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Conference proceedings ; Online: Standardising stratigraphic data reporting

Wouters, S. / Arts, M. / Cicone, A. / Crucifix, M. / Da Silva, A. / Hohmann, N. / Sinnesael, M. / Zeeden, C.

XXVIII General Assembly of the International Union of Geodesy and Geophysics (IUGG)

2023

Abstract: Transparent data reporting is crucial for an integrated and reproducible stratigraphic approach. However, standard data formats are lacking. Typically, lithological information is found as simple images in publications, rather than as vector or tabulated ...

Abstract	Transparent data reporting is crucial for an integrated and reproducible stratigraphic approach. However, standard data formats are lacking. Typically, lithological information is found as simple images in publications, rather than as vector or tabulated data. There is also confusion on stratigraphic depth, composite depth, and interpreted age. Standardised stratigraphic data formats and associated automated tests could solve these issues. We explore the cases of the quantified data in lithological logs [1], and of age-depth conversion models, or depth-depth models for correlation between sections or for splicing [2]. We define three types of numerical data in lithological logs: Bed nature and thickness (including thickness variations) Bed profile (to convey hardness, grain-size, etc.) Discrete feature occurrences (e.g. fossils, etc.) These data types are not defined based on geological arguments, but on the way they are digitised. Accordingly, these three data sub-formats can serve as building blocks for a larger single data format. Based on this, the open source StratigrapheR package (https://CRAN.R-project.org/package=StratigrapheR) has been updated (version 1.3) to digitise these types of information. For age-depth and depth-depth conversion models, we explore the ability to retrieve the initial signal from one that has been transformed, i.e., correlated, spliced, or tuned. This involves taking the precision in depth and age into account, formalizing hiatuses, and preserving relevant features of the original data/signals in all subsequent data files, such as parts of the signal removed for processing (e.g., turbidites). In the talk, we provide practical examples on how to use our software solutions.
Subject code	550
Language	English
Publishing country	de
Document type	Conference proceedings ; Online
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Article ; Online: Rapid Detection and Monitoring of Flavobacterium psychrophilum in Water by Using a Handheld, Field-Portable Quantitative PCR System.

Nguyen, Phong L / Sudheesh, Ponnerassery S / Thomas, Austen C / Sinnesael, Mieke / Haman, Katherine / Cain, Kenneth D

Journal of aquatic animal health

2018 Volume 30, Issue 4, Page(s) 302–311

Abstract: Advances in technology are making it easier for rapid field detection of microbes in aquaculture. Specifically, real-time quantitative PCR (qPCR) analysis, which has traditionally been confined to laboratory-based protocols, is now available in a ... ...

Abstract	Advances in technology are making it easier for rapid field detection of microbes in aquaculture. Specifically, real-time quantitative PCR (qPCR) analysis, which has traditionally been confined to laboratory-based protocols, is now available in a handheld, field-portable system. The feasibility of using the Biomeme handheld qPCR system for rapid (<50 min) on-site detection and monitoring of Flavobacterium psychrophilum from filtered water samples was evaluated. Paired water samples were collected over a 23-d period from microcosm tanks that housed fish injected with known levels of F. psychrophilum. Water samples were filtered through 0.45-μm nitrocellulose filters and were analyzed with both the Biomeme qPCR platform and a traditional bench qPCR protocol. The two methods identified similar fluctuations in F. psychrophilum DNA throughout the study. Standard curves relating quantification cycles to the number of F. psychrophilum colony-forming units (CFU) were constructed and analyzed; results indicated that CFU increased rapidly between days 6 and 8 of the trial and then progressively decreased during the remaining 15 d. Average calculated log
MeSH term(s)	Animals ; DNA, Bacterial/analysis ; Fish Diseases/microbiology ; Flavobacteriaceae Infections/microbiology ; Flavobacteriaceae Infections/veterinary ; Flavobacterium/genetics ; Flavobacterium/isolation & purification ; Oncorhynchus mykiss ; Real-Time Polymerase Chain Reaction/instrumentation ; Real-Time Polymerase Chain Reaction/methods ; Real-Time Polymerase Chain Reaction/veterinary ; Water Microbiology
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2018-11-22
Publishing country	United States
Document type	Evaluation Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1019919-6
ISSN	1548-8667 ; 0899-7659
ISSN (online)	1548-8667
ISSN	0899-7659
DOI	10.1002/aah.10046
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Article ; Online: Novel insights in the regulation and mechanism of androgen action on bone.

