Maximum Agreement Research Articles

Bounds on the Expected Size of the Maximum Agreement Subtree for a Given Tree Shape

We show that the expected size of the maximum agreement subtree of two $n$-leaf trees, uniformly random among all trees with the shape, is $\Theta(\sqrt{n})$. To derive the lower bound, we prove a global structural result on a decomposition of rooted binary trees into subgroups of leaves called blobs. To obtain the upper bound, we generalize a first moment argument from [D. I. Bernstein, et al., SIAM J. Discrete Math., 29 (2015), pp. 2065--2074] for random tree distributions that are exchangeable and not necessarily sampling consistent.

Comparison of the modeling results of nitrate concentrations in soil water below the root zone in the local and regional scale

The article presents a comparative analysis of the modeling results of nitrate concentrations in water below the root zone of the soil in the local and regional scale. In this research, the field-scale DNDC (Denitrification – Decomposition) and the regional-scale GROWA–DENUZ (ger. Großräumiges wasserhaushalt – Denitrifikation im durchwurzelten Boden) models were applied to the study area of the shallow aluvial aquifer of the Spodnje Savinjska dolina in the central part of Slovenia. Using the concept of Hydrological Response Unit (HRU) and Cohen Kappa statistical analysis of the degree of agreement and assessment of the reliability of the results of spatial modeling of nitrate in soil water below the root zone, we determined and interpreted the areas of maximum agreement and disagreement of model results. A good agreement was found at the highest modeled concentrations of nitrate in soil water, whereas the greatest deviations were detected primarily in the lower part of the range. The main reasons for disagreement were differences in the estimation of the denitrification conditions in the anaerobic environments of gley-soils with the shallow groundwater and differences in fertilisation scenarios and agricultural practices.

The consistency of neuropathological diagnoses in patients undergoing surgery for suspected recurrence of glioblastoma

PurposeClinical factors and neuro-imaging in patients with glioblastoma who appear to progress following standard chemoradiation are unable to reliably distinguish tumor progression from pseudo-progression. As a result, surgery is commonly recommended to establish a final diagnosis. However, studies evaluating the pathologists’ agreement on pathologic diagnoses in this setting have not been previously evaluated.MethodsA hypothetical clinical history coupled with images of histological sections from 13 patients with glioblastoma who underwent diagnostic surgery for suspected early recurrence were sent to 101 pathologists from 50 NCI-designated Cancer Centers. Pathologists were asked to provide a final diagnosis (active tumor, treatment effect, or unable to classify) and to report on percent active tumor, treatment effect, and degree of cellularity and degree of mitotic activity.ResultsForty-eight pathologists (48%) from 30 centers responded. In three cases > 75% of pathologists diagnosed active tumor. In two cases > 75% diagnosed treatment effect. However, in the remaining eight cases the disparity in diagnoses was striking (maximum agreement on final diagnosis ranged from 36 to 68%). Overall, only marginal agreement was observed in the overall assessment of disease status [kappa score 0.228 (95% CI 0.22–0.24)].ConclusionsConfidence in any clinical diagnostic assay requires that very similar results are obtained from identical specimens evaluated by sophisticated clinicians and institutions. The findings of this study illustrate that the diagnostic agreement between different cases of repeat resection for suspected recurrent glioblastoma can be variable. This raises concerns as pathological diagnoses are critical in directing standard and experimental care in this setting.

Human consistency evaluation of static video summaries

Automatic video summarization aims to provide brief representation of videos. Its evaluation is quite challenging, usually relying on comparison with user summaries. This study views it in a different perspective in terms of verifying the consistency of user summaries, as the outcome of video summarization is usually judged based on them. We focus on human consistency evaluation of static video summaries in which the user summaries are evaluated among themselves using the consistency modelling method we proposed recently. The purpose of such consistency evaluation is to check whether the users agree among themselves. The evaluation is performed on different publicly available datasets. Another contribution lies in the creation of static video summaries from the available video skims of the SumMe datatset. The results show that the level of agreement varies significantly between the users for the selection of key frames, which denotes the hidden challenge in automatic video summary evaluation. Moreover, the maximum agreement level of the users for a certain dataset, may indicate the best performance that the automatic video summarization techniques can achieve using that dataset.

