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Article ; Online: Management of Patients with Multidrug-Resistant Organisms in Outpatient Dialysis Facilities.

Dittrich, Mary / Silberzweig, Jeffrey / Hymes, Jeffrey L / Giullian, Jeff / Green, Gopa / Wong, Leslie P / Freedman, Barry I / Bhat, J Ganesh / Spry, Leslie / Taylor, Robert / Spech, Richard / Durvasula, Raghu / Blue, Sky R

Clinical journal of the American Society of Nephrology : CJASN

2023

Language	English
Publishing date	2023-12-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	2226665-3
ISSN	1555-905X ; 1555-9041
ISSN (online)	1555-905X
ISSN	1555-9041
DOI	10.2215/CJN.0000000000000419
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Article ; Online: Revitalizing antibiotic discovery and development through in vitro modelling of in-patient conditions.

Sollier, Julie / Basler, Marek / Broz, Petr / Dittrich, Petra S / Drescher, Knut / Egli, Adrian / Harms, Alexander / Hierlemann, Andreas / Hiller, Sebastian / King, Carolyn G / McKinney, John D / Moran-Gilad, Jacob / Neher, Richard A / Page, Malcolm G P / Panke, Sven / Persat, Alexandre / Picotti, Paola / Rentsch, Katharina M / Rivera-Fuentes, Pablo /

Sauer, Uwe / Stolz, Daiana / Tschudin-Sutter, Sarah / van Delden, Christian / van Nimwegen, Erik / Veening, Jan-Willem / Zampieri, Mattia / Zinkernagel, Annelies S / Khanna, Nina / Bumann, Dirk / Jenal, Urs / Dehio, Christoph

Nature microbiology

2024 Volume 9, Issue 1, Page(s) 1–3

MeSH term(s)	Humans ; Anti-Bacterial Agents/pharmacology ; Drug Discovery
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2024-01-04
Publishing country	England
Document type	Journal Article
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-023-01566-w
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Article ; Online: Spatial Rule-Based Simulations: The SRSim Software.

Henze, Richard / Grünert, Gerd / Ibrahim, Bashar / Dittrich, Peter

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1945, Page(s) 231–249

Abstract: SRSim combines rule-based reaction network models with spatial particle simulations allowing to simulate the dynamics of large molecular complexes changing according to a set of chemical reaction rules. As the rule can contain patterns of molecular ... ...

Abstract	SRSim combines rule-based reaction network models with spatial particle simulations allowing to simulate the dynamics of large molecular complexes changing according to a set of chemical reaction rules. As the rule can contain patterns of molecular complexes and specific states of certain binding sites, a combinatorially complex or even infinitely sized reaction network can be defined. Particles move in a three-dimensional space according to molecular dynamics implemented by LAMMPS, while the BioNetGen language is used to formulate reaction rules. Geometric information is added in a specific XML format. The simulation protocol is exemplified by two different variants of polymerization as well as a toy model of DNA helix formation. SRSim is open source and available for download.
MeSH term(s)	DNA/chemistry ; DNA/genetics ; Models, Biological ; Molecular Dynamics Simulation ; Nucleic Acid Conformation ; Software
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2019-04-03
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9102-0_10
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Article ; Online: Changes in Physical Activity Associated With a Multicomponent Weight-Loss Randomized Controlled Trial for Youth With Intellectual Disabilities.

Fleming, Richard K / Eliasziw, Misha / Dittrich, Gretchen A / Curtin, Carol / Maslin, Melissa / Must, Aviva / Bandini, Linda G

Adapted physical activity quarterly : APAQ

2023 Volume 41, Issue 2, Page(s) 287–305

Abstract: ... in moderate to vigorous PA between participants in FBBI-M and FBBI-C at 18 months was 14.0 (5.1) min/day (p ... 005); mean (SE) difference in light PA was 47.4 (27.4) min/day (p = .08). Increasing PA ...

