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Spinrad A, Taylor CB, Ruzek JI, Jefroykin S, Friedlander T, Feleke I, Lev-Ari H, Szapiro N, Sadeh-Sharvit S. Correction: Action recommendations review in community-based therapy and depression and anxiety outcomes: a machine learning approach. BMC Psychiatry 2024; 24:204. [PMID: 38481243 PMCID: PMC10938712 DOI: 10.1186/s12888-024-05655-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/17/2024] Open
Affiliation(s)
- Amit Spinrad
- Eleos Health, 117 Kendrick Street, Suite 300, 02494, Needham, MA, USA.
| | - C Barr Taylor
- Center for m2Health, Palo Alto University, Palo Alto, CA, USA
- Department of Psychiatry, Stanford Medical Center, Stanford, CA, USA
| | - Josef I Ruzek
- Center for m2Health, Palo Alto University, Palo Alto, CA, USA
- Department of Psychiatry, Stanford Medical Center, Stanford, CA, USA
| | - Samuel Jefroykin
- Eleos Health, 117 Kendrick Street, Suite 300, 02494, Needham, MA, USA
| | - Tamar Friedlander
- Eleos Health, 117 Kendrick Street, Suite 300, 02494, Needham, MA, USA
| | - Israela Feleke
- Eleos Health, 117 Kendrick Street, Suite 300, 02494, Needham, MA, USA
| | - Hila Lev-Ari
- Eleos Health, 117 Kendrick Street, Suite 300, 02494, Needham, MA, USA
| | - Natalia Szapiro
- Eleos Health, 117 Kendrick Street, Suite 300, 02494, Needham, MA, USA
| | - Shiri Sadeh-Sharvit
- Eleos Health, 117 Kendrick Street, Suite 300, 02494, Needham, MA, USA
- Center for m2Health, Palo Alto University, Palo Alto, CA, USA
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Spinard A, Taylor CB, Ruzek JI, Jefroykin S, Friedlander T, Feleke I, Lev-Ari H, Szapiro N, Sadeh-Sharvit S. Action recommendations review in community-based therapy and depression and anxiety outcomes: a machine learning approach. BMC Psychiatry 2024; 24:133. [PMID: 38365635 PMCID: PMC10870574 DOI: 10.1186/s12888-024-05570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND While the positive impact of homework completion on symptom alleviation is well-established, the pivotal role of therapists in reviewing these assignments has been under-investigated. This study examined therapists' practice of assigning and reviewing action recommendations in therapy sessions, and how it correlates with patients' depression and anxiety outcomes. METHODS We analyzed 2,444 therapy sessions from community-based behavioral health programs. Machine learning models and natural language processing techniques were deployed to discern action recommendations and their subsequent reviews. The extent of the review was quantified by measuring the proportion of session dialogues reviewing action recommendations, a metric we refer to as "review percentage". Using Generalized Estimating Equations modeling, we evaluated the correlation between this metric and changes in clients' depression and anxiety scores. RESULTS Our models achieved 76% precision in capturing action recommendations and 71.1% in reviewing them. Using these models, we found that therapists typically provided clients with one to eight action recommendations per session to engage in outside therapy. However, only half of the sessions included a review of previously assigned action recommendations. We identified a significant interaction between the initial depression score and the review percentage (p = 0.045). When adjusting for this relationship, the review percentage was positively and significantly associated with a reduction in depression score (p = 0.032). This suggests that more frequent review of action recommendations in therapy relates to greater improvement in depression symptoms. Further analyses highlighted this association for mild depression (p = 0.024), but not for anxiety or moderate to severe depression. CONCLUSIONS An observed positive association exists between therapists' review of previous sessions' action recommendations and improved treatment outcomes among clients with mild depression, highlighting the possible advantages of consistently revisiting therapeutic homework in real-world therapy settings. Results underscore the importance of developing effective strategies to help therapists maintain continuity between therapy sessions, potentially enhancing the impact of therapy.
