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Article ; Online: Artifact3-D

Leore Grosman / Antoine Muller / Itamar Dag / Hadas Goldgeier / Ortal Harush / Gadi Herzlinger / Keren Nebenhaus / Francesco Valetta / Talia Yashuv / Nir Dick

PLoS ONE, Vol 17, Iss

New software for accurate, objective and efficient 3D analysis and documentation of archaeological artifacts

2022 Volume 6

Abstract: ... and make available for academic-use Artifact3-D, a new software package comprised of a suite ... archaeological case studies to demonstrate its utility. Artifact3-D equips its users with a range ... but the Artifact3-D software can be used on any artifact type to address the needs of modern archaeology ...

Abstract	The study of artifacts is fundamental to archaeological research. The features of individual artifacts are recorded, analyzed, and compared within and between contextual assemblages. Here we present and make available for academic-use Artifact3-D, a new software package comprised of a suite of analysis and documentation procedures for archaeological artifacts. We introduce it here, alongside real archaeological case studies to demonstrate its utility. Artifact3-D equips its users with a range of computational functions for accurate measurements, including orthogonal distances, surface area, volume, CoM, edge angles, asymmetry, and scar attributes. Metrics and figures for each of these measurements are easily exported for the purposes of further analysis and illustration. We test these functions on a range of real archaeological case studies pertaining to tool functionality, technological organization, manufacturing traditions, knapping techniques, and knapper skill. Here we focus on lithic artifacts, but the Artifact3-D software can be used on any artifact type to address the needs of modern archaeology. Computational methods are increasingly becoming entwined in the excavation, documentation, analysis, database creation, and publication of archaeological research. Artifact3-D offers functions to address every stage of this workflow. It equips the user with the requisite toolkit for archaeological research that is accurate, objective, repeatable and efficient. This program will help archaeological research deal with the abundant material found during excavations and will open new horizons in research trajectories.
Keywords	Medicine ; R ; Science ; Q
Subject code	930
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Conversation With Karen Howard: Vitamin D.

Benson, Dick

Integrative medicine (Encinitas, Calif.)

2020 Volume 19, Issue 4, Page(s) 40–44

Language	English
Publishing date	2020-10-17
Publishing country	United States
Document type	Journal Article
ZDB-ID	2100529-1
ISSN	1945-7081 ; 1546-993X
ISSN (online)	1945-7081
ISSN	1546-993X
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Article ; Online: Transient potentiometry based d-serine sensor using engineered d-amino acid oxidase showing quasi-direct electron transfer property.

Takamatsu, Shouhei / Lee, Inyoung / Lee, Jinhee / Asano, Ryutaro / Tsugawa, Wakako / Ikebukuro, Kazunori / Dick, Jeffrey E / Sode, Koji

Biosensors & bioelectronics

2021 Volume 200, Page(s) 113927

Abstract: d-Serine biosensing has been extensively reported based on enzyme sensors using ... flavin adenine dinucleotide (FAD) -dependent d-amino acid oxidase (DAAOx), based on the monitoring of hydrogen peroxide ... environment in in vivo use. Here we report a novel sensing principle for d-serine, transient potentiometry ...

Abstract	d-Serine biosensing has been extensively reported based on enzyme sensors using flavin adenine dinucleotide (FAD) -dependent d-amino acid oxidase (DAAOx), based on the monitoring of hydrogen peroxide generated by the enzymatic reaction, which is affected by dissolved oxygen concentration in the measurement environment in in vivo use. Here we report a novel sensing principle for d-serine, transient potentiometry based d-serine sensor using engineered DAAOx showing quasi-direct electron transfer (DET) property. DAAOx Gly52Val mutant, revealed to possess dye-mediated dehydrogenase activity using artificial synthetic electron acceptors, while its oxidase activity was negligible. The enzyme was immobilized on electrode and was modified with amine-reactive phenazine ethosulfate, resulted an enzyme electrode showing quasi-DET type response. Although OCP based monitoring took more than several minutes to obtain steady state OCP value, the time dependent OCP change monitoring, transient potentiometry, provided rapid and sensitive sensor signals. While dOCP/dt based monitoring was suitable for sensing with longer than 5 s time resolution with d-serine concentration range between 0.5 mM and 5 mM, dOCP/d t based monitoring is suitable for d-serine monitoring with much shorter time resolution (less than 1 s) with high sensitivity with wider dynamic range (20 μM-30 mM). The maximum dOCP/d t was -39.2 ± 2.0 mV/s
MeSH term(s)	Biosensing Techniques ; Electrons ; Flavin-Adenine Dinucleotide ; Glucose ; Glucose 1-Dehydrogenase ; Potentiometry ; Serine
Chemical Substances	Flavin-Adenine Dinucleotide (146-14-5) ; Serine (452VLY9402) ; Glucose 1-Dehydrogenase (EC 1.1.1.47) ; Glucose (IY9XDZ35W2)
Language	English
Publishing date	2021-12-29
Publishing country	England
Document type	Journal Article
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2021.113927
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Article ; Online: Thermostable D-amino acid decarboxylases derived from Thermotoga maritima diaminopimelate decarboxylase.