Sinnesael, Mieke / Claessens, Frank / Boonen, Steven / Vanderschueren, Dirk

Current opinion in endocrinology, diabetes, and obesity

2013 Volume 20, Issue 3, Page(s) 240–244

Abstract: Purpose of review: This review provides an update on the associations of testosterone, estrogens, sex hormone binding globulin, GH-IGF-I, osteocalcin and mechanical loading with relevance to skeletal health.: Recent findings: The simple concept of a ... ...

Abstract	Purpose of review: This review provides an update on the associations of testosterone, estrogens, sex hormone binding globulin, GH-IGF-I, osteocalcin and mechanical loading with relevance to skeletal health. Recent findings: The simple concept of a dual model of action of androgens, i.e. either directly via the androgen receptor or indirectly by estrogens, is proving more complicated because of novel interactions of these hormones and their receptors with other hormonal as well as mechanical signals. Summary: Testosterone - in contrast with estrogen - is not uniformly associated with fracture risk in men. However, androgen receptor mediated action is clearly important for trabecular bone maintenance in male mice whereas both estrogens and androgens regulate cortical bone growth. The osteoblast and osteocyte appear to be involved in such androgen receptor mediated action on bone in male mice. Studies in mice also showed an unexpected interaction between osteocalcin and testosterone production in males and, vice versa, between ovarian production of follicle-stimulating hormone with testosterone and potentially bone formation.
MeSH term(s)	Androgens/metabolism ; Androgens/therapeutic use ; Animals ; Bone Density Conservation Agents/metabolism ; Bone Density Conservation Agents/therapeutic use ; Bone Development/drug effects ; Bone and Bones/drug effects ; Bone and Bones/physiology ; Estrogens/deficiency ; Estrogens/metabolism ; Estrogens/therapeutic use ; Female ; Humans ; Male ; Osteoblasts/drug effects ; Osteoblasts/metabolism ; Osteocalcin/metabolism ; Osteoclasts/drug effects ; Osteoclasts/metabolism ; Osteoporosis/epidemiology ; Osteoporosis/metabolism ; Osteoporosis/prevention & control ; Receptors, Androgen/chemistry ; Receptors, Androgen/metabolism ; Risk Factors ; Sex Characteristics ; Signal Transduction/drug effects ; Weight-Bearing
Chemical Substances	Androgens ; Bone Density Conservation Agents ; Estrogens ; Receptors, Androgen ; Osteocalcin (104982-03-8)
Language	English
Publishing date	2013-06
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2272017-0
ISSN	1752-2978 ; 1752-296X
ISSN (online)	1752-2978
ISSN	1752-296X
DOI	10.1097/MED.0b013e32835f7d04
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Book ; Online: Reconstructing seasonality through stable-isotope and trace-element analyses of the Proserpine stalagmite, Han-sur-Lesse cave, Belgium

Vansteenberge, Stef / Winter, Niels J. / Sinnesael, Matthias / Verheyden, Sophie / Goderis, Steven / Malderen, Stijn J. M. / Vanhaecke, Frank / Claeys, Philippe

eISSN: 1814-9332

indications for climate-driven changes during the last 400 years

2020

Abstract: Fast-growing speleothems allow for the reconstruction of palaeoclimate down to a seasonal scale. Additionally, annual lamination in some of these speleothems yields highly accurate age models for these palaeoclimate records, making these speleothems ... ...

