Publications by authors named "Christopher Dean"

75 Publications

Spatial sampling heterogeneity limits the detectability of deep time latitudinal biodiversity gradients.

Proc Biol Sci 2021 02 24;288(1945):20202762. Epub 2021 Feb 24.

Department of Earth Science and Engineering, Imperial College London, South Kensington, London SW7 2AZ, UK.

The latitudinal biodiversity gradient (LBG), in which species richness decreases from tropical to polar regions, is a pervasive pattern of the modern biosphere. Although the distribution of fossil occurrences suggests this pattern has varied through deep time, the recognition of palaeobiogeographic patterns is hampered by geological and anthropogenic biases. In particular, spatial sampling heterogeneity has the capacity to impact upon the reconstruction of deep time LBGs. Here we use a simulation framework to test the detectability of three different types of LBG (flat, unimodal and bimodal) over the last 300 Myr. We show that heterogeneity in spatial sampling significantly impacts upon the detectability of genuine LBGs, with known biodiversity patterns regularly obscured after applying the spatial sampling window of fossil collections. Sampling-standardization aids the reconstruction of relative biodiversity gradients, but cannot account for artefactual absences introduced by geological and anthropogenic biases. Therefore, we argue that some previous studies might have failed to recover the 'true' LBG type owing to incomplete and heterogeneous sampling, particularly between 200 and 20 Ma. Furthermore, these issues also have the potential to bias global estimates of past biodiversity, as well as inhibit the recognition of extinction and radiation events.
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http://dx.doi.org/10.1098/rspb.2020.2762DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7934898PMC
February 2021

Growth and development of the third permanent molar in Paranthropus robustus from Swartkrans, South Africa.

Sci Rep 2020 11 4;10(1):19053. Epub 2020 Nov 4.

UMR 7194 CNRS, Muséum National D'Histoire Naturelle, Musée de L'Homme, Paris, France.

Third permanent molars (M3s) are the last tooth to form but have not been used to estimate age at dental maturation in early fossil hominins because direct histological evidence for the timing of their growth has been lacking. We investigated an isolated maxillary M3 (SK 835) from the 1.5 to 1.8-million-year-old (Mya) site of Swartkrans, South Africa, attributed to Paranthropus robustus. Tissue proportions of this specimen were assessed using 3D X-ray micro-tomography. Thin ground sections were used to image daily growth increments in enamel and dentine. Transmitted light microscopy and synchrotron X-ray fluorescence imaging revealed fluctuations in Ca concentration that coincide with daily growth increments. We used regional daily secretion rates and Sr marker-lines to reconstruct tooth growth along the enamel/dentine and then cementum/dentine boundaries. Cumulative growth curves for increasing enamel thickness and tooth height and age-of-attainment estimates for fractional stages of tooth formation differed from those in modern humans. These now provide additional means for assessing late maturation in early hominins. M3 formation took ≥ 7 years in SK 835 and completion of the roots would have occurred between 11 and 14 years of age. Estimated age at dental maturation in this fossil hominin compares well with what is known for living great apes.
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http://dx.doi.org/10.1038/s41598-020-76032-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7642444PMC
November 2020

Early life of Neanderthals.

Proc Natl Acad Sci U S A 2020 11 2;117(46):28719-28726. Epub 2020 Nov 2.

Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy;

The early onset of weaning in modern humans has been linked to the high nutritional demand of brain development that is intimately connected with infant physiology and growth rate. In Neanderthals, ontogenetic patterns in early life are still debated, with some studies suggesting an accelerated development and others indicating only subtle differences vs. modern humans. Here we report the onset of weaning and rates of enamel growth using an unprecedented sample set of three late (∼70 to 50 ka) Neanderthals and one Upper Paleolithic modern human from northeastern Italy via spatially resolved chemical/isotopic analyses and histomorphometry of deciduous teeth. Our results reveal that the modern human nursing strategy, with onset of weaning at 5 to 6 mo, was present among these Neanderthals. This evidence, combined with dental development akin to modern humans, highlights their similar metabolic constraints during early life and excludes late weaning as a factor contributing to Neanderthals' demise.
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http://dx.doi.org/10.1073/pnas.2011765117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7682388PMC
November 2020

A comprehensive survey of Retzius periodicities in fossil hominins and great apes.

J Hum Evol 2020 12 15;149:102896. Epub 2020 Oct 15.

Institute of Human Origins, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA.

Recent studies have provided great insight into hominin life history evolution by utilizing incremental lines found in dental tissues to reconstruct and compare the growth records of extant and extinct humans versus other ape taxa. Among the hominins, studies that have examined Retzius periodicity (RP) variation have come to contradictory conclusions in some instances. To clarify RP variation among hominins and better place this variation in its broader evolutionary context, we conduct the most comprehensive analysis of published RP values for hominins and great apes to date. We gathered all available data from the literature on RP data from extant humans, great apes, and fossil hominins and assessed their variation using parametric and nonparametric analyses of variance. We also performed phylogenetic generalized least-squares regressions of RP data for these taxa as well as a larger set of hominoids for which RP data have been published against data for body mass, encephalization, and mean semicircular canal radius (a proxy for metabolic rate). Our results show that modern humans have a mean RP significantly differing from that of other hominins. Pongo also is significantly different from nearly all other taxa in all analyses. Our results also demonstrate that RP variation among hominins scales with respect to body mass, encephalization, and semicircular canal radius similarly to other hominids but that modern humans and Pongo stand out in this regard. Operating within the hypothesis that RP reflects autonomic biorhythms that regulate multiple life history variables, our results reinforce the idea that Homo sapiens has evolved a life history distinct from other hominins, even from other members of Homo, and suggest that many of these life history differences may be driven by hypothalamic output from the brain.
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http://dx.doi.org/10.1016/j.jhevol.2020.102896DOI Listing
December 2020

Synchrotron X-ray fluorescence imaging of strontium incorporated into the enamel and dentine of wild-shot orangutan canine teeth.

