Assignment Errors Research Articles

An open source software tool to assign the material properties of bone for ABAQUS finite element simulations

A new software tool to assign the material properties of bone to an ABAQUS finite element mesh was created and compared with Bonemat, a similar tool originally designed to work with Ansys finite element models. Our software tool (py_bonemat_abaqus) was written in Python, which is the chosen scripting language for ABAQUS. The purpose of this study was to compare the software packages in terms of the material assignment calculation and processing speed. Three element types were compared (linear hexahedral (C3D8), linear tetrahedral (C3D4) and quadratic tetrahedral elements (C3D10)), both individually and as part of a mesh.Comparisons were made using a CT scan of a hemi-pelvis as a test case. A small difference, of −0.05kPa on average, was found between Bonemat version 3.1 (the current version) and our Python package. Errors were found in the previous release of Bonemat (version 3.0 downloaded from www.biomedtown.org) during calculation of the quadratic tetrahedron Jacobian, and conversion of the apparent density to modulus when integrating over the Young׳s modulus field. These issues caused up to 2GPa error in the modulus assignment. For these reasons, we recommend users upgrade to the most recent release of Bonemat.Processing speeds were assessed for the three different element types. Our Python package took significantly longer (110s on average) to perform the calculations compared with the Bonemat software (10s). Nevertheless, the workflow advantages of the package and added functionality makes ‘py_bonemat_abaqus’ a useful tool for ABAQUS users.

Total Synthesis of the Proposed Structure of Maltepolide C.

The first total synthesis of the proposed structure of cytotoxic macrolide maltepolide C has been achieved via an E-selective intramolecular Heck cyclization as a key step. Other key features of the synthesis are Z-selective Wittig olefination, Sharpless asymmetric dihydroxylation followed by Williamson-type cyclo-etherification, Brown asymmetric allylation, and Noyori reduction of an alkynone. Detailed NMR study confirms the structure and stereochemistry of the synthetic maltepolide C unambiguously. However, the deviation of the spectra of the synthetic maltepolide C from those of the natural maltepolide C indicates a possible error in the original structural assignment.

Why RBE must be a variable and not a constant in proton therapy.

This article considered why the proton therapy (PT) relative biological effect (RBE) should be a variable rather than a constant. The reasons for a variable proton RBE are enumerated, with qualitative and quantitative arguments. The heterogeneous data sets collated by Paganetti et al (2002) and the more homogeneous data of Britten et al (2013) are further analyzed using linear regression fitting and RBE-inclusive adaptations of the linear-quadratic (LQ) radiation model. The in vitro data show RBE increasing as dose per fraction is lowered. In the Paganetti et al (2002) data sets, the differences between observed and expected effects are smaller when the LQ model is used, but with such data heterogeneity, firm statistical conclusions cannot be obtained. The more homogeneous data set shows an unequivocal variation in RBE with dose per faction. The in vivo data are inappropriate for assessments of late normal tissue effects in radiotherapy. Also, if there is the same degree of uncertainty in an RBE of 1.1 or in an RBE of 2-3 for C ions, the fractional and biological effective doses can vary considerably and be greater in the proton case. So, errors in RBE assignment are important for protons, just as with C ions. Further experimental programmes are proposed, including late normal tissue end points. Better RBE allocations might further improve PT outcomes. This study provides a rigorous critique of the 1.1 RBE used for protons, from theoretical and practical standpoints. Data analysis shows that the LQ model is more appropriate than simple linear regression. Comprehensive research programmes are suggested.

Extracting human antibody sequences from public databases for antibody humanization: high frequency of species assignment errors.

In antibody humanization, complementarity determining regions from a 'donor' antibody are often grafted onto a human framework selected by high sequence identity with the donor. In our own humanization experiments, we have found that species information is often incorrect. Here we take three mouse antibodies and perform BLAST searches against sequences annotated as being human. We find that the first genuine human hits for the six chains appear at Positions 30, 4, 11, 24, 18 and 29 in the hit lists. This illustrates both the need for caution in performing humanization and for improvements in annotation.

