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Article: Clapeyron.jl: An Extensible, Open-Source Fluid Thermodynamics Toolkit

Walker, Pierre J. / Yew, Hon-Wa / Riedemann, Andrés

Industrial & engineering chemistry process design and development. 2022 May 12, v. 61, no. 20

2022

Abstract: Thermodynamic models are often vital when characterizing complex systems, particularly natural gas, electrolyte, polymer, pharmaceutical, and biological systems. However, their implementations have historically been abstruse and cumbersome, and as such, ... ...

Abstract	Thermodynamic models are often vital when characterizing complex systems, particularly natural gas, electrolyte, polymer, pharmaceutical, and biological systems. However, their implementations have historically been abstruse and cumbersome, and as such, the only options available were black box commercial tools. In this article, we present Clapeyron.jl: a pioneering attempt at an open-source fluid thermodynamics toolkit to build and make use of thermodynamic models. This toolkit is built using Julia, a modern language for scientific computing known for its ease of use, extensibility, and first-class support for differentiable programming. We currently support more models than any package available, including standard cubic (SRK, PR, PSRK, etc.), activity coefficient (NRTL, UNIFAC, etc.), COSMO-based, and the venerable SAFT equations. The property estimation methods supported are extensive, including bulk, VLE, LLE, VLLE, and critical properties. With Clapeyron.jl, researchers and enthusiasts alike will be able to focus on the application and worry less about the implementation.
Keywords	chemistry ; electrolytes ; extensibility ; natural gas ; polymers ; process design ; thermodynamics
Language	English
Dates of publication	2022-0512
Size	p. 7130-7153.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1484436-9
ISSN	1520-5045 ; 0888-5885
ISSN (online)	1520-5045
ISSN	0888-5885
DOI	10.1021/acs.iecr.2c00326
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Cancer and Covid-19: Collectively catastrophic.

du Plessis, M / Fourie, C / Riedemann, J / de Villiers, W J S / Engelbrecht, A M

Cytokine & growth factor reviews

2021 Volume 63, Page(s) 78–89

Abstract: The Covid-19 pandemic has spread rapidly across the globe, resulting in more than 3 million deaths worldwide. The symptoms of Covid-19 are usually mild and non-specific, however in some cases patients may develop acute respiratory distress syndrome (ARDS) ...

Abstract	The Covid-19 pandemic has spread rapidly across the globe, resulting in more than 3 million deaths worldwide. The symptoms of Covid-19 are usually mild and non-specific, however in some cases patients may develop acute respiratory distress syndrome (ARDS) and systemic inflammation. Individuals with inflammatory or immunocompromising illnesses, such as cancer, are more susceptible to develop ARDS and have higher rates of mortality. This is mediated through an initial hyperstimulated immune response which results in elevated levels of pro-inflammatory cytokines and a subsequent cytokine storm. This potentiates positive feedback loops which are unable to be balanced by anti-inflammatory mediators. Therefore, elevated levels of IL-1β, as a result of NLRP3 inflammasome activation, as well as IL-6 and TNF-α amongst many others, contribute to the progression of various cancer types. Furthermore, Covid-19 progression is associated with the depletion of CD8
MeSH term(s)	COVID-19 ; Cytokine Release Syndrome ; Cytokines ; Humans ; Neoplasms ; Pandemics ; SARS-CoV-2 ; Tumor Microenvironment
Chemical Substances	Cytokines
Language	English
Publishing date	2021-10-23
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1330534-7
ISSN	1879-0305 ; 1359-6101
ISSN (online)	1879-0305
ISSN	1359-6101
DOI	10.1016/j.cytogfr.2021.10.005
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Article ; Online: [No title information]

Zeidler, Robert / Dudeck, Manuela / Frank, Udo / Gerlinger, Gabriel / Hesse, Dirk / Muysers, Jutta / Pollmächer, Thomas / Riedemann, Christian / Sander, Julia / Völlm, Birgit / Müller, Jürgen L

Der Nervenarzt

2024 Volume 95, Issue 1, Page(s) 9

Title translation	Erratum zu: Die Situation des deutschen Maßregelvollzugs – Ergebnisse einer Umfrage der DGPPN.
Language	German
Publishing date	2024-01-04
Publishing country	Germany
Document type	Published Erratum
ZDB-ID	123291-5
ISSN	1433-0407 ; 0028-2804
ISSN (online)	1433-0407
ISSN	0028-2804
DOI	10.1007/s00115-023-01582-5
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Article: Pharmacokinetic analysis of vilobelimab, anaphylatoxin C5a and antidrug antibodies in PANAMO: a phase 3 study in critically ill, invasively mechanically ventilated COVID-19 patients.