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Affiliation(s)
- Amit Spinard
- Eleos Health, 117 Kendrick Street, Suite 300, Needham, MA, 02494, USA.
| | - C Barr Taylor
- Center for m2Health, Palo Alto University, Palo Alto, CA, USA
- Department of Psychiatry, Stanford Medical Center, Stanford, CA, USA
| | - Josef I Ruzek
- Center for m2Health, Palo Alto University, Palo Alto, CA, USA
- Department of Psychiatry, Stanford Medical Center, Stanford, CA, USA
| | - Samuel Jefroykin
- Eleos Health, 117 Kendrick Street, Suite 300, Needham, MA, 02494, USA
| | - Tamar Friedlander
- Eleos Health, 117 Kendrick Street, Suite 300, Needham, MA, 02494, USA
| | - Israela Feleke
- Eleos Health, 117 Kendrick Street, Suite 300, Needham, MA, 02494, USA
| | - Hila Lev-Ari
- Eleos Health, 117 Kendrick Street, Suite 300, Needham, MA, 02494, USA
| | - Natalia Szapiro
- Eleos Health, 117 Kendrick Street, Suite 300, Needham, MA, 02494, USA
| | - Shiri Sadeh-Sharvit
- Eleos Health, 117 Kendrick Street, Suite 300, Needham, MA, 02494, USA
- Center for m2Health, Palo Alto University, Palo Alto, CA, USA
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Necchi A, Pouessel D, Leibowitz R, Gupta S, Fléchon A, García-Donas J, Bilen MA, Debruyne PR, Milowsky MI, Friedlander T, Maio M, Gilmartin A, Li X, Veronese ML, Loriot Y. Pemigatinib for metastatic or surgically unresectable urothelial carcinoma with FGF/FGFR genomic alterations: final results from FIGHT-201. Ann Oncol 2024; 35:200-210. [PMID: 37956738 DOI: 10.1016/j.annonc.2023.10.794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/17/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND Fibroblast growth factor receptor 3 (FGFR3) alterations are oncogenic drivers of urothelial carcinoma (UC). Pemigatinib is a selective, oral inhibitor of FGFR1-3 with antitumor activity. We report the efficacy and safety of pemigatinib in the open-label, single-arm, phase II study of previously treated, unresectable or metastatic UC with FGFR3 alterations (FIGHT-201; NCT02872714). PATIENTS AND METHODS Patients ≥18 years old with FGFR3 mutations or fusions/rearrangements (cohort A) and other FGF/FGFR alterations (cohort B) were included. Patients received pemigatinib 13.5 mg once daily continuously (CD) or intermittently (ID) until disease progression or unacceptable toxicity. The primary endpoint was centrally confirmed objective response rate (ORR) as per RECIST v1.1 in cohort A-CD. Secondary endpoints included ORR in cohorts A-ID and B, duration of response (DOR), progression-free survival (PFS), overall survival (OS), and safety. RESULTS Overall, 260 patients were enrolled and treated (A-CD, n = 101; A-ID, n = 103; B, n = 44; unconfirmed FGF/FGFR status, n = 12). All discontinued treatment, most commonly due to progressive disease (68.5%). ORR [95% confidence interval (CI)] in cohorts A-CD and A-ID was 17.8% (10.9% to 26.7%) and 23.3% (15.5% to 32.7%), respectively. Among patients with the most common FGFR3 mutation (S249C; n = 107), ORR was similar between cohorts (A-CD, 23.9%; A-ID, 24.6%). In cohorts A-CD/A-ID, median (95% CI) DOR was 6.2 (4.1-8.3)/6.2 (4.6-8.0) months, PFS was 4.0 (3.5-4.2)/4.3 (3.9-6.1) months, and OS was 6.8 (5.3-9.1)/8.9 (7.5-15.2) months. Pemigatinib had limited clinical activity among patients in cohort B. Of 36 patients with samples available at progression, 6 patients had 8 acquired FGFR3 secondary resistance mutations (V555M/L, n = 3; V553M, n = 1; N540K/S, n = 2; M528I, n = 2). The most common treatment-emergent adverse events overall were diarrhea (44.6%) and alopecia, stomatitis, and hyperphosphatemia (42.7% each). CONCLUSIONS Pemigatinib was generally well tolerated and demonstrated clinical activity in previously treated, unresectable or metastatic UC with FGFR3 mutations or fusions/rearrangements.
