109 results on '"Thomas M. Kaiser"'
Search Results
2. Prospective evaluation and success of a machine learning hit-to-lead drug development program against phosphatidylinositol 3-kinase α
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James P. Snyder, Dennis C. Liotta, Zackery W. Dentmon, Pieter B. Burger, Yuhong Du, Thomas M. Kaiser, Haian Fu, and Qi Shi
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chemistry.chemical_compound ,Drug development ,chemistry ,Kinase ,Organic Chemistry ,Hit to lead ,Phosphatidylinositol ,Bioinformatics ,Prospective evaluation - Published
- 2020
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3. Accelerated Discovery of Potent Fusion Inhibitors for Respiratory Syncytial Virus
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Perry W. Bartsch, Julien Sourimant, Thalia Le, Edgars Jecs, Nicole Pribut, Richard K. Plemper, Stephen C. Pelly, Robert Wilson, Zackery W. Dentmon, Savita Sharma, Pieter B. Burger, Jeong-Joong Yoon, Dennis C. Liotta, Thomas M. Kaiser, and Soyon S. Hwang
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0301 basic medicine ,Fusion ,Benzimidazole ,030106 microbiology ,Antiviral Agents ,Fusion protein ,Article ,Virus ,In vitro ,Structure-Activity Relationship ,03 medical and health sciences ,chemistry.chemical_compound ,030104 developmental biology ,Infectious Diseases ,Biochemistry ,chemistry ,Respiratory Syncytial Virus, Human ,Potency ,Benzimidazoles ,Respiratory system ,Viral Fusion Proteins ,EC50 - Abstract
A series of five benzimidazole-based compounds were identified using a machine learning algorithm as potential inhibitors of the respiratory syncytial virus (RSV) fusion protein. These compounds were synthesized, and compound 2 in particular exhibited excellent in vitro potency with an EC(50) value of 5 nM. This new scaffold was then further refined leading to the identification of compound 44, which exhibited a 10-fold improvement in activity with an EC(50) value of 0.5 nM.
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- 2020
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4. Accelerated Discovery of Novel Ponatinib Analogs with Improved Properties for the Treatment of Parkinson’s Disease
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Zackery W. Dentmon, Christopher E. Dalloul, Dennis C. Liotta, Thomas M. Kaiser, and Savita Sharma
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Parkinson's disease ,biology ,010405 organic chemistry ,business.industry ,Organic Chemistry ,Ponatinib ,hERG ,Disease ,medicine.disease ,Bioinformatics ,01 natural sciences ,Biochemistry ,QT interval ,0104 chemical sciences ,010404 medicinal & biomolecular chemistry ,chemistry.chemical_compound ,chemistry ,Nilotinib ,Drug development ,Drug Discovery ,medicine ,biology.protein ,business ,medicine.drug - Abstract
[Image: see text] Parkinson’s disease (PD) is a debilitating and common neurodegenerative disease. New insights implicating c-Abl activation as a driving force in PD have opened a new drug development avenue for PD treatment beyond the symptomatic relief by L-DOPA. BCR-Abl inhibitors, which include nilotinib and ponatinib, have been found to inhibit this process, and nilotinib has shown improvement in outcomes in a 12-patient, nonrandomized trial. However, nilotinib is a potent inhibitor of hERG, a cardiac K(+) channel whose inhibition increases risk of sudden death. We used our machine learning approach to predict novel molecules that would inhibit c-Abl while also having minimal liability against hERG. Of our six novel compounds tested, we identified two that had c-Abl potencies comparable to nilotinib, but with significantly improved profiles regarding the hERG channel. Our best compound exhibited a hERG IC(50) of 12.1 μM (compared to nilotinib with an IC(50) of 0.45 μM and ponatinib with IC(50) of 0.767 μM). This work is a step forward for a machine learning enabled, multiparameter optimization of a chemical space and represents a significant advance in the development of novel Parkinson’s therapies.
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- 2020
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5. Post-mortem enamel surface texture alteration during taphonomic processes—do experimental approaches reflect natural phenomena?
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Katrin Weber, Daniela E. Winkler, Ellen Schulz-Kornas, Thomas M. Kaiser, and Thomas Tütken
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General Neuroscience ,Experimental alteration ,Fluvial transport ,General Medicine ,General Biochemistry, Genetics and Molecular Biology ,Diet ,Dental microwear ,Vertebrate enamel ,560 Paläontologie ,560 Paleontology ,stomatognathic system ,Medicine ,Post-mortem wear ,General Agricultural and Biological Sciences - Abstract
Experimental approaches are often used to better understand the mechanisms behindand consequences of post-mortem alteration on proxies for diet reconstruction.Dental microwear texture analysis (DMTA) is such a dietary proxy, using dental wearfeatures in extant and extinct taxa to reconstruct feeding behaviour and mechanicalfood properties. In fossil specimens especially, DMTA can be biased by post-mortemalteration caused by mechanical or chemical alteration of the enamel surface. Herewe performed three different dental surface alteration experiments to assess the effectof common taphonomic processes by simplifying them: (1) tumbling in sedimentsuspension to simulate fluvial transport, (2) sandblasting to simulate mechanicalerosion due to aeolian sediment transport, (3) acid etching to simulate chemicaldissolution by stomach acid. For tumbling (1) we found alteration to be mainlydependent on sediment grain size fraction and that on specimens tumbled with sandfractions mainly post-mortem scratches formed on the dental surface, while specimenstumbled with a fine-gravel fraction showed post-mortem formed dales. Sandblasting(2) with loess caused only negligible alteration, however blasting with fine sand quartzparticles resulted in significant destruction of enamel surfaces and formation of largepost-mortem dales. Acid etching (3) using diluted hydrochloric acid solutions inconcentrations similar to that of predator stomachs led to a complete etching of thewhole dental surface, which did not resemble those of teeth recovered from owl pellets.The experiments resulted in post-mortem alteration comparable, but not identical tonaturally occurring post-mortem alteration features. Nevertheless, this study servesas a first assessment and step towards further, more refined taphonomic experimentsevaluating post-mortem alteration of dental microwear texture (DMT).
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- 2022
6. Dental microwear texture analysis of rats receiving experimental near-natural diets shows that seeds and insect exoskeletons cause high enamel surface complexity
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Daniela E. Winkler, Marcus Clauss, Mugino O. Kubo, Ellen Schulz-Kornas, Thomas M. Kaiser, Anja Tschudin, Annelies De Cuyper, Tai Kubo, Thomas Tütken
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- 2022
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7. Osteo-pathological analysis provides evidence for a survived historical ship strike in a Southern Hemisphere fin whale (Balaenoptera physalus)
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Hannah Viola Daume, Helena Herr, Heinrich Mallison, Matthias Glaubrecht, and Thomas M. Kaiser
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Multidisciplinary - Abstract
The life history of a fin whale (Balaenoptera physalus) caught during whaling operations in the 1950s was partly reconstructed. 3D surface models of the bones of the skeleton curated at the Zoological Museum of Hamburg were used for an osteopathological analysis. The skeleton revealed multiple healed fractures of ribs and a scapula. Moreover, the processus spinosi of several vertebrae were deformed and arthrosis was found. Together, the pathological findings provide evidence for large blunt trauma and secondary effects arising from it. Reconstruction of the likely cause of events suggests collision with a ship inflicting the fractures and leading to post traumatic posture damage as indicated by skeletal deformations. The injured bones had fully healed before the fin whale was killed by a whaler in the South Atlantic in 1952. This study is the first in-detail reconstruction of a historical whale—ship collision in the Southern Hemisphere, dating back to the 1940s, and the first documentation of a healed scapula fracture in a fin whale. The skeleton provides evidence for survival of a ship strike by a fin whale with severe injuries causing long-term impairment.
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- 2023
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8. Dental wear proxy correlation in a long-term feeding experiment on sheep (
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Nicole L, Ackermans, Daniela E, Winkler, Ellen, Schulz-Kornas, Thomas M, Kaiser, Louise F, Martin, Jean-Michel, Hatt, and Marcus, Clauss
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Sheep ,Animals ,Life Sciences–Physics interface ,Tooth Wear ,Molar ,Tooth ,Sheep, Domestic ,Diet - Abstract
Dietary reconstruction in vertebrates often relies on dental wear-based proxies. Although these proxies are widely applied, the contributions of physical and mechanical processes leading to meso- and microwear are still unclear. We tested their correlation using sheep (Ovis aries, n = 39) fed diets of varying abrasiveness for 17 months as a model. Volumetric crown tissue loss, mesowear change and dental microwear texture analysis (DMTA) were all applied to the same teeth. We hereby correlate: (i) 46 DMTA parameters with each other, for the maxillary molars (M1, M2, M3), and the second mandibular molar (m2); (ii) 10 mesowear variables to each other and to DMTA for M1, M2, M3 and m2; and (iii) volumetric crown tissue loss to mesowear and DMTA for M2. As expected, many DMTA parameters correlated strongly with each other, supporting the application of reduced parameter sets in future studies. Correlation results showed only few DMTA parameters correlated with volumetric tissue change and even less so with mesowear variables, with no correlation between mesowear and volumetric tissue change. These findings caution against interpreting DMTA and mesowear patterns in terms of actual tissue removal until these dental wear processes can be better understood at microscopic and macroscopic levels.
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- 2021
9. Dental microwear texture gradients in guinea pigs reveal that material properties of the diet affect chewing behaviour
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Thomas M. Kaiser, Ellen Schulz-Kornas, Marcus Clauss, Maximilian Rölle, Daniela E. Winkler, Thomas Tütken, Daryl Codron, University of Zurich, and Winkler, Daniela E
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0106 biological sciences ,Abrasion (dental) ,10253 Department of Small Animals ,1109 Insect Science ,Physiology ,Evolution ,Guinea Pigs ,Biology ,Aquatic Science ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Posterior Tooth ,Animal science ,stomatognathic system ,Behavior and Systematics ,medicine ,1312 Molecular Biology ,Animals ,Mastication ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Anterior teeth ,030304 developmental biology ,0303 health sciences ,Herbivore ,630 Agriculture ,1104 Aquatic Science ,Ecology ,1314 Physiology ,medicine.disease ,Animal Feed ,Diet ,Bite force quotient ,stomatognathic diseases ,1105 Ecology, Evolution, Behavior and Systematics ,Phytolith ,Tooth wear ,Insect Science ,570 Life sciences ,biology ,Animal Science and Zoology ,Tooth Wear ,1103 Animal Science and Zoology ,Tooth - Abstract
Dental microwear texture analysis (DMTA) is widely used for diet inferences in extant and extinct vertebrates. Often, a reference tooth position is analysed in extant specimens, while isolated teeth are lumped together in fossil datasets. It is therefore important to test whether dental microwear texture (DMT) is tooth position specific and, if so, what causes the differences in wear. Here, we present results from controlled feeding experiments with 72 guinea pigs, which received either fresh or dried natural plant diets of different phytolith content (lucerne, grass, bamboo) or pelleted diets with and without mineral abrasives (frequently encountered by herbivorous mammals in natural habitats). We tested for gradients in dental microwear texture along the upper cheek tooth row. Regardless of abrasive content, guinea pigs on pelleted diets displayed an increase in surface roughness along the tooth row, indicating that posterior tooth positions experience more wear compared with anterior teeth. Guinea pigs feedings on plants of low phytolith content and low abrasiveness (fresh and dry lucerne, fresh grass) showed almost no DMT differences between tooth positions, while individuals feeding on more abrasive plants (dry grass, fresh and dry bamboo) showed a gradient of decreasing surface roughness along the tooth row. We suggest that plant feeding involves continuous intake and comminution by grinding, resulting in posterior tooth positions mainly processing food already partly comminuted and moistened. Pelleted diets require crushing, which exerts higher loads, especially on posterior tooth positions, where bite forces are highest. These differences in chewing behaviour result in opposing wear gradients for plant versus pelleted diets.