Lim, Endry H T / Vlaar, Alexander P J / de Bruin, Sanne / Rückinger, Simon / Thielert, Claus / Habel, Maria / Guo, Renfeng / Burnett, Bruce P / Dickinson, James / Brouwer, Matthijs C / Riedemann, Niels C / van de Beek, Diederik

Intensive care medicine experimental

2023 Volume 11, Issue 1, Page(s) 37

Abstract: Background: Vilobelimab, a complement 5a (C5a)-specific monoclonal antibody, reduced mortality in critically ill COVID-19 patients in a phase 3 multicentre, randomized, double-blind, placebo-controlled study. As part of the study, vilobelimab ... ...

Abstract	Background: Vilobelimab, a complement 5a (C5a)-specific monoclonal antibody, reduced mortality in critically ill COVID-19 patients in a phase 3 multicentre, randomized, double-blind, placebo-controlled study. As part of the study, vilobelimab concentrations and C5a levels as well as antidrug antibodies (ADAs) to vilobelimab were analysed. Results: From Oct 1, 2020 to Oct 4, 2021, 368 invasively mechanically ventilated COVID-19 patients were randomized: 177 patients were randomly assigned to receive vilobelimab while 191 patients received placebo. Pharmacokinetic sampling was only performed at sites in Western Europe. Blood samples for vilobelimab measurements were available for 93 of 177 (53%) patients in the vilobelimab group and 99 of 191 (52%) patients in the placebo group. On day 8, after three infusions, mean vilobelimab (trough) concentrations ranged from 21,799.3 to 302,972.1 ng/mL (geometric mean 137,881.3 ng/mL). Blood samples for C5a measurements were available for 94 of 177 (53%) patients in the vilobelimab group and 99 of 191 (52%) patients in the placebo group. At screening, C5a levels were highly elevated and comparable between groups. In the vilobelimab group, median C5a levels were 118.3 ng/mL [IQR 71.2-168.2 ng/mL] and in the placebo group, median C5a levels were 104.6 ng/mL [IQR 77.5-156.6 ng/mL]. By day 8, median C5a levels were reduced by 87% in the vilobelimab group (median 14.5 ng/mL [IQR 9.5-21.0 ng/mL], p < 0.001) versus an 11% increase in the placebo group (median 119.2 ng/mL [IQR 85.9-152.1 ng/mL]). Beyond day 8, though plasma sampling was sparse, C5a levels did not reach screening levels in the vilobelimab group while C5a levels remained elevated in the placebo group. Treatment-emergent ADAs were observed in one patient in the vilobelimab group at hospital discharge on day 40 and in one patient in the placebo group at hospital discharge on day 25. Conclusions: This analysis shows that vilobelimab efficiently inhibits C5a in critically ill COVID-19 patients. There was no evidence of immunogenicity associated with vilobelimab treatment. Trial registration ClinicalTrials.gov, NCT04333420. Registered 3 April 2020, https://clinicaltrials.gov/ct2/show/NCT04333420.
Language	English
Publishing date	2023-06-19
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2740385-3
ISSN	2197-425X
ISSN	2197-425X
DOI	10.1186/s40635-023-00520-8
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Article ; Online: Die Situation des deutschen Maßregelvollzugs – Ergebnisse einer Umfrage der DGPPN.

Zeidler, Robert / Dudeck, Manuela / Frank, Udo / Gerlinger, Gabriel / Hesse, Dirk / Muysers, Jutta / Pollmächer, Thomas / Riedemann, Christian / Sander, Julia / Völlm, Birgit / Müller, Jürgen L

Der Nervenarzt

2023 Volume 95, Issue 1, Page(s) 1–8

Abstract: Background and objective: In German forensic psychiatry detention under Sections 63 and 64 of the German Penal Code have been repeatedly reformed over the past years; however, despite the most recent amendments to the law on detention, clinics and state ...