Marjanovic, Antonija / Ramírez-Palacios, Carlos J / Masman, Marcelo F / Drenth, Jeroen / Otzen, Marleen / Marrink, Siewert-Jan / Janssen, Dick B

Protein engineering, design & selection : PEDS

2021 Volume 34

Abstract: ... toward different D-amino acids. One of the mutants (E315T) had lost most of its activity toward DAP and primarily ...

Abstract	Diaminopimelate decarboxylases (DAPDCs) are highly selective enzymes that catalyze the common final step in different lysine biosynthetic pathways, i.e. the conversion of meso-diaminopimelate (DAP) to L-lysine. We examined the modification of the substrate specificity of the thermostable decarboxylase from Thermotoga maritima with the aim to introduce activity with 2-aminopimelic acid (2-APA) since its decarboxylation leads to 6-aminocaproic acid (6-ACA), a building block for the synthesis of nylon-6. Structure-based mutagenesis of the distal carboxylate binding site resulted in a set of enzyme variants with new activities toward different D-amino acids. One of the mutants (E315T) had lost most of its activity toward DAP and primarily acted as a 2-APA decarboxylase. We next used computational modeling to explain the observed shift in catalytic activities of the mutants. The results suggest that predictive computational protocols can support the redesign of the catalytic properties of this class of decarboxylating PLP-dependent enzymes.
MeSH term(s)	Amino Acids ; Carboxy-Lyases/genetics ; Carboxy-Lyases/metabolism ; Substrate Specificity ; Thermotoga ; Thermotoga maritima/genetics ; Thermotoga maritima/metabolism
Chemical Substances	Amino Acids ; Carboxy-Lyases (EC 4.1.1.-)
Language	English
Publishing date	2021-04-02
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1466729-0
ISSN	1741-0134 ; 1741-0126
ISSN (online)	1741-0134
ISSN	1741-0126
DOI	10.1093/protein/gzab016
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Artifact3-D: New software for accurate, objective and efficient 3D analysis and documentation of archaeological artifacts.

Grosman, Leore / Muller, Antoine / Dag, Itamar / Goldgeier, Hadas / Harush, Ortal / Herzlinger, Gadi / Nebenhaus, Keren / Valetta, Francesco / Yashuv, Talia / Dick, Nir

PloS one

2022 Volume 17, Issue 6, Page(s) e0268401

Abstract	The study of artifacts is fundamental to archaeological research. The features of individual artifacts are recorded, analyzed, and compared within and between contextual assemblages. Here we present and make available for academic-use Artifact3-D, a new software package comprised of a suite of analysis and documentation procedures for archaeological artifacts. We introduce it here, alongside real archaeological case studies to demonstrate its utility. Artifact3-D equips its users with a range of computational functions for accurate measurements, including orthogonal distances, surface area, volume, CoM, edge angles, asymmetry, and scar attributes. Metrics and figures for each of these measurements are easily exported for the purposes of further analysis and illustration. We test these functions on a range of real archaeological case studies pertaining to tool functionality, technological organization, manufacturing traditions, knapping techniques, and knapper skill. Here we focus on lithic artifacts, but the Artifact3-D software can be used on any artifact type to address the needs of modern archaeology. Computational methods are increasingly becoming entwined in the excavation, documentation, analysis, database creation, and publication of archaeological research. Artifact3-D offers functions to address every stage of this workflow. It equips the user with the requisite toolkit for archaeological research that is accurate, objective, repeatable and efficient. This program will help archaeological research deal with the abundant material found during excavations and will open new horizons in research trajectories.
MeSH term(s)	Archaeology/methods ; Artifacts ; Documentation ; Software ; Technology
Language	English
Publishing date	2022-06-16
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0268401
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: PDGF-C and PDGF-D signaling in vascular diseases and animal models.