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- 2021
10. Tooth Microwear Texture in the Eastern Atlantic Harbour Seals (Phoca vitulina vitulina) of the German Wadden Sea and Its Implications for Long Term Dietary and Ecosystem Changes
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Elehna Bethune, Thomas M. Kaiser, Kristina Lehnert, Ursula Siebert, and Ellen Schulz-Kornas
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0106 biological sciences ,0301 basic medicine ,lcsh:Evolution ,010603 evolutionary biology ,01 natural sciences ,Phoca ,Predation ,03 medical and health sciences ,Marine mammal ,Phoca vitulina (Harbour seal) ,Abundance (ecology) ,lcsh:QH540-549.5 ,lcsh:QH359-425 ,Ecosystem ,marine mammals ,Ecology, Evolution, Behavior and Systematics ,Ecology ,Dentition ,biology ,biology.organism_classification ,dental microwear texture analysis (DMTA) ,030104 developmental biology ,Geography ,Habitat ,pinnipeds ,Threatened species ,lcsh:Ecology ,diet ,German Wadden Sea - Abstract
Marine mammals are increasingly threatened in their habitat by various anthropogenic impacts. This is particularly evident in prey abundance. Understanding the dietary strategies of marine mammal populations can help predict implications for their future health status and is essential for their conservation. In this study we provide a striking example of a new dietary proxy in pinnipeds to document marine mammal diets using a dental record. In this novel approach, we used a combination of 49 parameters to establish a dental microwear texture (DMTA) as a dietary proxy of feeding behaviour in harbour seals. This method is an established approach to assess diets in terrestrial mammals, but has not yet been applied to pinnipeds. Our aim was to establish a protocol, opening DMTA to pinnipeds by investigating inter- and intra-individual variations. We analysed the 244 upper teeth of 78 Atlantic harbour seals (Phoca vitulina vitulina). The specimens were collected in 1988 along the North Sea coast (Wadden Sea, Germany) and are curated by the Zoological Institute of Kiel University, Germany. An increasing surface texture roughness from frontal to distal teeth was found and related to different prey processing biomechanics. Ten and five year old individuals were similar in their texture roughness, whereas males and females were similar to each other with the exception of their frontal dentition. Fall and summer specimens also featured no difference in texture roughness. We established the second to fourth postcanine teeth as reference tooth positions, as those were unaffected by age, sex, season, or intra-individual variation. In summary, applying indirect dietary proxies, such as DMTA, will allow reconstructing dietary traits of pinnipeds using existing skeletal collection material. Combining DMTA with time series analyses is a very promising approach to track health status in pinniped populations over the last decades. This approach opens new research avenues and could help detect dietary shifts in marine environments in the past and the future.
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- 2021
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11. The good, the bad and the ugly – A visual guide for common post-mortem wear patterns in vertebrate teeth
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Ellen Schulz-Kornas, Katrin Weber, Thomas Tütken, Thomas M. Kaiser, and Daniela E. Winkler
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Orthodontics ,Enamel paint ,Dental Wear ,Paleontology ,Extinct species ,Oceanography ,Texture (geology) ,stomatognathic diseases ,stomatognathic system ,Extant taxon ,visual_art ,visual_art.visual_art_medium ,Reference database ,Ecology, Evolution, Behavior and Systematics ,Geology ,Earth-Surface Processes - Abstract
Dental microwear texture analysis (DMTA) is a common wear proxy using dental wear features to reconstruct diet in extant and extinct taxa. Dietary reconstructions of extinct species can be biased due to post-mortem mechanical modification of the dental surface. These post-mortem surface alterations can be caused by material loss after death, or as the result of burial, excavation, or preparation processes. In this study, we explore post-mortem surface alterations that occur during excavation, preparation, and conservation processes. We present a first general overview of unsuitable and suspicious dental surface scans and describe them both qualitatively and quantitatively using dental microwear texture (DMT) parameters. Finally, we compare these taphonomically altered surfaces to dental surfaces formed only by contact with a natural, ingested diet. We show that non-ingesta-related surfaces vary widely in morphologies. While some altered surfaces such as large post-mortem scratches or cracks in the enamel are easy to distinguish from ante-mortem ingesta-related wear features, others, such as remaining varnish covering the dental surface, are more obscure. The compiled surface defects dataset reveals that post-mortem altered surfaces often overlap with the parameter space of ingesta-related dental surfaces, but usually also include outliers with extreme values. To best identify dental surfaces with strong post-mortem alteration, we suggest using quantitative thresholds for frequently used DMT parameters for ingesta-related enamel surfaces based on literature values. However, with sufficient training and a reference database, these altered surfaces are detectable by an experienced user. Here we have compiled a first visual database of non-ingesta-related dental wear to help DMTA users identify these features and improve future DMTA studies.
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- 2021
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12. Movement analysis of primate molar teeth under load using synchrotron X-ray microtomography
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Thomas M. Kaiser, Elke Zimmermann, Anthony Herrel, Alexander Hipp, Julian Moosmann, Ute Radespiel, Kornelius Kupczik, Alexander Rack, Ellen Schulz-Kornas, Maximilian Bemmann, Jörg U. Hammel, Mécanismes Adaptatifs et Evolution (MECADEV), and Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)
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Primates ,Molar ,Microcebus murinus ,X-ray microtomography ,Materials science ,Tooth Movement Techniques ,Periodontal Ligament ,[SDV]Life Sciences [q-bio] ,Connective tissue ,Mice ,03 medical and health sciences ,Imaging, Three-Dimensional ,stomatognathic system ,Structural Biology ,biology.animal ,medicine ,Animals ,Humans ,Periodontal fiber ,Primate ,Dental alveolus ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,Orthodontics ,0303 health sciences ,biology ,030302 biochemistry & molecular biology ,Biomechanics ,X-Ray Microtomography ,biology.organism_classification ,stomatognathic diseases ,medicine.anatomical_structure ,ddc:540 ,Female ,Stress, Mechanical ,Synchrotrons - Abstract
Journal of structural biology 213(1), 107658 (1-12) (2021). doi:10.1016/j.jsb.2020.107658, Mammalian teeth have to sustain repetitive and high chewing loads without failure. Key to this capability is the periodontal ligament (PDL), a connective tissue containing a collagenous fibre network which connects the tooth roots to the alveolar bone socket and which allows the teeth to move when loaded. It has been suggested that rodent molars under load experience a screw-like downward motion but it remains unclear whether this movement also occurs in primates. Here we use synchroton micro-computed tomography paired with an axial loading setup to investigate the form-function relationship between tooth movement and the morphology of the PDL space in a non-human primate, the mouse lemur (Microcebus murinus). The loading behavior of both mandibular and maxillary molars showed a three-dimensional movement with translational and rotational components, which pushes the tooth into the alveolar socket. Moreover, we found a non-uniform PDL thickness distribution and a gradual increase in volumetric proportion of the periodontal vasculature from cervical to apical. Our results suggest that the PDL morphology may optimize the three-dimensional tooth movement to avoid high stresses under loading., Published by Elsevier, San Diego, Calif.
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- 2021
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13. Dental microwear texture analysis on extant and extinct sharks : Ante- or post-mortem tooth wear?
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Thomas Tütken, Katrin Weber, Živilė Žigaitė, Daniela E. Winkler, and Thomas M. Kaiser
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010506 paleontology ,Dental Wear ,Zoology ,Extinct species ,chemical and pharmacologic phenomena ,Shark teeth ,010502 geochemistry & geophysics ,Oceanography ,01 natural sciences ,Texture (geology) ,DMTA ,Zoologi ,Predation ,Extant taxon ,stomatognathic system ,14. Life underwater ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Earth-Surface Processes ,biology ,Tumbling experiment ,Paleontology ,Geology ,biology.organism_classification ,stomatognathic diseases ,Habitat ,Tooth wear ,Carcharhinus ,Geologi ,Alteration ,human activities ,Elasmobranchii - Abstract
Sharks are apex-predators that play an important role in past and present aquatic food webs. However, their diet - especially in extinct species - is often not well constrained. Dental microwear texture analysis (DMTA) has been successfully applied to reconstruct diet and feeding behaviours of different aquatic and terrestrial vertebrates. However, unlike in mammals, food-to-tooth contact in sharks is rather limited because only larger prey is manipulated before swallowing. Together with a fast tooth replacement rate, this reduces wear on individual teeth. Here, we present an explorative study of dental microwear texture on extant and extinct sharks to test whether ante-mortem wear is related to ingested diet or habitat preferences and resistant to post-mortem alteration processes. Shark teeth from 24 modern species and 12 fossil species from different localities were measured. As an additional comparison, extant shark teeth of Carcharhinus plumbeus were tumbled in sedimentwater suspensions to simulate post-mortem mechanical alteration by sediment transport. Only three of the twelve extant shark species with three or more specimens had significantly different dental surface textures. Furthermore, no clear relation between food or habitat preferences and ante-mortem dental wear features was detected for this sample set. Tumbling modern shark teeth with siliciclastic sediment of four different grain size fractions led to increasing complexity of the dental surface. Fossil specimens resemble these experimentally altered shark teeth more in complexity and roughness. Thus, fossil shark teeth seem to display either very different (e.g. harder) diet-related wear or a strong degree of post-mortem alteration. Based on our restricted sample size, dental wear of shark teeth does overall not seem to simply reflect dietary differences; hence, it is difficult to use DMTA as reliable dietary reconstruction, in either extant nor extinct sharks.
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- 2021
14. Dental microwear texture gradients in guinea pigs reveal that physical and mechanical properties of the diet affect chewing behaviour
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Daniela E Winkler, Marcus Clauss, Maximilian Rölle, Ellen Schulz-Korna, Daryl Codron, Thomas M Kaiser, Thomas Tütken
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- 2021
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15. Distinct GluN1 and GluN2 Structural Determinants for Subunit-Selective Positive Allosteric Modulation of N-Methyl-d-aspartate Receptors
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Jing Zhang, Katie L. Strong, Riley E. Perszyk, Chad R. Camp, Kevin K. Ogden, Timothy J. Wilding, Subhrajit Bhattacharya, Dennis C. Liotta, Miranda J. McDaniel, Stephen F. Traynelis, David S. Menaldino, Pieter B. Burger, Tue G. Banke, Matthew P. Epplin, Hiro Kusumoto, Kasper B. Hansen, James E. Huettner, Phuong Le, Thomas M. Kaiser, and Gil Shaulsky
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Agonist ,Models, Molecular ,Physiology ,medicine.drug_class ,Stereochemistry ,Cognitive Neuroscience ,Protein subunit ,Allosteric regulation ,Kainate receptor ,Biochemistry ,Receptors, N-Methyl-D-Aspartate ,Synaptic Transmission ,Article ,03 medical and health sciences ,0302 clinical medicine ,Allosteric Regulation ,medicine ,Receptor ,030304 developmental biology ,0303 health sciences ,Chemistry ,Glutamate receptor ,Cell Biology ,General Medicine ,NMDA receptor ,030217 neurology & neurosurgery ,Ionotropic effect - Abstract
N-Methyl-d-aspartate receptors (NMDARs) are ionotropic ligand-gated glutamate receptors that mediate fast excitatory synaptic transmission in the central nervous system (CNS). Several neurological disorders may involve NMDAR hypofunction, which has driven therapeutic interest in positive allosteric modulators (PAMs) of NMDAR function. Here we describe modest changes to the tetrahydroisoquinoline scaffold of GluN2C/GluN2D-selective PAMs that expands activity to include GluN2A- and GluN2B-containing recombinant and synaptic NMDARs. These new analogues are distinct from GluN2C/GluN2D-selective compounds like (+)-(3-chlorophenyl)(6,7-dimethoxy-1-((4-methoxyphenoxy)methyl)-3,4-dihydroisoquinolin-2(1H)-yl)methanone (CIQ) by virtue of their subunit selectivity, molecular determinants of action, and allosteric regulation of agonist potency. The (S)-enantiomers of two analogues (EU1180-55, EU1180-154) showed activity at NMDARs containing all subunits (GluN2A, GluN2B, GluN2C, GluN2D), whereas the (R)-enantiomers were primarily active at GluN2C- and GluN2D-containing NMDARs. Determination of the actions of enantiomers on triheteromeric receptors confirms their unique pharmacology, with greater activity of (S) enantiomers at GluN2A/GluN2D and GluN2B/GluN2D subunit combinations than (R) enantiomers. Evaluation of the (S)-EU1180-55 and EU1180-154 response of chimeric kainate/NMDA receptors revealed structural determinants of action within the pore-forming region and associated linkers. Scanning mutagenesis identified structural determinants within the GluN1 pre-M1 and M1 regions that alter the activity of (S)-EU1180-55 but not (R)-EU1180-55. By contrast, mutations in pre-M1 and M1 regions of GluN2D perturb the actions of only the (R)-EU1180-55 but not the (S) enantiomer. Molecular modeling supports the idea that the (S) and (R) enantiomers interact distinctly with GluN1 and GluN2 pre-M1 regions, suggesting that two distinct sites exist for these NMDAR PAMs, each of which has different functional effects.
