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Article ; Online: Denver pain authenticity stimulus set (D-PASS).

Lloyd, E Paige / Summers, Kevin M / Gunderson, Christopher A / Weesner, Rachael E / Ten Brinke, Leanne / Hugenberg, Kurt / McConnell, Allen R

Behavior research methods

2023

Abstract: We introduce the Denver Pain Authenticity Stimulus Set (D-PASS), a free resource containing 315 ...

Abstract	We introduce the Denver Pain Authenticity Stimulus Set (D-PASS), a free resource containing 315 videos of 105 unique individuals expressing authentic and posed pain. All expressers were recorded displaying one authentic (105; pain was elicited via a pressure algometer) and two posed (210) expressions of pain (one posed expression recorded before [posed-unrehearsed] and one recorded after [posed-rehearsed] the authentic pain expression). In addition to authentic and posed pain videos, the database includes an accompanying codebook including metrics assessed at the expresser and video levels (e.g., Facial Action Coding System metrics for each video controlling for neutral images of the expresser), expressers' pain threshold and pain tolerance values, averaged pain detection performance by naïve perceivers who viewed the videos (e.g., accuracy, response bias), neutral images of each expresser, and face characteristic rating data for neutral images of each expresser (e.g., attractiveness, trustworthiness). The stimuli and accompanying codebook can be accessed for academic research purposes from https://digitalcommons.du.edu/lsdl_dpass/1/ . The relatively large number of stimuli allow for consideration of expresser-level variability in analyses and enable more advanced statistical approaches (e.g., signal detection analyses). Furthermore, the large number of Black (n = 41) and White (n = 56) expressers permits investigations into the role of race in pain expression, perception, and authenticity detection. Finally, the accompanying codebook may provide pilot data for novel investigations in the intergroup or pain sciences.
Language	English
Publishing date	2023-11-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	231560-9
ISSN	1554-3528 ; 0743-3808 ; 1554-351X
ISSN (online)	1554-3528
ISSN	0743-3808 ; 1554-351X
DOI	10.3758/s13428-023-02283-2
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Article: GIA imaging of 3-D mantle viscosity based on palaeo sea level observations - Part I: Sensitivity kernels for an Earth with laterally varying viscosity.

Lloyd, Andrew J / Crawford, Ophelia / Al-Attar, David / Austermann, Jacqueline / Hoggard, Mark J / Richards, Fred D / Syvret, Frank

Geophysical journal international

2023 Volume 236, Issue 2, Page(s) 1139–1171

Abstract: A key initial step in geophysical imaging is to devise an effective means of mapping the sensitivity of an observation to the model parameters, that is to compute its Fréchet derivatives or sensitivity kernel. In the absence of any simplifying ... ...

Abstract	A key initial step in geophysical imaging is to devise an effective means of mapping the sensitivity of an observation to the model parameters, that is to compute its Fréchet derivatives or sensitivity kernel. In the absence of any simplifying assumptions and when faced with a large number of free parameters, the adjoint method can be an effective and efficient approach to calculating Fréchet derivatives and requires just two numerical simulations. In the Glacial Isostatic Adjustment problem, these consist of a forward simulation driven by changes in ice mass and an adjoint simulation driven by
Language	English
Publishing date	2023-11-21
Publishing country	England
Document type	Journal Article
ZDB-ID	2006420-2
ISSN	1365-246X ; 0956-540X ; 0016-8009 ; 0955-419X
ISSN (online)	1365-246X
ISSN	0956-540X ; 0016-8009 ; 0955-419X
DOI	10.1093/gji/ggad455
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Article ; Online: Abatement of 2,4-D by H

Serra-Clusellas, Anna / De Angelis, Laura / Lin, Chung-Ho / Vo, Phuc / Bayati, Mohamed / Sumner, Lloyd / Lei, Zhentian / Amaral, Nathalia B / Bertini, Liliana M / Mazza, Jose / Pizzio, Luis R / Stripeikis, Jorge D / Rengifo-Herrera, Julián A / Fidalgo de Cortalezzi, María M

Water research

2018 Volume 144, Page(s) 572–580

Abstract: ... to eliminate the herbicide 2,4-D from water. PF-like experiments concerning ferric and H ...