Abstract	Youth with intellectual disabilities engage in low levels of physical activity (PA). An aim of this family-based weight-loss behavioral intervention (FBBI) trial was to increase and sustain PA in these youth. Accelerometry data were available from 21 individuals with intellectual disabilities, age 14-22 years. Each completed the 6-month FBBI, after which 10 completed a 6-month maintenance intervention (FBBI-M), and 11 received no further intervention (FBBI-C). Twenty participated in a further 6-month follow-up. Accelerometry data were analyzed using linear mixed models. During FBBI, mean (SE) moderate to vigorous PA increased by 4.1 (2.5) min/day and light PA by 24.2 (13.5) min/day. Mean (SE) difference in moderate to vigorous PA between participants in FBBI-M and FBBI-C at 18 months was 14.0 (5.1) min/day (p = .005); mean (SE) difference in light PA was 47.4 (27.4) min/day (p = .08). Increasing PA through behavioral intervention is possible in youth with intellectual disabilities.
MeSH term(s)	Humans ; Adolescent ; Young Adult ; Adult ; Intellectual Disability ; Exercise ; Sedentary Behavior ; Weight Loss ; Accelerometry
Language	English
Publishing date	2023-11-09
Publishing country	United States
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	995992-0
ISSN	1543-2777 ; 0736-5829
ISSN (online)	1543-2777
ISSN	0736-5829
DOI	10.1123/apaq.2023-0030
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Article ; Online: A Dynamical Model for Activating and Silencing the Mitotic Checkpoint.

Henze, Richard / Dittrich, Peter / Ibrahim, Bashar

Scientific reports

2017 Volume 7, Issue 1, Page(s) 3865

Abstract: The spindle assembly checkpoint (SAC) is an evolutionarily conserved mechanism, exclusively sensitive to the states of kinetochores attached to microtubules. During metaphase, the anaphase-promoting complex/cyclosome (APC/C) is inhibited by the SAC but ... ...

Abstract	The spindle assembly checkpoint (SAC) is an evolutionarily conserved mechanism, exclusively sensitive to the states of kinetochores attached to microtubules. During metaphase, the anaphase-promoting complex/cyclosome (APC/C) is inhibited by the SAC but it rapidly switches to its active form following proper attachment of the final spindle. It had been thought that APC/C activity is an all-or-nothing response, but recent findings have demonstrated that it switches steadily. In this study, we develop a detailed mathematical model that considers all 92 human kinetochores and all major proteins involved in SAC activation and silencing. We perform deterministic and spatially-stochastic simulations and find that certain spatial properties do not play significant roles. Furthermore, we show that our model is consistent with in-vitro mutation experiments of crucial proteins as well as the recently-suggested rheostat switch behavior, measured by Securin or CyclinB concentration. Considering an autocatalytic feedback loop leads to an all-or-nothing toggle switch in the underlying core components, while the output signal of the SAC still behaves like a rheostat switch. The results of this study support the hypothesis that the SAC signal varies with increasing number of attached kinetochores, even though it might still contain toggle switches in some of its components.
MeSH term(s)	Algorithms ; Cell Cycle Checkpoints ; Mitosis/physiology ; Models, Biological ; Mutation ; Spindle Apparatus/metabolism
Language	English
Publishing date	2017-06-20
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/s41598-017-04218-2
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Article ; Online: Picoplankton accumulate and recycle polyphosphate to support high primary productivity in coastal Lake Ontario.

Li, Jiying / Plouchart, Diane / Zastepa, Arthur / Dittrich, Maria

Scientific reports

2019 Volume 9, Issue 1, Page(s) 19563

Abstract: ... the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic bay ... phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle remain ... to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under ...

Abstract	Phytoplankton can accumulate polyphosphate (polyP) to alleviate limitation of essential nutrient phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle remain elusive. Previously reported polyP enrichment in low-phosphorus oligotrophic marine waters contradicts the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic bay of Lake Ontario, planktonic polyP is controlled by multiple mechanisms and responds strongly to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under acute P stress. Low phosphorus also triggers enrichment of polyP that can be preferentially recycled to attenuate P lost. We discover that picoplankton, despite their low production rates, are responsible for the dynamic polyP metabolisms. Picoplankton store and liberate polyP to support the high primary productivity of blooming algae. PolyP mechanisms enable efficient P recycling on ecosystem and even larger scales.
Language	English
Publishing date	2019-12-20
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/s41598-019-56042-5
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Article ; Online: A family-based weight loss randomized controlled trial for youth with intellectual disabilities.