Folestad, Erika / Kunath, Anne / Wågsäter, Dick

Molecular aspects of medicine

2018 Volume 62, Page(s) 1–11

Abstract: ... PDGF-D, in vascular diseases. There are clear implications for these growth factors ... important implications of PDGF-C and PDGF-D signaling in fibrosis, neovascularization, atherosclerosis and ...

Abstract	Members of the platelet-derived growth factor (PDGF) family are well known to be involved in different pathological conditions. The cellular and molecular mechanisms induced by the PDGF signaling have been well studied. Nevertheless, there is much more to discover about their functions and some important questions to be answered. This review summarizes the known roles of two of the PDGFs, PDGF-C and PDGF-D, in vascular diseases. There are clear implications for these growth factors in several vascular diseases, such as atherosclerosis and stroke. The PDGF receptors are broadly expressed in the cardiovascular system in cells such as fibroblasts, smooth muscle cells and pericytes. Altered expression of the receptors and the ligands have been found in various cardiovascular diseases and current studies have shown important implications of PDGF-C and PDGF-D signaling in fibrosis, neovascularization, atherosclerosis and restenosis.
MeSH term(s)	Animals ; Cardiovascular System/metabolism ; Disease Models, Animal ; Gene Expression Regulation ; Humans ; Lymphokines/genetics ; Lymphokines/metabolism ; Neovascularization, Physiologic ; Platelet-Derived Growth Factor/genetics ; Platelet-Derived Growth Factor/metabolism ; Polymorphism, Single Nucleotide ; Receptor, Platelet-Derived Growth Factor alpha/genetics ; Receptor, Platelet-Derived Growth Factor alpha/metabolism ; Receptor, Platelet-Derived Growth Factor beta/genetics ; Receptor, Platelet-Derived Growth Factor beta/metabolism ; Signal Transduction ; Vascular Diseases/genetics ; Vascular Diseases/metabolism
Chemical Substances	Lymphokines ; PDGFD protein, human ; Platelet-Derived Growth Factor ; platelet-derived growth factor C ; PDGFRB protein, human (EC 2.7.10.1) ; Receptor, Platelet-Derived Growth Factor alpha (EC 2.7.10.1) ; Receptor, Platelet-Derived Growth Factor beta (EC 2.7.10.1)
Language	English
Publishing date	2018-02-14
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	197640-0
ISSN	1872-9452 ; 0098-2997
ISSN (online)	1872-9452
ISSN	0098-2997
DOI	10.1016/j.mam.2018.01.005
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Zs.A 1189: Show issues

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Article: Transient potentiometry based d-serine sensor using engineered d-amino acid oxidase showing quasi-direct electron transfer property

Takamatsu, Shouhei / Lee, Inyoung / Lee, Jinhee / Asano, Ryutaro / Tsugawa, Wakako / Ikebukuro, Kazunori / Dick, Jeffrey E. / Sode, Koji

Biosensors & bioelectronics. 2022 Mar. 15, v. 200

2022

Abstract	d-Serine biosensing has been extensively reported based on enzyme sensors using flavin adenine dinucleotide (FAD) -dependent d-amino acid oxidase (DAAOx), based on the monitoring of hydrogen peroxide generated by the enzymatic reaction, which is affected by dissolved oxygen concentration in the measurement environment in in vivo use. Here we report a novel sensing principle for d-serine, transient potentiometry based d-serine sensor using engineered DAAOx showing quasi-direct electron transfer (DET) property. DAAOx Gly52Val mutant, revealed to possess dye-mediated dehydrogenase activity using artificial synthetic electron acceptors, while its oxidase activity was negligible. The enzyme was immobilized on electrode and was modified with amine-reactive phenazine ethosulfate, resulted an enzyme electrode showing quasi-DET type response. Although OCP based monitoring took more than several minutes to obtain steady state OCP value, the time dependent OCP change monitoring, transient potentiometry, provided rapid and sensitive sensor signals. While dOCP/dt based monitoring was suitable for sensing with longer than 5 s time resolution with d-serine concentration range between 0.5 mM and 5 mM, dOCP/d t based monitoring is suitable for d-serine monitoring with much shorter time resolution (less than 1 s) with high sensitivity with wider dynamic range (20 μM–30 mM). The maximum dOCP/d t was −39.2 ± 2.0 mV/s¹/², the Kₘ₍ₐₚₚ₎ was 1.9 mM, and the lower limit of detection was 20 μM. In addition, d-serine monitoring was also possible in the artificial cerebrospinal fluid. The transient potentiometry based sensing reported in this study will be further utilized to realize miniaturized, continuous, real-time, in vivo sensor for d-serine monitoring.
Keywords	D-amino-acid oxidase ; biosensors ; cerebrospinal fluid ; detection limit ; dissolved oxygen ; electrodes ; electron transfer ; enzymatic reactions ; flavin-adenine dinucleotide ; hydrogen peroxide ; mutants ; serine
Language	English
Dates of publication	2022-0315
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2021.113927
Database	NAL-Catalogue (AGRICOLA)