Abstract	The Photo-Fenton-like (PF-like) process with minute Fe(III) concentrations and the Hydrogen Peroxide Photolysis (HPP), using Xe-lamp or solar light as sources of irradiation, were efficiently applied to eliminate the herbicide 2,4-D from water. PF-like experiments concerning ferric and H
MeSH term(s)	2,4-Dichlorophenoxyacetic Acid/chemistry ; Hydrogen Peroxide/chemistry ; Hydrogen-Ion Concentration ; Iron/chemistry ; Photolysis ; Ultraviolet Rays ; Water Pollutants, Chemical/chemistry ; Water Purification/instrumentation ; Water Purification/methods
Chemical Substances	Water Pollutants, Chemical ; 2,4-Dichlorophenoxyacetic Acid (2577AQ9262) ; Hydrogen Peroxide (BBX060AN9V) ; Iron (E1UOL152H7)
Language	English
Publishing date	2018-07-31
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	202613-2
ISSN	1879-2448 ; 0043-1354
ISSN (online)	1879-2448
ISSN	0043-1354
DOI	10.1016/j.watres.2018.07.072
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Article ; Online: D-dimer Thresholds to Exclude Pulmonary Embolism among COVID-19 Patients in the Emergency Department: Derivation with Independent Validation.

Bledsoe, Joseph R / Knox, Daniel / Peltan, Ithan D / Woller, Scott C / Lloyd, James F / Snow, Gregory L / Horne, Benjamin D / Connors, Jean M / Kline, Jeffrey A

Clinical and applied thrombosis/hemostasis : official journal of the International Academy of Clinical and Applied Thrombosis/Hemostasis

2022 Volume 28, Page(s) 10760296221117997

Abstract: Objective: To derive and validate a D-dimer cutoff for ruling out pulmonary embolism (PE) in COVID ... data from 154 ED's from 26 US states. Consecutive ED patients with laboratory confirmed COVID-19, a D ... to those without PE. After identifying a D-dimer threshold at which the 95% confidence lower bound of the negative ...

Abstract	Objective: To derive and validate a D-dimer cutoff for ruling out pulmonary embolism (PE) in COVID-19 patients presenting to the emergency department (ED). Methods: A retrospective cohort study was performed in an integrated healthcare system including 22 adult ED's between March 1, 2020, and January 31, 2021. Results were validated among patients enrolled in the RECOVER Registry, representing data from 154 ED's from 26 US states. Consecutive ED patients with laboratory confirmed COVID-19, a D-dimer performed within 48 h of ED arrival, and with objectively confirmed PE were compared to those without PE. After identifying a D-dimer threshold at which the 95% confidence lower bound of the negative predictive value for PE was higher than 98% in the derivation cohort, it was validated using RECOVER registry data. Results: Among 3978 patients with a D-dimer result, 3583 with confirmed COVID-19 infection were included in the derivation cohort. Overall, PE incidence was 4.1% and a D-dimer cutoff of Conclusion: A D-dimer cutoff of
MeSH term(s)	Adult ; COVID-19/complications ; COVID-19/diagnosis ; Emergency Service, Hospital ; Fibrin Fibrinogen Degradation Products/metabolism ; Humans ; Predictive Value of Tests ; Pulmonary Embolism/diagnosis ; Pulmonary Embolism/epidemiology ; Retrospective Studies ; Sensitivity and Specificity
Chemical Substances	Fibrin Fibrinogen Degradation Products ; fibrin fragment D
Language	English
Publishing date	2022-08-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	1237357-6
ISSN	1938-2723 ; 1076-0296
ISSN (online)	1938-2723
ISSN	1076-0296
DOI	10.1177/10760296221117997
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Article ; Online: Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.

Batson, Sarah / de Chiara, Cesira / Majce, Vita / Lloyd, Adrian J / Gobec, Stanislav / Rea, Dean / Fülöp, Vilmos / Thoroughgood, Christopher W / Simmons, Katie J / Dowson, Christopher G / Fishwick, Colin W G / de Carvalho, Luiz Pedro S / Roper, David I

Nature communications

2017 Volume 8, Issue 1, Page(s) 1939

Abstract: D-cycloserine is an antibiotic which targets sequential bacterial cell wall peptidoglycan ... biosynthesis enzymes: alanine racemase and D-alanine:D-alanine ligase. By a combination of structural, chemical ... and mechanistic studies here we show that the inhibition of D-alanine:D-alanine ligase ...