Delphi poll to assess consensus on issues influencing long-term adherence to treatments in cystic fibrosis among Italian health care professionals.

PurposeThe aim of this study was to determine the level of consensus among Italian health care professionals (HCPs) regarding factors that influence adherence to cystic fibrosis (CF) treatments.MethodsA Delphi questionnaire with 94 statements of potential factors influencing adherence was developed based on a literature review and in consultation with a board of experts (n=4). This was distributed to a multidisciplinary expert panel of HCPs (n=110) from Italian CF centers. A Likert scale was used to indicate the level of agreement (1= no agreement to 9= maximum agreement) with each statement. Three rounds were distributed to establish a consensus (≥80% of participant ratings within one 3-point region) and, at the third round, assign a ranking to each statement with a high level of agreement (consensus in the 7–9 range) only.ResultsOf 110 HCPs (from 31 Italian CF centers who were surveyed), responses were obtained from 85 (77%) in the first, 78 (71%) in the second, and 72 (65%) in the third round. The highest degree of agreement (95.8%) was reached with the statement that the HCP needs to build a relationship with the patient to influence adherence. A high level of agreement was not reached for statements that morbidity and mortality are influenced by the level of adherence to therapy, and no consensus was reached on the statement that age of the patient influences adherence to treatment.ConclusionWe found that Italian HCPs endorsed a strong relationship with the patient as being a key driver in improving adherence. There were several areas, such as the influence of adherence on morbidity and mortality, where the consensus of Italian HCPs differed from the published literature. These areas require investigation to determine why these discrepancies exist.

The complexity of comparing multiply-labelled trees by extending phylogenetic-tree metrics

A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in biogeographical studies, to study the evolution of gene families, and also within approaches to construct phylogenetic networks. A multilabelled tree in which no leaf-labels are repeated is called a phylogenetic tree, and one in which every label is the same is also known as a tree-shape. In this paper, we consider the complexity of computing metrics on MUL-trees that are obtained by extending metrics on phylogenetic trees. In particular, by restricting our attention to tree shapes, we show that computing the metric extension on MUL-trees is NP-complete for two well-known metrics on phylogenetic trees, namely, the path-difference and Robinson Foulds distances. We also show that the extension of the Robinson Foulds distance is fixed parameter tractable with respect to the distance parameter. The path distance complexity result allows us to also answer an open problem concerning the complexity of solving the quadratic assignment problem for two matrices that are a Robinson similarity and a Robinson dissimilarity, which we show to be NP-complete. We conclude by considering the maximum agreement subtree (MAST) distance on phylogenetic trees to MUL-trees. Although its extension to MUL-trees can be computed in polynomial time, we show that computing its natural generalization to more than two MUL-trees is NP-complete, although fixed-parameter tractable in the maximum degree when the number of given trees is bounded.

Evaluation of real-time PCR, MAT, and recombinant LipL32-based ELISA for the diagnosis of canine leptospirosis in a disease-endemic South Indian state, Kerala

Canine samples (n = 425) collected from cases of suspected leptospirosis over a period of 6 years were tested using the microscopic agglutination test (MAT), recombinant LipL32-based IgM and IgG ELISA, and real-time PCR (RT PCR). A prevalence of 69.41% was recorded by MAT. Among the different tests, IgG ELISA was observed to have maximum agreement with that of MAT (k-0.810), followed by IgM ELISA (k-0.762.). RT PCR had only slight agreement with MAT (k-0.156). However, the percentage positivity of RT PCR with samples with MAT titers of 1:100 and 1:200 were 76.47% and 85.96%, respectively, indicating the reliability of RT PCR in the early phase of the disease. The values for the samples at higher MAT titers of 1:400 and 1:800 were 10.58% and 1.2%, respectively, clearly indicating the unreliability of the test for samples having high antibody titers. It was concluded that IgG ELISA could be used as the routine test for the diagnosis of canine leptospirosis in this disease-endemic region. Samples with negative results that have high symptomatic correlation with leptospirosis may be tested by PCR/RT PCR for the detection of the pathogen well ahead of antibody generation.