Arch Oral Biol 2020 Nov 29;119:104879. Epub 2020 Aug 29.

Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607, Hamburg, Germany.

Objectives: Dental hard tissues contain trace elements of both dietary and environmental origin. One objective was to demonstrate that a longitudinal record of synchronous Sr incorporation into enamel and dentine can be retrieved from museum specimens of once-free-living endangered species. Further objectives were to quantify sudden fluctuations in Sr concentration and estimate the extent of Sr overprinting back into dentine and enamel formed prior to the time of Sr ingestion.

Materials And Methods: Daily incremental markings were used to determine rates and times of tooth formation and synchrotron X-ray fluorescence of the same polished ground sections to image Sr distribution in a male and a female orangutan canine. The X-ray beam was monochromatised to 17.0 keV and focused to 500 × 500 nm. Scans were performed at either 25.0 or 5.0 μm resolution.

Results: Baseline Sr levels ranged between 215-750 ppm. Multiple short, intense Sr labels reaching 750- 1,625 ppm occurred randomly throughout 15-22 years of tooth formation. In dentine, Sr concentration increased gradually away from the EDJ, while in enamel, it reduced towards the enamel surface. Using daily incremental markings, Sr overprinting into earlier formed dentine and enamel was estimated to be ∼12-45 days. There was no evidence of Sr overprinting by maturational ameloblasts.

Conclusions: A good record of growth and trace element incorporation into tooth tissues can be retrieved from museum specimens. Short, intense Sr labels were equally well time-resolved in enamel and dentine and could be distinguished from more diffuse background levels. Enamel maturation appears to have no quantifiable effect.
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http://dx.doi.org/10.1016/j.archoralbio.2020.104879DOI Listing
November 2020

Dual-Mode Infrared Absorption by Segregating Dopants within Plasmonic Semiconductor Nanocrystals.

Nano Lett 2020 Oct 22;20(10):7498-7505. Epub 2020 Sep 22.

McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States.

When aliovalent dopants are sufficiently segregated to the core or near the surface of semiconductor nanocrystals, charge carriers donated by the dopants are also segregated to the core or near the surface, respectively. In Sn-doped indium oxide nanocrystals, we find that this contrast in free charge carrier concentration creates a core and shell with differing dielectric properties and results in two distinctly observable plasmonic extinction peaks. The trends in this dual-mode optical response with shell growth differ from core/shell nanoparticles composed of traditional plasmonic metals such as Au and Ag. We developed a model employing a core/shell effective medium approximation that can fit the dual-mode spectra and explain the trends in the extinction response. Lastly, we show that dopant segregation can improve sensitivity of plasmon spectra to changes in refractive index of the surrounding environment.
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http://dx.doi.org/10.1021/acs.nanolett.0c02992DOI Listing
October 2020

Mobilization of Antibiotic Resistance: Are Current Approaches for Colocalizing Resistomes and Mobilomes Useful?

Front Microbiol 2020 30;11:1376. Epub 2020 Jun 30.

Food-Centric Corridor, Infectious Disease Laboratory, Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, United States.

Antimicrobial resistance (AMR) poses a global human and animal health threat, and predicting AMR persistence and transmission remains an intractable challenge. Shotgun metagenomic sequencing can help overcome this by enabling characterization of AMR genes within all bacterial taxa, most of which are uncultivatable in laboratory settings. Shotgun sequencing, therefore, provides a more comprehensive glance at AMR "potential" within samples, i.e., the "resistome." However, the risk inherent within a given resistome is predicated on the genomic context of various AMR genes, including their presence within mobile genetic elements (MGEs). Therefore, resistome risk stratification can be advanced if AMR profiles are considered in light of the flanking mobilizable genomic milieu (e.g., plasmids, integrative conjugative elements (ICEs), phages, and other MGEs). Because such mediators of horizontal gene transfer (HGT) are involved in uptake by pathogens, investigators are increasingly interested in characterizing that resistome fraction in genomic proximity to HGT mediators, i.e., the "mobilome"; we term this "colocalization." We explored the utility of common colocalization approaches using alignment- and assembly-based techniques, on clinical (human) and agricultural (cattle) fecal metagenomes, obtained from antimicrobial use trials. Ordination revealed that tulathromycin-treated cattle experienced a shift in ICE and plasmid composition versus untreated animals, though the resistome was unaffected during the monitoring period. Contrarily, the human resistome and mobilome composition both shifted shortly after antimicrobial administration, though this rebounded to pre-treatment status. Bayesian networks revealed statistical AMR-MGE co-occurrence in 19 and 2% of edges from the cattle and human networks, respectively, suggesting a putatively greater mobility potential of AMR in cattle feces. Conversely, using Mobility Index (MI) and overlap analysis, abundance of -assembled contigs supporting resistomes flanked by MGE increased shortly post-exposure within human metagenomes, though > 40 days after peak dose such contigs were rare (∼2%). MI was not substantially altered by antimicrobial exposure across all cattle metagenomes, ranging 0.5-4.0%. We highlight that current alignment- and assembly-based methods estimating resistome mobility yield contradictory and incomplete results, likely constrained by approach-specific data inputs, and bioinformatic limitations. We discuss recent laboratory and computational advancements that may enhance resistome risk analysis in clinical, regulatory, and commercial applications.
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http://dx.doi.org/10.3389/fmicb.2020.01376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7338343PMC
June 2020

Reassessment of the TM 1517 odonto-postcranial assemblage from Kromdraai B, South Africa, and the maturational pattern of Paranthropus robustus.