Bandini, Linda G / Eliasziw, Misha / Dittrich, Gretchen A / Curtin, Carol / Maslin, Melissa / Must, Aviva / Boutelle, Kerri N / Fleming, Richard K

Pediatric obesity

2021 Volume 16, Issue 11, Page(s) e12816

Abstract: ... the FBBI lost, on average (SE), 5.1 (1.1) kg (P < .001) over 6 months. The 13 participants who were ... those who received FBBI-M lost, on average (SE), 4.4 (1.7) kg more than those who received FBBI-C (-7.6 vs -3.2 kg, P ...

Abstract	Background: Scant data exist on weight loss interventions for youth with intellectual disabilities (ID). Objective: To compare weight loss among youth with ID randomized to a 6-month, family-based behavioural intervention (FBBI) or a waitlist and to compare weight loss among youth who completed a 6-month maintenance (FBBI-M) intervention to a control group (FBBI-C). Methods: Youth with ID and overweight/obesity, aged 14-22 years, were randomized to the FBBI or to a waitlist and subsequently randomized to a maintenance intervention or a control group. Sessions were held weekly during the FBBI and biweekly during the FBBI-M. Using an intention-to-treat approach, we used linear mixed models to test differences in the change in weight and in BMI from the start of FBBI. Results: The 24 participants who received the FBBI lost, on average (SE), 5.1 (1.1) kg (P < .001) over 6 months. The 13 participants who were waitlisted gained, on average (SE), 1.2 (1.6) kg over the 6-month waiting period. At 12 months, those who received FBBI-M lost, on average (SE), 4.4 (1.7) kg more than those who received FBBI-C (-7.6 vs -3.2 kg, P-value = .008). Conclusion: Participation in an intensive FBBI for weight loss with ID was efficacious, and continued participation in a maintenance intervention yielded additional weight loss.
MeSH term(s)	Adolescent ; Humans ; Intellectual Disability/therapy ; Weight Loss
Language	English
Publishing date	2021-06-01
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2655527-X
ISSN	2047-6310 ; 2047-6302
ISSN (online)	2047-6310
ISSN	2047-6302
DOI	10.1111/ijpo.12816
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Article ; Online: Assessment of Pharmacokinetic Interaction Between Capecitabine and Cetuximab in Metastatic Colorectal Cancer Patients.

Rachar, Veronika / Czejka, Martin / Kitzmueller, Marie / Buchner, Philipp / Lichtneckert, Maria / Greil, Richard / Geiler, Herbert / Dittrich, Christian

Anticancer research

2016 Volume 36, Issue 9, Page(s) 4715–4723

Abstract: ... 1,000 mg/m(2) bid p.o.), followed by CCB plus CTX (loading dose (LD)=400 mg/m(2) followed by 250 mg ...

Abstract	Aim: This study focuses on the plasma disposition and metabolic activation of capecitabine (CCB) when administered alone or when combined with cetuximab (CTX). Patients and methods: Twenty-four chemo-naïve patients with KRAS wild-type colorectal cancer were randomized into two arms and received either CCB alone (1,000 mg/m(2) bid p.o.), followed by CCB plus CTX (loading dose (LD)=400 mg/m(2) followed by 250 mg/m(2) weekly i.v. maintenance dose) (Arm A; n=12 patients (patients)) or CCB plus CTX followed by CCB alone (Arm B; n=12 patients). Plasma samples were collected from the cubital vein and CCB, 5'-desoxy-5-fluorocytidine (5'-DFCR) and 5'-desoxy-5 fluorouridine (5'-DFUR) were quantified by a sensitive, selective reversed phase high-performance liquid chromatography (HPLC) assay. Non-compartment pharmacokinetic parameters have been calculated by Phoenix WinNonlin. Results: No clinically relevant impact of CTX on CCB pharmacokinetic parameters and metabolic conversion could be detected in both arms after statistical evaluation (ANOVA). Conclusion: From the pharmacokinetic point of view, co-administration of CTX to CCB seems to be safe.
MeSH term(s)	Adult ; Aged ; Antineoplastic Combined Chemotherapy Protocols/administration & dosage ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Capecitabine/administration & dosage ; Capecitabine/adverse effects ; Capecitabine/blood ; Capecitabine/pharmacokinetics ; Cetuximab/administration & dosage ; Cetuximab/adverse effects ; Cetuximab/blood ; Colorectal Neoplasms/blood ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/pathology ; Drug Interactions ; Female ; Humans ; Male ; Middle Aged ; Neoplasm Metastasis ; Proto-Oncogene Proteins p21(ras)/genetics
Chemical Substances	KRAS protein, human ; Capecitabine (6804DJ8Z9U) ; Proto-Oncogene Proteins p21(ras) (EC 3.6.5.2) ; Cetuximab (PQX0D8J21J)
Language	English
Publishing date	2016
Publishing country	Greece
Document type	Clinical Trial, Phase II ; Journal Article ; Randomized Controlled Trial
ZDB-ID	604549-2
ISSN	1791-7530 ; 0250-7005
ISSN (online)	1791-7530
ISSN	0250-7005
DOI	10.21873/anticanres.11026
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Article ; Online: Picoplankton accumulate and recycle polyphosphate to support high primary productivity in coastal Lake Ontario

