). The template was created from the samples in first set by using 3D generalized Procrustes analysis and thin-plate splines. Subsequently, the template and 2D BMD image were utilized to estimate the shape and internal density distribution of the femurs in the second set. Finally, FEA was conducted based on the original and the estimated bone models to evaluate the effect of geometrical and density distributional errors on the mechanical strength. The volumetric errors induced by the estimation itself were low (<1.4%). In the estimation of bones in the second set, the mean distance difference between the estimated and the original bone surfaces was 0.80 ± 0.19 mm, suggesting feasible estimation of the femoral shape. The mean absolute error in voxel-by-voxel BMD was 120±8 mg cm?3. In FEA, the stiffness of the proximal femur differed by -7±16% between the original and estimated bones. The present method, in comparison with methods used in previous studies, improved the prediction of the geometry, the BMD distribution and the mechanical characteristics of the proximal femur. Potentially, the proposed method could ultimately improve the determination of bone fracture risk.     

Phenotypic variation along a cline in allozyme and karyotype frequencies, and its relationship with habitat, in the dog-whelk Nucella lapillus, L.

The dog-whelk Nucella lapillus exhibits a number of phenotypic variations and genetic polymorphisms which correlate with habitat-specific environmental pressures, especially those associated with wave action and temperature. This study investigates the relationship between genetic composition (karyotypic and electrophoretic variation) and phenotypic differentiation in N. lapillus sampled at 15 points along an 8 km stretch of coastline. Coincident clinal variation in gene frequencies and shell shape is described; they covary with differences in karyotype and also with growth. Laboratory-reared young show that differences in phenotype (shell shape and growth) are inherited. Experimental evidence is presented that specific shell shapes are adaptive under conditions of thermal stress. Together with the well-established correlations between shell shape and shore exposure, this association provides an argument for a relationship between genetic composition, phenotype and habitat in this species.     

Mandibular size and shape variation in the hominins at Dmanisi, Republic of Georgia

The hominin fossils of Dmanisi, Republic of Georgia, present an ideal means of assessing levels of skeletal size and shape variation in a fossil hypodigm belonging to the genus Homo because they have been recovered from a spatially and temporally restricted context. We compare variation in mandible size and shape at Dmanisi to that of extant hominoids and extinct hominins. We use height and breadth measurements of the mandibular corpus at the first molar and the symphysis to assess size, and analyze shape based on size-adjusted (using a geometric mean) versions of these four variables. We compare size and shape variation at Dmanisi relative to all possible pairs of individuals within each comparative taxon using an exact resampling procedure of the ratio of D2600 to D211 and the average Euclidean distance (AED) between D2600 and D211, respectively. Comparisons to extant hominoids were conducted at both the specific and subspecific taxonomic levels and to extinct hominins by adopting both a more, and less speciose, hominin taxonomy. Results indicate that the pattern of variation for the Dmanisi hominins does not resemble that of any living species: they exhibit significantly more size variation when compared to modern humans, and they have significantly more corpus shape variation and size variation in corpus heights and overall mandible size than any extant ape species. When compared to fossil hominins they are also more dimorphic in size (although this result is influenced by the taxonomic hypothesis applied to the hominin fossil record). These results highlight the need to re-examine expectations of levels of sexual dimorphism in members of the genus Homo and to account for marked size and shape variation between D2600 and D211 under the prevailing view of a single hominin species at Dmanisi.     

Biochemical variation and shell shape in populations of the fresh-water snail Lymnaea peregra (Mollusca, Gastropoda, Pulmonata) from south-west Ireland

Lymnaea peregra was collected at sites, predominantly from the Caha plateau, in south-west Ireland. These included sites investigated by previous workers and found to contain populations with a distinctive pattern of variation in shell-shape. Normally spired populations and non-spired ( involuta, sub-involuta ) could occur in adjacent loughs in the same watershed. The biochemical variation in some of these populations was investigated using horizontal starch-gel zone electrophoresis. Fourteen biochemical loci were investigated. Although circumscribed by difficulties in collecting and low sample numbers, the investigation showed that the pattern of variation in shell shape was still present and was not correlated or associated with the biochemical variation. While this did not support hypotheses of geographic race formation or incipient speciation, it was in agreement with the current view of variation and speciation in fresh-water pulmonates.     