Am J Phys Anthropol 2020 08 24;172(4):714-722. Epub 2020 May 24.

UMR 7194 CNRS, Muséum national d'Histoire naturelle, Musée de l'Homme, Paris, France.

Objectives: The Pleistocene taxon Paranthropus robustus was established in 1938 following the discovery at Kromdraai B, South Africa, of the partial cranium TM 1517a and associated mandible TM 1517b. Shortly thereafter, a distal humerus (TM 1517g), a proximal ulna (TM 1517e), and a distal hallucial phalanx (TM 1517k) were collected nearby at the site, and were considered to be associated with the holotype. TM 1517a-b represents an immature individual; however, no analysis of the potentially associated postcranial elements has investigated the presence of any endostructural remnant of recent epiphyseal closure. This study aims at tentatively detecting such traces in the three postcranial specimens from Kromdraai B.

Materials And Methods: By using μXCT techniques, we assessed the developmental stage of the TM 1517b's C-M3 roots and investigated the inner structure of TM 1517g, TM 1517e, and TM 1517k.

Results: The M2 shows incompletely closed root apices and the M3 a half-completed root formation stage. The distal humerus was likely completely fused, while the proximal ulna and the distal hallucial phalanx preserve endosteal traces of the diaphyseo-epiphyseal fusion process.

Discussion: In the hominin fossil record, there are few unambiguously associated craniodental and postcranial remains sampling immature individuals, an essential condition for assessing the taxon-specific maturational patterns. Our findings corroborate the original association of the craniodental and postcranial remains representing the P. robustus type specimen. As with other Plio-Pleistocene hominins, the odonto-postcranial maturational pattern of TM 1517 more closely fits an African great ape rather than the extant human pattern.
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http://dx.doi.org/10.1002/ajpa.24082DOI Listing
August 2020

Variation in the timing of enamel formation in modern human deciduous canines.

Arch Oral Biol 2020 Jun 19;114:104719. Epub 2020 Apr 19.

Department of Earth Sciences, Centre for Human Evolution Research, Natural History Museum, Cromwell Road, London SW7 5BD, UK; Institute of Archaeology, University College London, Gordon Square, London, WC1H 0PY, UK.

Objectives: Deciduous canines are now used increasingly in archaeological and forensic studies to establish the time of birth and as a retrospective source of trace elements incorporated into enamel before and after birth. However, data on the variability of deciduous enamel formation times are scarce. Our objectives were to use daily incremental markings to estimate daily secretion rates, the timing of prenatal, postnatal and total enamel formation and any changes in enamel coverage or prism and stria orientation that occur during enamel formation.

Materials And Methods: Longitudinal ground sections of 81 deciduous canines were studied with transmitted light microscopy. High-resolution digital images were imported from an Olympus VS-120 virtual slide scanning system into a geographic information system (ArcGIS, ESRI USA) for quantitative and statistical analyses of linear, angular and area measurements of buccal enamel.

Results: Daily rates of enamel secretion close to the EDJ were faster than in permanent enamel (3.23 μm/day, SD = 0.54). Prism and stria angles subtended to the EDJ both increased through crown formation. Enamel coverage was low in the cusp and cervix but maximal ∼150 days after birth. The mean prenatal enamel formation time was 118 days (range 60-150, SD, 29.2, n = 24). The overall mean postnatal enamel formation time was 319 days (range 210-420, SD 50.6, n = 67).

Conclusions: Daily enamel secretion rates compared well with previous studies of deciduous enamel, however, enamel extension rates in deciduous cuspal enamel were notably lower. The variability of both prenatal and postnatal deciduous enamel formation times was greater than previously reported.
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http://dx.doi.org/10.1016/j.archoralbio.2020.104719DOI Listing
June 2020

Anders Retzius and the Dental Histologists of the Mid-Nineteenth Century: Their Contribution to Comparative Anatomy, Histology and Anthropology.

J Hist Dent 2019 ;67(2):58-97

Professor Emeritus, Department of Cell and Developmental Biology University College London, WC1E 6BT, UK Calleva Dental Histologist, Centre for Human Evolution Research, Earth Sciences Natural History Museum, London, SW7 5BD, UK.

Anatomy, comparative anatomy and embryology are fundamental to taxonomy and evolutionary biology. In the mid-nineteenth century many anatomists and zoologists made major contributions to more than one of these disciplines and a surprising number of them were also histologists. Historical accounts of discoveries and developments in anatomy, and in particular dental histology, rarely consider broader contributions and have tended to be concerned with establishing historical priority about who discovered or described what first. The period 1830 to 1840 saw new developments in light microscopy that enabled studies of histology, cellular pathology and embryology. It also saw a shift away from older ideas such as Naturphilosophie and vitalism towards a more rigorous experimental approach to scientific investigation. Many scientists with diverse research interests were working in parallel on comparative dental histology and were in many cases largely unaware of each other's work. One researcher, Anders Retzius, travelled widely across Europe, corresponded regularly with his scientific colleagues and, probably unbeknownst to himself in his own lifetime, made a lasting contribution to dental histology. Anders Retzius was a clinician, an anatomist, a comparative anatomist, a histologist and latterly an anthropologist. His life and career spanned the whole of this fast-moving period in the history of anatomy and histology.
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April 2020

Short and long period growth markers of enamel formation distinguish European Pleistocene hominins.

