Evaluation of computational methods for the reconstruction of HLA haplotypes

Human leukocyte antigen (HLA) haplotypes are frequently evaluated for population history inferences and association studies. However, the available typing techniques for the main HLA loci usually do not allow the determination of the allele phase and the constitution of a haplotype, which may be obtained by a very time-consuming and expensive family-based segregation study. Without the family-based study, computational inference by probabilistic models is necessary to obtain haplotypes. Several authors have used the expectation-maximization (EM) algorithm to determine HLA haplotypes, but high levels of erroneous inferences are expected because of the genetic distance among the main HLA loci and the presence of several recombination hotspots. In order to evaluate the efficiency of computational inference methods, 763 unrelated individuals stratified into three different datasets had their haplotypes manually defined in a family-based study of HLA-A, -B, -DRB1 and -DQB1 segregation, and these haplotypes were compared with the data obtained by the following three methods: the Expectation-Maximization (EM) and Excoffier-Laval-Balding (ELB) algorithms using the arlequin 3.11 software, and the PHASE method. When comparing the methods, we observed that all algorithms showed a poor performance for haplotype reconstruction with distant loci, estimating incorrect haplotypes for 38%-57% of the samples considering all algorithms and datasets. We suggest that computational haplotype inferences involving low-resolution HLA-A, HLA-B, HLA-DRB1 and HLA-DQB1 haplotypes should be considered with caution.

Fractured Orbital Wall Reconstruction With an Auricular Cartilage Graft or Absorbable Polyacid Copolymer

Objective: The objective of the study was to compare the functional and aesthetic results of fractured orbital wall reconstruction with an auricular cartilage graft or absorbable polyacid copolymer. Materials and Methods: Twenty patients with blow-out orbital fracture/orbital floor associated or not with the medial wall were assessed by the same craniofacial surgical group. All were evaluated preoperatively and postoperatively by an ophthalmologist for diplopia, enophthalmos, exophthalmos, sensitivity, ophthalmic reflexes, intraocular pressure, and visual field. The patients were subjected to a preoperative facial multislice computed tomographic scan, repeated 6 months after surgery. Eight patients underwent reconstruction with an auricular cartilage graft, and 12 patients, with blade absorbable polyacid copolymer. Subtarsal access was used for all patients. Results: Two patients showed temporary ectropion, 1 in each group. All patients presented satisfactory ocular function, and all tests revealed good orbital delineation, orbital symmetry, periorbital sinus individualization, and reduction of blow-out. Conclusions: The blow-out orbital wall reconstruction can be performed with the use of an auricular cartilage or with a blade absorbable copolymer without differences regarding functional or aesthetic complications and sequelae.

Reconstruction of two mandible defects with one fibular flap

The present report describes an original surgical procedure for the mandibular reconstruction of 2 different defects using a single fibular flap. In addition to the habitual osteotomies, we resected a bone fragment from the middle portion of the flap, with care taken to maintain the integrity of the pedicle throughout its extension to guarantee an adequate blood supply also for the distal portion of the bone flap used for the treatment of the smaller mandibular defect. This simple maneuver permitted the reconstruction of 2 mandibular regions with well-vascularized bone tissue using a single microsurgical flap. (C) 2008 Published by Elsevier Inc.

Reconstruction of mandibular segmental defects using the guided-bone regeneration technique with polylactide membranes and/or autogenous bone graft: A preliminary study on the influence of membrane permeability