Length and sequence variation in the mitochondrialDNA control region of the Etruscan freshwater goby Padogobius nigricans (Teleostei, Gobiidae)

The primary structures of the mtDNA control region, the flanking tRNA^Pro and tRNA^Phe genes and the partial 12S rRNA gene of the freshwater Etruscan goby Padogobius nigricans (Teleostei, Gobiidae) were determined. A tandem array of variable 17-bp repeats, named R1–7, was found to be responsible for most of the observed length and sequence variation between individuals.     

Developmental plasticity, morphological variation and evolvability: a multilevel analysis of morphometric integration in the shape of compound leaves

The structure of compound leaves provides flexibility for morphological change by variation in the shapes, sizes and arrangement of leaflets. Here, we conduct a multilevel analysis of shape variation in compound leaves to explore the developmental plasticity and evolutionary potential that are the basis of diversification in leaf shape. We use the methods of geometric morphometrics to study the shapes of individual leaflets and whole leaves in 20 taxa of Potentilla (sensu lato). A newly developed test based on the bootstrap approach suggests that uncertainty in the molecular phylogeny precludes firm conclusions whether there is a phylogenetic signal in the data on leaf shape. For variation among taxa, variation within taxa, as well as fluctuating asymmetry, there is evidence of strong morphological integration. The patterns of variation are similar across all three levels, suggesting that integration within taxa may act as a constraint on evolutionary change.     

Stability of HIV-1 subtype B and C Tat is associated with variation in the carboxyl-terminal region

The multifunctional trans-activator Tat is an essential regulatory protein for HIV-1 replication and is characterized by high sequence diversity. Numerous experimental studies have examined Tat in HIV-1 subtype B, but research on subtype C Tat is lacking, despite the high prevalence of infections caused by subtype C worldwide. We hypothesized that amino acid differences contribute to functional differences among Tat proteins. In the present study, we found that subtype B NL4-3Tat and subtype C isolate HIV1084 i Tat exhibited differences in stability by overexpressing the fusion protein Tat-Flag. In addition, 1084 i Tat can activate LTR and NF-κB more efficiently than NL4-3 Tat. In analyses of the activities of the truncated forms of Tat, we found that the carboxylterminal region of Tat regulates its stability and transactivity. According to our results, we speculated that the differences in stability between B-Tat and C-Tat result in differences in transactivation ability.     

Mapping of the ben, ant and cat genes of Pseudomonas aeruginosa and evolutionary relationship of the ben region of P. aeruginosa and P. putida

Abstract Genes responsible for the utilization of benzoate, anthranilate or catechol ( ben, ant, cat ) of Pseudomonas aeruginosa PAO were mapped precisely using a cosmid clone carrying all these genes. Genes were localized either by subcloning and complementation or by Tn 5 mutagenesis and mapping of the Tn 5 insertion. To achieve this, a novel Tn 5 mutagenesis procedure was developed by constructing a Tn 5 insertion derivative of the Escherichia coli strain S17-1. Preliminary mapping of the ben cat genes of P. putida PPN was accomplished by complementation using a PPN cosmid bank. Sequence homology was demonstrated by Southern hybridization between the ben regions of both P. aeruginosa and P. putida , implying an evolutionary relationship of this chromosomal region of these two pseudomonads.     

Genomic sequence analysis of the 238-kb swine segment with a cluster of TRIM and olfactory receptor genes located, but with no class I genes, at the distal end of the SLA class I region

Continuous genomic sequence has been previously determined for the swine leukocyte antigen (SLA) class I region from the TNF gene cluster at the border between the major histocompatibility complex (MHC) class III and class I regions to the UBD gene at the telomeric end of the classical class I gene cluster (SLA-1 to SLA-5, SLA-9, SLA-11). To complete the genomic sequence of the entire SLA class I genomic region, we have analyzed the genomic sequences of two BAC clones carrying a continuous 237,633-bp-long segment spanning from the TRIM15 gene to the UBD gene located on the telomeric side of the classical SLA class I gene cluster. Fifteen non-class I genes, including the zinc finger and the tripartite motif (TRIM) ring-finger-related family genes and olfactory receptor genes, were identified in the 238-kilobase (kb) segment, and their location in the segment was similar to their apparent human homologs. In contrast, a human segment (alpha block) spanning about 375 kb from the gene ETF1P1 and from the HLA-J to HLA-F genes was absent from the 238-kb swine segment. We conclude that the gene organization of the MHC non-class I genes located in the telomeric side of the classical SLA class I gene cluster is remarkably similar between the swine and the human segments, although the swine lacks a 375-kb segment corresponding to the human alpha block. The nucleotide sequence data reported in this paper have been submitted to DDBJ, EMBL, and GenBank databases under accession numbers AB158486 and AB158487     