Sci Rep 2020 03 13;10(1):4665. Epub 2020 Mar 13.

Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Paseo Sierra de Atapuerca 3, 09002, Burgos, Spain.

Characterizing dental development in fossil hominins is important for distinguishing between them and for establishing where and when the slow overall growth and development of modern humans appeared. Dental development of australopiths and early Homo was faster than modern humans. The Atapuerca fossils (Spain) fill a barely known gap in human evolution, spanning ~1.2 to ~0.4 million years (Ma), during which H. sapiens and Neandertal dental growth characteristics may have developed. We report here perikymata counts, perikymata distributions and periodicities of all teeth belonging to the TE9 level of Sima del Elefante, level TD6.2 of Gran Dolina (H. antecessor) and Sima de los Huesos. We found some components of dental growth in the Atapuerca fossils resembled more recent H. sapiens. Mosaic evolution of perikymata counts and distribution generate three distinct clusters: H. antecessor, Sima de los Huesos and H. sapiens.
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http://dx.doi.org/10.1038/s41598-020-61659-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7069994PMC
March 2020

Effects of maternal, gestational, and perinatal variables on neonatal line width observed in a modern UK birth cohort.

Am J Phys Anthropol 2020 06 10;172(2):314-332. Epub 2020 Mar 10.

Natural History Museum, London, UK.

Objectives: The objective of this study was to explore potential relationships between neonatal line (NNL) width and early life history variables such as maternal health, gestation, the birth process, and perinatal health.

Materials And Methods: Histological thin sections of deciduous canines were studied from 71 children from the Avon Longitudinal Study of Parents and Children (ALSPAC). The width of the NNL was measured in three locations on the tooth crown using spatial mapping techniques (ArcGIS) from digital images from an Olympus VS-120 microscope. Life history variables were collected prospectively through a combination of clinical observations and questionnaires.

Results: Infants born late term or post term had narrower neonatal lines than those born prematurely or at full term. Infants born in Autumn (September to November) had narrower NNLs than those born at other times of year. NNLs in infants born to mothers with hypertension were wider than those without. Infants resuscitated at birth or born to obese mothers had narrower NNLs than those that were not. There was no association between NNL width and either the type or duration of delivery.

Discussion: The NNL in enamel is an irregular accentuated line, but the factors underlying its formation and width remain unclear. In contrast to some previous studies, we found no association between wider NNLs and long or difficult births. Instead, we found that the width of the neonatal line NNL varied in relation to parameters that reflected the prenatal environment and length of gestation.
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http://dx.doi.org/10.1002/ajpa.24042DOI Listing
June 2020

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data.

Nucleic Acids Res 2020 01;48(D1):D561-D569

Veterinary Education, Research, and Outreach (VERO) Program, Texas A&M University and West Texas A&M University, Canyon, TX 79016, USA.

Antimicrobial resistance (AMR) is a threat to global public health and the identification of genetic determinants of AMR is a critical component to epidemiological investigations. High-throughput sequencing (HTS) provides opportunities for investigation of AMR across all microbial genomes in a sample (i.e. the metagenome). Previously, we presented MEGARes, a hand-curated AMR database and annotation structure developed to facilitate the analysis of AMR within metagenomic samples (i.e. the resistome). Along with MEGARes, we released AmrPlusPlus, a bioinformatics pipeline that interfaces with MEGARes to identify and quantify AMR gene accessions contained within a metagenomic sequence dataset. Here, we present MEGARes 2.0 (https://megares.meglab.org), which incorporates previously published resistance sequences for antimicrobial drugs, while also expanding to include published sequences for metal and biocide resistance determinants. In MEGARes 2.0, the nodes of the acyclic hierarchical ontology include four antimicrobial compound types, 57 classes, 220 mechanisms of resistance, and 1,345 gene groups that classify the 7,868 accessions. In addition, we present an updated version of AmrPlusPlus (AMR ++ version 2.0), which improves accuracy of classifications, as well as expanding scalability and usability.
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http://dx.doi.org/10.1093/nar/gkz1010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145535PMC
January 2020

Rare Orbital Metastasis Originating From a Neuroendocrine Tumor.

Radiol Technol 2019 Nov;91(2):112-119

Background: This case study details a rare orbital metastasis originating from the gastrointestinal tract. A patient presented with proptosis of the right eye precipitated by a slow-growing orbital tumor. A biopsy confirmed a low-grade neuroendocrine tumor. Imaging studies were completed, with magnetic resonance (MR) imaging of the orbits providing the most detailed images of the mass. Fusion software images were created from the MR images and indium In 111 pentetreotide (octreoscan) studies, which confirmed the presence of the neuroendocrine carcinoid tumor.

Discussion: Orbital metastases are a rare condition associated with various symptoms, most commonly proptosis and diplopia. Imaging modalities, such as MR, computed tomography, and nuclear medicine technology, are instrumental in detecting and assessing these masses. Fusion imaging software can provide additional opportunities for facilities without hybrid scanners. The treatment of choice for orbital metastases is octreotide therapy; however, radiation therapy, partial or complete surgical removal of the tumor, and chemotherapy also are used.