Abstract	Fast-growing speleothems allow for the reconstruction of palaeoclimate down to a seasonal scale. Additionally, annual lamination in some of these speleothems yields highly accurate age models for these palaeoclimate records, making these speleothems valuable archives for terrestrial climate. In this study, an annually laminated stalagmite from the Han-sur-Lesse cave (Belgium) is used to study the expression of the seasonal cycle in northwestern Europe during the Little Ice Age. More specifically, two historical 12-year-long growth periods (ca. 1593–1605 CE and 1635–1646 CE) and one modern growth period (1960–2010 CE) are analysed on a sub-annual scale for their stable-isotope ratios ( δ 13 C and δ 18 O) and trace-element (Mg, Sr, Ba, Zn, Y, Pb, U) contents. Seasonal variability in these proxies is confirmed with frequency analysis. Zn, Y and Pb show distinct annual peaks in all three investigated periods related to annual flushing of the soil during winter. A strong seasonal in-phase relationship between Mg, Sr and Ba in the modern growth period reflects a substantial influence of enhanced prior calcite precipitation (PCP). In particular, PCP occurs during summers when recharge of the epikarst is low. This is also evidenced by earlier observations of increased δ 13 C values during summer. In the 17th century intervals, there is a distinct antiphase relationship between Mg, Sr and Ba, suggesting that processes other than PCP, i.e. varying degrees of incongruent dissolution of dolomite, eventually related to changes in soil activity and/or land-use change are more dominant. The processes controlling seasonal variations in Mg, Sr and Ba in the speleothem appear to change between the 17th century and 1960–2010 CE. The Zn, Y, Pb, and U concentration profiles; stable-isotope ratios; and morphology of the speleothem laminae all point towards increased seasonal amplitude in cave hydrology. Higher seasonal peaks in soil-derived elements (e.g. Zn and Y) and lower concentrations of host-rock-derived elements (e.g. Mg, Sr, Ba) point towards lower residence times in the epikarst and higher flushing rates during the 17th century. These observations reflect an increase in water excess above the cave and recharge of the epikarst, due to a combination of lower summer temperatures and increased winter precipitation during the 17th century. This study indicates that the transfer function controlling Mg, Sr and Ba seasonal variability varies over time. Which process is dominant – either PCP, soil activity or dolomite dissolution – is clearly climate driven and can itself be used as a palaeoenvironment proxy.
Subject code	333
Language	English
Publishing date	2020-01-16
Publishing country	de
Document type	Book ; Online
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Article ; Online: Anchoring the Late Devonian mass extinction in absolute time by integrating climatic controls and radio-isotopic dating.

Da Silva, Anne-Christine / Sinnesael, Matthias / Claeys, Philippe / Davies, Joshua H F L / de Winter, Niels J / Percival, L M E / Schaltegger, Urs / De Vleeschouwer, David

Scientific reports

2020 Volume 10, Issue 1, Page(s) 12940

Abstract: The Devonian Frasnian-Famennian (F-F) boundary marks one of the five main extinction intervals of the Phanerozoic Aeon. This time was characterized by two pulses of oceanic anoxia, named the Lower and Upper Kellwasser events, during which massive marine ... ...

Abstract	The Devonian Frasnian-Famennian (F-F) boundary marks one of the five main extinction intervals of the Phanerozoic Aeon. This time was characterized by two pulses of oceanic anoxia, named the Lower and Upper Kellwasser events, during which massive marine biodiversity losses occurred. This paper presents high-resolution magnetic susceptibility, X-ray fluorescence elemental geochemistry and carbon isotope datasets obtained from the Steinbruch Schmidt F-F boundary section (Germany). These records lead to an astronomical time calibration of the environmental changes associated with the two ocean anoxia pulses. Cyclostratigraphic interpretation indicates deposition of the black argillaceous Lower and Upper Kellwasser horizons over ~ 90 and ~ 110 kyr, respectively; approximately equivalent to the duration of one short eccentricity cycle. This study confirms that the succession of events within the Upper Kellwasser event is paced by obliquity, under a low-eccentricity orbit. Hence, astronomical insolation forcing likely contributed to the expansion of ocean anoxia and other environmental perturbations associated with these two crises. The new floating chronology established for the Steinbruch Schmidt section is anchored in numerical time by means of a radio-isotopic date, obtained from a bentonite layer interbedded between the two Kellwasser horizons. After anchoring, this time scale gives a high-precision age of 371.870 ± 0.108 Ma for the F-F boundary.
Language	English
Publishing date	2020-07-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-69097-6
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Article ; Online: Timing and pacing of the Late Devonian mass extinction event regulated by eccentricity and obliquity.

