Patch Count Research Articles

Surfaces and spaces: troubleshooting the study of dietary niche space overlap between North American stem primates and rodents

Dental topographic metrics provide quantitative, biologically meaningful data on the three-dimensional (3D) form of teeth. In this study, three dental topographic metrics (Dirichlet normal energy (DNE), relief index (RFI), and orientation patch count rotated (OPCR)) are used to evaluate the presence of dietary niche overlap between North American plesiadapoid primates (Plesiadapidae, Carpolestidae, and Saxonellidae) and early rodents. Calculation of these metrics requires researchers to modify the 3D surface models of the teeth by cropping them to a region of interest and/or orienting them. The current study therefore also examines the error introduced by cropping and orientation, and evaluates the contribution of these metrics to the niche overlap hypothesis. Our results indicate that cropping creates significantly more variation in RFI than DNE. Furthermore, orientation is an even larger source of variation in the calculation of RFI than cropping. Orientation does not strongly influence OPCR values. However, none of these sources of error are significant enough to undermine the extent to which these metrics can speak to the niche overlap hypothesis. The DNE and RFI results suggest that carpolestids and saxonellids had very different molar morphologies from early rodents, and thus these groups were not adapted to consume the same resources. Some plesiadapids show similar levels of occlusal curvature, relief, and complexity to early rodents. The plesiadapid Chiromyoides, which has distinctively low cusps and weak shearing crest development, has molars that are the most rodent-like of all taxa compared. This suggests that Chiromyoides had a dietary niche that overlapped with early rodents and would have been the most likely to be competing over food resources. Results from the plesiadapoid-rodent dental topographic analysis highlight the utility of DNE for detecting more fine-scaled differences in occlusal surface morphology than OPCR, whereas RFI provided valuable data on the degree to which teeth were high crowned.

Age-related changes in molar topography and shearing crest length in a wild population of mountain Gorillas from Volcanoes National Park, Rwanda.

Great ape teeth must remain functional over long lifespans. The molars of the most folivorous apes, the mountain gorillas, must maintain shearing function for 40+ years while the animals consume large quantities of mechanically challenging foods. While other folivorous primates experience dental senescence, which compromises their occlusal surfaces and affects their reproductive success as they age, it is unknown whether dental senescence also occurs in mountain gorillas. In this article, we quantified and evaluated how mountain gorilla molars change throughout their long lifespans. We collected high-resolution replicas of M(1)s (n = 15), M(2)s (n = 13), and M(3)s (n = 11) from a cross-sectional sample of wild mountain gorilla skeletons from the Virunga Volcanoes, ranging in age from 4 to 43 years. We employed dental topographic analyses to track how aspects of occlusal slope, angularity, relief index, and orientation patch count rotated change with age. In addition, we measured the relative length of shearing crests in two- and three-dimensions. Occlusal topography was found to decrease, while 2D relative shearing crest length increased, and 3D relative crest lengths were maintained with age. Our findings indicate that shearing function is maintained throughout the long lifetimes of mountain gorillas. Unlike the dental senescence experienced by other folivorous primates, mountain gorillas do not appear to possess senesced molars despite their long lifetimes, mechanically challenging diets, and decreases in occlusal topography with age.

MorphoTester: An Open Source Application for Morphological Topographic Analysis.