Abstract	D-cycloserine is an antibiotic which targets sequential bacterial cell wall peptidoglycan biosynthesis enzymes: alanine racemase and D-alanine:D-alanine ligase. By a combination of structural, chemical and mechanistic studies here we show that the inhibition of D-alanine:D-alanine ligase by the antibiotic D-cycloserine proceeds via a distinct phosphorylated form of the drug. This mechanistic insight reveals a bimodal mechanism of action for a single antibiotic on different enzyme targets and has significance for the design of future inhibitor molecules based on this chemical structure.
MeSH term(s)	Alanine Racemase ; Antibiotics, Antitubercular/metabolism ; Antibiotics, Antitubercular/pharmacology ; Cycloserine/metabolism ; Cycloserine/pharmacology ; Escherichia coli ; Escherichia coli Proteins/antagonists & inhibitors ; Escherichia coli Proteins/drug effects ; Peptide Synthases/antagonists & inhibitors ; Peptide Synthases/drug effects ; Phosphorylation
Chemical Substances	Antibiotics, Antitubercular ; Escherichia coli Proteins ; Cycloserine (95IK5KI84Z) ; Alanine Racemase (EC 5.1.1.1) ; Peptide Synthases (EC 6.3.2.-) ; D-alanylalanine synthetase (EC 6.3.2.4)
Language	English
Publishing date	2017-12-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-017-02118-7
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Article ; Online: Mapping the Binding Interactions between Human Gasdermin D and Human Caspase-1 Using Carbene Footprinting.

Lloyd, James R / Biasutto, Antonio / Dürr, Katharina L / Jazayeri, Ali / Hopper, Jonathan T S / Oldham, Neil J

JACS Au

2023 Volume 3, Issue 7, Page(s) 2025–2035

Abstract: ... interactions between the protease human Caspase-1 (C285A) and full-length human Gasdermin D (hGSDMD), which are ...

Abstract	Carbene footprinting is a recently developed mass spectrometry-based chemical labeling technique that probes protein interactions and conformation. Here, we use the methodology to investigate binding interactions between the protease human Caspase-1 (C285A) and full-length human Gasdermin D (hGSDMD), which are important in inflammatory cell death. GSDMD is cleaved by Caspase-1, releasing its N-terminal domain which oligomerizes in the membrane to form large pores, resulting in lytic cell death. Regions of reduced carbene labeling (masking), caused by protein binding, were observed for each partner in the presence of the other and were consistent with hCaspase-1 exosite and active-site interactions. Most notably, the results showed direct occupancy of hCaspase-1 (C285A) active-site by hGSDMD for the first time. Differential carbene labeling of full-length hGSDMD and the pore-forming N-terminal domain assembled in liposomes showed masking of the latter, consistent with oligomeric assembly and insertion into the lipid bilayer. Interactions between Caspase-1 and the specific inhibitor VRT-043198 were also studied by this approach. In wild-type hCaspase-1, VRT-043198 modifies the active-site Cys285 through the formation of a S,O-hemiacetal. Here, we showed by carbene labeling that this inhibitor can noncovalently occupy the active site of a C285A mutant. These findings add considerably to our knowledge of the hCaspase-1-hGSDMD system.
Language	English
Publishing date	2023-06-23
Publishing country	United States
Document type	Journal Article
ISSN	2691-3704
ISSN (online)	2691-3704
DOI	10.1021/jacsau.3c00236
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Article ; Online: Application of PCSWMM for the 1-D and 1-D–2-D Modeling of Urban Flooding in Damansara Catchment, Malaysia

Lariyah Mohd Sidek / Lloyd Hock Chye Chua / Aqilah Syasya Mohd Azizi / Hidayah Basri / Aminah Shakirah Jaafar / Wei Chek Moon

Applied Sciences, Vol 11, Iss 9300, p

2021 Volume 9300

Abstract: ... developed for the 1-D river flow modeling and 1-D–2-D drainage overflow modeling. The reliability of the 1-D ... model efficiency coefficient (NSE), and relative error (RE). The performance of the 1-D–2-D model was ...