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Article: Progrès dans l’application de la télédétection pour les besoins en matière d’information sur les forêts au Canada : leçons tirées d’une collaboration nationale d’intervenants universitaires, industriels et gouvernementaux

Coops, Nicholas C. / Achim, Alexis / Arp, Paul / Bater, Christopher W. / Caspersen, John P. / Côté, Jean-François / Dech, Jeffery P. / Dick, Adam R. / van Ewijk, Karin / Fournier, Richard / Goodbody, Tristan R. H. / Hennigar, Chris R. / Leboeuf, Antoine / van Lier, Olivier R. / Luther, Joan E. / MacLean, David A. / McCartney, Grant / Pelletier, Gaetan / Prieur, Jean-Francois /

Tompalski, Piotr / Treitz, Paul M. / White, Joanne C. / Woods, Murray E.

Forestry chronicle. 2021 June, v. 97, no. 2

2021

Abstract: The Canadian forest sector requires detailed information regarding the amount and characteristics of the forest resource. To address these needs, inventory systems that spatially quantify timber and other forest related ecosystem services are required, ... ...

Abstract	The Canadian forest sector requires detailed information regarding the amount and characteristics of the forest resource. To address these needs, inventory systems that spatially quantify timber and other forest related ecosystem services are required, that are accurate, comprehensive and timely. The Assessment of Wood properties using Remote Sensing (AWARE) was a five-year project involving collaboration between seven Canadian universities, and seven forest companies with support provided by provincial and federal forestry agencies and other non-for-profit forestry focused organisations. AWARE provided methods and tools to enhance the characterization of forests at national, landscape and individual tree scales. The project supported 24 post-doctoral fellows, PhD and MSc students that examined the roles that advanced three-dimensional remote sensing technologies can play in the development of accurate forest inventory systems across Canada. In this review we examine the AWARE research project, review research highlights, key outcomes, future research needs, and provide an assessment of successes and challenges the project faced over its five-year lifetime.
Keywords	ecosystems ; forest industries ; forest inventory ; forests ; landscapes ; research projects ; trees ; wood ; Canada
Language	English
Dates of publication	2021-06
Size	p. 127-147.
Publishing place	NRC Research Press
Document type	Article
ZDB-ID	348848-2
ISSN	0015-7546
ISSN	0015-7546
DOI	10.5558/tfc2021-015
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Seasonal variation of vitamin D among healthy adult men in a subtropical region.

Fontanive, Tiago Oselame / Dick, Nidea Rita Michels / Valente, Mariana Costa Silva / Laranjeira, Vani Dos Santos / Antunes, Marina Venzon / Corrêa, Marcelo de Paula / Alves, Rita de Cássia Marques / Linden, Rafael / Furlanetto, Tania Weber

Revista da Associacao Medica Brasileira (1992)

2020 Volume 66, Issue 10, Page(s) 1431–1436

Abstract: Objective: To evaluate seasonal variation of 25(OH)vitamin D [25(OH)D3] levels, and factors ... Ultraviolet irradiation was estimated by radiometer, calculating the daily photobiological response to vitamin D synthesis ... in human skin (D-VitD). The prevalence of 25(OH)D3 <20ng/mL changed with the seasons (p=0.000): 8.7% (n=6 ...