Morphological differentiation amongst Zulu sheep populations in KwaZulu-Natal, South Africa, as revealed by multivariate analysis

Understanding morphological structure and variation of Zulu sheep is crucial for its identification and preservation. We measured 14 linear body measurements and scored 5 qualitative traits to evaluate the morphological variation and relationships among eight Zulu sheep populations in KwaZulu-Natal. Sheep were sampled from Empangeni, Escourt, Eshowe, Jozini, Msinga, Mtubatuba, Nongoma, and Nquthu rural communities. Dark brown coat colour, either in solid form or white patched, was most frequent amongst studied sheep. There were significant variations in body measurements amongst sheep populations from different areas. Sheep from Nqutu measured highest in most morphometric variables while sheep from Empangeni measured lowest. Discriminant analysis identified rump-width, head-width, heart-girth, thorax-depth and tail-length as the most distinguishing variables amongst sheep populations. Hierarchical cluster analysis revealed two major groups, one formed by Empangeni, Mtubatuba and Nongoma, the other by Jozini, Msinga and Eshowe populations. Estcourt and Nqutu distanced themselves from these groups as individual entities. About 62% of individual sheep could be correctly identified with the populations from which they were sampled. Nqutu had the highest percentage (88.9%) of correct assignment whilst Mtubatuba had the lowest (46.7%). High assignment errors were ascribed to a certain gene flow between sheep populations. The overall significant morphostructural variation amongst Zulu sheep populations, infers considerable genetic variability within the breed and its populations. Maintaining this genetic variation is very crucial for the continuity of the breed, as it provides animals with options to respond to change in climate, disease or consumer preference.

TH‐CD‐206‐07: Determination of Patient‐Specific Myocardial Mass at Risk Using Computed Tomography Angiography

Purpose:To evaluate the accuracy of a patient‐specific coronary perfusion territory assignment algorithm that uses CT angiography (CTA) and a minimum‐cost‐path approach to assign coronary perfusion territories on a voxel‐by‐voxel basis for determination of myocardial mass at risk.Methods:Intravenous (IV) contrast (370 mg/mL iodine, 25 mL, 7 mL/s) was injected centrally into five swine (35–45 kg) and CTA was performed using a 320‐slice CT scanner at 100 kVp and 200 mA. Additionally, a 4F catheter was advanced into the left anterior descending (LAD), left circumflex (LCX), and right coronary artery (RCA) and contrast (30 mg/mL iodine, 10 mL, 1.5 mL/s) was directly injected into each coronary artery for isolation of reference coronary perfusion territories. Semiautomatic myocardial segmentation of the CTA data was then performed and the centerlines of the LAD, LCX, and RCA were digitally extracted through image processing. Individual coronary perfusion territories were then assigned using a minimum‐cost‐path approach, and were quantitatively compared to the reference coronary perfusion territories.Results:The results of the coronary perfusion territory assignment algorithm were in good agreement with the reference coronary perfusion territories. The average volumetric assignment error from mitral orifice to apex was 5.5 ± 1.1%, corresponding to 2.1 ± 0.7 grams of myocardial mass misassigned for each coronary perfusion territory.Conclusion:The results indicate that accurate coronary perfusion territory assignment is possible on a voxel‐by‐voxel basis using CTA data and an assignment algorithm based on a minimum‐cost‐path approach. Thus, the technique can potentially be used to accurately determine patient‐specific myocardial mass at risk distal to a coronary stenosis, improving coronary lesion assessment and treatment.Conflict of Interest (only if applicable): Grant funding from Toshiba America Medical Systems.