Purpose: Bone maintenance after mandibular reconstruction with autogenous iliac crest may be disappointing due to extensive resorption in the long term. The potential of the guided-bone regeneration (GBR) technique to enhance the healing process in segmental defects lacks comprehensive scientific documentation. This study aimed to investigate the influence of polylactide membrane permeability on the fate of iliac bone graft (BG) used to treat mandibular segmental defects. Materials and Methods: Unilateral 10-mm-wide segmental defects were created through the mandibles of 34 mongrel dogs. All defects were mechanically stabilized, and the animals were divided into 6 treatment groups: control, BG alone, microporous membrane (poly L/DL-lactide 80/20%) (Mi); Mi plus BG; microporous laser-perforated (15 cm(2) ratio) membrane (Mip), and Mip plus BG. Calcein fluorochrome was injected intravenously at 3 months, and animal euthanasia was carried out at 6 months postoperatively. Results: Histomorphometry showed that BG protected by Mip was consistently related to larger amounts of bone compared with other groups (P <= .0001). No difference was found between defects treated with Mip alone and BG alone. Mi alone rendered the least bone area and reduced the amount of grafted bone to control levels. Data from bone labeling indicated that the bone formation process was incipient in the BG group at 3 months postoperatively regardless of whether or not it was covered by membrane. In contrast, GBR with Mip tended to enhance bone formation activity at 3 months. Conclusions: The use of Mip alone could be a useful alternative to BG. The combination of Mip membrane and BG efficiently delivered increased bone amounts in segmental defects compared with other treatment modalities. (C) 2008 American Association of Oral and Maxillofacial Surgeons.

Surgical planning for resection of an ameloblastoma and reconstruction of the mandible using a selective laser sintering 3D biomodel

Ameloblastoma is a benign locally aggressive infiltrative odontogenic lesion. It is characterized by slow growth and painless swelling. The treatment for ameloblastoma varies from curettage to en bloc resection, and the reported recurrence rates after treatment are high; the safety margin of resection is important to avoid recurrence. Advances in technology brought about great benefits in dentistry; a new generation of computed tomography scanners and 3-dimensional images enhance the surgical planning and management of maxillofacial tumors. The development of new prototyping systems provides accurate 3D biomodels on which surgery can be simulated, especially in cases of ameloblastoma, in which the safety margin is important for treatment success. A case of mandibular follicular ameloblastoma is reported where a 3D biomodel was used before and during surgery.

Outcome Analysis of Immediate and Delayed Conservative Breast Surgery Reconstruction With Mastopexy and Reduction Mammaplasty Techniques

Background: Bilateral mammaplasty or mastopexy is frequently used for oncoplastic objectives. However, little information has been available regarding outcome following immediate and delayed reconstruction. Method: Patients were divided into Group I (immediate reconstruction) and Group II (delayed reconstruction). Retrospective review was performed to compare complications, length of hospital stay, revision surgeries, and satisfaction. The associations between the complications with potential risk factors (timing, age, body mass index, smoking, and comorbid medical conditions) were analyzed. Results: There were a total of 144 patients with a mean follow-up of 47 months. Of the 106 patients in Group I, complications occurred in 24 (22.6%), skin necrosis was observed in 7.5%, fat necrosis in 5.6%, and 6.6% patients developed local recurrence. Mean period of hospitalization was 1.89 days. Of the 38 patients of the Group II, complications occurred in 12 (31.5%), skin necrosis was observed in 7 (18.4%), fat necrosis in 4 (10.5%), and 5.2% patients developed local recurrence. Mean period of hospitalization was 1.35 days. Increased length of hospital stay greater than 1 day (P < 0.001) and the number of revision surgeries (P = 0.043) were associated with the timing of the reconstruction. In univariate analysis, no difference between groups was found with respect to complication incidence (P = 0.275); however, after adjusting for other risk factors, the probability of complications tend to be higher for Group II (OR = 2.65; 95% confidence interval - 1.01-7.00; P = 0.049). Conclusions: On the basis of the results of our study, the probability of complications tends to be higher for delayed reconstructions, and it is demonstrated that obesity and smoking are risk factors for complications. Ultimately, these data may facilitate the provision of individualized risk information for shared medical decision-making.

Immediate reconstruction following breast-conserving surgery: Management of the positive surgical margins and influence on secondary reconstruction