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Affiliation(s)
- A Necchi
- Vita-Salute San Raffaele University, Department of Medical Oncology, IRCCS San Raffaele Hospital, Milan, Italy.
| | - D Pouessel
- Institut Claudius Regaud-IUCT Oncopole, Toulouse, France
| | - R Leibowitz
- Chaim Sheba Medical Center, Ramat Gan; Shamir Medical Center, Zerifin, Israel
| | - S Gupta
- Huntsman Cancer Institute, Salt Lake City, USA
| | | | | | - M A Bilen
- Winship Cancer Institute of Emory University, Atlanta, USA
| | - P R Debruyne
- Kortrijk Cancer Centre, General Hospital Groeninge, Kortrijk, Belgium; Medical Technology Research Centre (MTRC), School of Life Sciences, Anglia Ruskin University, Cambridge; School of Nursing and Midwifery, University of Plymouth, Plymouth, UK
| | - M I Milowsky
- University of North Carolina Lineberger Comprehensive Cancer Center, Chapel Hill
| | - T Friedlander
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, USA
| | - M Maio
- University of Siena and Center for Immuno-Oncology, Department of Oncology, University Hospital, Siena, Italy
| | | | - X Li
- Incyte Corporation, Wilmington, USA
| | - M L Veronese
- Incyte International Biosciences Sàrl, Morges, Switzerland
| | - Y Loriot
- Gustave Roussy, DITEP, Université Paris-Saclay, INSERM 981, Villejuif, France.
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Engelen C, Wechsler T, Bakhshian O, Smoly I, Flaks I, Friedlander T, Ben-Ari G, Samach A. Studying Parameters Affecting Accumulation of Chilling Units Required for Olive Winter Flower Induction. Plants (Basel) 2023; 12:1714. [PMID: 37111937 PMCID: PMC10143890 DOI: 10.3390/plants12081714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/30/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
With global warming, mean winter temperatures are predicted to increase. Therefore, understanding how warmer winters will affect the levels of olive flower induction is essential for predicting the future sustainability of olive oil production under different climactic scenarios. Here, we studied the effect of fruit load, forced drought in winter, and different winter temperature regimes on olive flower induction using several cultivars. We show the necessity of studying trees with no previous fruit load as well as provide evidence that soil water content during winter does not significantly affect the expression of an FT-encoding gene in leaves and the subsequent rate of flower induction. We collected yearly flowering data for 5 cultivars for 9 to 11 winters, altogether 48 data sets. Analyzing hourly temperatures from these winters, we made initial attempts to provide an efficient method to calculate accumulated chill units that are then correlated with the level of flower induction in olives. While the new models tested here appear to predict the positive contribution of cold temperatures, they lack in accurately predicting the reduction in cold units caused by warm temperatures occurring during winter.