Análisis de los errores en la lectura y en el lenguaje escrito en niños de Educación Primaria

El objetivo del presente estudio es caracterizar los tipos de error en lectura y lenguaje escrito que presentan niños colombianos de segundo grado de primaria sin antecedentes neuropsicológicos. Para esto, fueron evaluados 61 niños (7-9 años) divididos en dos grupos, uno con rendimiento alto o superior y otro con básico o bajo en Lengua Castellana. Los resultados permitieron identificar y comparar los tipos de error y las categorías gramaticales utilizadas por cada grupo. Se encontraron diferencias y semejanzas entre los grupos en errores como omisión sustituciones, adiciones, traslocaciones, errores ortográficos, escritura en espejo, unión de palabras y segmentación. Estas características dependen de las tareas de lectura y lenguaje escrito a las que está expuesto el niño. Los errores más frecuentes fueron la omisión y la adición. Se encontró que la aparición de errores en las tareas de lectura es menos frecuente en los niños con rendimiento alto, presentando mejor precisión y, por lo tanto, mayor generalización de estructura fonológica de las palabras. No obstante, se encontró mayor número de errores en las tareas de escritura de estos niños, relacionado con una mayor cantidad de palabras escritas.

Erratum: Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature.

Scientific Reports 6: Article number: 23499; published online: 23 March 2016; updated: 29 April 2016. In the Supplementary Information file originally published with this Article, references 31 and 32 were incorrectly given as references 44 and 45 respectively. These errors have been corrected in the Supplementary Information that now accompanies the Article.

Structural revisions of small molecules reported to cross-link G-quadruplex DNA in vivo reveal a repetitive assignment error in the literature.

Two molecules of mistaken identity are addressed. Uncovering these assignment errors led us to formulate more general guidelines about additional misassignments in cases of published bis-imines derived from 1,2-phenylenediamine and hydroxybenzaldehydes having no substituent in ortho-positions. The main purpose of this article is to highlight this repetitive assignment error in the literature and thus increase the likelihood of correct assignments in future papers.

Improved Multi-Bernoulli Filter for Extended Stealth Targets Tracking Based on Sub-Random Matrices

In this paper, we address a radar detection and tracking of multi-stealth targets. Multi-Bernoulli filter is a provable optimal Bayes approach of multi-target filtering and shows excellent performance over the other filters. The original multi-Bernoulli filters rely on the assumption that the interest targets are point source objects. Normally, in realistic scenarios, the point source assumption is not suitable for estimating the extent stealth targets (ESTs) scenarios. Recently, the random matrices approach has been proposed for ellipsoidal extended object tracking by additional state variables. In multiple EST scenarios, although the extension ellipsoid is efficient, it may not be accurate enough because of lacking useful information, such as size, shape, and orientation. To this point, we introduce a non-ellipsoidal EST composed of multiple ellipsoidal sub-objects, and each one is represented by a random matrix. Based on such models, a multi-Bernoulli filter is used to estimate kinematic states and extensions of sub-objects for each EST. However, in multiple EST scenarios, the detection profile is prior unknown due to fluctuation of EST parameters. The parameter, such as detection probability, is of critical importance in this extended filter. To tackle these problems, a beta Gaussian inverse Wishart implementation is proposed to estimate the EST extent augment with unknown detection probability and kinematic state. The results show that the proposed filter has more accurate cardinality estimation and smaller optimal sub-pattern assignment errors than the recently extended probability hypothesis density (PHD) and cardinalized PHD filters.

Operon Gene Order Is Optimized for Ordered Protein Complex Assembly.

SummaryThe assembly of heteromeric protein complexes is an inherently stochastic process in which multiple genes are expressed separately into proteins, which must then somehow find each other within the cell. Here, we considered one of the ways by which prokaryotic organisms have attempted to maximize the efficiency of protein complex assembly: the organization of subunit-encoding genes into operons. Using structure-based assembly predictions, we show that operon gene order has been optimized to match the order in which protein subunits assemble. Exceptions to this are almost entirely highly expressed proteins for which assembly is less stochastic and for which precisely ordered translation offers less benefit. Overall, these results show that ordered protein complex assembly pathways are of significant biological importance and represent a major evolutionary constraint on operon gene organization.