Title translation	The situation in the German forensic commitment-Results of a survey by the DGPPN.
Abstract	Background and objective: In German forensic psychiatry detention under Sections 63 and 64 of the German Penal Code have been repeatedly reformed over the past years; however, despite the most recent amendments to the law on detention, clinics and state authorities warn of insufficient capacities and worrying conditions. Media reports paint a defiant picture. At the same time, there is a lack of valid data that would allow an objective description of the situation in forensic psychiatry. Against this background the management of institutions in Germany has been surveyed. Material and methods: The survey was conducted as an online survey and sent to all 78 forensic hospitals in Germany. The survey covered topics such as structural data of the facilities, the occupancy and staffing situation, incidents, support from supervisory authorities and funding agencies, and patient characteristics. The results are presented descriptively. Results: Of the 78 facilities contacted, 45 (approximately 60%) participated at least partially in the survey. Many of the clinics (68.5%) complained of significant overcrowding. A clear lack of staff and rooms was reported, at the same time it was stated that patients do not receive adequate treatment. Approximately 1 in 5 patients have a length of stay for more than 10 years and one third of the clinics reported an increasing number of physical assaults by patients. Conclusion: This overview shows that the forensic psychiatric hospitals are in very different but generally strained situations. A significant number of clinics are under great pressure. Financial, structural, spatial and personnel resources were described as insufficient to properly and professionally fulfill the legal mandate. The treatment standards presented by the DGPPN in 2017 are not met in many clinics.
MeSH term(s)	Humans ; Forensic Psychiatry ; Surveys and Questionnaires ; Hospitals, Psychiatric ; Germany
Language	German
Publishing date	2023-11-09
Publishing country	Germany
Document type	English Abstract ; Journal Article
ZDB-ID	123291-5
ISSN	1433-0407 ; 0028-2804
ISSN (online)	1433-0407
ISSN	0028-2804
DOI	10.1007/s00115-023-01564-7
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Article ; Online: A Novel Intron-Encoded Neuropilin-1 Isoform in Pancreatic Islets Associated With Very Young Age of Onset of Type 1 Diabetes.

MacDonald, Michael J / Ansari, Israr-Ul H / Riedemann, Amy S / Stoker, Scott W / Eickhoff, Jens C / Chlebeck, Peter J / Fernandez, Luis A / Longacre, Melissa J

Diabetes

2022 Volume 71, Issue 9, Page(s) 2058–2063

Abstract: Net synthesis of pancreatic β-cells peaks before 2 years of life. β-Cell mass is set within the first 5 years of life. In-frame translational readthrough of the NRP1 gene exon 9 into intron 9 generates a truncated neuropilin-1 protein lacking downstream ... ...

Abstract	Net synthesis of pancreatic β-cells peaks before 2 years of life. β-Cell mass is set within the first 5 years of life. In-frame translational readthrough of the NRP1 gene exon 9 into intron 9 generates a truncated neuropilin-1 protein lacking downstream sequence necessary for binding VEGF that stimulates β-cell replication. VEGF is critical for developing but not adult islet neogenesis. Herein we show that cells in human pancreatic islets containing the full-length neuropilin-1 possess insulin but cells that contain the truncated neuropilin-1 are devoid of insulin. Decreased insulin cells increases susceptibility to onset of type 1 diabetes at a younger age. We also show that the frequency of a genetic marker in NRP1 intron 9 is higher among patients with onset of type 1 diabetes before age 4 years (31.8%), including those with onset at 0.67-2.00 and 2-4 years, compared with that in patients with onset at 4-8 years, at 8-12 years, and after 16 years (16.1%) with frequency equal to that in subjects without diabetes (16.0%). Decreased insulin cells plus the genetic data are consistent with a low effect mechanism that alters the onset of type 1 diabetes to a very young age in some patients, thus supporting the endotype concept that type 1 diabetes is a heterogeneous disease.
MeSH term(s)	Age of Onset ; Child, Preschool ; Diabetes Mellitus, Type 1/genetics ; Diabetes Mellitus, Type 1/metabolism ; Humans ; Insulin/metabolism ; Introns/genetics ; Islets of Langerhans/metabolism ; Neuropilin-1/genetics ; Neuropilin-1/metabolism ; Protein Isoforms/genetics ; Vascular Endothelial Growth Factor A/metabolism
Chemical Substances	Insulin ; Protein Isoforms ; Vascular Endothelial Growth Factor A ; Neuropilin-1 (144713-63-3)
Language	English
Publishing date	2022-06-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80085-5
ISSN	1939-327X ; 0012-1797
ISSN (online)	1939-327X
ISSN	0012-1797
DOI	10.2337/db21-1070
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Article ; Online: Community-wide consequences of nonconsumptive predator effects on a foundation species.