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- 2020
16. The turnover of dental microwear texture: Testing the' last supper' effect in small mammals in a controlled feeding experiment
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Ellen Schulz-Kornas, Daniela E. Winkler, Jennifer Leichliter, Thomas M. Kaiser, Louise F. Martin, Thomas Tütken, Daryl Codron, Jürgen Hummel, Marcus Clauss, University of Zurich, and Winkler, Daniela E
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Molar ,010506 paleontology ,10253 Department of Small Animals ,Diet switch ,Evolution ,Dental Wear ,1904 Earth-Surface Processes ,Texture (music) ,010502 geochemistry & geophysics ,Oceanography ,01 natural sciences ,Mandibular second molar ,Animal science ,Behavior and Systematics ,1910 Oceanography ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Earth-Surface Processes ,2. Zero hunger ,Enamel paint ,630 Agriculture ,Ecology ,Palaeontology ,Paleontology ,Earth ,1911 Paleontology ,1105 Ecology, Evolution, Behavior and Systematics ,Surface Processes ,visual_art ,visual_art.visual_art_medium ,570 Life sciences ,biology ,Geology - Abstract
Dental microwear texture (DMT) analysis is commonly applied for dietary reconstruction of vertebrates. The temporal scale on which dietarily informative microscopic wear forms on enamel surfaces is crucial to infer dietary flexibility and seasonality. Microwear is assumed to form shortly before the individual's death, reflecting information pertaining to the last meals consumed (“last supper” effect). In primate feeding experiments, microwear features formed within hours, suggesting rates of turnover within one to two weeks. As DMT formation experiments testing the persistence of microwear three-dimensionally (textures) are still lacking, we test how quickly DMTs form and pre-existing ones are overwritten in a terminal feeding experiment with 72 rats. In two groups of 36, rats received either a standard pelleted diet or the same pelleted diet containing 4% loess, an aeolian, silt-sized sediment, for 24 consecutive days. Then 6 individuals from each group were sacrificed, while the rest (n=30) were switched to the diet they had not received before. On day 1, 2, 4, 8, 16, and 24 after the diet switch, 5 of the remaining individuals were sacrificed, creating a cohort of n=5 each for each time point. We applied DMT analysis on first and second upper molars. For upper second molars, rats show a subsequent change in DMT after the switch, with visible differences from day 2 on. On upper first molars, microwear textures were variable for individuals sacrificed directly after the initial 24-day feeding period, thus obscuring significant differences in diet-induced dental wear. We find turnover faster and more pronounced when switching from loess-containing to standard pellet as compared to the opposite switch. The trend for either decreasing or increasing parameter values after the diet switch approaches a plateau between 16 and 24days for many DMT parameters, suggesting that, under these experimental conditions, the “last supper” effect needs at least two weeks to overwrite previous DMT patterns.
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- 2020
17. Synthesis and Antiviral Activity of a Series of 2'
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Zackery W, Dentmon, Thomas M, Kaiser, and Dennis C, Liotta
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Thionucleosides ,Drug Evaluation, Preclinical ,Nucleosides ,Hepacivirus ,Viral Nonstructural Proteins ,Amides ,Antiviral Agents ,Hepatitis C ,Article ,nucleotides ,Cell Line ,Phosphates ,antivirals ,prodrugs ,medicinal chemistry ,Humans ,Phosphoric Acids - Abstract
The NS5B RNA-dependent RNA polymerase of the hepatitis C virus (HCV) is a validated target for nucleoside antiviral drug therapy. We endeavored to synthesize and test a series of 4′-thionucleosides with a monophosphate prodrug moiety for their antiviral activity against HCV and other related viruses in the Flaviviridae family. Nucleoside analogs were prepared via the stereoselective Vorbrüggen glycosylation of various nucleobases with per-acetylated 2-C-methyl-4-thio-d-ribose built in a 10-step synthetic sequence from the corresponding ribonolactone. Conjugation of the thionucleoside to a ProTide phosphoramidate allowed for evaluation of the prodrugs in the cellular HCV replicon assay with anti-HCV activities ranging from single-digit micromolar (μM) to >200 μM. The diminished anti-HCV potency of our best compound compared to its 4′-oxo congener is the subject of ongoing research in our lab and is proposed to stem from changes in sugar geometry imparted by the larger sulfur atom.
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- 2020
18. Mesowear represents a lifetime signal in sheep (Ovis aries) within a long-term feeding experiment
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Thomas M. Kaiser, Henning Richter, Louise F. Martin, Jürgen Hummel, Nicole L. Ackermans, Daryl Codron, Marcus Clauss, Patrick R Kircher, Jean-Michel Hatt, University of Zurich, and Ackermans, Nicole L
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010506 paleontology ,10253 Department of Small Animals ,Evolution ,1904 Earth-Surface Processes ,010502 geochemistry & geophysics ,Oceanography ,01 natural sciences ,Mesowear ,Small magnitude ,Animal science ,Behavior and Systematics ,1910 Oceanography ,Ovis ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Earth-Surface Processes ,Herbivore ,biology ,630 Agriculture ,Ecology ,Palaeontology ,Paleontology ,Earth ,biology.organism_classification ,1911 Paleontology ,1105 Ecology, Evolution, Behavior and Systematics ,Surface Processes ,Tooth wear ,11404 Department of Clinical Diagnostics and Services ,570 Life sciences ,Geology - Abstract
A herbivore's diet can affect its teeth by causing different types of wear. Browsers typically have sharper, higher cusps, while grazers show lower, blunter cusps, presumably due to the more abrasive nature of their diet. On the macroscopic scale, this allows the reconstruction of herbivore diets based on the shape of the tooth's profile, using the mesowear method. However, the timeframe involved in constituting a stable dietary signal represented by mesowear has not been precisely defined. To obtain a more precise delimitation of this timeframe, sheep (Ovis aries, n = 39) were fed pelleted diets containing external abrasives of different sizes (⌀ 4 μm, ⌀ 50 μm, and ⌀ 130 μm), and concentrations (4%, or 8%) for 17 months. Mesowear was scored on the skulls at the end of the experiment, as well as on computer-tomographic scans and on resin casts of the teeth taken at different timepoints along the experiment. These datasets were compared, and changes in score were calculated using the CT and cast data from the beginning and end of the experiment. Overall, even though a visual trend appeared of more wear on higher abrasion diets, it was of an extremely small magnitude, and the dietary effect on the mesowear scores or the change of the mesowear scores in these animals was never significant. This leads us to conclude that, at least in small ruminants, mesowear is more of a general signal than a seasonal one, and needs to be considered as such for tooth wear-based palaeodietary reconstructions. Experiments with natural forages are required to corroborate this conclusion.
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- 2020
19. Root growth compensates for molar wear in adult goats (Capra aegagrus hircus)
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Nicole L. Ackermans, Daniela E. Winkler, Thomas M. Kaiser, Jürgen Hummel, Patrick R Kircher, Ellen Schulz-Kornas, Marcus Clauss, Jean-Michel Hatt, and Dennis W. H. Müller
- Subjects
0106 biological sciences ,0301 basic medicine ,Molar ,Root growth ,Physiology ,Capra aegagrus ,Biology ,010603 evolutionary biology ,01 natural sciences ,Mandibular second molar ,03 medical and health sciences ,Animal science ,stomatognathic system ,Genetics ,medicine ,Cementum ,Root volume ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,2. Zero hunger ,Herbivore ,stomatognathic diseases ,030104 developmental biology ,medicine.anatomical_structure ,Volume (thermodynamics) ,Animal Science and Zoology - Abstract
One reason for the mammalian clade’s success is the evolutionary diversity of their teeth. In herbivores, this is represented by high‐crowned teeth evolved to compensate for wear caused by dietary abrasives like phytoliths and grit. Exactly how dietary abrasives wear teeth is still not understood completely. We fed four different pelleted diets of increasing abrasiveness (L: Lucerne; G: grass; GR: grass and rice husks; GRS: grass, rice husks, and sand) to four groups of a total of 28 adult goats, all with completely erupted third molars, over a six‐month period. Tooth morphology was captured by medical computed tomography scans at the beginning and end of the controlled feeding experiment, and separation lines between the crown and root segments were defined in the upper right second molar (M2), to gauge absolute wear. Using bootstrapping, significant differences in volume loss between diets L/G and GR/GRS were detected. A small but nevertheless consistent volume gain was noted in the roots, and there was a significant, positive correlation between crown volume loss and root volume gain. This growth could possibly be attributed to the well‐known process of cementum deposition and its relation with a putative feedback mechanism, in place to attenuate wear caused by abrasive diets.
- Published
- 2018
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20. The phylogenetic signal in tooth wear: What does it mean?
- Author
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Mark F. Teaford, Mark A. Purnell, Juha Saarinen, Thomas M. Kaiser, Peter S. Ungar, Indrė Žliobaitė, Ellen Schulz-Kornas, Christine M. Janis, Larisa R.G. DeSantis, Frederick E. Grine, Mikael Fortelius, Gildas Merceron, Department of Geosciences and Geography [Helsinki], Falculty of Science [Helsinki], University of Helsinki-University of Helsinki, Universität Hamburg (UHH), Laboratoire de paléontologie, évolution, paléoécosystèmes, paléoprimatologie (PALEVOPRIM ), Université de Poitiers-Centre National de la Recherche Scientifique (CNRS), Max Planck Weizmann Center for Integrative Archaeology and Anthropology (WPWC), Max Planck Institute for Evolutionary Anthropology [Leipzig], Max-Planck-Gesellschaft-Max-Planck-Gesellschaft-Weizmann Institute of Science [Rehovot, Israël], and University of Helsinki
- Subjects
0106 biological sciences ,010506 paleontology ,Ecology ,Phylogenetic tree ,SIGNAL (programming language) ,Phylogenetic comparative methods ,phylogenetic methods ,mesowear ,010603 evolutionary biology ,01 natural sciences ,microwear ,Tooth wear ,Research community ,tooth wear ,sort ,[SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology ,Set (psychology) ,Clade ,Psychology ,Letter to the Editor ,ComputingMilieux_MISCELLANEOUS ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Nature and Landscape Conservation ,Cognitive psychology - Abstract
A new study by Fraser et al (2018) urges the use of phylogenetic comparative methods, whenever possible, in analyses of mammalian tooth wear. We are concerned about this for two reasons. First, this recommendation may mislead the research community into thinking that phylogenetic signal is an artifact of some sort rather than a fundamental outcome of the evolutionary process. Secondly, this recommendation may set a precedent for editors and reviewers to enforce phylogenetic adjustment where it may unnecessarily weaken or even directionally alter the results, shifting the emphasis of analysis from common patterns manifested by large clades to rare cases.