The problematic issue of grammatical gender in Arabic as a foreign language

Abstract Many languages of the world have a grammatical gender system that divides all nouns into gendered categories. The gender assigned to a given noun requires gender agreement with associated items in the sentence, such as: determiners, adjectives, and demonstrative pronouns. Research in the area of grammatical gender acquisition has found that this grammatical category poses considerable difficulty for L2 learners. However, rarely was this area of difficulty the focus of L2 studies in Arabic. The present study focuses on the problematic issue of grammatical gender in Arabic as a foreign language. It examines advanced Arabic L2 learners’ written errors of gender assignment and agreement in the Arabic Learner Corpus (ALC) v2, compiled by Alfaifi, Atwel, and Hedaya (2014). Based on the classification and analysis of the errors, possible factors of the difficulty facing L2 learners in assigning the correct gender are discussed, and recommendations to reduce their effects are suggested.

Quality Assurance of UMLS Semantic Type Assignments Using SNOMED CT Hierarchies.

The Unified Medical Language System (UMLS) is one of the largest biomedical terminological systems, with over 2.5 million concepts in its Metathesaurus repository. The UMLS's Semantic Network (SN) with its collection of 133 high-level semantic types serves as an abstraction layer on top of the Metathesaurus. In particular, the SN elaborates an aspect of the Metathesaurus's concepts via the assignment of one or more types to each concept. Due to the scope and complexity of the Metathesaurus, errors are all but inevitable in this semantic-type assignment process. To develop a semi-automated methodology to help assure the quality of semantic-type assignments within the UMLS. The methodology uses a cross-validation strategy involving SNOMED CT's hierarchies in combination with UMLS semantic types. Semantically uniform, disjoint concept groups are generated programmatically by partitioning the collection of all concepts in the same SNOMED CT hierarchy according to their respective semantic-type assignments in the UMLS. Domain experts are then called upon to review the concepts in any group having a small number of concepts. It is our hypothesis that a semantic-type assignment combination applicable only to a very small number of concepts in a SNOMED CT hierarchy is an indicator of potential problems. The methodology was applied to the UMLS 2013AA release along with the SNOMED CT from January 2013. An overall error rate of 33% was found for concepts proposed by the quality-assurance methodology. Supporting our hypothesis, that number was four times higher than the error rate found in control samples. The results show that the quality-assurance methodology can aid in effective and efficient identification of UMLS semantic-type assignment errors.

가우시안 군집분석을 이용한 천리안 위성의 대기운동벡터 표적추적 알고리듬 개발 및 분석

Atmospheric Motion Vector (AMV) from satellite images have shown Slow Speed Bias (SSB) in comparison with rawinsonde. The causes of SSB are originated from tracking, selection, and height assignment error, which is known to be the leading error. However, recent works have shown that height assignment error cannot be fully explained the cause of SSB. This paper attempts a new approach to examine the possibility of SSB reduction of COMS AMV by using a new target tracking algorithm. Tracking error can be caused by averaging of various wind patterns within a target and changing of cloud shape in searching process over time. To overcome this problem, Gaussian Mixture Model (GMM) has been adopted to extract the coldest cluster as target since the shape of such target is less subject to transformation. Then, an image filtering scheme is applied to weigh more on the selected coldest pixels than the other, which makes it easy to track the target. When AMV derived from our algorithm with sum of squared distance method and current COMS are compared with rawindsonde, our products show noticeable improvement over COMS products in mean wind speed by an increase of and SSB reduction by 29%. However, the statistics regarding the bias show negative impact for mid/low level with our algorithm, and the number of vectors are reduced by 40% relative to COMS. Therefore, further study is required to improve accuracy for mid/low level winds and increase the number of AMV vectors.

Taxonomic Characterization of Honey Bee (Apis mellifera) Pollen Foraging Based on Non-Overlapping Paired-End Sequencing of Nuclear Ribosomal Loci.

