9 results on '"Karim TS"'
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2. An image dataset of cleared, x-rayed, and fossil leaves vetted to plant family for human and machine learning.
- Author
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Wilf P, Wing SL, Meyer HW, Rose JA, Saha R, Serre T, Cúneo NR, Donovan MP, Erwin DM, Gandolfo MA, González-Akre E, Herrera F, Hu S, Iglesias A, Johnson KR, Karim TS, and Zou X
- Abstract
Leaves are the most abundant and visible plant organ, both in the modern world and the fossil record. Identifying foliage to the correct plant family based on leaf architecture is a fundamental botanical skill that is also critical for isolated fossil leaves, which often, especially in the Cenozoic, represent extinct genera and species from extant families. Resources focused on leaf identification are remarkably scarce; however, the situation has improved due to the recent proliferation of digitized herbarium material, live-plant identification applications, and online collections of cleared and fossil leaf images. Nevertheless, the need remains for a specialized image dataset for comparative leaf architecture. We address this gap by assembling an open-access database of 30,252 images of vouchered leaf specimens vetted to family level, primarily of angiosperms, including 26,176 images of cleared and x-rayed leaves representing 354 families and 4,076 of fossil leaves from 48 families. The images maintain original resolution, have user-friendly filenames, and are vetted using APG and modern paleobotanical standards. The cleared and x-rayed leaves include the Jack A. Wolfe and Leo J. Hickey contributions to the National Cleared Leaf Collection and a collection of high-resolution scanned x-ray negatives, housed in the Division of Paleobotany, Department of Paleobiology, Smithsonian National Museum of Natural History, Washington D.C.; and the Daniel I. Axelrod Cleared Leaf Collection, housed at the University of California Museum of Paleontology, Berkeley. The fossil images include a sampling of Late Cretaceous to Eocene paleobotanical sites from the Western Hemisphere held at numerous institutions, especially from Florissant Fossil Beds National Monument (late Eocene, Colorado), as well as several other localities from the Late Cretaceous to Eocene of the Western USA and the early Paleogene of Colombia and southern Argentina. The dataset facilitates new research and education opportunities in paleobotany, comparative leaf architecture, systematics, and machine learning.
- Published
- 2021
- Full Text
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3. Utility of Zwolle Risk Score in Guiding Low-Risk STEMI Discharge.
- Author
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Lim TW, Karim TS, Fernando M, Haydar J, Lightowler R, Yip B, Sriamareswaran R, Tong DC, and Layland J
- Subjects
- Female, Humans, Male, Middle Aged, Patient Discharge, Risk Assessment, Risk Factors, Time Factors, Treatment Outcome, Percutaneous Coronary Intervention, ST Elevation Myocardial Infarction diagnosis, ST Elevation Myocardial Infarction surgery
- Abstract
Background: Despite emerging evidence suggesting that selected patients presenting with ST-segment elevation myocardial infarction (STEMI) treated successfully with primary percutaneous coronary intervention (PPCI) may be considered for early discharge, STEMI patients are typically hospitalised longer to monitor for serious complications., Methods: We assessed the feasibility of identifying low-risk STEMI patients in our institution for early discharge using the Zwolle risk score (ZRS). We evaluated consecutive STEMI patients who underwent successful PPCI within the period 1 January 2016 to 31 December 2017. Low-risk was defined as ZRS≤3. Demographic, angiographic characteristics, length of stay (LOS), and 30-day major adverse cardiovascular events (MACE) defined as cardiac death, stroke, congestive cardiac failure, and non-fatal myocardial infarction, were recorded., Results: There were 183 STEMI patients in our study cohort (mean age 62.0±12.2 years, 77.0% male). The median ZRS was 2 (interquartile range 1-4) with 132 (72.1%) patients classified as low-risk. The overall 30-day MACE and mortality rates were 10.4% and 3.3% respectively. None of the 35 (26.5%) low-risk patients who were discharged within 72 hours experienced MACE at 30 days. Low-risk STEMI patients had significantly shorter median LOS (86.3 vs. 93.2 hours, p=0.002), lower 30-day MACE (4.5% vs. 25.5%, p<0.0001) and mortality (0% vs. 11.8%, p<0.0001) compared to high-risk group (ZRS>3). Receiver operating characteristic (ROC) curve analyses for ZRS in predicting 30-day MACE and mortality yielded C-statistics of 0.79 (95%CI 0.68-0.90, p<0.0001) and 0.98 (95%CI 0.95-1.00, p<0.0001) respectively., Conclusion: Low-risk STEMI patients stratified by Zwolle risk score, who were treated successfully with PPCI, experienced low 30-day MACE and mortality rates, indicating that early discharge may be safe in these patients. Larger studies are warranted to evaluate the safety of ZRS-guided early discharge of STEMI patients, as well as the economic and psychological impacts., (Copyright © 2020 Australian and New Zealand Society of Cardiac and Thoracic Surgeons (ANZSCTS) and the Cardiac Society of Australia and New Zealand (CSANZ). Published by Elsevier B.V. All rights reserved.)