A parameterized algorithm for the Maximum Agreement Forest problem on multiple rooted multifurcating trees

The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem on multiple rooted multifurcating phylogenetic trees, from the perspective of parameterized algorithms. By taking advantage of a new branch-and-bound strategy, a parameterized algorithm with running time O(2.42km3n4) is presented for the problem, assuming that all polytomies in the multifurcating phylogenetic trees are hard.

Novel platinum-based anticancer drug: a complete vibrational study.

The introduction of cisplatin to oncology, in the 1970s, marked the onset of the search for novel and improved metal-based anticancer drugs. Polynuclear PtII and PdII complexes with linear alkylamines as bridging ligands are a class of potential antineoplastic agents that have shown promising cytotoxicity against low-prognosis human cancers, such as metastatic breast adenocarcinoma and osteosarcoma. The present study reports an analysis of [μ-N,N'-bis(3-aminopropyl)butane-1,4-diamine-κ4N,N':N'',N''']bis[dichloridoplatinum(II)], [Pt2Cl4(C10H26N4)], denoted Pt2Spm (Spm is spermine), by vibrational spectroscopy coupled to theoretical calculations. Within the latter, the Density Functional Theory (DFT - mPW1PW/6-31G*) and Effective Core Potential (ECP - LANL2DZ) approaches were used, in order to ensure the most accurate representation of the molecule and achieve a maximum agreement with the experimental data. The solid-state geometry of Pt2Spm corresponds to Ci symmetry, displaying 132 vibrational modes. A complete assignment of the experimental vibrational profile of the system was attained through the combined application of complementary Raman, FT-IR and Inelastic Neutron Scattering (INS) techniques. INS allowed an unequivocal identification of the CH2 and NH2 rocking modes, not clearly detected by the optical techniques, while Raman measurements led to a clear discrimination of the Pt-N stretching frequencies from the two distinct Pt-N moieties within the chelate. The metal-to-metal distances calculated for the molecule under study were found to allow the establishment of effective inter- and intrastrand crosslinks with DNA. These results will hopefully help to clarify the mode of action of the compound, at the molecular level, contributing to the development of improved cisplatin-like chemotherapeutic drugs having a higher efficacy and specificity coupled to lower acquired resistance and deleterious side effects.

Correlation Of Various Cytological Grading Systems With Histopathological Grading In Breast Carcinoma

Background: The nuclear grading of breast carcinoma is well established on histopathology, but not in cytology. There is no single standardised grading system yet in cytology for predicting breast carcinoma prognosis in spite of various cytological grading systems.Aim: The study was performed with an aim of evaluating various cytological grading systems on needle aspirates of breast carcinoma and to determine the best possible cytological grading system that correlates with the Nottingham modification of Scarf Bloom Richardson(SBR) histological grading.Materials & Methods: The study consisted of 30 cases of infiltrating ductal carcinoma diagnosed on cytology for which the corresponding histopathology was available. These cases were graded cytologically by eight grading systems and histologically by SBR method. The various cytological grading systems were evaluated for concordance, association, and correlation with the histopathological grading to select best possible cytological grading system. The various grading systems were also evaluated for interobserver reproducibilityResults: A positive correlation was noted between the various grading systems on cytology with SBR method on histopathology. A strong correlation (r =0.925), maximum percent agreement (93.3%), and a substantial kappa value of agreement (k = 0.885) was noted for Robinson’s grading with the Nottingham modification of SBR grading system. It also showed better interobserver agreement (93.3%; k = 0.889).Conclusion: The various cytological grading systems evaluated in this study showed a positive correlation with SBR method. Among them, Robinson’s grading showed best concordance, correlation with histological grade and hence, may be included in the routine cytology reports.DOI:10.21276/APALM.1837

Antifungal Susceptibility of the Aspergillus viridinutans Complex: Comparison of Two In Vitro Methods.