- Published
- 2018
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21. Nano-indentation of native phytoliths and dental tissues: implications for herbivore-plant combat and dental wear proxies
- Author
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Gerhard Kalinka, Ellen Schulz-Kornas, Thomas M. Kaiser, and Caroline Braune
- Subjects
0106 biological sciences ,0301 basic medicine ,lcsh:Evolution ,lcsh:Life ,010603 evolutionary biology ,01 natural sciences ,Indentation hardness ,03 medical and health sciences ,stomatognathic system ,lcsh:QH359-425 ,medicine ,Ecology, Evolution, Behavior and Systematics ,Herbivore ,Enamel paint ,Chemistry ,Metallurgy ,Abrasive ,indentation hardness phytolith enamel dentine tooth wear ,Nanoindentation ,Tooth enamel ,lcsh:QH501-531 ,stomatognathic diseases ,030104 developmental biology ,medicine.anatomical_structure ,Tooth wear ,Phytolith ,Insect Science ,visual_art ,visual_art.visual_art_medium ,Animal Science and Zoology - Abstract
Tooth wear induced by abrasive particles is a key process affecting dental function and life expectancy in mammals. Abrasive particles may be plant endogenous opal phytoliths, exogene wind-blown quartz dust or rain borne mineral particles ingested by mammals. Nano-indentation hardness of abrasive particles and dental tissues is a significant yet not fully established parameter of this tribological system. We provide consistent nano-indentation hardness data for some of the major antagonists in the dental tribosystem (tooth enamel, tooth dentine and opaline phytoliths from silica controlled cultivation). All indentation data were gathered from native tissues under stable and controlled conditions and thus maximize comparability to natural systems. Here we show that native (hydrated) wild boar enamel exceeds any hardness measures known for dry herbivore tooth enamel by at least 3 GPa. The native tooth enamel is not necessarily softer then environmental quartz grit, although there is little overlap. The native hardness of the tooth enamel exceeds that of any silica phytolith hardness recently published. Further, we find that native reed phytoliths equal native suine dentine in hardness, but does not exceed native suine enamel. We also find that native suine enamel is significantly harder than dry enamel and dry phytoliths are harder than native phytoliths. Our data challenge the claim that the culprit of tooth wear may be the food we chew, but suggest instead that wear may relates more to exogenous than endogenous abrasives.
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- 2018
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22. Does silica concentration and phytolith ultrastructure relate to phytolith hardness?
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Thomas M. Kaiser, Ellen Schulz-Kornas, Daniela E. Winkler, and Caroline Braune
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0106 biological sciences ,0301 basic medicine ,lcsh:Biotechnology ,Biomedical Engineering ,Biophysics ,Phytolith ,Material property ,Forage ,010603 evolutionary biology ,01 natural sciences ,Biomaterials ,lcsh:Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,lcsh:TP248.13-248.65 ,Botany ,medicine ,lcsh:QD415-436 ,biology ,Mechanical Engineering ,Tooth wear ,Themeda triandra ,biology.organism_classification ,Tooth enamel ,Silicate ,Surfaces, Coatings and Films ,030104 developmental biology ,medicine.anatomical_structure ,chemistry ,Ultrastructure ,Silicate availability ,Hordeum vulgare ,Indentation - Abstract
Grasses are an important part of the forage of many herbivorous mammals and their phytoliths have long been regarded as the most important agent of tooth wear. Recent work has challenged this “paradigm” in finding evidence 1. of native phytoliths to be much softer then tooth enamel and 2. indicating, that phytolith hardness is highly variable, 3. prone to methodology and 4. not easy to be related to habitat conditions. We conduct controlled silica-cultivations measuring SiO2 content in the common forage grass Themeda triandra. Phytoliths are extracted natively, and nano-indentation values are measured. Phytolith hardness in Themeda triandra is found to be independent of silicate availability in the substrate. We further investigate the phytolith ultrastructure of Hordeum vulgare phytoliths. Phytoliths are shown to be an anisotropic composite of at least 3 components, silica bodies, inter-body matrix (both mineralised) and globular inclusions (likely non-mineralised). It can be argued, that indentation will be largely influenced by the heterogeneity of the structure and thus nano-indentation measurements will largely reflect the matrix and its mechanical properties but not necessarily the silicate bodies, which make up the vast majority of a phytolith.
- Published
- 2017
23. Chewing, dental morphology and wear in tapirs (Tapirus spp.) and a comparison of free-ranging and captive specimens
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Clemens J M, Hohl, Daryl, Codron, Thomas M, Kaiser, Louise F, Martin, Dennis W H, Müller, Jean-Michel, Hatt, and Marcus, Clauss
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Teeth ,Physiology ,Digestive Physiology ,Mandible ,Molars ,Tooth Eruption ,Eating ,stomatognathic system ,Medicine and Health Sciences ,Maxilla ,Animals ,Dentition ,Musculoskeletal System ,Perissodactyla ,Skeleton ,Mouth ,Biology and Life Sciences ,Biomechanical Phenomena ,stomatognathic diseases ,Jaw ,Dentin ,Mastication ,Anatomy ,Physiological Processes ,Tooth ,Digestive System ,Head ,Research Article - Abstract
Feeding practice in herbivorous mammals can impact their dental wear, due to excessive or irregular abrasion. Previous studies indicated that browsing species display more wear when kept in zoos compared to natural habitats. Comparable analyses in tapirs do not exist, as their dental anatomy and chewing kinematics are assumed to prevent the use of macroscopic wear proxies such as mesowear. We aimed at describing tapir chewing, dental anatomy and wear, to develop a system allowing comparison of free-ranging and captive specimens even in the absence of known age. Video analyses suggest that in contrast to other perissodactyls, tapirs have an orthal (and no lateral) chewing movement. Analysing cheek teeth from 74 museum specimens, we quantified dental anatomy, determined the sequence of dental wear along the tooth row, and established several morphometric measures of wear. In doing so, we showcase that tapir maxillary teeth distinctively change their morphology during wear, developing a height differential between less worn buccal and more worn lingual cusps, and that quantitative wear corresponds to the eruption sequence. We demonstrate that mesowear scoring shows a stable signal during initial wear stages but results in a rather high mesowear score compared to other browsing herbivores. Zoo specimens had lesser or equal mesowear scores as specimens from the wild; additionally, for the same level of third molar wear, premolars and other molars of zoo specimens showed similar or less wear compared specimens from the wild. While this might be due to the traditional use of non-roughage diet items in zoo tapirs, these results indicate that in contrast to the situation in other browsers, excessive tooth wear appears to be no relevant concern in ex situ tapir management.
- Published
- 2020
24. Dust and grit matter: abrasives of different size lead to opposing dental microwear textures in experimentally fed sheep (Ovis aries)
- Author
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Nicole L. Ackermans, Louise F. Martin, Thomas M. Kaiser, Daniela E. Winkler, Marcus Clauss, Jean-Michel Hatt, and University of Zurich
- Subjects
0106 biological sciences ,Molar ,010506 paleontology ,10253 Department of Small Animals ,1109 Insect Science ,Physiology ,Evolution ,Ruminant ,Dental Wear ,Aquatic Science ,010603 evolutionary biology ,01 natural sciences ,Texture (geology) ,Microtexture ,Animal science ,Behavior and Systematics ,1312 Molecular Biology ,Animals ,Grit ,Ovis ,Molecular Biology ,Sheep, Domestic ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Feeding experiment ,biology ,630 Agriculture ,1104 Aquatic Science ,Ecology ,Chemistry ,Abrasive ,Tooth wear ,Dust ,1314 Physiology ,biology.organism_classification ,Abrasives ,Animal Feed ,Diet ,1105 Ecology, Evolution, Behavior and Systematics ,Insect Science ,570 Life sciences ,Particulate Matter ,Animal Science and Zoology ,1103 Animal Science and Zoology - Abstract
External abrasives ingested along with the herbivore diet are considered main contributors to dental wear, though how the different sizes and concentrations of these abrasives influence wear remains unclear. Dental microwear texture analysis (DMTA) is an established method for dietary reconstruction which describes a tooth9s surface topography on a micrometre scale. The method has yielded conflicting results as to the effect of external abrasives. In the present study, a feeding experiment was performed on sheep (Ovis aries) fed seven diets of different abrasiveness. Our aim was to discern the individual effects of size (4, 50 and 130 µm) and concentration (0%, 4% and 8% of dry matter) of abrasives on dental wear, applying DMTA to four tooth positions. Microwear textures differed between individual teeth, but surprisingly, showed no gradient along the molar tooth row, and the strongest differentiation of experimental groups was achieved when combining data of all maxillary molars. Overall, a pattern of increasing height, volume and complexity of the tooth9s microscopic surface appeared with increasing size of dietary abrasives, and when compared with the control, the small abrasive diets showed a polishing effect. The results indicate that the size of dietary abrasives is more important for dental microwear texture traces than their concentration, and that different sizes can have opposing effects on the dietary signal. The latter finding possibly explains conflicting evidence from previous experimental DMTA applications. Further exploration is required to understand whether and how microscopic traces created by abrasives translate quantitatively to tissue loss.
- Published
- 2020
25. Everything matters: Molar microwear texture in goats (Capra aegagrus hircus) fed diets of different abrasiveness
- Author
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Nicole L. Ackermans, Jessica Carlsson, Thomas M. Kaiser, Ellen Schulz-Kornas, Louise F. Martin, Dennis W. H. Müller, Marcus Clauss, Daniela E. Winkler, Jean-Michel Hatt, Jürgen Hummel, University of Zurich, and Clauss, Marcus
- Subjects
Molar ,010506 paleontology ,10253 Department of Small Animals ,Evolution ,Phytolith ,1904 Earth-Surface Processes ,Grazer ,Grit ,010502 geochemistry & geophysics ,Oceanography ,01 natural sciences ,Mesowear ,Animal science ,Behavior and Systematics ,Grazing ,1910 Oceanography ,media_common.cataloged_instance ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Earth-Surface Processes ,media_common ,2. Zero hunger ,Enamel paint ,biology ,630 Agriculture ,Ecology ,Palaeontology ,Tooth wear ,Paleontology ,Earth ,biology.organism_classification ,1911 Paleontology ,1105 Ecology, Evolution, Behavior and Systematics ,Texture analysis ,Connochaetes taurinus ,Surface Processes ,visual_art ,visual_art.visual_art_medium ,570 Life sciences ,Geology ,Giraffa camelopardalis - Abstract
There is an ongoing discourse about whether or not external abrasives influence the microscopic wear in herbivore teeth, including a statement that “dust does not matter”. We submitted the maxillary and mandibular second molar of 28 goats (Capra aegagrus hircus) to dental microwear texture analysis (DMTA). The study animals were divided into four groups, which received diets of increasing phytolith-based abrasiveness (L: lucerne based pellets, very low phytolith abrasion diet, acting as control; G: grass-based pellets, medium abrasive phytolith diet; GR: grass and rice husk pellets, high abrasion phytolith diet), or a diet with added external abrasives (GRS: the GR diet with addition of large-grained sand as source of external abrasives), for 6 months. Generally, the three diets without sand (L, G, GR) were ranked in the expected sequence by DMTA parameters. For some parameters, in particular those relating to area, complexity, peak sharpness and plateau size of the enamel surface, diet GRS differed from diet GR, whereas the two were not distinct in other parameters, mostly relating to direction, height or volume. Additionally, diets triggered different patterns on the maxillary or mandibular molar for several parameters. For some DMTA parameters, the range covered in the experimental goats corresponded to that observed in free-ranging browsing giraffe (Giraffa camelopardalis) and grazing wildebeest (Connochaetes taurinus), with goats receiving diet L resembling the giraffe, while the other diets G, GR and GRS more resembled the wildebeest. However, the previously reported mesowear in the goats did not cover the browser-grazer range, and DMTA measurements showed no correlation to the development of mesowear scores or measures of absolute tissue loss in the same animals. In summary, the results confirm DMTA measurements as generally recording properties related to both internal and external abrasives, but also indicate that our understanding of how DMTA characteristics actually originate, and how they relate to other proxies of dental wear, is still very limited.