Abstract	Coupled with climate change, the urbanization-driven increase in the frequency and intensity of floods can be seen in both developing and developed countries, and Malaysia is no exemption. As part of flood hazard mitigation, this study aimed to simulate the urban flood scenarios in Malaysia’s urbanized catchments. The flood simulation was performed using the Personal Computer Storm Water Management Model (PCSWMM) modeling of the Damansara catchment as a case study. An integrated hydrologic-hydraulic model was developed for the 1-D river flow modeling and 1-D–2-D drainage overflow modeling. The reliability of the 1-D river flow model was confirmed through the calibration and validation, in which the water level in TTDI Jaya was satisfactorily predicted, supported by the coefficient of determination (R 2 ), Nash–Sutcliffe model efficiency coefficient (NSE), and relative error (RE). The performance of the 1-D–2-D model was further demonstrated based on the flood depth, extent, and risk caused by the drainage overflow. Two scenarios were tested, and the comparison results showed that the current drainage effectively reduced the drainage overflow due to the increased size of drains compared to the historic drainage in 2015. The procedure and findings of this study could serve as references for the application in flood mitigation planning worldwide, especially for developing countries.
Keywords	urban flood ; PCSWMM ; river flow ; drainage overflow ; risk mapping ; Technology ; T ; Engineering (General). Civil engineering (General) ; TA1-2040 ; Biology (General) ; QH301-705.5 ; Physics ; QC1-999 ; Chemistry ; QD1-999
Subject code	550
Language	English
Publishing date	2021-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: Base excision repair of the N-(2-deoxy-d-erythro-pentofuranosyl)-urea lesion by the hNEIL1 glycosylase.

Tomar, Rachana / Minko, Irina G / Sharma, Pankaj / Kellum, Andrew H / Lei, Li / Harp, Joel M / Iverson, T M / Lloyd, R Stephen / Egli, Martin / Stone, Michael P

Nucleic acids research

2023 Volume 51, Issue 8, Page(s) 3754–3769

Abstract: The N-(2-deoxy-d-erythro-pentofuranosyl)-urea DNA lesion forms following hydrolytic fragmentation ...

Abstract	The N-(2-deoxy-d-erythro-pentofuranosyl)-urea DNA lesion forms following hydrolytic fragmentation of cis-5R,6S- and trans-5R,6R-dihydroxy-5,6-dihydrothymidine (thymine glycol, Tg) or from oxidation of 7,8-dihydro-8-oxo-deoxyguanosine (8-oxodG) and subsequent hydrolysis. It interconverts between α and β deoxyribose anomers. Synthetic oligodeoxynucleotides containing this adduct are efficiently incised by unedited (K242) and edited (R242) forms of the hNEIL1 glycosylase. The structure of a complex between the active site unedited mutant CΔ100 P2G hNEIL1 (K242) glycosylase and double-stranded (ds) DNA containing a urea lesion reveals a pre-cleavage intermediate, in which the Gly2 N-terminal amine forms a conjugate with the deoxyribose C1' of the lesion, with the urea moiety remaining intact. This structure supports a proposed catalytic mechanism in which Glu3-mediated protonation of O4' facilitates attack at deoxyribose C1'. The deoxyribose is in the ring-opened configuration with the O4' oxygen protonated. The electron density of Lys242 suggests the 'residue 242-in conformation' associated with catalysis. This complex likely arises because the proton transfer steps involving Glu6 and Lys242 are hindered due to Glu6-mediated H-bonding with the Gly2 and the urea lesion. Consistent with crystallographic data, biochemical analyses show that the CΔ100 P2G hNEIL1 (K242) glycosylase exhibits a residual activity against urea-containing dsDNA.
MeSH term(s)	Deoxyribose/chemistry ; DNA/chemistry ; DNA Damage ; DNA Repair ; Urea ; DNA Glycosylases/metabolism ; Humans
Chemical Substances	Deoxyribose (533-67-5) ; DNA (9007-49-2) ; Urea (8W8T17847W) ; NEIL1 protein, human (EC 3.2.2.-) ; DNA Glycosylases (EC 3.2.2.-)
Language	English
Publishing date	2023-04-03
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkad164
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Article ; Online: Magnetic Resonance Imaging and Freehand 3-D Ultrasound Provide Similar Estimates of Free Achilles Tendon Shape and 3-D Geometry.