- Published
- 2021
- Full Text
- View/download PDF
4. Atlanticalymene, a new genus of Middle Ordovician (Darriwilian) calymenine trilobites, and revision of the calymenoidean genus Protocalymene Ross.
- Author
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Adrain JM, Karim TS, and McADAMS NEB
- Subjects
- Animals, Environment, Invertebrates, Fossils
- Abstract
Middle Ordovician (Darriwilian) species representing early Laurentian occurrences of the Subfamily Calymeninae Milne Edwards, 1840 (=Flexicalymeninae Siveter, 1977) are assigned to Atlanticalymene n. gen. (type species: A. bardensis n. sp. from the Table Cove Formation, western Newfoundland, Canada). They have routinely been confused with the older (Dapingian) calymenoidean taxon Protocalymene Ross, 1967. Revision of the type species of Protocalymene, P. mcallisteri Ross, 1967, from the Antelope Valley Formation, Funeral Mountains, California, indicates that it is not a calymenine, and that while it is clearly a calymenoidean its close affinity is otherwise difficult to determine. A single genuine calymenine species is known from the Laurentian Dapingian, and revised here as "Calymeninae n. gen.? n. sp. A" from the Antelope Valley Formation, Nevada, USA. A species from the Dapingian of Tarim, known from a single partial cranidium, appears to represent an older, extra-Laurentian species of Atlanticalymene.
- Published
- 2020
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5. Revision of the Early Ordovician (late Tremadocian; Stairsian) cheirurid trilobite Tesselacauda Ross, with species from the Great Basin, western USA.
- Author
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Adrain JM and Karim TS
- Subjects
- Animals, Idaho, Utah, Arthropods, Fossils
- Abstract
The Stairsian genus Tesselacauda Ross, 1951, has historically included two species, the poorly known type, T. depressa Ross, 1951 (Bearriverops loganensis Zone), and the even less well known T. flabella Kobayashi, 1955 (Bearriverops alsacharovi Zone), which may not belong to the genus. The family assignment of the genus has long been in question, with some workers assigning it to Cheiruridae and some to Pliomeridae. New field collections from western Utah and southeastern Idaho yield abundant material of T. depressa, which facilitates revision on the basis of multiple specimens of most exoskeletal parts. Two additional well known species are proposed, T. morrisoni (Rossaspis leboni Zone), and T. kriegerae (Bearriverops alsacharovi Zone). A third new species, very similar to T. depressa, is described in open nomenclature from the Rossaspis leboni Zone. Knowledge of hypostomes from silicified material helps to clarify the basal morphologies of cheirurid versus pliomerid trilobites. Pliomerids have anteroposteriorly elongate hypostomes with a basic pattern of three pairs of lateral hypostomal spines and a single posteromedian spine. Some or all of the spines are reduced or lost in various taxa. Cheirurids either lack paired spines or have only one or two pairs, and never have a posteromedian spine. Cheirurid hypostomes tend to be much shorter and more subquadrate than pliomerids. Other differences between the families are: a small, triangular or trapezoidal rostral plate in pliomerids versus a wide, short plate in cheirurids; a thoracic segment count commonly of 11-13 in Cheiruridae (fewer in one derived subfamily) versus commonly 15 or more in pliomerids (fewer in two derived subfamilies); thoracic pleurae with subequal bands and a prominent furrow in cheirurids versus a much more inflated and rib-like posterior band, reduced anterior band, and short, anteriorly placed furrow; and pygidia with four or fewer segments in cheirurids versus commonly five in pliomerids (again, fewer in two derived subfamilies). On these and other criteria, Tesselacauda is clearly a cheirurid, assigned for the present to the presumptively basal and possibly paraphyletic Subfamily Pilekiinae.