- Published
- 2020
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26. Broad-scale morpho-functional traits of the mandible suggest no hard food adaptation in the hominin lineage
- Author
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Alexander Daasch, Jordi Marcé-Nogué, Thomas M. Kaiser, and Thomas A. Püschel
- Subjects
Primates ,0106 biological sciences ,0301 basic medicine ,Support Vector Machine ,Lineage (evolution) ,Biological anthropology ,Finite Element Analysis ,lcsh:Medicine ,Context (language use) ,Mandible ,Biology ,010603 evolutionary biology ,01 natural sciences ,Article ,03 medical and health sciences ,Animals ,Biomechanics ,lcsh:Science ,Clade ,Morphometrics ,Multidisciplinary ,Fossils ,lcsh:R ,Skull ,Hominidae ,Morpho ,biology.organism_classification ,Adaptation, Physiological ,Biological Evolution ,Diet ,030104 developmental biology ,Taxon ,Jaw ,Food ,Evolutionary biology ,Mastication ,Paranthropus ,lcsh:Q ,Adaptation - Abstract
An on-going debate concerning the dietary adaptations of archaic hominins and early Homo has been fuelled by contradictory inferences obtained using different methodologies. This work presents an extensive comparative sample of 30 extant primate species that was assembled to perform a morpho-functional comparison of these taxa with 12 models corresponding to eight fossil hominin species. Finite Element Analysis and Geometric Morphometrics were employed to analyse chewing biomechanics and mandible morphology to, firstly, establish the variation of this clade, secondly, relate stress and shape variables, and finally, to classify fossil individuals into broad ingesta related hardness categories using a support vector machine algorithm. Our results suggest that some hominins previously assigned as hard food consumers (e.g. the members of the Paranthropus clade) in fact seem to rely more strongly on soft foods, which is consistent with most recent studies using either microwear or stable isotope analyses. By analysing morphometric and stress results in the context of the comparative framework, we conclude that in the hominin clade there were probably no hard-food specialists. Nonetheless, the biomechanical ability to comminute harder items, if required as fallback option, adds to their strategy of increased flexibility.
- Published
- 2020
27. Shape, size, and quantity of ingested external abrasives influence dental microwear texture formation in guinea pigs
- Author
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Ellen Schulz-Kornas, Jacqueline Müller, Marcus Clauss, Jean-Michel Hatt, Jennifer Leichliter, Daniela E. Winkler, Thomas Tütken, Katrin Weber, Thomas M. Kaiser, and University of Zurich
- Subjects
0106 biological sciences ,10253 Department of Small Animals ,Guinea Pigs ,Dental Wear ,Mineral dust ,diet reconstruction ,010603 evolutionary biology ,01 natural sciences ,Texture (geology) ,Texture formation ,010104 statistics & probability ,chemistry.chemical_compound ,stomatognathic system ,Animals ,Herbivory ,Particle Size ,0101 mathematics ,Quartz ,grit ,2. Zero hunger ,1000 Multidisciplinary ,Multidisciplinary ,630 Agriculture ,Metallurgy ,Plants ,Biological Sciences ,Animal Feed ,Silicate ,Diet ,Tooth Abrasion ,chemistry ,Tooth wear ,tooth wear ,570 Life sciences ,biology ,Particle size ,dust ,feeding experiment - Abstract
Food processing wears down teeth, thus affecting tooth functionality and evolutionary success. Other than intrinsic silica phytoliths, extrinsic mineral dust/grit adhering to plants causes tooth wear in mammalian herbivores. Dental microwear texture analysis (DMTA) is widely applied to infer diet from microscopic dental wear traces. The relationship between external abrasives and dental microwear texture (DMT) formation remains elusive. Feeding experiments with sheep have shown negligible effects of dust-laden grass and browse, suggesting that intrinsic properties of plants are more important. Here, we explore the effect of clay- to sand-sized mineral abrasives (quartz, volcanic ash, loess, kaolin) on DMT in a controlled feeding experiment with guinea pigs. By adding 1, 4, 5, or 8% mineral abrasives to a pelleted base diet, we test for the effect of particle size, shape, and amount on DMT. Wear by fine-grained quartz (>5/ abrasive-free control diet. Fine silt-sized quartz (∼5 μm) results in higher surface anisotropy and lower roughness (polishing effect). Coarse-grained volcanic ash leads to significantly higher complexity, while fine sands (130 to 166 μm) result in significantly higher roughness. Complexity and roughness values exceed those from feeding experiments with guinea pigs who received plants with different phytolith content. Our results highlight that large (>95-μm) external silicate abrasives lead to distinct microscopic wear with higher roughness and complexity than caused bymineral abrasive-free herbivorous diets. Hence, high loads of mineral dust and grit in natural diets might be identified by DMTA, also in the fossil record.
- Published
- 2020
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28. New drugs: where did we go wrong and what can we do better?
- Author
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Thomas M. Kaiser, Natalie McGauran, and Beate Wieseler
- Subjects
Evidence-Based Medicine ,business.industry ,education ,General Medicine ,030204 cardiovascular system & hematology ,Public relations ,language.human_language ,Drug Costs ,German ,03 medical and health sciences ,0302 clinical medicine ,Drug development ,Drug Development ,Germany ,language ,Drug Evaluation ,Humans ,030212 general & internal medicine ,Business ,Drug Approval ,health care economics and organizations ,Healthcare system - Abstract
More than half of new drugs entering the German healthcare system have not been shown to add benefit. Beate Wieseler and colleagues argue that international drug development processes and policies are responsible and must be reformed
- Published
- 2019
29. Machine Learning Algorithms for Biological Targets: Investigating the Error Tolerance in Various Computational Methods
- Author
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Thomas M. Kaiser and Pieter B. Burger
- Abstract
Machine learning continues to make strident advances in the prediction of desired properties concerning drug development. Problematically, the efficacy of machine learning in these arenas is reliant upon highly accurate and abundant data. These two limitations, high accuracy and abundance, are often taken together; however, insight into the dataset accuracy limitation of contemporary machine learning algorithms may yield insight into whether non-bench experimental sources of data may be used to generate useful machine learning models where there is a paucity of experimental data. We took highly accurate data across six kinase types, one GPCR, one polymerase, a human protease, and HIV protease, and intentionally introduced error at varying population proportions in the datasets for each target. With the generated error in the data, we explored how the retrospective accuracy of a Naïve Bayes Network, a Random Forest Model, and a Probabilistic Neural Network model decayed as a function of error. Additionally, we explored the ability of a training dataset with an error profile resembling that produced by the Free Energy Perturbation method (FEP+) to generate machine learning models with useful retrospective capabilities. The categorical error tolerance was quite high for a Naïve Bayes Network algorithm averaging 39% error in the training set required to lose predictivity on the test set. Additionally, a Random Forest tolerated a significant degree of categorical error introduced into the training set with an average error of 29% required to lose predictivity. However, we found the Probabilistic Neural Network algorithm did not tolerate as much categorical error requiring an average of 20% error to lose predictivity. Finally, we found that a Naïve Bayes Network and a Random Forest could both use datasets with an error profile resembling that of FEP+. This work demonstrates that computational methods of known error distribution like FEP+ may be useful in generating machine learning models not based on extensive and expensive in vitro-generated datasets.
- Published
- 2019
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30. The Application in the Sensitization of Titania : Zinc Porphyrin-Functionalized Fullerenes as a Visible-Light Active Photocatalyst
- Author
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Thomas M. Kaiser and Danisha Maria Rivera-Nazario
- Abstract
Zinc porphyrin-functionalized fullerene [C60] derivatives have been synthesized and usedto prepare titania-based composites. The electrochemical properties and HOMO andLUMO levels of the photosensitizers were determined by electrochemical measurements.Raman and IR techniques were used to study chemical groups present on the titaniasurface. Absorption properties of the composites were measured in the solid state bydiffuse reflectance UV-Vis spectra (DRS).
- Published
- 2019
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31. Post-mortem alteration of diet-related enamel surface textures through artificial biostratinomy: A tumbling experiment using mammal teeth
- Author
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Thomas M. Kaiser, Daniela E. Winkler, Katrin Böhm, and Thomas Tütken
- Subjects
Abrasion (dental) ,010506 paleontology ,Mammal teeth ,Dental wear ,Mineralogy ,010502 geochemistry & geophysics ,Oceanography ,01 natural sciences ,Biostratinomy ,Capreolus ,stomatognathic system ,Surface roughness ,medicine ,Surface texture ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Earth-Surface Processes ,Diagenetic alteration ,biology ,Enamel paint ,Paleontology ,15. Life on land ,biology.organism_classification ,medicine.disease ,Equus ,Grain size ,Otomys ,Microwear ,visual_art ,visual_art.visual_art_medium ,Geology - Abstract
In the fossil record, teeth are often all that remains of a fossil organism. Dental microwear texture analysis (DMTA) is a common proxy for diet using dental wear features at the μm-scale, enabling comparative and quantitative assessments of various feeding traits in extant and extinct species. In extinct species, original diet-related dental wear features may be overprinted by post-mortem alteration including fluvial transport. Here we experimentally investigate the effects of mechanical alteration on diet-related 3D enamel surface texture (3DST) patterns of different mammal teeth. Post canine teeth of Equus sp., Capreolus capreolus and Otomys sp. are tumbled in sediment-water suspensions using three different grain size fractions of sand. The 3DST of the enamel surfaces are measured prior to and after each tumbling interval and characterised using ISO normed surface texture and SSFA parameters. In all species, we find several parameters to be almost unaffected by tumbling (stable parameters), while other parameters show inconsistent-directional shifts (unstable parameters). For Otomys, all three sediment grain size fractions result in abrasion of peaks and a reduction of overall surface roughness. For Equus, tumbling results in visible abrasive changes in the original wear patterns and the introduction of new wear features. Capreolus capreolus shows high variability in surface texture patterns prior to and after the experiment, hence we see ambiguous trends for changes in parameter values. However, even after 336 h of tumbling the browsing C. capreolus can still be distinguished from the grazing Equus sp. Thus, biostratinomy may potentially modify diet-related 3DST causing non-systematic bias via mechanical abrasion, which is related to sediment grain size, duration of transport and geometry of teeth. However, the original diet-related 3DST is still preserved and a more prominent characteristic in DMT than the experimentally induced diagenetic alteration.
- Published
- 2019
32. Dental wear proxy correlation in a long-term feeding experiment on sheep ( Ovis aries )
- Author
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Daniela E. Winkler, Ellen Schulz-Kornas, Marcus Clauss, Jean-Michel Hatt, Nicole L. Ackermans, Louise F. Martin, and Thomas M. Kaiser
- Subjects
0106 biological sciences ,Orthodontics ,Molar ,0303 health sciences ,Future studies ,biology ,Chemistry ,Dental Wear ,Biomedical Engineering ,Biophysics ,Bioengineering ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Biochemistry ,Mesowear ,Biomaterials ,Correlation ,03 medical and health sciences ,stomatognathic system ,Proxy (statistics) ,Mandibular molar ,Ovis ,030304 developmental biology ,Biotechnology - Abstract
Dietary reconstruction in vertebrates often relies on dental wear-based proxies. Although these proxies are widely applied, the contributions of physical and mechanical processes leading to meso- and microwear are still unclear. We tested their correlation using sheep ( Ovis aries , n = 39) fed diets of varying abrasiveness for 17 months as a model. Volumetric crown tissue loss, mesowear change and dental microwear texture analysis (DMTA) were all applied to the same teeth. We hereby correlate: (i) 46 DMTA parameters with each other, for the maxillary molars (M1, M2, M3), and the second mandibular molar (m2); (ii) 10 mesowear variables to each other and to DMTA for M1, M2, M3 and m2; and (iii) volumetric crown tissue loss to mesowear and DMTA for M2. As expected, many DMTA parameters correlated strongly with each other, supporting the application of reduced parameter sets in future studies. Correlation results showed only few DMTA parameters correlated with volumetric tissue change and even less so with mesowear variables, with no correlation between mesowear and volumetric tissue change. These findings caution against interpreting DMTA and mesowear patterns in terms of actual tissue removal until these dental wear processes can be better understood at microscopic and macroscopic levels.