Conclusion: Traditional imaging techniques and fusion imaging techniques are essential for diagnosing and treating orbital metastases.
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November 2019

Multi-center evaluation of dose conformity in stereotactic body radiotherapy.

Phys Imaging Radiat Oncol 2019 Jul 28;11:41-46. Epub 2019 Aug 28.

National Radiotherapy Trials QA Group, Mount Vernon Hospital, London HA6 2RN, UK.

Background And Purpose: Stereotactic body radiotherapy (SBRT) is an emerging technique for treating oligometastases, but limited data is available on what plan quality is achievable for a range of modalities and clinical sites.

Methods: SBRT plans for lung, spine, bone, adrenal, liver and node sites from 17 participating centers were reviewed. Centers used various delivery techniques including static and rotational intensity-modulation and multiple non-coplanar beams. Plans were split into lung and other body sites and evaluated with different plan quality metrics, including two which are independent of target coverage; "prescription dose spillage" (PDS) and "modified gradient index" (MGI). These were compared to constraints from the ROSEL and RTOG 0813 clinical trials.

Results: Planning target volume (PTV) coverage was compromised (PTV V100% < 90%) in 29% of patient plans in order to meet organ-at-risk (OAR) tolerances, supporting the use of plan quality metrics which are independent of target coverage. Both lung (n = 48) and other body (n = 99) site PDS values agreed well with ROSEL constraints on dose spillage, but RTOG 0813 values were too high to detect sub-optimal plans. MGI values for lung plans were mis-matched to both sets of previous constraints, with ROSEL values too high and RTOG 0813 values too low. MGI values were lower for other body plans as expected, though this was only statistically significant for PTV volumes <20 cm.

Conclusions: Updated guidance for lung and other body site SBRT plan quality using the PDS and MGI metrics is presented.
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http://dx.doi.org/10.1016/j.phro.2019.08.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807546PMC
July 2019

Synchrotron X-ray fluorescence mapping of Ca, Sr and Zn at the neonatal line in human deciduous teeth reflects changing perinatal physiology.

Arch Oral Biol 2019 Aug 25;104:90-102. Epub 2019 May 25.

Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.

Objectives: Our first objective was to review the evidence describing the appearance and microstructure of the neonatal line in human deciduous teeth and to link this with known changes in neonatal physiology occurring at and around birth. A second objective was to explore ways to improve identification of the neonatal line by mapping the pre- and postnatal distribution of Ca, Sr and Zn in deciduous cuspal enamel and superimposing these maps onto transmitted light micrographs that included a clear true section of the neonatal line.

Materials And Methods: We used synchrotron X-ray fluorescence to map elemental distributions in pre- and postnatal enamel and dentine. Two deciduous canines and 5 deciduous molars were scanned with an X-ray beam monochromatised to 17.0 keV at either 10.0, 2.5 or 1.0 μm resolution and 10 ms integration time.

Results: Calcium maps distinguished enamel and dentine but did not clearly demarcate tissues formed pre- or postnatally. Strontium maps reflected presumed pre- and postnatal maternal serum levels and what are likely to be diet-dependent regions of Sr enrichment or depletion. Prenatal Zn maps, particularly for dentine, mirror elevated levels in the fetus and in colostrum during the first few days of life.

Conclusions: The neonatal line, enamel dentine junction and surface enamel were all Zn-rich. Within the neonatal line Zn may be associated with increased crystallinity but also with caries resistance, both of which have been reported previously. Elemental mapping may improve the identification of ambiguous NNLs and so be useful in forensic and archaeological studies.
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http://dx.doi.org/10.1016/j.archoralbio.2019.05.024DOI Listing
August 2019

Investigating Effects of Tulathromycin Metaphylaxis on the Fecal Resistome and Microbiome of Commercial Feedlot Cattle Early in the Feeding Period.

Front Microbiol 2018 30;9:1715. Epub 2018 Jul 30.

Microbial Ecology Group, Colorado State University, Fort Collins, CO, United States.

The objective was to examine effects of treating commercial beef feedlot cattle with therapeutic doses of tulathromycin, a macrolide antimicrobial drug, on changes in the fecal resistome and microbiome using shotgun metagenomic sequencing. Two pens of cattle were used, with all cattle in one pen receiving metaphylaxis treatment (800 mg subcutaneous tulathromycin) at arrival to the feedlot, and all cattle in the other pen remaining unexposed to parenteral antibiotics throughout the study period. Fecal samples were collected from 15 selected cattle in each group just prior to treatment (Day 1), and again 11 days later (Day 11). Shotgun sequencing was performed on isolated metagenomic DNA, and reads were aligned to a resistance and a taxonomic database to identify alignments to antimicrobial resistance (AMR) gene accessions and microbiome content. Overall, we identified AMR genes accessions encompassing 9 classes of AMR drugs and encoding 24 unique AMR mechanisms. Statistical analysis was used to identify differences in the resistome and microbiome between the untreated and treated groups at both timepoints, as well as over time. Based on composition and ordination analyses, the resistome and microbiome were not significantly different between the two groups on Day 1 or on Day 11. However, both the resistome and microbiome changed significantly between these two sampling dates. These results indicate that the transition into the feedlot-and associated changes in diet, geography, conspecific exposure, and environment-may exert a greater influence over the fecal resistome and microbiome of feedlot cattle than common metaphylactic antimicrobial drug treatment.
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http://dx.doi.org/10.3389/fmicb.2018.01715DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6077226PMC
July 2018

Novel 3D geometry and models of the lower regions of large trees for use in carbon accounting of primary forests.