Devaprakash, Daniel / Lloyd, David G / Barrett, Rod S / Obst, Steven J / Kennedy, Ben / Adams, Kahlee L / Hunter, Adam / Vlahovich, Nicole / Pease, David L / Pizzolato, Claudio

Ultrasound in medicine & biology

2019 Volume 45, Issue 11, Page(s) 2898–2905

Abstract: The purpose of this study was to assess the similarity of free Achilles tendon shape and 3-D ... geometry between magnetic resonance imaging (MRI) and freehand 3-D ultrasound (3-DUS) imaging methods ... of the Achilles tendon were acquired on two separate imaging sessions, and all 3-D reconstructions were performed using ...

Abstract	The purpose of this study was to assess the similarity of free Achilles tendon shape and 3-D geometry between magnetic resonance imaging (MRI) and freehand 3-D ultrasound (3-DUS) imaging methods. Fourteen elite/sub-elite middle-distance runners participated in the study. MRI and 3-DUS scans of the Achilles tendon were acquired on two separate imaging sessions, and all 3-D reconstructions were performed using identical methods. Shape similarity of free Achilles tendon reconstructed from MRI and 3-DUS data was assessed using Jaccard index, Hausdorff distance and root mean square error (RMSE). The Jaccard index, Hausdorff distance and RMSE values were 0.76 ± 0.05, 2.70 ± 0.70 and 0.61 ± 0.10 mm, respectively. The level of agreement between MRI and 3-DUS for free Achilles tendon volume, length and average cross-sectional area (CSA) was assessed using Bland-Altman analysis. Compared to MRI, freehand 3-DUS overestimated volume, length and average CSA by 30.6 ± 15.8 mm
MeSH term(s)	Achilles Tendon/diagnostic imaging ; Adult ; Athletes ; Female ; Humans ; Image Interpretation, Computer-Assisted ; Imaging, Three-Dimensional/methods ; Magnetic Resonance Imaging/methods ; Male ; Ultrasonography/methods
Language	English
Publishing date	2019-08-27
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186150-5
ISSN	1879-291X ; 0301-5629
ISSN (online)	1879-291X
ISSN	0301-5629
DOI	10.1016/j.ultrasmedbio.2019.07.679
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Article ; Online: Substrate specificity of human metallocarboxypeptidase D

Javier Garcia-Pardo / Sebastian Tanco / Lucía Díaz / Sayani Dasgupta / Juan Fernandez-Recio / Julia Lorenzo / Francesc X Aviles / Lloyd D Fricker

PLoS ONE, Vol 12, Iss 11, p e

Comparison of the two active carboxypeptidase domains.

2017 Volume 0187778

Abstract: Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network ...

Abstract	Metallocarboxypeptidase D (CPD) is a membrane-bound component of the trans-Golgi network that cycles to the cell surface through exocytic and endocytic pathways. Unlike other members of the metallocarboxypeptidase family, CPD is a multicatalytic enzyme with three carboxypeptidase-like domains, although only the first two domains are predicted to be enzymatically active. To investigate the enzymatic properties of each domain in human CPD, a critical active site Glu in domain I and/or II was mutated to Gln and the protein expressed, purified, and assayed with a wide variety of peptide substrates. CPD with all three domains intact displays >50% activity from pH 5.0 to 7.5 with a maximum at pH 6.5, as does CPD with mutation of domain I. In contrast, the domain II mutant displayed >50% activity from pH 6.5-7.5. CPD with mutations in both domains I and II was completely inactive towards all substrates and at all pH values. A quantitative peptidomics approach was used to compare the activities of CPD domains I and II towards a large number of peptides. CPD cleaved C-terminal Lys or Arg from a subset of the peptides. Most of the identified substrates of domain I contained C-terminal Arg, whereas comparable numbers of Lys- and Arg-containing peptides were substrates of domain II. We also report that some peptides with C-terminal basic residues were not cleaved by either domain I or II, showing the importance of the P1 position for CPD activity. Finally, the preference of domain I for C-terminal Arg was validated through molecular docking experiments. Together with the differences in pH optima, the different substrate specificities of CPD domains I and II allow the enzyme to perform distinct functions in the various locations within the cell.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
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