- Published
- 2021
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33. Synthesis and Antiviral Activity of a Series of 2′-C-Methyl-4′-thionucleoside Monophosphate Prodrugs
- Author
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Dennis C. Liotta, Thomas M. Kaiser, and Zackery W. Dentmon
- Subjects
medicine.drug_class ,Stereochemistry ,viruses ,Pharmaceutical Science ,Protide ,010402 general chemistry ,01 natural sciences ,Analytical Chemistry ,lcsh:QD241-441 ,chemistry.chemical_compound ,antivirals ,lcsh:Organic chemistry ,prodrugs ,medicinal chemistry ,Drug Discovery ,medicine ,Physical and Theoretical Chemistry ,NS5B ,Nucleoside analogue ,010405 organic chemistry ,Chemistry ,Organic Chemistry ,virus diseases ,Phosphoramidate ,Prodrug ,digestive system diseases ,nucleotides ,0104 chemical sciences ,Thionucleosides ,Chemistry (miscellaneous) ,Molecular Medicine ,hepatitis C ,Antiviral drug ,Nucleoside ,nucleosides ,medicine.drug - Abstract
The NS5B RNA-dependent RNA polymerase of the hepatitis C virus (HCV) is a validated target for nucleoside antiviral drug therapy. We endeavored to synthesize and test a series of 4&prime, thionucleosides with a monophosphate prodrug moiety for their antiviral activity against HCV and other related viruses in the Flaviviridae family. Nucleoside analogs were prepared via the stereoselective Vorbrü, ggen glycosylation of various nucleobases with per-acetylated 2-C-methyl-4-thio-d-ribose built in a 10-step synthetic sequence from the corresponding ribonolactone. Conjugation of the thionucleoside to a ProTide phosphoramidate allowed for evaluation of the prodrugs in the cellular HCV replicon assay with anti-HCV activities ranging from single-digit micromolar (&mu, M) to >, 200 &mu, M. The diminished anti-HCV potency of our best compound compared to its 4&prime, oxo congener is the subject of ongoing research in our lab and is proposed to stem from changes in sugar geometry imparted by the larger sulfur atom.
- Published
- 2020
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34. Correction to 'Accelerated Discovery of Novel Ponatinib Analogs with Improved Properties for the Treatment of Parkinson’s Disease'
- Author
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Savita Sharma, Christopher E. Dalloul, Dennis C. Liotta, Thomas M. Kaiser, and Zackery W. Dentmon
- Subjects
Oncology ,medicine.medical_specialty ,Parkinson's disease ,business.industry ,Organic Chemistry ,Ponatinib ,medicine.disease ,Biochemistry ,chemistry.chemical_compound ,chemistry ,Internal medicine ,Drug Discovery ,medicine ,business - Published
- 2020
- Full Text
- View/download PDF
35. Root growth compensates for molar wear in adult goats (Capra aegagrus hircus)
- Author
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Nicole L, Ackermans, Marcus, Clauss, Daniela E, Winkler, Ellen, Schulz-Kornas, Thomas M, Kaiser, Dennis W H, Müller, Patrick R, Kircher, Jürgen, Hummel, and Jean-Michel, Hatt
- Subjects
Goats ,Animals ,Tooth Wear ,Animal Feed ,Molar - Abstract
One reason for the mammalian clade's success is the evolutionary diversity of their teeth. In herbivores, this is represented by high-crowned teeth evolved to compensate for wear caused by dietary abrasives like phytoliths and grit. Exactly how dietary abrasives wear teeth is still not understood completely. We fed four different pelleted diets of increasing abrasiveness (L: Lucerne; G: grass; GR: grass and rice husks; GRS: grass, rice husks, and sand) to four groups of a total of 28 adult goats, all with completely erupted third molars, over a six-month period. Tooth morphology was captured by medical computed tomography scans at the beginning and end of the controlled feeding experiment, and separation lines between the crown and root segments were defined in the upper right second molar (M2), to gauge absolute wear. Using bootstrapping, significant differences in volume loss between diets L/G and GR/GRS were detected. A small but nevertheless consistent volume gain was noted in the roots, and there was a significant, positive correlation between crown volume loss and root volume gain. This growth could possibly be attributed to the well-known process of cementum deposition and its relation with a putative feedback mechanism, in place to attenuate wear caused by abrasive diets.
- Published
- 2018
36. Why ruminating ungulates chew sloppily: Biomechanics discern a phylogenetic pattern
- Author
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Thomas M. Kaiser, Daniela E. Winkler, Zupeng Zhou, Josep Fortuny, and Jordi Marcé-Nogué
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0106 biological sciences ,Male ,Models, Anatomic ,Ungulate ,Science ,Finite Element Analysis ,Zoology ,Rhinoceros ,Mandible ,010603 evolutionary biology ,01 natural sciences ,biomechanics ,Ruminantia ,Bite Force ,Evolution, Molecular ,03 medical and health sciences ,Imaging, Three-Dimensional ,Species Specificity ,Animals ,Cluster Analysis ,Ruminating ,FEA ,Perissodactyla ,Phylogeny ,030304 developmental biology ,Artiodactyla ,functional morphology ,0303 health sciences ,Multidisciplinary ,biology ,Reproducibility of Results ,Ruminants ,biology.organism_classification ,Tylopoda ,Biomechanical Phenomena ,Diet ,Bite force quotient ,Phylogenetic Pattern ,Medicine ,Mastication ,Female ,Adaptation - Abstract
Altres ajuts: "Beatriu de Pinos" 2014 - BP-A 00048 There is considerable debate regarding whether mandibular morphology in ungulates primarily reflects phylogenetic affinities or adaptation to specific diet. In an effort to help resolve this debate, we use three-dimensional finite element analysis (FEA) to assess the biomechanical performance of mandibles in eleven ungulate taxa with well-established but distinct dietary preferences. We found notable differences in the magnitude and the distribution of von Mises stress between Artiodactyla and Perissodactyla, with the latter displaying lower overall stress values. Additionally, within the order Artiodactyla the suborders Ruminantia and Tylopoda showed further distinctive stress patterns. Our data suggest that a strong phylogenetic signal can be detected in biomechanical performance of the ungulate mandible. In general, Perissodactyla have stiffer mandibles than Artiodactyla. This difference is more evident between Perissodactyla and ruminant species. Perissodactyla likely rely more heavily on thoroughly chewing their food upon initial ingestion, which demands higher bite forces and greater stress resistance, while ruminants shift comminution to a later state (rumination) where less mechanical effort is required by the jaw to obtain sufficient disintegration. We therefore suggest that ruminants can afford to chew sloppily regardless of ingesta, while hindgut fermenters cannot. Additionally, our data support a secondary degree of adaptation towards specific diet. We find that mandibular morphologies reflect the masticatory demands of specific ingesta within the orders Artiodactyla and Perissodactyla. Of particular note, stress patterns in the white rhinoceros (C. simum) look more like those of a general grazer than like other rhinoceros' taxa. Similarly, the camelids (Tylopoda) appear to occupy an intermediate position in the stress patterns, which reflects the more ancestral ruminating system of the Tylopoda.
- Published
- 2018
37. Controlled feeding experiments with diets of different abrasiveness reveal slow development of mesowear signal in goats (
- Author
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Nicole L, Ackermans, Daniela E, Winkler, Ellen, Schulz-Kornas, Thomas M, Kaiser, Dennis W H, Müller, Patrick R, Kircher, Jürgen, Hummel, Marcus, Clauss, and Jean-Michel, Hatt
- Subjects
Goats ,Animals ,Female ,Tooth Wear ,Tomography, X-Ray Computed ,Animal Feed ,Tooth ,Diet - Abstract
Dental mesowear is applied as a proxy to determine the general diet of mammalian herbivores based on tooth-cusp shape and occlusal relief. Low, blunt cusps are considered typical of grazers and high, sharp cusps typical of browsers. However, how internal or external abrasives impact mesowear, and the time frame the wear signature takes to develop, still need to be explored. Four different pelleted diets of increasing abrasiveness (lucerne, grass, grass and rice husks, and grass, rice husks and sand) were fed to four groups of a total of 28 adult goats in a controlled feeding experiment over a 6-month period. Tooth morphology was captured by medical CT scans at the beginning and end of the experiment. These scans, as well as the crania obtained post mortem, were scored using the mesowear method. Comparisons between diet groups showed few significant differences after 6 months, irrespective of whether CT scans or the real teeth were scored. Only when assessing the difference in signal between the beginning and the end of the experiment did relevant, significant diet-specific effects emerge. Diets containing lower phytolith content caused a more pronounced change in mesowear towards sharper cusps/higher reliefs, while the feed containing sand did not result in more extreme changes in mesowear when compared with the same feed without sand. Our experiment suggests that the formation of a stable and hence reliable mesowear signal requires more time to develop than 6 months.
- Published
- 2018
38. Wie das Internet der Dinge neue Geschäftsmodelle ermöglicht
- Author
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Daniel Huber and Thomas M. Kaiser
- Abstract
Bis 2020 werden mehr als 50 Milliarden Gerate mit dem Internet verbunden sein. Mit Hilfe Cyber-Physikalischer Systeme und digitaler Zwillinge, die die reale mit der virtuellen Welt verbinden, konnen Prozesse automatisiert und wertvolle Erkenntnisse gewonnen werden. Dies ermoglicht neue Geschaftsmodelle auf Basis intelligenter Produkte und Dienstleistungen.
- Published
- 2015
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39. Methodological approach to determine minor, considerable, and major treatment effects in the early benefit assessment of new drugs
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Ralf Bender, Guido Skipka, Jürgen Windeler, Stefan Lange, Beate Wieseler, Thomas M. Kaiser, and Stefanie Thomas
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Magnitude of effects ,Statistics and Probability ,Biometry ,Drug Industry ,media_common.quotation_subject ,Early benefit assessment ,Context (language use) ,Risk Assessment ,03 medical and health sciences ,0302 clinical medicine ,Drug Therapy ,Statutory law ,Health care ,Humans ,Quality (business) ,030212 general & internal medicine ,Drug Approval ,media_common ,Actuarial science ,Operationalization ,business.industry ,030503 health policy & services ,AMNOG ,General Medicine ,Research Papers ,Clinical relevance ,restrict ,Value (economics) ,Government Regulation ,Business ,Statistics, Probability and Uncertainty ,0305 other medical science ,Monte Carlo Method ,Shifted hypotheses ,Research Paper ,Added benefit - Abstract
At the beginning of 2011, the early benefit assessment of new drugs was introduced in Germany with the Act on the Reform of the Market for Medicinal Products (AMNOG). The Federal Joint Committee (G‐BA) generally commissions the Institute for Quality and Efficiency in Health Care (IQWiG) with this type of assessment, which examines whether a new drug shows an added benefit (a positive patient‐relevant treatment effect) over the current standard therapy. IQWiG is required to assess the extent of added benefit on the basis of a dossier submitted by the pharmaceutical company responsible. In this context, IQWiG was faced with the task of developing a transparent and plausible approach for operationalizing how to determine the extent of added benefit. In the case of an added benefit, the law specifies three main extent categories (minor, considerable, major). To restrict value judgements to a minimum in the first stage of the assessment process, an explicit and abstract operationalization was needed. The present paper is limited to the situation of binary data (analysis of 2 × 2 tables), using the relative risk as an effect measure. For the treatment effect to be classified as a minor, considerable, or major added benefit, the methodological approach stipulates that the (two‐sided) 95% confidence interval of the effect must exceed a specified distance to the zero effect. In summary, we assume that our approach provides a robust, transparent, and thus predictable foundation to determine minor, considerable, and major treatment effects on binary outcomes in the early benefit assessment of new drugs in Germany. After a decision on the added benefit of a new drug by G‐BA, the classification of added benefit is used to inform pricing negotiations between the umbrella organization of statutory health insurance and the pharmaceutical companies.