AoB Plants 2018 Mar 28;10(2):ply015. Epub 2018 Feb 28.

CSIRO Land & Water, Canberra, ACT, Australia.

There is high uncertainty in the contribution of land-use change to anthropogenic climate change, especially pertaining to below-ground carbon loss resulting from conversion of primary-to-secondary forest. Soil organic carbon (SOC) and coarse roots are concentrated close to tree trunks, a region usually unmeasured during soil carbon sampling. Soil carbon estimates and their variation with land-use change have not been correspondingly adjusted. Our aim was to deduce allometric equations that will allow improvement of SOC estimates and tree trunk carbon estimates, for primary forest stands that include large trees in rugged terrain. Terrestrial digital photography, photogrammetry and GIS software were used to produce 3D models of the buttresses, roots and humus mounds of large trees in primary forests dominated by in Tasmania. Models of 29, eucalypts were made and analysed. 3D models of example eucalypt roots, logging debris, rainforest tree species, fallen trees, branches, root and trunk slices, and soil profiles were also derived. Measurements in 2D, from earlier work, of three buttress 'logs' were added to the data set. The 3D models had high spatial resolution. The modelling allowed checking and correction of field measurements. Tree anatomical detail was formulated, such as buttress shape, humus volume, root volume in the under-sampled zone and trunk hollow area. The allometric relationships developed link diameter at breast height and ground slope, to SOC and tree trunk carbon, the latter including a correction for senescence. These formulae can be applied to stand-level carbon accounting. The formulae allow the typically measured, inter-tree SOC to be corrected for not sampling near large trees. The 3D models developed are irreplaceable, being for increasingly rare, large trees, and they could be useful to other scientific endeavours.
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http://dx.doi.org/10.1093/aobpla/ply015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5861447PMC
March 2018

Response to Comment on "The growth pattern of Neandertals, reconstructed from a juvenile skeleton from El Sidrón (Spain)".

Science 2018 03;359(6380)

Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK.

The comment by DeSilva challenges our suggestion that brain growth of the El Sidrón J1 Neandertal was still incomplete at 7.7 years of age. Evidence suggests that endocranial volume is likely to represent less than 90% adult size at El Sidrón as well as Neandertal male plus Krapina samples, in line with further evidence from endocranial surface histology and dural sinus groove size.
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http://dx.doi.org/10.1126/science.aar3820DOI Listing
March 2018

Incremental distribution of strontium and zinc in great ape and fossil hominin cementum using synchrotron X-ray fluorescence mapping.

J R Soc Interface 2018 01;15(138)

Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, 22607 Hamburg, Germany.

Cementum and the incremental markings it contains have been widely studied as a means of ageing animals and retrieving information about diet and nutrition. The distribution of trace elements in great ape and fossil hominin cementum has not been studied previously. Synchrotron X-ray fluorescence (SXRF) enables rapid scanning of large tissue areas with high resolution of elemental distributions. First, we used SXRF to map calcium, phosphorus, strontium and zinc distributions in great ape dentine and cementum. At higher resolution, we compared zinc and strontium distributions in cellular and acellular cementum in regions where clear incremental markings were expressed. We then mapped trace element distributions in fossil hominin dentine and cementum from the 1.55-1.65 million year old site of Koobi Fora, Kenya. Zinc, in particular, is a precise marker of cementum increments in great apes, and is retained in fossil hominin cementum, but does not correspond well with the more diffuse fluctuations observed in strontium distribution. Cementum is unusual among mineralized tissues in retaining so much zinc. This is known to reduce the acid solubility of hydroxyapatite and so may confer resistance to resorption by osteoclasts in the dynamic remodelling environment of the periodontal ligament and alveolar bone.
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http://dx.doi.org/10.1098/rsif.2017.0626DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5805964PMC
January 2018

The role of identity in committing acts of violent extremism - and in desisting from them.

Authors:
Christopher Dean

Crim Behav Ment Health 2017 10;27(4):281-285

Identify Psychological Services (Ltd), Warrington, UK.

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http://dx.doi.org/10.1002/cbm.2048DOI Listing
October 2017

The growth pattern of Neandertals, reconstructed from a juvenile skeleton from El Sidrón (Spain).

Science 2017 09;357(6357):1282-1287

Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK.

Ontogenetic studies help us understand the processes of evolutionary change. Previous studies on Neandertals have focused mainly on dental development and inferred an accelerated pace of general growth. We report on a juvenile partial skeleton (El Sidrón J1) preserving cranio-dental and postcranial remains. We used dental histology to estimate the age at death to be 7.7 years. Maturation of most elements fell within the expected range of modern humans at this age. The exceptions were the atlas and mid-thoracic vertebrae, which remained at the 5- to 6-year stage of development. Furthermore, endocranial features suggest that brain growth was not yet completed. The vertebral maturation pattern and extended brain growth most likely reflect Neandertal physiology and ontogenetic energy constraints rather than any fundamental difference in the overall pace of growth in this extinct human.
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http://dx.doi.org/10.1126/science.aan6463DOI Listing
September 2017

New regression formula to estimate the prenatal crown formation time of human deciduous central incisors derived from a Roman Imperial sample (Velia, Salerno, Italy, I-II cent. CE).