The increased prevalence and affordability of 3D scanning technology is beginning to have significant effects on the research questions and approaches available for studies of morphology. As the current trend of larger and more precise 3D datasets is unlikely to slow in the future, there is a need for efficient and capable tools for high-throughput quantitative analysis of biological shape. The promise and the challenge of implementing relatively automated methods for characterizing surface shape can be seen in the example of dental topographic analysis. Dental topographic analysis comprises a suite of techniques for quantifying tooth surfaces and component features. Topographic techniques have provided insight on mammalian molar form-function relationships and these methods could be applied to address other topics and questions. At the same time implementing multiple complementary topographic methods can have high time and labor costs, and comparability of data formats and approaches is difficult to predict. To address these challenges I present MorphoTester, an open source application for visualizing and quantifying topography from 3D triangulated polygon meshes. This application is Python-based and is free to use. MorphoTester implements three commonly used dental topographic metrics–Dirichlet normal energy, relief index, and orientation patch count rotated (OPCR). Previous OPCR algorithms have used raster-based grid data, which is not directly interchangeable with vector-based triangulated polygon meshes. A 3D-OPCR algorithm is provided here for quantifying complexity from polygon meshes. The efficacy of this metric is tested in a sample of mandibular second molars belonging to four species of cercopithecoid primates. Results suggest that 3D-OPCR is at least as effective for quantifying complexity as previous approaches, and may be more effective due to finer resolution of surface data considered here. MorphoTester represents an advancement in the automated quantification of morphology, and can be modified to adapt to future needs and priorities.

To What Extent is Primate Second Molar Enamel Occlusal Morphology Shaped by the Enamel-Dentine Junction?

The form of two hard tissues of the mammalian tooth, dentine and enamel, is the result of a combination of the phylogenetic inheritance of dental traits and the adaptive selection of these traits during evolution. Recent decades have been significant in unveiling developmental processes controlling tooth morphogenesis, dental variation and the origination of dental novelties. The enamel-dentine junction constitutes a precursor for the morphology of the outer enamel surface through growth of the enamel cap which may go along with the addition of original features. The relative contribution of these two tooth components to morphological variation and their respective response to natural selection is a major issue in paleoanthropology. This study will determine how much enamel morphology relies on the form of the enamel-dentine junction. The outer occlusal enamel surface and the enamel-dentine junction surface of 76 primate second upper molars are represented by polygonal meshes and investigated using tridimensional topometrical analysis. Quantitative criteria (elevation, inclination, orientation, curvature and occlusal patch count) are introduced to show that the enamel-dentine junction significantly constrains the topographical properties of the outer enamel surface. Our results show a significant correlation for elevation, orientation, inclination, curvature and occlusal complexity between the outer enamel surface and the enamel dentine junction for all studied primate taxa with the exception of four modern humans for curvature (p<0.05). Moreover, we show that, for all selected topometrical parameters apart from occlusal patch count, the recorded correlations significantly decrease along with enamel thickening in our sample. While preserving tooth integrity by providing resistance to wear and fractures, the variation of enamel thickness may modify the curvature present at the occlusal enamel surface in relation to enamel-dentine junction, potentially modifying dental functionalities such as blunt versus sharp dental tools. In terms of natural selection, there is a balance between increasing tooth resistance and maintaining efficient dental tools. In this sense the enamel cap acts as a functional buffer for the molar occlusal pattern. In primates, results suggest a primary emergence of dental novelties on the enamel-dentine junction and a secondary transposition of these novelties with no or minor modifications of dental functionalities by the enamel cap. Whereas enamel crenations have been reported by previous studies, our analysis do not support the presence of enamel tubercles without dentine relief nuclei. As is, the enamel cap is, at most, a secondary source of morphological novelty.

The Evolution of High Dental Complexity in the Horse Lineage

The horse lineage (family Equidae) represents one of the clearest acquisitions of complicated derived dental morphology from a more generalized ancestor. Here we investigate the change in dental complexity (orientation patch count rotated, OPCR) during the evolution of key members of this group. A clear linear increase in dental complexity over evolutionary time is apparent when complexity is measured at high resolution (125 to 175 rows per tooth). The taxa examined also show a linear scaling of OPCR with varying resolution. The slope of this relationship is also a key distinguishing factor among taxa, designated as OPCRS. We found that successive increases in dental complexity are due to the addition of finer-scale morphological features. The study sets the scene for a more detailed investigation into additional members of the Equidae.