De Vleeschouwer, David / Da Silva, Anne-Christine / Sinnesael, Matthias / Chen, Daizhao / Day, James E / Whalen, Michael T / Guo, Zenghui / Claeys, Philippe

Nature communications

2017 Volume 8, Issue 1, Page(s) 2268

Abstract: The Late Devonian envelops one of Earth's big five mass extinction events at the Frasnian-Famennian boundary (374 Ma). Environmental change across the extinction severely affected Devonian reef-builders, besides many other forms of marine life. Yet, ... ...

Abstract	The Late Devonian envelops one of Earth's big five mass extinction events at the Frasnian-Famennian boundary (374 Ma). Environmental change across the extinction severely affected Devonian reef-builders, besides many other forms of marine life. Yet, cause-and-effect chains leading to the extinction remain poorly constrained as Late Devonian stratigraphy is poorly resolved, compared to younger cataclysmic intervals. In this study we present a global orbitally calibrated chronology across this momentous interval, applying cyclostratigraphic techniques. Our timescale stipulates that 600 kyr separate the lower and upper Kellwasser positive δ
Language	English
Publishing date	2017-12-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/s41467-017-02407-1
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Article ; Online: Androgens and estrogens in skeletal sexual dimorphism.

Laurent, Michaël / Antonio, Leen / Sinnesael, Mieke / Dubois, Vanessa / Gielen, Evelien / Classens, Frank / Vanderschueren, Dirk

Asian journal of andrology

2014 Volume 16, Issue 2, Page(s) 213–222

Abstract: Bone is an endocrine tissue expressing androgen and estrogen receptors as well as steroid metabolizing enzymes. The bioactivity of circulating sex steroids is modulated by sex hormone-binding globulin and local conversion in bone tissue, for example, ... ...

Abstract	Bone is an endocrine tissue expressing androgen and estrogen receptors as well as steroid metabolizing enzymes. The bioactivity of circulating sex steroids is modulated by sex hormone-binding globulin and local conversion in bone tissue, for example, from testosterone (T) to estradiol (E2) by aromatase, or to dihydrotestosterone by 5α-reductase enzymes. Our understanding of the structural basis for gender differences in bone strength has advanced considerably over recent years due to increasing use of (high resolution) peripheral computed tomography. These microarchitectural insights form the basis to understand sex steroid influences on male peak bone mass and turnover in cortical vs trabecular bone. Recent studies using Cre/LoxP technology have further refi ned our mechanistic insights from global knockout mice into the direct contributions of sex steroids and their respective nuclear receptors in osteoblasts, osteoclasts, osteocytes, and other cells to male osteoporosis. At the same time, these studies have reinforced the notion that androgen and estrogen defi ciency have both direct and pleiotropic effects via interaction with, for example, insulin-like growth factor 1, inflammation, oxidative stress, central nervous system control of bone metabolism, adaptation to mechanical loading, etc., This review will summarize recent advances on these issues in the fi eld of sex steroid actions in male bone homeostasis.
MeSH term(s)	Androgens/physiology ; Bone Density ; Bone and Bones/physiology ; Estrogens/physiology ; Female ; Humans ; Male ; Sex Characteristics
Chemical Substances	Androgens ; Estrogens
Language	English
Publishing date	2014-01-03
Publishing country	China
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2075824-8
ISSN	1745-7262 ; 1008-682X
ISSN (online)	1745-7262
ISSN	1008-682X
DOI	10.4103/1008-682X.122356
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Article ; Online: Testosterone and the male skeleton: a dual mode of action.