Cryptic species of Aspergillus fumigatus, including the Aspergillus viridinutans species complex, are increasingly reported to be causes of invasive aspergillosis. Their identification is clinically relevant, as these species frequently have intrinsic resistance to common antifungals. We evaluated the susceptibilities of 90 environmental and clinical isolates from the A. viridinutans species complex, identified by DNA sequencing of the calmodulin gene, to seven antifungals (voriconazole, posaconazole, itraconazole, amphotericin B, anidulafungin, micafungin, and caspofungin) using the reference European Committee on Antimicrobial Susceptibility Testing (EUCAST) method. The majority of species demonstrated elevated MICs of voriconazole (geometric mean [GM] MIC, 4.46 mg/liter) and itraconazole (GM MIC, 9.85 mg/liter) and had variable susceptibility to amphotericin B (GM MIC, 2.5 mg/liter). Overall, the MICs of posaconazole and the minimum effective concentrations of echinocandins were low. The results obtained by the EUCAST method were compared with the results obtained with Sensititre YeastOne (YO) panels. Overall, there was 67% agreement (95% confidence interval [CI], 62 to 72%) between the results obtained by the EUCAST method and those obtained with YO panels when the results were read at 48 h and 82% agreement (95% CI, 78 to 86%) when the results were read at 72 h. There was a significant difference in agreement between antifungals; agreement was high for amphotericin B, voriconazole, and posaconazole (70 to 86% at 48 h and 88 to 93% at 72 h) but was very low for itraconazole (37% at 48 h and 57% at 72 h). The agreement was also variable between species, with the maximum agreement being observed for A. felis isolates (85 and 93% at 48 and 72 h, respectively). Elevated MICs of voriconazole and itraconazole were cross-correlated, but there was no correlation between the other azoles tested.

Calculating the Unrooted Subtree Prune-and-Regraft Distance.

The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo phylogenetic inference. Although the rooted version of SPR distance can be computed relatively efficiently between rooted trees using fixed-parameter-tractable maximum agreement forest (MAF) algorithms, no MAF formulation is known for the unrooted case. Correspondingly, previous algorithms are unable to compute unrooted SPR distances larger than 7.

Material structure generation of concrete and its further usage in numerical simulations

The execution of an experiment is a complex affair. It includes the preparation of test specimens, the measurement process itself and also the evaluation of the experiment as such. Financial requirements can differ significantly. In contrast, the cost of numerical simulations can be negligible, but what is the credibility of a simulated experiment? Discussions frequently arise concerning the methodology used in simulations, and particularly over the geometric model used. Simplification, rounding or the complete omission of details are frequent reasons for differences that occur between simulation results and the results of executed experiments. However, the creation of a very complex geometry, perhaps all the way down to the resolution of the very structure of the material, can be complicated. The subject of the article is therefore a means of creating the material structure of concrete contained in a test specimen. Because a complex approach is taken right from the very start of the numerical simulation, maximum agreement with experimental results can be achieved. With regard to the automation of the process described, countless material structures can be generated and randomly produced samples simulated in this way. Subsequently, a certain degree of randomness can be observed in the results obtained, e.g., the shape of the failure – just as is the case with experiments. The first part of the article presents a description of a complex approach to the creation of a geometry representing real concrete test specimens. The second part presents a practical application in which the numerical simulation of the compressive testing of concrete is executed using the generated geometry.

Phylogenetic studies on assam rice (Oryza sativa L.) accessions for nitrogen use efficiency

In the present investigation, phylogenetic analysis was carried out on 26 rice genotypes for nitrogen use efficiency (NUE) related traits and grain yield in order to identify similar performing genotypes over varying nitrogen (N) level. The phylogenic trees at both N0 and N60 clustered all the genotypes into four main groups. To identify genotypes performing uniformly over the different N levels, a maximal length MAST (maximum agreement sub-tree) on rooted trees was constructed for comparison between the clustering at N0 and N60, which identified seven genotypes grouped into four clusters in the MAST. Phylogenetic analysis revealed that for NUE related traits and grain yield, the clustering pattern for these seven genotypes was independent of the N levels. The study further suggests stability analysis to get more realistic picture.

The influence of geometric design variables on the kinematic performance of a surface-guided total knee replacement.