Identifying plant taxa that honey bees (Apis mellifera) forage upon is of great apicultural interest, but traditional methods are labor intensive and may lack resolution. Here we evaluate a high-throughput genetic barcoding approach to characterize trap-collected pollen from multiple North Dakota apiaries across multiple years. We used the Illumina MiSeq platform to generate sequence scaffolds from non-overlapping 300-bp paired-end sequencing reads of the ribosomal internal transcribed spacers (ITS). Full-length sequence scaffolds represented ~530 bp of ITS sequence after adapter trimming, drawn from the 5’ of ITS1 and the 3’ of ITS2, while skipping the uninformative 5.8S region. Operational taxonomic units (OTUs) were picked from scaffolds clustered at 97% identity, searched by BLAST against the nt database, and given taxonomic assignments using the paired-read lowest common ancestor approach. Taxonomic assignments and quantitative patterns were consistent with known plant distributions, phenology, and observational reports of pollen foraging, but revealed an unexpected contribution from non-crop graminoids and wetland plants. The mean number of plant species assignments per sample was 23.0 (+/- 5.5) and the mean species diversity (effective number of equally abundant species) was 3.3 (+/- 1.2). Bray-Curtis similarities showed good agreement among samples from the same apiary and sampling date. Rarefaction plots indicated that fewer than 50,000 reads are typically needed to characterize pollen samples of this complexity. Our results show that a pre-compiled, curated reference database is not essential for genus-level assignments, but species-level assignments are hindered by database gaps, reference length variation, and probable errors in the taxonomic assignment, requiring post-hoc evaluation. Although the effective per-sample yield achieved using custom MiSeq amplicon primers was less than the machine maximum, primarily due to lower “read2” quality, further protocol optimization and/or a modest reduction in multiplex scale should offset this difficulty. As small quantities of pollen are sufficient for amplification, our approach might be extendable to other questions or species for which large pollen samples are not available.

A pedigree gone bad: increased offspring survival after using DNA‐based relatedness to minimize inbreeding in a captive population

AbstractCaptive breeding programs often use a pedigree to identify breeding pairs that maintain genetic diversity and limit inbreeding. However, unintentional breeding of closely related individuals can occur when errors exist in the pedigree and may subsequently result in inbreeding depression. In this study, a DNA‐based approach was used to identify parentage assignment errors in the captive pedigree of the critically endangered Attwater's prairie‐chicken Tympanuchus cupido attwateri, and tested whether clutch survival increased using DNA‐relatedness values for assigning breeding pairs instead of the pedigree and mean kinship. Parentage assignment error was observed in each year surveyed ranging from 2.4 to 7.3%. After correcting identified errors prior to the 2013 breeding season, 11 of 38 assigned pedigree‐based breeding pairs still possessed DNA‐based relatedness coefficients (rDNA) ≥0.125 suggesting that additional errors remained in the pedigree. Two approaches were used to prevent breeding among close relatives in 2013 and 2014. Assigned pedigree‐based breeding pairs in 2013 that possessed rDNA ≥0.125 were reassigned unrelated breeding partners, while all individuals in 2014 were used to identify the minimum overall rDNA for the breeding population without reference to the pedigree other than to verify founder representation. Both years resulted in a significant reduction in mean parental relatedness among chicks (P < 0.001) and a significant increase in the proportion of the clutch surviving to 5 weeks post‐hatch (P ≤ 0.006) compared to 2012 when breeding pairs were assigned using only the pedigree. No significant difference in the proportion of the clutch surviving was observed between 2013 and 2014 (P > 0.300). These results have important implications for the captive management of endangered species, and highlight the importance of periodically evaluating for pedigree errors. To what degree pedigree errors limit fitness in other endangered species captive populations deserves further attention.

A regression method for estimating performance in a rapid serial visual presentation target detection task

BackgroundEstimating target detection performance in the rapid serial visual presentation (RSVP) target detection paradigm can be challenging when the inter-stimulus interval is small relative to the variability in human response time. The challenge arises because assigning a particular response to the correct image cannot be done with certainty. Existing solutions to this challenge establish a heuristic for assigning responses to images and thereby determining which responses are hits and which are false alarms. New methodWe developed a regression-based method for estimating hit rate and false alarm rate that corrects for expected errors in a likelihood-based assignment of responses to stimuli. ResultsSimulations show that this regression method results in an unbiased and accurate estimate of target detection performance. Comparison with existing methodsThe regression method had lower estimation error compared to three existing methods, and in contrast to the existing methods, the errors made by the regression method do not depend strongly on the true values of hit rate and false alarm rate. The most commonly used existing method performed well when simulated performance was nearly perfect, but not when behavioral error rates increased. ConclusionsBased on its better estimation of hit rate and false alarm rate, the regression method proposed here would seem the best choice when estimating the hit rate and false alarm rate is the primary interest.