- Published
- 2015
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- View/download PDF
40. Comparative analyses of tooth wear in free-ranging and captive wild equids
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Ellen Schulz-Kornas, J C Castell, Christoph Schwitzer, Thomas M. Kaiser, Marcus Clauss, Dennis W. H. Müller, and Lucy A. Taylor
- Subjects
0106 biological sciences ,Abrasion (dental) ,education.field_of_study ,040301 veterinary sciences ,business.industry ,Population ,Captivity ,Zoology ,Dentistry ,Rhinoceros ,04 agricultural and veterinary sciences ,General Medicine ,Biology ,medicine.disease ,010603 evolutionary biology ,01 natural sciences ,Mesowear ,0403 veterinary science ,stomatognathic system ,Tooth wear ,Cheek teeth ,Captive breeding ,medicine ,business ,education - Abstract
Reasons for performing study: Captive breeding has played a crucial role in the conservation of threatened equid species. Grazing ruminants and rhinoceros in captivity have less abrasion-dominated tooth wear than their free-ranging conspecifics, with potential negative consequences for their health. However, a similar study on wild equids in captivity is missing. Objectives: The aim was to establish if different tooth wear patterns are exhibited by free-ranging and captive equids. Study design: Cross-sectional study of museum specimens comparing free-ranging and captive equids. Methods: Dental casts of maxillary cheek teeth of 228 museum specimens (122 from free-ranging and 106 from captive individuals) of 7 wild equid species were analysed using the extended mesowear method. Although teeth showing specific abnormalities were not scored, the presence of focal overgrowths (hooks) of the rostral premolars (106, 206) was recorded. Results: Captive Equus ferus przewalskii, E. grevyi, E. hemionus, E. quagga boehmi and E. zebra hartmannae have less abrasion-dominated tooth wear on their premolars than their free-ranging conspecifics (P
- Published
- 2015
- Full Text
- View/download PDF
41. Design and Validation of FRESH, a Drug Discovery Paradigm Resting on Robust Chemical Synthesis
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Qi Shi, Zackery W. Dentmon, Claudiu T. Supuran, Thomas M. Kaiser, Daniela Vullo, James P. Snyder, and Mariangela Ceruso
- Subjects
Quantitative structure–activity relationship ,business.industry ,Computer science ,Drug discovery ,High-throughput screening ,Pipeline (computing) ,Organic Chemistry ,Modular design ,Biochemistry ,Combinatorial chemistry ,Fragment (logic) ,Fragment processing ,Drug Discovery ,Biochemical engineering ,business ,ADME - Abstract
A method capable of identifying novel synthetic targets for small molecule lead optimization has been developed. The FRESH (FRagment-based Exploitation of modular Synthesis by vHTS) approach relies on a multistep synthetic route to a target series of compounds devised by a close collaboration between synthetic and computational chemists. It combines compound library generation, quantitative structure-acitvity relationship construction, fragment processing, virtual high throughput screening and display of results within the Pipeline Pilot framework. Outcomes enumerate tailored selection of novel synthetic targets with improved potency and optimized physical properties for an emerging compound series. To validate the application of FRESH, three retrospective case studies have been performed to pinpoint reported potent analogues. One prospective case study was performed to demonstrate that FRESH is able to capture additional potent analogues.
- Published
- 2015
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- View/download PDF
42. Controlled feeding experiments with diets of different abrasiveness reveal slow development of mesowear signal in goats ( Capra aegagrus hircus )
- Author
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Dennis W. H. Müller, Thomas M. Kaiser, Nicole L. Ackermans, Ellen Schulz-Kornas, Jürgen Hummel, Patrick R Kircher, Marcus Clauss, Jean-Michel Hatt, Daniela E. Winkler, and University of Zurich
- Subjects
0106 biological sciences ,010506 paleontology ,10253 Department of Small Animals ,1109 Insect Science ,Evolution ,Physiology ,Capra aegagrus ,Aquatic Science ,General diet ,010603 evolutionary biology ,01 natural sciences ,Mesowear ,Animal science ,Time frame ,Behavior and Systematics ,stomatognathic system ,1312 Molecular Biology ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,2. Zero hunger ,Herbivore ,Crania ,630 Agriculture ,1104 Aquatic Science ,Ecology ,biology ,1314 Physiology ,biology.organism_classification ,Tooth morphology ,1105 Ecology, Evolution, Behavior and Systematics ,Tooth wear ,Insect Science ,11404 Department of Clinical Diagnostics and Services ,570 Life sciences ,Animal Science and Zoology ,1103 Animal Science and Zoology - Abstract
Dental mesowear is applied as a proxy to determine the general diet of mammalian herbivores based on tooth-cusp shape and occlusal relief. Low, blunt cusps are considered typical of grazers and high, sharp cusps typical of browsers. However, how internal or external abrasives impact mesowear, and the time frame the wear signature takes to develop, still need to be explored. Four different pelleted diets of increasing abrasiveness (lucerne, grass, grass and rice husks, and grass, rice husks and sand) were fed to four groups of a total of 28 adult goats in a controlled feeding experiment over a 6-month period. Tooth morphology was captured by medical CT scans at the beginning and end of the experiment. These scans, as well as the crania obtained post mortem, were scored using the mesowear method. Comparisons between diet groups showed few significant differences after 6 months, irrespective of whether CT scans or the real teeth were scored. Only when assessing the difference in signal between the beginning and the end of the experiment did relevant, significant diet-specific effects emerge. Diets containing lower phytolith content caused a more pronounced change in mesowear towards sharper cusps/higher reliefs, while the feed containing sand did not result in more extreme changes in mesowear when compared with the same feed without sand. Our experiment suggests that the formation of a stable and hence reliable mesowear signal requires more time to develop than 6 months.
- Published
- 2018
- Full Text
- View/download PDF
43. The Bioactive Protein-Ligand Conformation of GluN2C-Selective Positive Allosteric Modulators Bound to the NMDA Receptor
- Author
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Hirofumi Kusumoto, Eric J. Miller, Steven A. Kell, David S. Menaldino, Bryan Cox, Stephen F. Traynelis, Pieter B. Burger, Dennis C. Liotta, Gil Shaulsky, Katie L. Strong, Matthew P. Epplin, Subhrajit Bhattacharya, and Thomas M. Kaiser
- Subjects
0301 basic medicine ,Agonist ,Models, Molecular ,Magnetic Resonance Spectroscopy ,Patch-Clamp Techniques ,medicine.drug_class ,Protein Conformation ,Proton Magnetic Resonance Spectroscopy ,Allosteric regulation ,Molecular Dynamics Simulation ,Ligands ,Receptors, N-Methyl-D-Aspartate ,03 medical and health sciences ,Xenopus laevis ,Allosteric Regulation ,medicine ,Animals ,Homology modeling ,Excitatory Amino Acid Agents ,Binding site ,Receptor ,Pharmacology ,Binding Sites ,Chemistry ,Reproducibility of Results ,Long-term potentiation ,Stereoisomerism ,Articles ,030104 developmental biology ,Biophysics ,Molecular Medicine ,NMDA receptor ,Binding domain - Abstract
N-methyl-d-aspartate (NMDA) receptors are ligand-gated, cation-selective channels that mediate a slow component of excitatory synaptic transmission. Subunit-selective positive allosteric modulators of NMDA receptor function have therapeutically relevant effects on multiple processes in the brain. A series of pyrrolidinones, such as PYD-106, that selectively potentiate NMDA receptors that contain the GluN2C subunit have structural determinants of activity that reside between the GluN2C amino terminal domain and the GluN2C agonist binding domain, suggesting a unique site of action. Here we use molecular biology and homology modeling to identify residues that line a candidate binding pocket for GluN2C-selective pyrrolidinones. We also show that occupancy of only one site in diheteromeric receptors is required for potentiation. Both GluN2A and GluN2B can dominate the sensitivity of triheteromeric receptors to eliminate the actions of pyrrolidinones, thus rendering this series uniquely sensitive to subunit stoichiometry. We experimentally identified NMR-derived conformers in solution, which combined with molecular modeling allows the prediction of the bioactive binding pose for this series of GluN2C-selective positive allosteric modulators of NMDA receptors. These data advance our understanding of the site and nature of the ligand-protein interaction for GluN2C-selective positive allosteric modulators for NMDA receptors.
- Published
- 2017
44. A biomechanical approach to understand the ecomorphological relationship between primate mandibles and diet
- Author
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Thomas M. Kaiser, Thomas A. Püschel, and Jordi Marcé-Nogué
- Subjects
Primates ,0106 biological sciences ,0301 basic medicine ,Molar ,Science ,Dentistry ,Mandible ,010603 evolutionary biology ,01 natural sciences ,Article ,03 medical and health sciences ,stomatognathic system ,biology.animal ,Premolar ,medicine ,Animals ,Primate ,General ,Orthodontics ,Multidisciplinary ,biology ,business.industry ,Feeding Behavior ,Biomechanical Phenomena ,Diet ,030104 developmental biology ,medicine.anatomical_structure ,Medicine ,ORDER PRIMATES ,business - Abstract
The relationship between primate mandibular form and diet has been previously analysed by applying a wide array of techniques and approaches. Nonetheless, most of these studies compared few species and/or infrequently aimed to elucidate function based on an explicit biomechanical framework. In this study, we generated and analysed 31 Finite Element planar models of different primate jaws under different loading scenarios (incisive, canine, premolar and molar bites) to test the hypothesis that there are significant differences in mandibular biomechanical performance due to food categories and/or food hardness. The obtained stress values show that in primates, hard food eaters have stiffer mandibles when compared to those that rely on softer diets. In addition, we find that folivores species have the weakest jaws, whilst omnivores have the strongest mandibles within the order Primates. These results are highly relevant because they show that there is a strong association between mandibular biomechanical performance, mandibular form, food hardness and diet categories and that these associations can be studied using biomechanical techniques rather than focusing solely on morphology.
- Published
- 2017
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45. Multiproxy dietary trait reconstruction in Pleistocene Hippopotamidae from the Mediterranean islands
- Author
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Elehna Bethune, Thomas M. Kaiser, Ellen Schulz-Kornas, and Daniela E. Winkler
- Subjects
Ecological niche ,010506 paleontology ,biology ,Ecology ,Hippopotamus creutzburgi ,Paleontology ,15. Life on land ,010502 geochemistry & geophysics ,Oceanography ,biology.organism_classification ,01 natural sciences ,Hippopotamus amphibius ,Hippopotamidae ,biology.animal ,Hippopotamus pentlandi ,Hypsodont ,Paleoecology ,Hippopotamus melitensis ,14. Life underwater ,Ecology, Evolution, Behavior and Systematics ,Geology ,0105 earth and related environmental sciences ,Earth-Surface Processes - Abstract
Geographically isolated insular species face energetic restrictions and commonly evolve adaptations that distinguish them from their mainland ancestors. During the Pleistocene, several Mediterranean islands were inhabited by now extinct Hippopotamidae. They underwent diverse changes in locomotion, dentition and body size. Based on these differences, it is supposed that they occupied different ecological niches depending on their respective faunal complexes and available resources. In this paper, we assess the paleoecology of dwarfed hippopotami from Crete, Malta, Sicily and Cyprus using a novel dental multiproxy approach. We applied dental topography analysis (SAGA-GIS) to measure the mean slope of the dental occlusal surface, mirroring dietary adaptations, as well as 3D surface texture analysis (3DST) to quantify the surface of occlusal wear facets, which correlate with dietary abrasiveness. Low slope values were found in the larger, more hypsodont hippopotami, whilst the smaller Phanourios minor displayed the highest occlusal relief with large compression basins. Since Hippopotamus pentlandi exhibited lower mean slope values than the larger, more hypsodont Hippopotamus amphibius, we conclude that lower occlusal reliefs reflect adaptations to lower diet quality and arid environments, which are characteristic of freshwater-limited island habitats. The 3DST analysis revealed distinct ecological niches for the investigated insular hippos. Hippopotamus creutzburgi exhibited enamel surface textures analogous to those of Hippopotamus amphibius, a fresh grass grazer, thus confirming a semiaquatic lifestyle at the upland lake at Katharo, Crete. Hippopotamus pentlandi was bound to a similar niche to the extant form, probably due to the mainland character of its fauna, but experienced more dust intake. Hippopotamus melitensis had to cope with high ingestion of abrasives, seemingly on account of a more generalistic diet in its resource-limited and small habitat. Results point to either Phanourios minor broadening its dietary niche in its almost competition-free habitat, or suggest a dietary shift following a climatic change. The adopted multiproxy approach proved to be useful in identifying dental adaptations and individual foraging strategies linked to energetically restricted habitats, and therefore contributes to a better understanding of basic evolutionary and ecological principles.