Dental topography of platyrrhines and prosimians: Convergence and contrasts

Dental topographic analysis is the quantitative assessment of shape of three-dimensional models of tooth crowns and component features. Molar topographic curvature, relief, and complexity correlate with aspects of feeding behavior in certain living primates, and have been employed to investigate dietary ecology in extant and extinct primate species. This study investigates whether dental topography correlates with diet among a diverse sample of living platyrrhines, and compares platyrrhine topography with that of prosimians. We sampled 111 lower second molars of 11 platyrrhine genera and 121 of 20 prosimian genera. For each tooth we calculated Dirichlet normal energy (DNE), relief index (RFI), and orientation patch count (OPCR), quantifying surface curvature, relief, and complexity respectively. Shearing ratios and quotients were also measured. Statistical analyses partitioned effects of diet and taxon on topography in platyrrhines alone and relative to prosimians. Discriminant function analyses assessed predictive diet models. Results indicate that platyrrhine dental topography correlates to dietary preference, and platyrrhine-only predictive models yield high rates of accuracy. The same is true for prosimians. Topographic variance is broadly similar among platyrrhines and prosimians. One exception is that platyrrhines display higher average relief and lower relief variance, possibly related to lower relative molar size and functional links between relief and tooth longevity distinct from curvature or complexity. Explicitly incorporating phylogenetic distance matrices into statistical analyses of the combined platyrrhine-prosimian sample results in loss of significance of dietary effects for OPCR and SQ, while greatly increasing dietary significance of RFI.

Dental topography indicates ecological contraction of lemur communities

Understanding the paleoecology of extinct subfossil lemurs requires reconstruction of dietary preferences. Tooth morphology is strongly correlated with diet in living primates and is appropriate for inferring dietary ecology. Recently, dental topographic analysis has shown great promise in reconstructing diet from molar tooth form. Compared with traditionally used shearing metrics, dental topography is better suited for the extraordinary diversity of tooth form among subfossil lemurs and has been shown to be less sensitive to phylogenetic sources of shape variation. Specifically, we computed orientation patch counts rotated (OPCR) and Dirichlet normal energy (DNE) of molar teeth belonging to 14 species of subfossil lemurs and compared these values to those of an extant lemur sample. The two metrics succeeded in separating species in a manner that provides insights into both food processing and diet. We used them to examine the changes in lemur community ecology in Southern and Southwestern Madagascar that accompanied the extinction of giant lemurs. We show that the poverty of Madagascar's frugivore community is a long-standing phenomenon and that extinction of large-bodied lemurs in the South and Southwest resulted not merely in a loss of guild elements but also, most likely, in changes in the ecology of extant lemurs.

Designing a smoking cessation intervention for the unique needs of homeless persons: a community-based randomized clinical trial

Although smoking prevalence remains strikingly high in homeless populations (~70% and three times the US national average), smoking cessation studies usually exclude homeless persons. Novel evidence-based interventions are needed for this high-risk subpopulation of smokers. To describe the aims and design of a first-ever smoking cessation clinical trial in the homeless population. The study was a two-group randomized community-based trial that enrolled participants (n = 430) residing across eight homeless shelters and transitional housing units in Minnesota. The study objective was to test the efficacy of motivational interviewing (MI) for enhancing adherence to nicotine replacement therapy (NRT; nicotine patch) and smoking cessation outcomes. Participants were randomized to one of the two groups: active (8 weeks of NRT + 6 sessions of MI) or control (NRT + standard care). Participants attended six in-person assessment sessions and eight retention visits at a location of their choice over 6 months. Nicotine patch in 2-week doses was administered at four visits over the first 8 weeks of the 26-week trial. The primary outcome was cotinine-verified 7-day point-prevalence abstinence at 6 months. Secondary outcomes included adherence to nicotine patch assessed through direct observation and patch counts. Other outcomes included the mediating and/or moderating effects of comorbid psychiatric and substance abuse disorders. Lessons learned from the community-based cessation randomized trial for improving recruitment and retention in a mobile and vulnerable population included: (1) the importance of engaging the perspectives of shelter leadership by forming and convening a Community Advisory Board; (2) locating the study at the shelters for more visibility and easier access for participants; (3) minimizing exclusion criteria to allow enrollment of participants with stable psychiatric comorbid conditions; (4) delaying the baseline visit from the eligibility visit by a week to protect against attrition; and (5) regular and persistent calls to remind participants of upcoming appointments using cell phones and shelter-specific channels of communication. The study's limitations include generalizability due to the sample drawn from a single Midwestern city in the United States. Since inclusion criteria encompassed willingness to use NRT patch, all participants were motivated and were ready to quit smoking at the time of enrollment in the study. Findings from the self-select group will be generalizable only to those motivated and ready to quit smoking. High incentives may limit the degree to which the intervention is replicable. Lessons learned reflect the need to engage communities in the design and implementation of community-based clinical trials with vulnerable populations.