Catalán, Alexis M / Büchner-Miranda, Joseline / Riedemann, Bárbara / Chaparro, Oscar R / Valdivia, Nelson / Scrosati, Ricardo A

The Journal of animal ecology

2021 Volume 90, Issue 5, Page(s) 1307–1316

Abstract: Predators can exert nonconsumptive effects (NCEs) on prey, which often take place through prey behavioural adjustments to minimise predation risk. As NCEs are widespread in nature, interest is growing to determine whether NCEs on a prey species can ... ...

Abstract	Predators can exert nonconsumptive effects (NCEs) on prey, which often take place through prey behavioural adjustments to minimise predation risk. As NCEs are widespread in nature, interest is growing to determine whether NCEs on a prey species can indirectly influence several other species simultaneously, thus leading to changes in community structure. In this study, we investigate whether a predator can exert NCEs on a foundation species and indirectly affect community structure. Through laboratory experiments, we first tested whether the predatory marine snail Acanthina monodon exerts negative NCEs on larviphagy (consumption of pelagic larvae) and phytoplankton filtration rates of the mussel Perumytilus purpuratus, an intertidal foundation species. These hypotheses stem from the notion that mussels may decrease feeding activities in the presence of predator cues to limit detection by predators. Afterwards, a field experiment tested whether the presence of A. monodon near mussel beds leads to higher colonisation rates of invertebrates that reproduce through pelagic larvae (expected under a lower larviphagy in P. purpuratus) and to a lower algal biomass on P. purpuratus shells (expected under a lower metabolite excretion in the mussels), thereby changing the community structure of the species typically found in P. purpuratus beds. The laboratory experiments revealed that waterborne cues from A. monodon limit the larviphagy and filtration rates of P. purpuratus. In turn, the field experiment showed that A. monodon cues led to greater abundances of barnacles and bivalves and a lower algal biomass in P. purpuratus beds, thus altering community structure. Overall, this study shows that a predator can indirectly affect community structure through NCEs on an invertebrate foundation species. As invertebrate foundation species are ubiquitous worldwide, understanding predator NCEs on these organisms could help to better understand community regulation in systems structured by such species.
MeSH term(s)	Animals ; Bivalvia ; Ecosystem ; Food Chain ; Predatory Behavior ; Snails ; Thoracica
Language	English
Publishing date	2021-03-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/1365-2656.13455
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Article ; Online: Accurate prostate cancer detection based on enrichment and characterization of prostate cancer specific circulating tumor cells.

Limaye, Sewanti / Chowdhury, Simon / Rohatgi, Nitesh / Ranade, Anantbhushan / Syed, Nelofer / Riedemann, Johann / Patil, Darshana / Akolkar, Dadasaheb / Datta, Vineet / Patel, Shoeb / Chougule, Rohit / Shejwalkar, Pradyumna / Bendale, Kiran / Apurwa, Sachin / Schuster, Stefan / John, Jinumary / Srinivasan, Ajay / Datar, Rajan

Cancer medicine

2023 Volume 12, Issue 8, Page(s) 9116–9127

Abstract: Background: The low specificity of serum PSA resulting in the inability to effectively differentiate prostate cancer from benign prostate conditions is a persistent clinical challenge. The low sensitivity of serum PSA results in false negatives and can ... ...