- Published
- 2019
- Full Text
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46. Error Tolerance of Machine Learning Algorithms across Contemporary Biological Targets
- Author
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Pieter B. Burger and Thomas M. Kaiser
- Subjects
Computer science ,Pharmaceutical Science ,computer.software_genre ,Workflow ,Analytical Chemistry ,Probabilistic neural network ,0302 clinical medicine ,Drug Discovery ,Molecular Targeted Therapy ,0303 health sciences ,education.field_of_study ,Artificial neural network ,cheminformatics ,Naïve Bayes Network ,error ,Random forest ,machine learning ,Chemistry (miscellaneous) ,Cheminformatics ,030220 oncology & carcinogenesis ,Molecular Medicine ,Algorithm ,Algorithms ,Population ,Neural Network ,Antineoplastic Agents ,Machine learning ,Models, Biological ,Article ,lcsh:QD241-441 ,03 medical and health sciences ,Naive Bayes classifier ,lcsh:Organic chemistry ,Biomarkers, Tumor ,Humans ,Physical and Theoretical Chemistry ,education ,Categorical variable ,030304 developmental biology ,Random Forest ,business.industry ,Organic Chemistry ,Reproducibility of Results ,Bayes Theorem ,FEP ,ROC Curve ,anaplastic lymphoma kinase (ALK) ,Test set ,Neural Networks, Computer ,Artificial intelligence ,business ,computer - Abstract
Machine learning continues to make strident advances in the prediction of desired properties concerning drug development. Problematically, the efficacy of machine learning in these arenas is reliant upon highly accurate and abundant data. These two limitations, high accuracy and abundance, are often taken together, however, insight into the dataset accuracy limitation of contemporary machine learning algorithms may yield insight into whether non-bench experimental sources of data may be used to generate useful machine learning models where there is a paucity of experimental data. We took highly accurate data across six kinase types, one GPCR, one polymerase, a human protease, and HIV protease, and intentionally introduced error at varying population proportions in the datasets for each target. With the generated error in the data, we explored how the retrospective accuracy of a Naï, ve Bayes Network, a Random Forest Model, and a Probabilistic Neural Network model decayed as a function of error. Additionally, we explored the ability of a training dataset with an error profile resembling that produced by the Free Energy Perturbation method (FEP+) to generate machine learning models with useful retrospective capabilities. The categorical error tolerance was quite high for a Naï, ve Bayes Network algorithm averaging 39% error in the training set required to lose predictivity on the test set. Additionally, a Random Forest tolerated a significant degree of categorical error introduced into the training set with an average error of 29% required to lose predictivity. However, we found the Probabilistic Neural Network algorithm did not tolerate as much categorical error requiring an average of 20% error to lose predictivity. Finally, we found that a Naï, ve Bayes Network and a Random Forest could both use datasets with an error profile resembling that of FEP+. This work demonstrates that computational methods of known error distribution like FEP+ may be useful in generating machine learning models not based on extensive and expensive in vitro-generated datasets.
- Published
- 2019
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47. Dietary divergence in space and time – Lessons from the dwarf-goat Myotragus balearicus (Pleisto-Holocene, Mallorca, Spain)
- Author
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Ivan Calandra, Christina Landwehr, Juan-Pablo Gailer, Thomas M. Kaiser, Ellen Schulz, Daniela E. Winkler, Lars W. van den Hoek Ostende, Biozentrum Grindel und Zoologisches Museum, Universität Hamburg ( UHH ), Netherlands Centre for Biodiversity Naturalis, Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Research supported by the 'Deutsche Forschungsgemeinschaft' (DFG, German Research Foundation, KA 1525/8-1), and AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université de Bourgogne ( UB ) -Centre National de la Recherche Scientifique ( CNRS )
- Subjects
Ecological niche ,Candiacervus ,biology ,Tooth morphology ,Ecology ,Hoplitomeryx ,Island evolution ,Niche differentiation ,biology.organism_classification ,Myotragus ,Diet ,Bovids ,Habitat ,Animal ecology ,Adaptive radiation ,Animal Science and Zoology ,Surface texture ,Ecology, Evolution, Behavior and Systematics ,[ SDU.STU.PG ] Sciences of the Universe [physics]/Earth Sciences/Paleontology - Abstract
8 pages; International audience; Newly colonised, isolated habitats, like islands, provide diverse niches to be filled and are prone to facilitate ecological separation which might lead to an adaptive radiation. Examples of such radiations can be found in the Mediterranean for the genera Candiacervus (Crete), Nesogoral (Sardinia) and Hoplitomeryx (Gargano). A different strategy to cope with limited resources on islands is generalism. We test whether populations of the endemic bovid Myotragus balearicus from two sites and Pleistocene as well as Holocene levels on Mallorca island displays ecological separation indicated by diet, or whether the species shifted its dietary trait towards generalism. We expect to find either: (1) dietary divergence in space and time (between sites and stratigraphic levels), which would indicate niche partitioning and/or a shift in dietary traits due to environmental influences; or (2) dietary congruence in a less specialised, generalistic dietary strategy in space and time which would indicate a flexible trait to cope with instable resource availability. We compare individuals from a fossil assemblage at a northern site and one assemblage from the eastern coast in terms of their dietary traits. Traits are reconstructed using dental dietary proxies, complementary in time scale and resolution. (1) 3D-dental topometry and (2) enamel surface texture analysis. Data suggest that individuals from both assemblages of M. balearicus behaved as variable browse dominated intermediate feeders. We thus conclude that the observed variability relates to a shift towards generalism as a subsistence strategy. We consider hypsodonty the pre-adaptation for this life style that enabled M. balearicus to exploit almost any food source in its energetically restricted island habitat.
- Published
- 2013
- Full Text
- View/download PDF
48. Regiochemistry Discoveries in the Use of Isoxazole as a Handle for the Rapid Construction of an All-Carbon Macrocyclic Precursor in the Synthetic Studies of Celastrol
- Author
-
Thomas M. Kaiser, Jiong Yang, and Jinhua Huang
- Subjects
chemistry.chemical_classification ,Nitrile ,Enyne ,Chemistry ,Stereochemistry ,Organic Chemistry ,Alkyne ,Regioselectivity ,Hydrogen Bonding ,Stereoisomerism ,Isoxazoles ,Catalysis ,Triterpenes ,Cycloaddition ,chemistry.chemical_compound ,Cyclization ,Alkynes ,Nitriles ,Moiety ,Isoxazole ,Pentacyclic Triterpenes ,Isomerization - Abstract
We have developed a convergent synthetic route to an all-carbon, 14-membered Z,E-macrocyclic bis-enone during our synthetic study of celastrol. The 1,3-dipolar cycloaddition of nitrile oxide and alkyne was employed for fragment coupling and introducing the 1,3-diketone moiety masked in the form of an isoxazole. We discovered that cycloaddition of the nitrile oxide and the enyne gave the rare 3,4-disubstituted isoxazole adduct under kinetic reaction conditions. The cycloaddition was found to be reversible, and the thermodynamic 3,5-disubstituted isoxazole could be obtained by isomerization of its 3,4-disubstituted isomer under elevated temperature. Our mechanistic studies support the role of hydrogen bonding in accelerating the isomerization. Consistent with our previous studies, the Z,E-macrocyclic bis-enone was found to be inactive toward the transannular bis-Michael reaction under the conditions evaluated.
- Published
- 2013
- Full Text
- View/download PDF
49. Catalytic Enantioconvergent Decarboxylative Allylic Alkylation of Allyl Indolenin-3-carboxylates
- Author
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Jiong Yang and Thomas M. Kaiser
- Subjects
Tsuji–Trost reaction ,Chemistry ,Organic Chemistry ,Enantioselective synthesis ,Organic chemistry ,chemistry.chemical_element ,Boranes ,Physical and Theoretical Chemistry ,Chirality (chemistry) ,Catalysis ,Quaternary carbon ,Palladium - Abstract
A catalytic enantioconvergent process has been developed for the conversion of racemic allyl indolenin-3-carboxylates into enantiomerically enriched C3-quaternary indolenines. A Pd-catalyzed decarboxylative allylic alkylation reaction was employed for both stereoablation of the racemic allyl indolenin-3-carboxylates and enantioselective formation of the quaternary carbon center.
- Published
- 2013
- Full Text
- View/download PDF
50. Modular Wear Facet Nomenclature for mammalian post-canine dentitions
- Author
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Ottmar Kullmer, Ulrike Menz, Irina Ruf, Thomas Martin, Karl-Heinz Südekum, Thomas M. Kaiser, Daniela E. Winkler, Julia A. Schultz, Wighart von Koenigswald, Sandra Engels, Daniela C. Kalthoff, and Ellen Schulz-Kornas
- Subjects
0106 biological sciences ,Orthodontics ,Molar ,musculoskeletal diseases ,010506 paleontology ,Facet (geometry) ,business.industry ,Dental Wear ,musculoskeletal system ,010603 evolutionary biology ,01 natural sciences ,Masticatory force ,antagonist ,crown surface ,dental wear ,functional units ,Occlusion ,stomatognathic diseases ,stomatognathic system ,Occlusal surface ,Medicine ,General Agricultural and Biological Sciences ,business ,Mastication ,0105 earth and related environmental sciences - Abstract
Dental wear facets on the occlusal surface of premolars and molars are traces of their main function, the mastication and therefore reflect masticatory movements and also paramasticatory (i.e. non-dietary use of teeth) behavior. Here we present the Modular Wear Facet Nomenclature applicable to most mammalian dentitions. Topographic positions of wear facets in relation to the major cusps and crests of the teeth are used to designate the areas of the occlusal surface the facets occupy (e.g. their mesial, distal, lingual, or buccal position). Previous published systems for labeling wear facets have been inconsistent with each other. Therefore, we provide a synoptic review of the most widely-used terminologies, and introduce the alternative Modular Wear Facet Nomenclature. This nomenclature aims to overcome the difficulties caused by the existing inconsistent wear facet terminologies. Our new approach is applicable to dentitions where the occlusal morphology does not change significantly for most of the lifetime of the animal. In those dentitions, the primary occlusal surfaces are not significantly modified as wear facets become more extensive with wearing. This appears to be a common pattern in pre-tribosphenic, tribosphenic molars, and the teeth derived from tribosphenic precursors (e.g. bunodont molar morphologies). In teeth where the secondary occlusal surface is functionally intensely modified (i.e. high-crowned and evergrowing teeth with large areas of dentine exposed) any facet labeling system appears to be challenging, since the identification of individual facets is blurred and their spatial position may be indeterminable.
- Published
- 2017
- Full Text
- View/download PDF
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