- Published
- 2019
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6. The pliomerid trilobite Ibexaspis and related new genera, with species from the Early Ordovician (Floian; Tulean, Blackhillsian) of the Great Basin, western USA.
- Author
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Mcadams NEB, Adrain JM, and Karim TS
- Subjects
- Animals, Fossils, Idaho, Nevada, Utah, Phylogeny
- Abstract
Field-based revision and phylogenetic analysis demonstrate that the pliomerid trilobite taxon Ibexaspis Přibyl and Vaněk (in Přibyl et al., 1985), previously known from a single formally named species (I. brevis [Young, 1973]), belongs to a complex of 14 mostly newly discovered, related species from the Early Ordovician (Floian; Tulean and Blackhillsian) of the northern Laurentian margin. The species are known from silicified samples recovered from sections in eastern Nevada, western Utah, and southeastern Idaho. The stratigraphically early Tuleaspis n. gen. (type species: T. jeneki n. sp.; Tulean; low Protopliomerella contracta Zone) includes its type and two species described in open nomenclature. Tuleaspis is sister to the remainder of the clade. Ibexaspis now includes three additional species: I. coadyi n. sp. (Blackhillsian; Carolinites nevadensis Zone), I. leuppi n. sp. (Blackhillsian; Presbynileus ibexensis Zone), and I. rupauli n. sp. (Blackhillsian; "Pseudocybele nasuta Zone"). Ibexapsis is sister to a clade of Millardaspis n. gen. + Deltapliomera n. gen. Millardaspis (type species M. milsteadi n. sp.; Tulean; Heckethornia hyndeae Zone) also includes M. knoxi n. sp. (Tulean; Panisaspis sevierensis Zone). Deltapliomera (type species D. humphriesi n. sp.; Blackhillsian, Carolinites nevadensis Zone) also includes D. inglei n. sp. (Tulean; Heckethornia bowiei Zone), D. heimbergi (Tulean; Panisaspis sevierensis Zone), D. eppersoni n. sp. (Blackhillsian; Bathyurina plicolabeona Zone), and a species described in open nomenclature.
- Published
- 2018
- Full Text
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7. Probing the global kinome and phosphoproteome in Chlamydomonas reinhardtii via sequential enrichment and quantitative proteomics.
- Author
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Werth EG, McConnell EW, Gilbert TS, Couso Lianez I, Perez CA, Manley CK, Graves LM, Umen JG, and Hicks LM
- Subjects
- Cell Wall chemistry, Chemical Fractionation, Mass Spectrometry methods, Phosphoproteins analysis, Plant Proteins analysis, Plant Proteins isolation & purification, Protein Kinases analysis, Reproducibility of Results, Chlamydomonas reinhardtii metabolism, Phosphoproteins metabolism, Plant Proteins metabolism, Protein Kinases metabolism, Proteomics methods
- Abstract
The identification of dynamic protein phosphorylation events is critical for understanding kinase/phosphatase-regulated signaling pathways. To date, protein phosphorylation and kinase expression have been examined independently in photosynthetic organisms. Here we present a method to study the global kinome and phosphoproteome in tandem in a model photosynthetic organism, the alga Chlamydomonas reinhardtii (Chlamydomonas), using mass spectrometry-based label-free proteomics. A dual enrichment strategy targets intact protein kinases via capture on immobilized multiplexed inhibitor beads with subsequent proteolytic digestion of unbound proteins and peptide-based phosphorylation enrichment. To increase depth of coverage, both data-dependent and data-independent (via SWATH, Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) mass spectrometric acquisitions were performed to obtain a more than 50% increase in coverage of the enriched Chlamydomonas kinome over coverage found with no enrichment. The quantitative phosphoproteomic dataset yielded 2250 phosphopeptides and 1314 localized phosphosites with excellent reproducibility across biological replicates (90% of quantified sites with coefficient of variation below 11%). This approach enables simultaneous investigation of kinases and phosphorylation events at the global level to facilitate understanding of kinase networks and their influence in cell signaling events., (© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.)