Tibiofemoral geometries in a total knee replacement (TKR) affect the performance of an implant during activities of daily living. The specially shaped components of a surface-guided TKR aim to control the tibiofemoral motion, such that a normal pattern of motion is achieved, even at high flexion angles. The purpose of this study was to assess the influence of the design parameters on the kinematic behavior of such an implant. A combination of design variables was determined that resulted in the least deviation from the design kinematic target. Six major design variables were considered to generate customized surface-guided TKR candidates. The contribution of these variables was evaluated by principal component analysis considering the input design variables and the results of the kinematic performance from a virtual simulation of deep squatting. The tibial internal-external rotation and the anterior-posterior translation of the medial and lateral femoral condyles were recorded for each design candidate. A quantified objective function of the kinematic behavior was used to define the design with a maximum agreement with the target pattern of motion. The location and orientation of the flexion-extension axis and the tibial slope were the most contributing parameters on the modes of variation. On the other hand, the conformity between the lateral guiding arcs had the least contribution. Virtual simulation showed that the current TKR reached deep flexion angles under squat load, while the tibia pivoted around the medial center. The tibial rotation was within the expected range of the IE rotation from healthy joints.

Evidence-based Draft Guideline for Prevention of Midwifery Malpractices based on Referred Cases to the Forensic Medicine Commission and the Medical Council from 2006-2011.

Background:Medical errors are the main concerns in health systems, which considering their ascending rate in the recent years, especially in the field of midwifery, have caused a medical crisis. Considering the importance of evidence-based health services as a way to improve health systems, the aim of this study was to suggest a guideline for preventing malpractice in midwifery services.Materials and Methods:In this cross-sectional study that was conducted in 2013, we investigated 206 cases that were referred to the Isfahan Legal Medicine Organization and Medical Council of Forensic Medicine from 2006–2011. Data were collected by a checklist and were analyzed using SPSS-16 software. Descriptive statistical tests (mean, maximum, minimum, standard deviation, frequency, and percentage agreement) were used to describe the data. Then, we used the Delphi technique with the participation from 17 experts in midwifery, gynecology, and legal medicine to provide an evidence-based draft guideline for prevention of midwifery errors.Results:A total of 206 cases were reviewed. In 66 cases (32%) the verdict for malpractice in midwifery services was approved. A practical draft guideline for preventing clinical errors for midwifery in the fields of pregnancy, delivery, and postpartum period was developed.Conclusions:This evidence-based draft guideline can improve the attention of all the healthcare providers, especially midwives and physicians to prevent urgent problems and offer effective health services for mothers and infants.

Perception of Dentists about the Functioning of Emergency Public Dental Services

Objective: To know the perception of dentists about the functioning of emergency public dental services (PEDS). Material and Methods: Cross-sectional exploratory study performed in Goiania, a large municipality in the mid-west of Brazil. Participated as subjects the dentists of all ten municipal PEDS. The perception was measured by Likert scale ranging from 1 to 5, where value 5 represented maximum agreement with assertions contained in a questionnaire about the functioning of the services. Results: The final sample consisted of 44 dentists (Response rate=70%.) The perception of the professionals, measured by average agreement with the assertions, ranged from 3.54 and 4.68 in a maximum score of 5.00. Conclusion: For all items discussed there was a favorable perception of the participants. In the perception of the professionals, emergency public dental services meet a spontaneous demand, commonly of endodontic emergencies, with performance of non-conclusive procedures and dental extraction. The professionals recognize that there is a need to improve the embracement of patients, as well as to adopt clinical protocols for the treatment, yet there are flaws in the system of reference of patients, in continuing education of professionals and in the conditions of provision of the services to the population.

Comparison of photographic and conventional methods for tooth shade selection: A clinical evaluation.