Sinnesael, Mieke / Boonen, Steven / Claessens, Frank / Gielen, Evelien / Vanderschueren, Dirk

Journal of osteoporosis

2011 Volume 2011, Page(s) 240328

Abstract: Testosterone is an important hormone for both bone gain and maintenance in men. Hypogonadal men have accelerated bone turnover and increased fracture risk. In these men, administration of testosterone inhibits bone resorption and maintains bone mass. ... ...

Abstract	Testosterone is an important hormone for both bone gain and maintenance in men. Hypogonadal men have accelerated bone turnover and increased fracture risk. In these men, administration of testosterone inhibits bone resorption and maintains bone mass. Testosterone, however, is converted into estradiol via aromatization in many tissues including male bone. The importance of estrogen receptor alpha activation as well of aromatization of androgens into estrogens was highlighted by a number of cases of men suffering from an inactivating mutation in the estrogen receptor alpha or in the aromatase enzyme. All these men typically had low bone mass, high bone turnover and open epiphyses. In line with these findings, cohort studies have confirmed that estradiol contributes to the maintenance of bone mass after reaching peak bone mass, with an association between estradiol and fractures in elderly men. Recent studies in knock-out mice have increased our understanding of the role of androgens and estrogens in different bone compartments. Estrogen receptor activation, but not androgen receptor activation, is involved in the regulation of male longitudinal appendicular skeletal growth in mice. Both the androgen and the estrogen receptor can independently mediate the cancellous bone-sparing effects of sex steroids in male mice. Selective KO studies of the androgen receptor in osteoblasts in male mice suggest that the osteoblast in the target cell for androgen receptor mediated maintenance of trabecular bone volume and coordination of bone matrix synthesis and mineralization. Taken together, both human and animal studies suggest that testosterone has a dual mode of action on different bone surfaces with involvement of both the androgen and estrogen receptor.
Language	English
Publishing date	2011-09-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	2549002-3
ISSN	2042-0064 ; 2042-0064
ISSN (online)	2042-0064
ISSN	2042-0064
DOI	10.4061/2011/240328
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Article ; Online: Skeletal sexual dimorphism: relative contribution of sex steroids, GH-IGF1, and mechanical loading.

Callewaert, Filip / Sinnesael, Mieke / Gielen, Evelien / Boonen, Steven / Vanderschueren, Dirk

The Journal of endocrinology

2010 Volume 207, Issue 2, Page(s) 127–134

Abstract: Structural gender differences in bone mass - characterized by wider but not thicker bones - are generally attributed to opposing sex steroid actions in men and women. Recent findings have redefined the traditional concept of sex hormones as the main ... ...