- Published
- 2017
- Full Text
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8. Origin of origami cockroach reveals long-lasting (11 Ma) phenotype instability following viviparity.
- Author
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Vršanský PV, Šmídová L, Valaška D, Barna P, Vidlička Ľ, Takáč P, Pavlik L, Kúdelová T, Karim TS, Zelagin D, and Smith D
- Subjects
- Adaptation, Physiological physiology, Animals, Cockroaches anatomy & histology, Cockroaches classification, Biological Evolution, Cockroaches physiology, Phenotype, Viviparity, Nonmammalian physiology
- Abstract
Viviparity evolved in bacteria, plants, ˃141 vertebrate lineages (ichthyosaurs, lizards, fishes, mammals, and others), and in 11 of 44 insect orders. Live-birth cockroaches preserved with brood sac (3D recovered two times optically) included Diploptera vladimir, Diploptera savba, Diploptera gemini spp.n., D. sp.1-2, and Stegoblatta irmgardgroehni from Green River, Colorado; Quilchena, Republic; McAbee, Canada; and Baltic amber, Russia (49, 54, and 45 Ma). They evolved from rare and newly evolved Blaberidae; they radiated circumtropically, later expanded into SE Asia, and have now spread to Hawaii and the SE USA. Association of autapomorphic characters that allow for passive and active protections from parasitic insects (unique wing origami pleating identical with its egg case-attacking wasp) suggest a response to high parasitic loads. Synchronized with global reorganization of the biota, morphotype destabilization in roaches lasted approximately 11-22 Ma, including both the adaptation of novel characters and the reduction of others. Thus, while viviparity can be disadvantageous, in association with new Bauplans and/or behaviors, it can contribute to the evolution of taxa with viviparous representatives that are slightly selectively preferred.
- Published
- 2016
- Full Text
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9. Tracing the trilobite tree from the root to the tips: a model marriage of fossils and phylogeny.
- Author
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Lieberman BS and Karim TS
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- Animals, Evolution, Molecular, Models, Anatomic, Models, Theoretical, Paleontology methods, Phylogeny, Time Factors, Arthropods genetics, Arthropods physiology, Fossils
- Abstract
Trilobites are a highly diverse group of extinct arthropods that persisted for nearly 300 million years. During that time, there was a profusion of morphological form, and they occupied a plethora of marine habitats. Their diversity, relative abundance, and complex morphology make them excellent candidates for phylogenetic analysis, and partly as a consequence they have been the subject of many cladistic studies. Although phylogenetic knowledge is certainly incomplete, our understanding of evolutionary patterns within the group has dramatically increased over the last 30 years. Moreover, trilobites have formed an important component of various studies of macroevolutionary processes. Here, we summarize the phylogenetic breadth of knowledge on the Trilobita, and present various hypotheses about phylogenetic patterns within the group, from the highest to the lowest taxonomic levels. Key topics we consider include the question of trilobite monophyly, the phylogenetic position of trilobites vis à vis extant arthropod groups, and inter- and intra-ordinal relationships., (Copyright (c) 2009 Elsevier Ltd. All rights reserved.)
- Published
- 2010
- Full Text
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