Prevention of menstrual migraine with perimenstrual transdermal 17-β-estradiol: a randomized, placebo-controlled, double-blind crossover study

The effect of treatment with percutaneous E(2) (100 μg/24 h) during 2 weeks perimenstrually on the number and severity of menstrual migraine attacks was studied in 27 women in a randomized, placebo-controlled, double-blind, crossover trial. We were not able to demonstrate any difference between E(2) supplementation and placebo on the number or severity of migraine attacks, but both regimens showed significant effects compared with before treatment. CLINICAL TRIAL IDENTIFICATION NUMBER: NCT00204074.

Comparing Dirichlet normal surface energy of tooth crowns, a new technique of molar shape quantification for dietary inference, with previous methods in isolation and in combination

Inferred dietary preference is a major component of paleoecologies of extinct primates. Molar occlusal shape correlates with diet in living mammals, so teeth are a potentially useful structure from which to reconstruct diet in extinct taxa. We assess the efficacy of Dirichlet normal energy (DNE) calculated for molar tooth surfaces for reflecting diet. We evaluate DNE, which uses changes in normal vectors to characterize curvature, by directly comparing this metric to metrics previously used in dietary inference. We also test whether combining methods improves diet reconstructions. The study sample consisted of 146 lower (mandibular) second molars belonging to 24 euarchontan taxa. Five shape quantification metrics were calculated on each molar: DNE, shearing quotient, shearing ratio, relief index, and orientation patch count rotated (OPCR). Statistical analyses were completed for each variable to assess effects of taxon and diet. Discriminant function analysis was used to assess ability of combinations of variables to predict diet. Values differ significantly by diets for all variables, although shearing ratios and OPCR do not distinguish statistically between insectivores and folivores or omnivores and frugivores. Combined analyses were much more effective at predicting diet than any metric alone. Alone, relief index and DNE were most effective at predicting diet. OPCR was the least effective alone but is still valuable as the only quantitative measure of surface complexity. Of all methods considered, DNE was the least methodologically sensitive, and its effectiveness suggests it will be a valuable tool for dietary reconstruction.

An investigation for improvement of the 3D‐digitization process: a reverse engineering approach

PurposeThe purpose of this paper is to provide a comprehensive work flow for the improvement of the Reverse Engineering (RE) process in producing non‐uniform rational B‐splines (NURBS) models from scanned point cloud data. This should become a reliable guide in the creation of desired 3D‐CAD models in order to improve efficiency of downstream operations and further to make decisions regarding quality control.Design/methodology/approachThe paper deals with a detailed investigation of operations in achieving an object's accuracy in the data editing phase and data fitting phase that employs the use of a 3D scanner. A case example involving the ShapeGrabber® AI310 laser scanner was used in digitizing the physical object. Operations considered for investigation at the data editing phase include relaxation, decimation of triangles and sharpening of edges. Contour detection, construct patches, target patch count, grid construction and grid resolution are selected as the operations for investigation in the data fitting phase. Evaluation of the generated digitized models was carried out by performing tests which include 3D Comparisons and Geometric Dimensioning and Tolerance (GD &amp; T) testing.FindingsThe process of data editing is considered to be extremely time consuming which requires a high degree of skill in order to carry out the data manipulation steps. For the purpose of investigation, an electrical socket cover was considered as the object for digitization. The study found some contributors to enhance the quality of the digital model that can be used in the first piece inspection. The results indicate that although the operations associated with the data fitting phase affect the overall quality of the digitized model; they are however, limited by whatever the quality achieved at the data editing phase.Practical implicationsThe RE work flow described in this research will assist designers and practitioners in improving both the efficiency and effectiveness of design and manufacturing functions.Originality/valueThe data editing and fitting processes are time consuming due to various adjustments necessary in obtaining a NURBS model from the digitized data. Thus, the proposed RE work flow identified the steps to realize the desired CAD models from the point cloud data. Moreover, from this study, practitioners will get a concise overall understanding about which geometrical features need to be adjusted so that the required model can be achieved; instead of the need to develop this procedure by themselves through the process of trial and error.