Abstract	Structural gender differences in bone mass - characterized by wider but not thicker bones - are generally attributed to opposing sex steroid actions in men and women. Recent findings have redefined the traditional concept of sex hormones as the main regulators of skeletal sexual dimorphism. GH-IGF1 action is likely to be the most important determinant of sex differences in bone mass. Estrogens limit periosteal bone expansion but stimulate endosteal bone apposition in females, whereas androgens stimulate radial bone expansion in males. Androgens not only act directly on bone through the androgen receptor (AR) but also activate estrogen receptor-α or -β (ERα or ERβ) following aromatization into estrogens. Both the AR and ERα pathways are needed to optimize radial cortical bone expansion, whereas AR signaling alone is the dominant pathway for normal male trabecular bone development. Estrogen/ERα-mediated effects in males may - at least partly - depend on interaction with IGF1. In addition, sex hormones and their receptors have an impact on the mechanical sensitivity of the growing skeleton. AR and ERβ signaling may limit the osteogenic response to loading in males and females respectively, while ERα may stimulate the response of bone to mechanical stimulation in the female skeleton. Overall, current evidence suggests that skeletal sexual dimorphism is not just the end result of differences in sex steroid secretion between the sexes, but depends on gender differences in GH-IGF1 and mechanical sensitivity to loading as well.
MeSH term(s)	Biomechanical Phenomena ; Bone Development/physiology ; Female ; Growth Hormone/metabolism ; Humans ; Insulin-Like Growth Factor I/metabolism ; Male ; Sex Characteristics
Chemical Substances	Insulin-Like Growth Factor I (67763-96-6) ; Growth Hormone (9002-72-6)
Language	English
Publishing date	2010-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	3028-4
ISSN	1479-6805 ; 0022-0795
ISSN (online)	1479-6805
ISSN	0022-0795
DOI	10.1677/JOE-10-0209
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Article ; Online: Androgen receptor (AR) in osteocytes is important for the maintenance of male skeletal integrity: evidence from targeted AR disruption in mouse osteocytes.

Sinnesael, Mieke / Claessens, Frank / Laurent, Michaël / Dubois, Vanessa / Boonen, Steven / Deboel, Ludo / Vanderschueren, Dirk

Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research

2012 Volume 27, Issue 12, Page(s) 2535–2543

Abstract: Androgens play a key role in the maintenance of male skeletal integrity. The regulation of this integrity by androgen receptor (AR) signaling has been mainly attributed to osteoblasts. Although osteocytes have emerged as key regulators of bone remodeling, ...

Abstract	Androgens play a key role in the maintenance of male skeletal integrity. The regulation of this integrity by androgen receptor (AR) signaling has been mainly attributed to osteoblasts. Although osteocytes have emerged as key regulators of bone remodeling, the influence of sex steroids on these cells has been poorly studied. We aimed to investigate the role of AR signaling, specifically in osteocytes using the Cre/LoxP system in male mice (driven by dentin matrix protein 1 [ocy-ARKOs]). Osteocyte fractions of control (AR(ex2)/Y) and ocy-ARKO (ARflox(ex2)/Y; DMP1-cre) mice isolated through sequential collagenase digestion showed increasing AR expression toward the mature osteocyte fraction of control males compared with the more immature fractions, whereas this was reduced by >80% in ocy-ARKO osteocytes. The skeletal phenotype of mutant mice was further assessed by histomorphometry and quantitative micro-computed tomography at 12 and 32 weeks of age. Ocy-ARKOs had significantly lower trabecular bone volume and number in femora and tibias at 32 weeks as well as decreased trabecular number in the L(5) vertebra at 12 weeks. Biomechanical testing showed that ocy-ARKO femora were also stiffer and required a lower ultimate force to induce failure at 32 weeks. However, femoral cortical structure was not significantly different at any time point. The absence of AR in osteocyte also did not appear to affect trabecular bone formation nor its response to mechanical loading. In conclusion, selective inactivation of the AR in osteocytes of male mice accelerates age-related deterioration of skeletal integrity. These findings provide evidence for a direct role of androgens in the maintenance of trabecular bone through actions of the AR in osteocytes.
MeSH term(s)	Animals ; Biomechanical Phenomena ; Bone Diseases/physiopathology ; Bone and Bones/pathology ; Extracellular Matrix Proteins/genetics ; Femur/pathology ; Femur/physiology ; Male ; Mice ; Mice, Knockout ; Osteocytes/drug effects ; Osteocytes/metabolism ; Receptors, Androgen/deficiency ; Receptors, Androgen/physiology ; Tibia/pathology
Chemical Substances	Dmp1 protein, mouse ; Extracellular Matrix Proteins ; Receptors, Androgen
Language	English
Publishing date	2012-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	632783-7
ISSN	1523-4681 ; 0884-0431
ISSN (online)	1523-4681
ISSN	0884-0431
DOI	10.1002/jbmr.1713
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