Jiying Li / Diane Plouchart / Arthur Zastepa / Maria Dittrich

Scientific Reports, Vol 9, Iss 1, Pp 1-

2019 Volume 10

Abstract: ... contradicts the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic ... nutrient phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle ... to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under ...

Abstract	Abstract Phytoplankton can accumulate polyphosphate (polyP) to alleviate limitation of essential nutrient phosphorus (P). Yet polyP metabolisms in aquatic systems and their roles in P biogeochemical cycle remain elusive. Previously reported polyP enrichment in low-phosphorus oligotrophic marine waters contradicts the common view of polyP as a luxury P-storage molecule. Here, we show that in a P-rich eutrophic bay of Lake Ontario, planktonic polyP is controlled by multiple mechanisms and responds strongly to seasonal variations. Plankton accumulate polyP as P storage under high-P conditions via luxury uptake and use it under acute P stress. Low phosphorus also triggers enrichment of polyP that can be preferentially recycled to attenuate P lost. We discover that picoplankton, despite their low production rates, are responsible for the dynamic polyP metabolisms. Picoplankton store and liberate polyP to support the high primary productivity of blooming algae. PolyP mechanisms enable efficient P recycling on ecosystem and even larger scales.
Keywords	Medicine ; R ; Science ; Q
Subject code	333
Language	English
Publishing date	2019-12-01T00:00:00Z
Publisher	Nature Publishing Group
Document type	Article ; Online
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Article ; Online: Structural analysis of in silico mutant experiments of human inner-kinetochore structure.

Henze, Richard / Huwald, Jan / Mostajo, Nelly / Dittrich, Peter / Ibrahim, Bashar

Bio Systems

2015 Volume 127, Page(s) 47–59

Abstract: Large multi-molecular complexes like the kinetochore are lacking of suitable methods to determine their spatial structure. Here, we use and evaluate a novel modeling approach that combines rule-bases reaction network models with spatial molecular ... ...

Abstract	Large multi-molecular complexes like the kinetochore are lacking of suitable methods to determine their spatial structure. Here, we use and evaluate a novel modeling approach that combines rule-bases reaction network models with spatial molecular geometries. In particular, we introduce a method that allows to study in silico the influence of single interactions (e.g. bonds) on the spatial organization of large multi-molecular complexes and apply this method to an extended model of the human inner-kinetochore. Our computational analysis method encompasses determination of bond frequency, geometrical distances, statistical moments, and inter-dependencies between bonds using mutual information. For the analysis we have extend our previously reported human inner-kinetochore model by adding 13 new protein interactions and three protein geometry details. The model is validated by comparing the results of in silico with reported in vitro single protein deletion experiments. Our studies revealed that most simulations mimic the in vitro behavior of the kinetochore complex as expected. To identify the most important bonds in this model, we have created 39 mutants in silico by selectively disabling single protein interactions. In a total of 11,800 simulation runs we have compared the resulting structures to the wild-type. In particular, this allowed us to identify the interaction Cenp-W-H3 and Cenp-S-Cenp-X as having the strongest influence on the inner-kinetochore's structure. We conclude that our approach can become a useful tool for the in silico dynamical study of large, multi-molecular complexes.
MeSH term(s)	Computer Simulation ; Humans ; Kinetochores/chemistry ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Interaction Mapping
Language	English
Publishing date	2015-01
Publishing country	Ireland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	186234-0
ISSN	1872-8324 ; 0303-2647
ISSN (online)	1872-8324
ISSN	0303-2647
DOI	10.1016/j.biosystems.2014.11.004
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