Recovery of the Vulnerable Pemba flying foxPteropus voeltzkowi: population and conservation status

AbstractFlying foxes of the genusPteropusare predominantly island taxa, with high levels of endemism, and face high risks of extinction. Their ecological and economic importance in island ecosystems has been widely recognized. Here we investigate the population size and conservation status of the VulnerablePteropus voeltzkowi, endemic to the western Indian Ocean island of Pemba, Tanzania. Direct counts and patch counts were used to determine abundance of flying foxes at roost sites, supplemented with evening dispersal counts, which were conducted to test accuracy of counting techniques under varying conditions of visibility. We estimate that the population size is now a minimum of 18,200–22,100, thus validating reports of annual increases by in-country monitoring teams since the last documented population survey of 4,600–5,500 bats in 1995. Taking into account differences in the counting methodologies for roosting bats we estimate that the population size could be as high as 35,600 individuals. We identified 44 occupied roosting sites, with just four of these supporting up to 87% of the population. Roost disturbance represents a continuing threat to this species and was found to influence roost occupancy and colony size. The implications of the population increase for the local human community are discussed and recommendations provided for continued monitoring and future management of this species on Pemba Island.

Brief communication: Contributions of enamel‐dentine junction shape and enamel deposition to primate molar crown complexity

Molar crown morphology varies among primates from relatively simple in some taxa to more complex in others, with such variability having both functional and taxonomic significance. In addition to the primary cusps, crown surface complexity derives from the presence of crests, cuspules, and crenulations. Developmentally, this complexity results from the deposition of an enamel cap over a basement membrane (the morphology of which is preserved as the enamel-dentine junction, or EDJ, in fully formed teeth). However, the relative contribution of the enamel cap and the EDJ to molar crown complexity is poorly characterized. In this study we examine the complexity of the EDJ and enamel surface of a broad sample of primate (including fossil hominin) lower molars through the application of micro-computed tomography and dental topographic analysis. Surface complexity of the EDJ and outer enamel surface (OES) is quantified by first mapping, and then summing, the total number of discrete surface orientation patches. We investigate the relative contribution of the EDJ and enamel cap to crown complexity by assessing the correlation in patch counts between the EDJ and OES within taxa and within individual teeth. We identify three patterns of EDJ/OES complexity which demonstrate that both crown patterning early in development and the subsequent deposition of the enamel cap contribute to overall crown complexity in primates.

Factor structure and validity of the Medication Adherence Questionnaire (MAQ) with cigarette smokers trying to quit

The Medication Adherence Questionnaire (MAQ) is a scale used to evaluate adherence to medications. The present study assessed the factor structure and validity of the MAQ with cigarette smokers. A principal components analysis was conducted on MAQ scores from a sample of smokers presenting for treatment in a clinical trial of naltrexone and nicotine patch for smoking cessation (N = 385). Indices of convergent and predictive validity were tested using electronic medication caps for naltrexone, nicotine patch counts, plasma drug levels of naltrexone, and treatment outcomes. The principal components analysis revealed two factors. Factor 1, labeled "unintentional nonadherence," measured the extent to which individuals were nonadherent because they were careless or forgot to take their medications. Factor 2, labeled "purposeful nonadherence," assessed nonadherence related to purposefully stopping medication use after feeling better or worse. Only the second factor was shown to have good convergent and predictive validity. Specifically, this factor was related to pill-taking behavior measured with electronic medication caps and drug plasma levels and nicotine patch use based on nicotine patch count data, and it was associated with smoking cessation outcome. Thus the purposeful nonadherence factor of the MAQ may be used as a brief screening tool for medication adherence with cigarette smokers seeking treatment. Information obtained with this questionnaire could be used to counsel patients regarding the importance of medication adherence.