On sulfur core level binding energies in thiol self-assembly and alternative adsorption sites: An experimental and theoretical study.

Characteristic core level binding energies (CLBEs) are regularly used to infer the modes of molecular adsorption: orientation, organization, and dissociation processes. Here, we focus on a largely debated situation regarding CLBEs in the case of chalcogen atom bearing molecules. For a thiol, this concerns the case when the CLBE of a thiolate sulfur at an adsorption site can be interpreted alternatively as due to atomic adsorption of a S atom, resulting from dissociation. Results of an investigation of the characteristics of thiol self-assembled monolayers (SAMs) obtained by vacuum evaporative adsorption are presented along with core level binding energy calculations. Thiol ended SAMs of 1,4-benzenedimethanethiol (BDMT) obtained by evaporation on Au display an unconventional CLBE structure at about 161.25 eV, which is close to a known CLBE of a S atom on Au. Adsorption and CLBE calculations for sulfur atoms and BDMT molecules are reported and allow delineating trends as a function of chemisorption on hollow, bridge, and atop sites and including the presence of adatoms. These calculations suggest that the 161.25 eV peak is due to an alternative adsorption site, which could be associated to an atop configuration. Therefore, this may be an alternative interpretation, different from the one involving the adsorption of atomic sulfur resulting from the dissociation process of the S-C bond. Calculated differences in S(2p) CLBEs for free BDMT molecules, SH group sulfur on top of the SAM, and disulfide are also reported to clarify possible errors in assignments.

HaploPOP: a software that improves population assignment by combining markers into haplotypes.

BackgroundIn ecology and forensics, some population assignment techniques use molecular markers to assign individuals to known groups. However, assigning individuals to known populations can be difficult if the level of genetic differentiation among populations is small. Most assignment studies handle independent markers, often by pruning markers in Linkage Disequilibrium (LD), ignoring the information contained in the correlation among markers due to LD.ResultsTo improve the accuracy of population assignment, we present an algorithm, implemented in the HaploPOP software, that combines markers into haplotypes, without requiring independence. The algorithm is based on the Gain of Informativeness for Assignment that provides a measure to decide if a pair of markers should be combined into haplotypes, or not, in order to improve assignment. Because complete exploration of all possible solutions for constructing haplotypes is computationally prohibitive, our approach uses a greedy algorithm based on windows of fixed sizes. We evaluate the performance of HaploPOP to assign individuals to populations using a split-validation approach. We investigate both simulated SNPs data and dense genotype data from individuals from Spain and Portugal.ConclusionsOur results show that constructing haplotypes with HaploPOP can substantially reduce assignment error. The HaploPOP software is freely available as a command-line software at www.ieg.uu.se/Jakobsson/software/HaploPOP/.

Quantifying uncertainty and confusion in land change analyses: a case study from central Mexico using MODIS data

Land cover classifications of coarse-resolution data can aid the identification and quantification of natural variability and anthropogenic change at regional scales, but true landscape change can be distorted by misrepresentation of map classes. The Lerma–Chapala–Santiago (LCS) is biophysically diverse and heavily modified by urbanization and agricultural expansion. Land cover maps classified with a Mahalanobis distance algorithm and possibilistic metrics of class membership were used to quantify uncertainty (potential error in class assignment) and change confusion (potential error in land change identification). While land change analysis suggests that ~33% of the landscape underwent a change in class, led by changes from or to the mosaic class (~19% of landscape), classification uncertainty values for 2001 and 2007 were 0.59 and 0.62, respectively, with highest uncertainty among bare soil classes, and an average confusion index value of 0.65, with pixels experiencing change at 0.67 and pixels experiencing persistence at 0.61 on average. These results indicate that uncertainty and potential error in land cover classifications estimates may inhibit accurate assessments of land change. Estimates of land change may be refined using these metrics to more confidently identify true landscape change and to find classes and locations that are contributing to errors in land change assessments.