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Affiliation(s)
- Chaim Engelen
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Tahel Wechsler
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Ortal Bakhshian
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Ilan Smoly
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Idan Flaks
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Tamar Friedlander
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
| | - Giora Ben-Ari
- Institute of Plant Sciences, Agricultural Research Organization (ARO), Volcani Center, Rishon LeZion 7528809, Israel
| | - Alon Samach
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, P.O. Box 12, Rehovot 7610001, Israel
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Rosenberg J, Milowsky M, Ramamurthy C, Mar N, McKay R, Friedlander T, Ferrario C, Bracarda S, George S, Moon H, Geynisman D, Petrylak D, Borchiellini D, Burgess E, Rey JM, Carret AS, Yu Y, Guseva M, Moreno BH, O'Donnell P. LBA73 Study EV-103 Cohort K: Antitumor activity of enfortumab vedotin (EV) monotherapy or in combination with pembrolizumab (P) in previously untreated cisplatin-ineligible patients (pts) with locally advanced or metastatic urothelial cancer (la/mUC). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.08.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Deshmukh P, De Kouchkovsky I, Zhang L, Jindal T, Reyes K, Hernandez Romero E, Chan E, Desai A, Borno H, Kwon D, Wong A, Bose R, Aggarwal R, Porten S, Fong L, Small E, Chou J, Friedlander T, Koshkin V. 1751P Impact of squamous histology on clinical outcomes and molecular profiling in metastatic urothelial carcinoma (mUC) patients (pts) treated with newer therapies. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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7
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Jindal T, Han H, Deshmukh P, De Kouchkovsky I, Kwon D, Borno H, Koshkin V, Desai A, Bose R, Chou J, Friedlander T, Small E, Angelidakis A, Johnson M, Feng S, Patnaik A, Fong L, Alumkal J, Aggarwal R. 1404P A phase II study of ZEN-3694 (ZEN), enzalutamide (ENZ), and pembrolizumab (P) in metastatic castration resistant prostate cancer (mCRPC): Interim safety results. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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8
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Grivas P, Agarwal P, Al-Ahmadie H, Friedlander T, Geynisman D, Hussain I, Lotan Y, Morgans A, Tesic-Schnell M, Meeks J. 1775P Prevalence of PD-L1 high expression in advanced urothelial carcinoma (aUC): Results from the PREVAIL prospective cohort study. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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9
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Aggarwal R, Trihy L, Hernandez Romero E, Luch Sam S, Rastogi M, De Kouchkovsky I, Small E, Feng F, Kwon D, Friedlander T, Borno H, Bose R, Chou J, Koshkin V, Desai A, Feng S, Angelidakis A, Johnson M, Fong L, Hope T. 1379P A phase Ib study of a single priming dose of 177Lu-PSMA-617 coupled with pembrolizumab in metastatic castration resistant prostate cancer (mCRPC). Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.1511] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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10
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Gabzi T, Pilpel Y, Friedlander T. Fitness landscape analysis of a tRNA gene reveals that the wild type allele is sub-optimal, yet mutationally robust. Mol Biol Evol 2022; 39:6670756. [PMID: 35976926 PMCID: PMC9447856 DOI: 10.1093/molbev/msac178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Fitness landscape mapping and the prediction of evolutionary trajectories on these landscapes are major tasks in evolutionary biology research. Evolutionary dynamics is tightly linked to the landscape topography, but this relation is not straightforward. Here, we analyze a fitness landscape of a yeast tRNA gene, previously measured under four different conditions. We find that the wild type allele is sub-optimal, and 8–10% of its variants are fitter. We rule out the possibilities that the wild type is fittest on average on these four conditions or located on a local fitness maximum. Notwithstanding, we cannot exclude the possibility that the wild type might be fittest in some of the many conditions in the complex ecology that yeast lives at. Instead, we find that the wild type is mutationally robust (“flat”), while more fit variants are typically mutationally fragile. Similar observations of mutational robustness or flatness have been so far made in very few cases, predominantly in viral genomes.