Abstract	Objective: To evaluate seasonal variation of 25(OH)vitamin D [25(OH)D3] levels, and factors associated with it, in healthy adult men, who exercised outdoors for 50 min., at least twice a week, from 10AM to 4PM, in a Brazilian semitropical region. Methods: Blood samples were collected at the end of each season for 25(OH)D3, measured by liquid chromatography with tandem mass spectrometry. Ultraviolet irradiation was estimated by radiometer, calculating the daily photobiological response to vitamin D synthesis in human skin (D-VitD). The prevalence of 25(OH)D3 <20ng/mL changed with the seasons (p=0.000): 8.7% (n=6/69), 1.5% (n=1/66), 0 (n=0/64), and 21.7% (n=13/60), respectively, at the end of winter, spring, summer, and autumn. The prevalence, adjusted for multiple comparisons, was higher in winter than summer (p=0.026), and in autumn than spring (p=0.001) and summer (p=0.000). There were no associations of 25(OH) D3 levels with BMI (p=0.207), body fat (p=0.064), and phototype (p=0.485), in univariate analysis. It was associated with D-VitD in the 30 days before blood sampling (p=0.000), after adjustment to body fat. The prevalence of 25(OH)D3 <30ng/mL varied seasonally (p=0.000): 69.6% (n=48/69), 68.2% (n=45/66), 43.8% (n=28/64), and 88.4% (n=53/60), respectively, in winter, spring, summer, and autumn. Conclusions: In a Brazilian subtropical region, a seasonal variation in 25(OH)D3 was observed in healthy adult males, although they spent at least 50 min outdoors twice a week, wearing shorts and T-shirts. 25(OH)D3 <20ng/mL was 21.7% in autumn; D-vitD 30 days prior to blood sampling was the only factor independently associated with 25(OH)D3 levels.
MeSH term(s)	Adult ; Brazil/epidemiology ; Calcifediol ; Dietary Supplements ; Humans ; Male ; Seasons ; Vitamin D ; Vitamin D Deficiency/epidemiology ; Vitamins
Chemical Substances	Vitamins ; Vitamin D (1406-16-2) ; Calcifediol (P6YZ13C99Q)
Language	English
Publishing date	2020-11-10
Publishing country	Brazil
Document type	Journal Article
ZDB-ID	731969-1
ISSN	1806-9282 ; 0104-4230 ; 0004-5241 ; 0102-843X
ISSN (online)	1806-9282
ISSN	0104-4230 ; 0004-5241 ; 0102-843X
DOI	10.1590/1806-9282.66.10.1431
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Article ; Online: Possible Role and Therapeutic Target of PDGF-D Signalling in Colorectal Cancer.

Olsen, Renate Slind / Dimberg, Jan / Geffers, Robert / Wågsäter, Dick

Cancer investigation

2019 Volume 37, Issue 2, Page(s) 99–112

Abstract: Platelet-derived growth factor D (PDGF-D) has been shown to mediate cellular processes ... of PDGF-D signaling in colorectal carcinogenesis. PDGF-D was expressed in vascular endothelial cells ... in tumor and normal tissues. PDGF-D stimulation of cells altered genes of importance in carcinogenic ...

Abstract	Platelet-derived growth factor D (PDGF-D) has been shown to mediate cellular processes of importance in cancer progression. This study aimed to investigate the expression and putative involvement of PDGF-D signaling in colorectal carcinogenesis. PDGF-D was expressed in vascular endothelial cells in tumor and normal tissues. PDGF-D stimulation of cells altered genes of importance in carcinogenic processes. In addition, PDGF-D increased the proliferation rate while imatinib inhibited these effects. PDGF-D and its PDGF receptor beta (PDGFR-β) are expressed in colorectal cancer and blockage of PDGF-D/PDGFR-β signaling using tyrosine kinase inhibitors, such as imatinib, might be important in inhibiting tumor-promoting actions.
MeSH term(s)	Caco-2 Cells ; Carcinogenesis/drug effects ; Carcinogenesis/metabolism ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Cell Proliferation/physiology ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/metabolism ; Endothelial Cells/drug effects ; Endothelial Cells/metabolism ; HT29 Cells ; Humans ; Imatinib Mesylate/pharmacology ; Lymphokines/metabolism ; Platelet-Derived Growth Factor/metabolism ; Protein Kinase Inhibitors/pharmacology ; Signal Transduction/drug effects ; Signal Transduction/physiology
Chemical Substances	Lymphokines ; PDGFD protein, human ; Platelet-Derived Growth Factor ; Protein Kinase Inhibitors ; Imatinib Mesylate (8A1O1M485B)
Language	English
Publishing date	2019-03-05
Publishing country	England
Document type	Journal Article
ZDB-ID	604942-4
ISSN	1532-4192 ; 0735-7907
ISSN (online)	1532-4192
ISSN	0735-7907
DOI	10.1080/07357907.2019.1576191
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