PLoS One 2017 12;12(7):e0180104. Epub 2017 Jul 12.

Laboratoire AMIS, UMR 5288, Université Toulouse III, Toulouse, France.

The characterization and quantification of human dental enamel microstructure, in both permanent and deciduous teeth, allows us to document crucial growth parameters and to identify stressful events, thus contributing to the reconstruction of the past life history of an individual. Most studies to date have focused on the more accessible post-natal portion of the deciduous dental enamel, even though the analysis of prenatal enamel is pivotal in understanding fetal growth, and reveals information about the mother's health status during pregnancy. This contribution reports new data describing the prenatal enamel development of 18 central deciduous incisors from the Imperial Roman necropolis of Velia (I-II century CE, Salerno, Italy). Histomorphometrical analysis was performed to collect data on prenatal crown formation times, daily secretion rates and enamel extension rates. Results for the Velia sample allowed us to derive a new regression formula, using a robust statistical approach, that describes the average rates of deciduous enamel formation. This can now be used as a reference for pre-industrial populations. The same regression formula, even when daily incremental markings are difficult to visualize, may provide a clue to predicting the proportion of infants born full term and pre-term in an archaeological series.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0180104PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507505PMC
September 2017

Dental development and age at death of the holotype of Anapithecus hernyaki (RUD 9) using synchrotron virtual histology.

J Hum Evol 2017 07 23;108:161-175. Epub 2017 May 23.

Department of Anthropology, University of Toronto, Toronto, ONT M5S 3G3, Canada. Electronic address:

The chronology of dental development and life history of primitive catarrhines provides a crucial comparative framework for understanding the evolution of hominoids and Old World monkeys. Among the extinct groups of catarrhines are the pliopithecoids, with no known descendants. Anapithecus hernyaki is a medium-size stem catarrhine known from Austria, Hungary and Germany around 10 Ma, and represents a terminal lineage of a clade predating the divergence of hominoids and cercopithecoids, probably more than 30 Ma. In a previous study, Anapithecus was characterized as having fast dental development. Here, we used non-destructive propagation phase contrast synchrotron micro-tomography to image several dental microstructural features in the mixed mandibular dentition of RUD 9, the holotype of A. hernyaki. We estimate its age at death to be 1.9 years and describe the pattern, sequence and timing of tooth mineralization. Our results do not support any simplistic correlation between body mass and striae periodicity, since RUD 9 has a 3-day periodicity, which was previously thought unlikely based on body mass estimates in Anapithecus. We demonstrate that the teeth in RUD 9 grew even faster and initiated even earlier in development than suggested previously. Permanent first molars and the canine initiated 49 and 38 days prenatally, respectively. These results contribute to a better understanding of dental development in Anapithecus and may provide a window into the dental development of the last common ancestor of hominoids and cercopithecoids.
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http://dx.doi.org/10.1016/j.jhevol.2017.03.007DOI Listing
July 2017

New methodology to reconstruct in 2-D the cuspal enamel of modern human lower molars.

Am J Phys Anthropol 2017 08 15;163(4):824-834. Epub 2017 May 15.

Centro Nacional de Investigación sobre la Evolución Humana (CENIEH), Burgos, 09002, Spain.

Objectives: In the last years different methodologies have been developed to reconstruct worn teeth. In this article, we propose a new 2-D methodology to reconstruct the worn enamel of lower molars. Our main goals are to reconstruct molars with a high level of accuracy when measuring relevant histological variables and to validate the methodology calculating the errors associated with the measurements.

Methods: This methodology is based on polynomial regression equations, and has been validated using two different dental variables: cuspal enamel thickness and crown height of the protoconid. In order to perform the validation process, simulated worn modern human molars were employed. The associated errors of the measurements were also estimated applying methodologies previously proposed by other authors.

Results: The mean percentage error estimated in reconstructed molars for these two variables in comparison with their own real values is -2.17% for the cuspal enamel thickness of the protoconid and -3.18% for the crown height of the protoconid. This error significantly improves the results of other methodologies, both in the interobserver error and in the accuracy of the measurements.

Conclusions: The new methodology based on polynomial regressions can be confidently applied to the reconstruction of cuspal enamel of lower molars, as it improves the accuracy of the measurements and reduces the interobserver error. The present study shows that it is important to validate all methodologies in order to know the associated errors. This new methodology can be easily exportable to other modern human populations, the human fossil record and forensic sciences.
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http://dx.doi.org/10.1002/ajpa.23243DOI Listing
August 2017

Structural organization and tooth development in a Homo aff. erectus juvenile mandible from the Early Pleistocene site of Garba IV at Melka Kunture, Ethiopian highlands.

Am J Phys Anthropol 2017 Mar 24;162(3):533-549. Epub 2016 Nov 24.

Laboratoire HNHP, UMR 7194 CNRS, Muséum national d'Histoire naturelle, Paris, France.

Objectives: The immature partial mandible GAR IVE from the c. 1.7 Ma old Garba IV site at Melka Kunture (Upper Awash Basin, Ethiopia), the earliest human representative from a mountain-like environment, represents one of the oldest early Homo specimens bearing a mixed dentition. Following its first description (Condemi, ), we extended the analytical and comparative record of this specimen by providing unreported details about its inner morphology, tooth maturational pattern and age at death, crown size, and tooth tissue proportions.