Aim:This study aimed to compare three different methods used for shade selection, i.e., visual method, spectrophotometer, and digital photography method.Materials and Methods:Fifty participants were selected from the Out Patient Department of Prosthodontics. Presence of the maxillary right central incisor with no history of any restorative or endodontic procedures was the primary inclusion criterion. The shade of the right maxillary central incisor was determined using all the three shade selection procedures, namely, visual, spectrophotometric, and digital photography method for all the selected participants. The shades obtained in the visual method using a shade guide were noted down for further comparisons. The spectrophotometer reported the L*, a*, and b* values along with the actual shade whereas the digital photography method reported only the L*, a*, and b* values. The agreement between the readings obtained by the three different methods was compared and subjected to appropriate statistical analysis.Results:The results showed that when the three methods studied were compared, there was a statistically significant proportion of agreement between spectrophotometric and visual method (P < 0.01) with higher proportion of “yes” (agreement) and between the spectrophotometric and digital photography method (P < 0.01) with higher proportion of “yes” (agreement). Coefficient of agreement (using Kappa coefficient) between spectrophotometric and visual shades revealed a fair agreement. The mean ΔE was 1.69. There was a statistically significant difference between the proportion of ΔE more than and <2, between spectrophotometric and digital photography methods (P < 0.01) with higher proportion of <2 ΔE. Furthermore, percentage of agreement between shades obtained by the visual and spectrophotometric method showed maximum agreement with A1 shade.Conclusion:It was concluded that the digital photography method emerged as a reliable method for shade selection in a clinical setup.

A note on convex characters, Fibonacci numbers and exponential-time algorithms

Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species (“taxa”) and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in which the subset of species (both contemporary and extinct) that share a given state, forms a connected subtree. Given an unrooted, binary phylogenetic tree T on a set of n≥2 taxa, a closed (but fairly opaque) expression for the number of convex characters on T has been known since 1992, and this is independent of the exact topology of T. In this note we prove that this number is actually equal to the (2n−1)th Fibonacci number. Next, we define gk(T) to be the number of convex characters on T in which each state appears on at least k taxa. We show that, somewhat curiously, g2(T) is also independent of the topology of T, and is equal to the (n−1)th Fibonacci number. As we demonstrate, this topological neutrality subsequently breaks down for k≥3. However, we show that for each fixed k≥1, gk(T) can be computed in O(n) time and the set of characters thus counted can be efficiently listed and sampled. We use these insights to give a simple but effective exact algorithm for the NP-hard maximum parsimony distance problem that runs in time Θ(ϕn⋅n2), where ϕ≈1.618... is the golden ratio, and an exact algorithm which computes the tree bisection and reconnection distance (equivalently, a maximum agreement forest) in time Θ(ϕ2n⋅poly(n)), where ϕ2≈2.619.

MPTH-48. INTER-INTERPRETER CONSISTENCY IN REVIEWING HISTOPATHOLOGY FROM PATIENTS WITH GLIOBLASTOMA AND RADIOGRAPHIC PROGRESSION FOLLOWING STANDARD RADIATION AND TEMOZOLOMIDE

As clinical and imaging assessments are often insufficient to determine if glioblastoma patients after standard treatment have true progression versus pseudo-progression, surgery is frequently recommended to obtain tissue to answer this critical question. However, inter-interpreter consistency of pathologic interpretation in this setting has never been formally addressed. 101 neuropathologists from 50 NCI-designated Cancer Centers were identified, mailed a case scenario, and asked to review histologic sections. The scenario involved a patient who underwent surgery within one year of diagnosis for progressive symptoms and imaging changes. Tissue sections were provided from 13 different cases. Neuropathologic evaluations requested the (1) percent active tumor, (2) percent treatment effect, (3) degree of cellularity, (4) degree of mitotic activity, and (5) overall assessment of disease activity (‘active tumor’ vs. ‘pseudo-progression’ vs. ‘unable to classify’). Fleiss’ kappa statistics were assessed for inter-interpreter consistency among all readers. The patterns of pathologists’ readings per patient case were also characterized. Responses were received from 48 pathologists (48%) at 30 centers (44 were neuropathologists). The kappa score for agreement in overall assessment of disease activity was 0.228 (95% CI: 0.22-0.24), which indicates marginal agreement. Percentages of maximum agreement in pathology assessment among the 13 cases ranged from 36%-98%. The pathology reading diversity in the overall assessment of disease activity (5) was highly consistent with the pathology reading diversity on percent active tumor (1) and percent treatment effect (2) with p=0.03 and 0.001, respectively. However, it was less consistent with cellularity (3) and mitotic activity (4). These data demonstrate marginal inter-interpreter consistency when experienced neuropathologists review the same images with an identical clinical scenario. This study strongly suggests that efforts to standardize pathologic interpretation in patients with glioblastoma with progressive imaging abnormalities post-therapy are critical to improving patient care and conduct of clinical research.