北疆地区15种豆科植物种子对绵羊消化道作用的响应

为揭示北疆地区豆科植物种子对绵羊消化道作用的响应, 采集了北疆地区天然草地中常见的15种豆科植物种子。首先测定种子的长、宽、厚和质量, 并计算种子的形状指数。其次, 用种子饲喂绵羊, 收粪试验在种子摄食后的第6、12、24、36、48和72 h进行, 测定种子经绵羊消化道作用后的回收率、种子在绵羊消化道内的平均滞留时间以及消化道作用前后种子的萌发行为, 并研究了种子大小及形状指数对平均滞留时间和种子回收率的影响。结果如下: 15种植物种子质量在1.50-37.68 mg之间, 形状指数在0.001-0.12之间, 均为中等或较大类型的球(圆)形种子; 种子被绵羊采食后的排放动态符合高斯模型: Y = 0.02 + 0.74e ^{-0.5(( X - 29.61)/9.41)2}, 种子排放高峰期集中在采食后的24-36 h时间段内; 种子回收率最大的是洋甘草(Glycyrrhiza glabra)(39.25%), 最小的是草木犀(Melilotus officinalis)(4.28%); 平均滞留时间最长的是草木犀(37.19 h), 最短的是新疆棘豆(Oxytropis sinkiangensis)(22.33 h); 种子回收率与种子大小和形状指数之间分别具有符合形如Y = 6.45 + 2.05X - 0.04X ²和Y = 2.59 + 36.97e ^{-24.47 X}的函数关系模型; 平均滞留时间与种子大小和形状指数之间分别具有符合形如Y = 12.48 + 37.44e ^{-0.07 X}和Y = 3.93 + 2055.33X - 21757.99X ²的函数关系模型, 此结果表明, 较大、较小和形状不规则的豆科种子较易被绵羊消化和排泄。经绵羊消化道作用后, 多叶锦鸡儿(Caragana pleiophylla)种子的萌发率由消化前的96.22%显著降低至35.17%, 野火球(Trifolium lupinaster)和狐尾黄耆(Astragalus alopecurus)种子萌发率和消化前相比差异不显著, 其余12种种子的萌发率均显著提高(p < 0.05)。     

Epidemiological study and variation analysis of the porcine kobuvirus 3D gene in Sichuan province,China

<正>Dear Editor,As a member of the Kobuvirus genus in the Picornaviridae family,porcine kobuvirus is prevalent worldwide in pigs with or without diarrhea.Picornaviruses are classified into 12 genera(Aphthovirus,Cardiovirus,Enterovirus,Hepatovirus,Kobuvirus,Parechovirus,Sapelovirus,Avihepatovirus,Erbovirus,Senecavirus,     

Airborne pollen concentration in the region of Braga, Portugal, and its relationship with meteorological parameters

The variation in airborne pollen concentrationof the Braga region (Portugal) was studied inspringtime, during the flowering of Vitisvinifera. The data set was obtained for twoconsecutive years (1999 and 2000), using aCour-type sampler.During this period, thirty-six taxa wereobserved in a total of 3,200 pollengrains m^-3 of air (CPA). The main pollentypes observed were Olea, Poaceaea,nd Castanea, representing 74% of thepollen spectrum.The airborne pollen concentration (CPA) wassignificantly correlated with certainmeteorological parameters. Pollen concentrationwas positively correlated with temperature andwind direction (East and Northeast) andnegatively correlated with rainfall and numberof rainy days.     

Length variation in a specific region of the period gene correlates with differences in pupal diapause incidence in the flesh fly, Sarcophaga bullata

We report differences in the length of a specific region of the circadian clock gene period (per) that correlate with different capacities for pupal diapause in the flesh fly, Sarcophaga bullata. The conspicuous difference is located in a region we refer to as the putative C-terminal photoperiodic (CP) region. The length of the CP region correlates inversely with the incidence of diapause. A deletion of 33 amino acids in this region correlates with a significant increase in the incidence of diapause, from 78.1% to 93.0%, and an insertion of 9 amino acids in the same area correlates with a drop in the diapause incidence to 4.0%. This correlation suggests a possible functional role for this region of per in photoperiodism.