Materials And Methods: The new body of quantitative structural information and virtual imaging derives from a medical CT record performed in 2013.

Results: Compared to the extant human condition and to some fossil representatives of comparable individual age, the GAR IVE mandible reveals absolutely and relatively thick cortical bone. Crown size of the permanent lateral incisor and the canine fit the estimates of H. erectus s.l., while the dm2 and the M1 more closely approach those of H. habilis-rudolfensis. Molar crown pulp volumes are lower than reported in other fossil specimens and in extant humans. The mineralization sequence of the permanent tooth elements is represented four times in our reference sample of extant immature individuals (N = 795).

Conclusions: The tooth developmental pattern displayed by the immature individual from Garba IV falls within the range of variation of extant human populations and is also comparable with that of other very young early fossil hominins. Taken together, the evidence presented here for mandibular morphology and dental development suggest GAR IVE is a robust 2.5- to 3.5-year old early Homo specimen.
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http://dx.doi.org/10.1002/ajpa.23135DOI Listing
March 2017

New genetic and morphological evidence suggests a single hoaxer created 'Piltdown man'.

R Soc Open Sci 2016 Aug 10;3(8):160328. Epub 2016 Aug 10.

Department of Earth Sciences , Natural History Museum , London SW7 5BD , UK.

In 1912, palaeontologist Arthur Smith Woodward and amateur antiquarian and solicitor Charles Dawson announced the discovery of a fossil that supposedly provided a link between apes and humans: (Dawson's dawn man). The publication generated huge interest from scientists and the general public. However, 'Piltdown man's' initial celebrity has long been overshadowed by its subsequent infamy as one of the most famous scientific frauds in history. Our re-evaluation of the Piltdown fossils using the latest scientific methods (DNA analyses, high-precision measurements, spectroscopy and virtual anthropology) shows that it is highly likely that a single orang-utan specimen and at least two human specimens were used to create the fake fossils. The was found consistent throughout the assemblage (specimens are stained brown, loaded with gravel fragments and restored using filling materials), linking all specimens from the Piltdown I and Piltdown II sites to a single forger-Charles Dawson. Whether Dawson acted alone is uncertain, but his hunger for acclaim may have driven him to risk his reputation and misdirect the course of anthropology for decades. The Piltdown hoax stands as a cautionary tale to scientists not to be led by preconceived ideas, but to use scientific integrity and rigour in the face of novel discoveries.
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http://dx.doi.org/10.1098/rsos.160328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5108962PMC
August 2016

Measures of maturation in early fossil hominins: events at the first transition from australopiths to early Homo.

Philos Trans R Soc Lond B Biol Sci 2016 07;371(1698)

Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK

An important question in palaeoanthropology is whether, among the australopiths and the first fossil hominins attributed to early Homo, there was a shift towards a more prolonged period of growth that can be distinguished from that of the living great apes and whether between the end of weaning and the beginning of puberty there was a slow period of growth as there is in modern humans. Evidence for the pace of growth in early fossil hominins comes from preserved tooth microstructure. A record of incremental growth in enamel and dentine persists, which allows us to reconstruct tooth growth and compare key measures of dental maturation with modern humans and living great apes. Despite their diverse diets and way of life, it is currently difficult to identify any clear differences in the timing of dental development among living great apes, australopiths and the earliest hominins attributed to the genus Homo There is, however, limited evidence that some early hominins may have attained a greater proportion of their body mass and stature relatively earlier in the growth period than is typical of modern humans today.This article is part of the themed issue 'Major transitions in human evolution'.
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http://dx.doi.org/10.1098/rstb.2015.0234DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920291PMC
July 2016

Conventional intensive logging promotes loss of organic carbon from the mineral soil.

Glob Chang Biol 2017 01 13;23(1):1-11. Epub 2016 Jul 13.

Environmental Studies Program, Dartmouth College, Hanover, NH, 03755, USA.

There are few data, but diametrically opposed opinions, about the impacts of forest logging on soil organic carbon (SOC). Reviews and research articles conclude either that there is no effect, or show contradictory effects. Given that SOC is a substantial store of potential greenhouse gasses and forest logging and harvesting is routine, resolution is important. We review forest logging SOC studies and provide an overarching conceptual explanation for their findings. The literature can be separated into short-term empirical studies, longer-term empirical studies and long-term modelling. All modelling that includes major aboveground and belowground biomass pools shows a long-term (i.e. ≥300 years) decrease in SOC when a primary forest is logged and then subjected to harvesting cycles. The empirical longer-term studies indicate likewise. With successive harvests the net emission accumulates but is only statistically perceptible after centuries. Short-term SOC flux varies around zero. The long-term drop in SOC in the mineral soil is driven by the biomass drop from the primary forest level but takes time to adjust to the new temporal average biomass. We show agreement between secondary forest SOC stocks derived purely from biomass information and stocks derived from complex forest harvest modelling. Thus, conclusions that conventional harvests do not deplete SOC in the mineral soil have been a function of their short time frames. Forest managers, climate change modellers and environmental policymakers need to assume a long-term net transfer of SOC from the mineral soil to the atmosphere when primary forests are logged and then undergo harvest cycles. However, from a greenhouse accounting perspective, forest SOC is not the entire story. Forest wood products that ultimately reach landfill, and some portion of which produces some soil-like material there rather than in the forest, could possibly help attenuate the forest SOC emission by adding to a carbon pool in landfill.
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http://dx.doi.org/10.1111/gcb.13387DOI Listing
January 2017