The efficacy of breast-conserving Surgery for the local control of early breast cancer has been repeatedly evidenced. Although immediate reconstruction following breast-conserving Surgery has been described, little information is available regarding surgical management in reoperative settings due to positive margins. We studied the influence of intraoperatively assessed and postoperatively controlled Surgical margin status on the type of breast-conserving Surgery and report our results regarding complications in a reoperative breast reconstruction scenario. All patients were seen by a multidisciplinary team who recommended breast-conserving surgery. According to the breast volume, ptosis and tumor size/location, the patients were also evaluated by a plastic Surgeon, who recommended reconstruction with the appropriate technique. Intraoperative assessment Of Surgical margins was determined by histological examination of frozen sections. The mean follow-up time was 48 months. Two hundred and eighteen patients (88.5%) underwent breast-conserving Surgery and immediate reconstruction. Twelve (5.5%) patients had a positive tumor margin after review of the permanent section. All patients underwent re-exploration. In 1.3%, a second reconstructive technique was indicated and in 2.2% a skin-sparing mastectomy with total reconstruction was performed. Our findings support the important role of the intraoperative assessment of surgical margins and its interference in the selection of reconstruction techniques and negative margins: however, it will not guarantee complete excision of the tumor. Success depends on coordinated planning with the oncologic Surgeon and careful intraoperative management, (C) 2008 Elsevier Ltd. All rights reserved.

Immediate conservative breast surgery reconstruction with perforator flaps: New challenges in the era of partial mastectomy reconstruction?

Introduction: Although the use of local flaps in conservative breast surgery (CBS) reconstruction is a reliable technique, little information has been available regarding outcome following the use of perforator flaps. The purpose of this study is to analyze the feasibility, surgical planning and outcome following CBS reconstruction with intercostal artery perforator (ICAP) flap. Patients/methods: Thirteen patients underwent CBS reconstructions with an ICAP flap. These flaps were raised from adjacent tissue located on the lateral and thoracic region and based on perforators originating from the costal and muscular segment of the intercostal vessels. The technique was indicated in patients with small/moderate volume breasts. Results: Mean time of follow-up was 32 months. Flap complications were evaluated and information on patient satisfaction were collected. 61.5 percent had tumors located in the lower-outer quadrants and 69.2 percent had tumors measuring 2 cm or less (T1). Complications occurred in 3 patients (23%), including wound dehiscence in 2 patients and fat necrosis in one. All cases were treated by conservative approach with a good result. No flap loss or wound infection were reported. 90 percent were either satisfied or very satisfied with their result. Conclusion: The ICAP flap is a reliable technique for immediate CBS reconstruction. The technique is advantageous because it does not require the use of muscle transfer, with minimum donor site morbidity. Success depends on patient selection, coordinated planning with the oncological surgeon and careful intra-operative management. (C) 2011 Elsevier Ltd. All rights reserved.

Optimizing the nipple-areola sparing mastectomy with double concentric periareolar incision and biodimensional expander-implant reconstruction: Aesthetic and technical refinements

Although the biodimensional anatomical expander-implant system (BEIS) is a reliable technique, little information has been available regarding outcome following nipple-areola sparing mastectomy (NSM). To perform the resection of glandular tissue, while improving the surgical access and maintaining the nipple-areola vascularization we have developed a new approach for NSM based on the double concentric periareolar incision (DCPI). The purpose of this study is to analyze the feasibility, surgical planning and its outcome following NSM. 18 patients underwent NSM reconstructions. Mean time of follow-up was 29 months. The technique was indicated in patients with small/moderate volume breasts. Flap complications were evaluated and information on aesthetic results and patient satisfaction were collected. 83.3% had tumors measuring 2 cm or less (T1) and 72.1% were stage 0 and 1. All patients presented peripherally tumors located (at least 5 cm from the nipple). Skin complications occurred in 11.1%. One patient (5.5%) presented small skin necrosis and a wound dehiscence was observed in one patient (5.5%). The aesthetic result was good/very good in 94.4 percent and the majority of patients were very satisfied/satisfied. No local recurrences were observed. All complications except one were treated by a conservative approach. DCPI-BEIS is a simple and reliable technique for NSM reconstruction. The success depends on patient selection, coordinated planning with the oncologic surgeon and careful intra-operative and post-operative management. (C) 2009 Elsevier Ltd. All rights reserved.