Recovery of gut-associated lymphoid tissue and upper respiratory tract immunity after parenteral nutrition.

The authors characterize the recovery of parenteral nutrition-induced changes in gut-associated lymphoid tissue (GALT) and upper respiratory tract immunity with enteral nutrition and provide further information defining the effects of enteral feeding on mucosal immunity. The small intestine plays a prominent role in development and maintenance of mucosal immunity, both intestinal and extraintestinal, primarily through immunoglobulin A (IgA)-mediated mechanisms. Prior research has shown that mice fed total parenteral nutrition (TPN) have reduced GALT T and B cells, the cells responsible for IgA production, as well as impaired upper respiratory tract immunity to viral challenge of previously immunized animals. The recovery of TPN-induced changes in GALT and upper respiratory tract immunity after enteral refeeding is studied. Male institute of Cancer Research mice received 5 days of TPN followed by 0 to 4 days of chow. Small intestinal GALT was characterized by flow cytometry. In a second experiment, animals were immunized intranasally with moused-adapted influenza virus. Three weeks later, one group received a 5-day course of TPN followed by enteral refeeding for 5 days. A second group received TPN alone. Both groups were challenged with intranasal virus and killed 40 hours postchallenge to determine viral shedding from the upper respiratory tract. Animals fed TPN only had significantly fewer GALT lymphocytes compared with those chow-fed control subjects. Peyer's patch counts increased after a single day of refeeding, returning to normal levels by 48 hours. Lamina propria counts remained significantly depressed after 24 hours of refeeding, but also returned to normal after 48 hours of refeeding. The T-cell and B-cell populations mimicked total cell patterns. Lamina propria CD4+/CD8+ ratio returned to normal only after 72 hours of refeeding. None of the 9 animals refed enterally for 5 days were positive for viral shedding, compared with 8 of 12 matched TPN-fed animals. Enteral refeeding after TPN is associated with rapid repletion of GALT cellularity, initially within Peyer's patches and subsequently within the lamina propria. Refeeding corrects the impairment of IgA-mediated upper respiratory tract antiviral immunity occurring with TPN administration. This work further enhances the authors' knowledge of the underlying immunologic differences influenced by routes of nutrition.

A comparison of surface sampling methods for coarse fluvial sediments

In order to characterize variability associated with sampling coarse fluvial sediment, surface grain‐size distributions were characterized at eight sample sites within gravel‐ to boulder‐bed channels. Four methods were used: (1) a random walk, (2) a sampling grid spaced at an interval equal to the intermediate diameter of the largest clast in the sampling area, (3) a sampling grid spaced at one half the interval of method 2, and (4) a randomly chosen subsection within which a patch count of most clasts at least partially exposed at the surface was conducted. At each site, six replicates of each method were performed, with each replicate consisting of 100 clasts. Sampling was performed by a single operator at six of the sites and by multiple operators at two of the same sites and at two additional sites. The research objectives were to characterize variability among replicates of a method, among methods, and among operators. Sample sites were divided into relatively well sorted (inclusive graphic standard deviation &lt;1.4) and poorly sorted (≥1.5). The first three methods produce statistically indistinguishable values of D50 and D84 for both well‐sorted and poorly sorted sites when performed by a single operator. Multiple operators may produce statistically different population measures (D50, D84, sample distributions, and variance) using any of the four methods at either type of site. Because of operator‐induced variability, we caution against direct comparisons of grain‐size distributions between channels or within a single channel through time if more than one operator performs the sampling.