Abstract	Background: The low specificity of serum PSA resulting in the inability to effectively differentiate prostate cancer from benign prostate conditions is a persistent clinical challenge. The low sensitivity of serum PSA results in false negatives and can miss high-grade prostate cancers. We describe a non-invasive test for detection of prostate cancer based on functional enrichment of prostate adenocarcinoma associated circulating tumor cells (PrAD-CTCs) from blood samples followed by their identification by immunostaining for pan-cytokeratins (PanCK), prostate specific membrane antigen (PSMA), alpha methyl-acyl coenzyme-A racemase (AMACR), epithelial cell adhesion molecule (EpCAM), and common leucocyte antigen (CD45). Methods: Analytical validation studies were performed to establish the performance characteristics of the test using VCaP prostate cancer cells spiked into healthy donor blood (HDB). The clinical performance characteristics of the test were evaluated in a case-control study with 160 known prostate cancer cases and 800 healthy males, followed by a prospective clinical study of 210 suspected cases of prostate cancer. Results: Analytical validation established analyte stability as well as acceptable performance characteristics. The test showed 100% specificity and 100% sensitivity to differentiate prostate cancer cases from healthy individuals in the case control study and 91.2% sensitivity and 100% specificity to differentiate prostate cancers from benign prostate conditions in the prospective clinical study. Conclusions: The test accurately detects PrAD-CTCs with high sensitivity and specificity irrespective of stage, serum PSA or Gleason score, which translates into low risks of false negatives or overdiagnosis. The high accuracy of the test could offer advantages over PSA based prostate cancer detection.
MeSH term(s)	Male ; Humans ; Prostate-Specific Antigen ; Prostate/pathology ; Case-Control Studies ; Neoplastic Cells, Circulating ; Prospective Studies ; Prostatic Neoplasms/pathology ; Biomarkers, Tumor
Chemical Substances	Prostate-Specific Antigen (EC 3.4.21.77) ; Biomarkers, Tumor
Language	English
Publishing date	2023-01-30
Publishing country	United States
Document type	Journal Article
ZDB-ID	2659751-2
ISSN	2045-7634 ; 2045-7634
ISSN (online)	2045-7634
ISSN	2045-7634
DOI	10.1002/cam4.5649
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Article ; Online: Clinical efficacy of complement C5a inhibition by IFX-1 in hidradenitis suppurativa: an open-label single-arm trial in patients not eligible for adalimumab.

Giamarellos-Bourboulis, E J / Argyropoulou, M / Kanni, T / Spyridopoulos, T / Otto, I / Zenker, O / Guo, R / Riedemann, N C

The British journal of dermatology

2020 Volume 183, Issue 1, Page(s) 176–178

MeSH term(s)	Adalimumab/therapeutic use ; Antibodies, Monoclonal ; Complement C5a ; Hidradenitis Suppurativa/drug therapy ; Humans ; Treatment Outcome
Chemical Substances	Antibodies, Monoclonal ; Complement C5a (80295-54-1) ; vilobelimab (F5T0RF9ZJA) ; Adalimumab (FYS6T7F842)
Language	English
Publishing date	2020-03-04
Publishing country	England
Document type	Clinical Trial ; Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	80076-4
ISSN	1365-2133 ; 0007-0963
ISSN (online)	1365-2133
ISSN	0007-0963
DOI	10.1111/bjd.18877
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Article ; Conference proceedings: Potential role of BMP-9 in the regulation of PD-L1/PD1-mediated immune evasion of HCC cells

Riedemann, G / Gaitantzi, H / Araos, J / Ebert, M / Breitkopf-Heinlein, K

Zeitschrift für Gastroenterologie

2020 Volume 58, Issue 08

Event/congress	DGVS Digital: BEST OF DGVS, online, 2020-09-16
Language	German
Publishing date	2020-08-01
Publisher	© Georg Thieme Verlag KG
Publishing place	Stuttgart ; New York
Document type	Article ; Conference proceedings
ZDB-ID	201387-3
ISSN	1439-7803 ; 0044-2771 ; 0172-8504
ISSN (online)	1439-7803
ISSN	0044-2771 ; 0172-8504
DOI	10.1055/s-0040-1716205
Database	Thieme publisher's database

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