The timing of Neotropical speciation dynamics: A reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data

Neotropical forests have brought forth a large proportion of the world`s terrestrial biodiversity, but the underlying evolutionary mechanisms and their timing require further elucidation. Despite insights gained from phylogenetic studies, uncertainties about molecular clock rates have hindered efforts to determine the timing of diversification processes. Moreover, most molecular research has been detached from the extensive body of data on Neotropical geology and paleogeography. We here examine phylogenetic relationships and the timing of speciation events in a Neotropical flycatcher genus (Myiopagis) by using calibrations from modern geologic data in conjunction with a number of recently developed DNA sequence dating algorithms and by comparing these estimates with those based on a range of previously proposed molecular clock rates. We present a well-supported hypothesis of systematic relationships within the genus. Our age estimates of Myiopagis speciation events based on paleogeographic data are in close agreement with nodal ages derived from a ""traditional"" avian mitochondrial 2%/My clock, while contradicting other clock rates. Our comparative approach corroborates the consistency of the traditional avian mitochondrial clock rate of 2%/My for tyrant-flycatchers. Nevertheless, our results argue against the indiscriminate use of molecular clock rates in evolutionary research and advocate the verification of the appropriateness of the traditional clock rate by means of independent calibrations in individual studies. (C) 2009 Elsevier Inc. All rights reserved.

Three-dimensional Reconstruction of Ovaries of Leaf-cutting Ant (Atta sexdens rubropilosa) Queens (Hymenoptera: Formicidae)

In this study, the ovary morphology of newly emerged ant queens of Atta sexdens rubropilosa was studied in whole mount preparations by confocal microscopy. The ovaries are composed of approximately 40 ovarioles, showing non-synchronic oocyte maturation. The terminal filament with clusters of undifferentiated cells was found at the distal end of the ovarioles. Next to this region is the germarium, composed of several elongated cystocytes interconnected by cytoplasmic bridges. The nurse cells (23-28 cells) result from asymmetric mitosis. Cytoskeleton analysis showed F-actin concentrated at the muscle cells of the external tunica and in fusomes inside the ovarioles. Microtubules were concentrated around the nuclei of the nurse and follicular cells. In contrast, the oocytes and the external tunica showed faint staining for tubulin.

Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

The role of carbon impurities on the Si(001)-c(4 x 4) surface reconstruction: Theoretical calculations

In this work we employ the state-of-the-art pseudopotential method, within a generalized gradient approximation to the density functional theory, combined with a recently developed method for the calculation of HREELS spectra to study a series of different proposed models for carbon incorporation on the silicon (001) surface. A fully discussion on the geometry, energetics and specially the comparison between experimental and theoretical STM images and electron energy loss spectra indicate that the Si(100)-c(4 x 4) is probably induced by Si-C surface dinners, in agreement with recent experimental findings. (C) 2009 Elsevier B.V. All rights reserved.

Performance Improvement of Tomographic Image Reconstruction Based on DSP Processors

This paper presents the use of a multiprocessor architecture for the performance improvement of tomographic image reconstruction. Image reconstruction in computed tomography (CT) is an intensive task for single-processor systems. We investigate the filtered image reconstruction suitability based on DSPs organized for parallel processing and its comparison with the Message Passing Interface (MPI) library. The experimental results show that the speedups observed for both platforms were increased in the same direction of the image resolution. In addition, the execution time to communication time ratios (Rt/Rc) as a function of the sample size have shown a narrow variation for the DSP platform in comparison with the MPI platform, which indicates its better performance for parallel image reconstruction.

Recording from Two Neurons: Second-Order Stimulus Reconstruction from Spike Trains and Population Coding

We study the reconstruction of visual stimuli from spike trains, representing the reconstructed stimulus by a Volterra series up to second order. We illustrate this procedure in a prominent example of spiking neurons, recording simultaneously from the two H1 neurons located in the lobula plate of the fly Chrysomya megacephala. The fly views two types of stimuli, corresponding to rotational and translational displacements. Second-order reconstructions require the manipulation of potentially very large matrices, which obstructs the use of this approach when there are many neurons. We avoid the computation and inversion of these matrices using a convenient set of basis functions to expand our variables in. This requires approximating the spike train four-point functions by combinations of two-point functions similar to relations, which would be true for gaussian stochastic processes. In our test case, this approximation does not reduce the quality of the reconstruction. The overall contribution to stimulus reconstruction of the second-order kernels, measured by the mean squared error, is only about 5% of the first-order contribution. Yet at specific stimulus-dependent instants, the addition of second-order kernels represents up to 100% improvement, but only for rotational stimuli. We present a perturbative scheme to facilitate the application of our method to weakly correlated neurons.