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Affiliation(s)
- Tzahi Gabzi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yitzhak Pilpel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tamar Friedlander
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture Faculty of Agriculture, Hebrew University of Jerusalem, 229 Herzl St., Rehovot 7610001, Israel
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Xu M, Sinha S, Wang S, Friedlander T, Braunstein S. Comparison of Radiation Initiation Timelines Among Varied Referral Streams to Identify Sources of Delay. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.1423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Friedlander T, Prizak R, Barton NH, Tkačik G. Evolution of new regulatory functions on biophysically realistic fitness landscapes. Nat Commun 2017; 8:216. [PMID: 28790313 PMCID: PMC5548793 DOI: 10.1038/s41467-017-00238-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 06/13/2017] [Indexed: 12/12/2022] Open
Abstract
Gene expression is controlled by networks of regulatory proteins that interact specifically with external signals and DNA regulatory sequences. These interactions force the network components to co-evolve so as to continually maintain function. Yet, existing models of evolution mostly focus on isolated genetic elements. In contrast, we study the essential process by which regulatory networks grow: the duplication and subsequent specialization of network components. We synthesize a biophysical model of molecular interactions with the evolutionary framework to find the conditions and pathways by which new regulatory functions emerge. We show that specialization of new network components is usually slow, but can be drastically accelerated in the presence of regulatory crosstalk and mutations that promote promiscuous interactions between network components.Gene networks evolve by transcription factor (TF) duplication and divergence of their binding site specificities, but little is known about the global constraints at play. Here, the authors study the coevolution of TFs and binding sites using a biophysical-evolutionary approach, and show that the emerging complex fitness landscapes strongly influence regulatory evolution with a role for crosstalk.
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Affiliation(s)
- Tamar Friedlander
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.,The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture Hebrew University of Jerusalem, P.O. Box 12, Rehovot, 7610001, Israel
| | - Roshan Prizak
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Nicholas H Barton
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria
| | - Gašper Tkačik
- Institute of Science and Technology Austria, Am Campus 1, A-3400, Klosterneuburg, Austria.
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Abstract
Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved. Many biological systems show bow-tie (also called hourglass) architecture. A bow-tie means that a large number of inputs are converted to a small number of intermediates, which then fan out to generate a large number of outputs. For example, cells use a wide variety of nutrients; process them into 12 metabolic precursors, which are then used to make all of the cells biomass. Similar principles exist in biological signaling and in the information processing in the visual system. Despite the ubiquity of bow-tie structures in biology, there is no explanation of how they evolved. Here, we find that bow-ties spontaneously evolve when the information in the evolutionary goal they evolved to satisfy can be compressed. Mathematically, this means that the matrix representing the goal has deficient rank. The maximal compression possible determines the width of the bow-tie—the narrowest part in the network (equal to the rank of the goal matrix). This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the rank of the goals under which they evolved.
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Affiliation(s)
- Tamar Friedlander
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Avraham E. Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tsvi Tlusty
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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Friedlander T, Mayo AE, Tlusty T, Alon U. Mutation rules and the evolution of sparseness and modularity in biological systems. PLoS One 2013; 8:e70444. [PMID: 23936433 PMCID: PMC3735639 DOI: 10.1371/journal.pone.0070444] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 06/18/2013] [Indexed: 11/21/2022] Open
Abstract
Biological systems exhibit two structural features on many levels of organization: sparseness, in which only a small fraction of possible interactions between components actually occur; and modularity – the near decomposability of the system into modules with distinct functionality. Recent work suggests that modularity can evolve in a variety of circumstances, including goals that vary in time such that they share the same subgoals (modularly varying goals), or when connections are costly. Here, we studied the origin of modularity and sparseness focusing on the nature of the mutation process, rather than on connection cost or variations in the goal. We use simulations of evolution with different mutation rules. We found that commonly used sum-rule mutations, in which interactions are mutated by adding random numbers, do not lead to modularity or sparseness except for in special situations. In contrast, product-rule mutations in which interactions are mutated by multiplying by random numbers – a better model for the effects of biological mutations – led to sparseness naturally. When the goals of evolution are modular, in the sense that specific groups of inputs affect specific groups of outputs, product-rule mutations also lead to modular structure; sum-rule mutations do not. Product-rule mutations generate sparseness and modularity because they tend to reduce interactions, and to keep small interaction terms small.
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Affiliation(s)
- Tamar Friedlander
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Avraham E. Mayo
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Tsvi Tlusty
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America
| | - Uri Alon
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
- * E-mail:
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15
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Arbel-Goren R, Tal A, Friedlander T, Meshner S, Costantino N, Court DL, Stavans J. Effects of post-transcriptional regulation on phenotypic noise in Escherichia coli. Nucleic Acids Res 2013; 41:4825-34. [PMID: 23519613 PMCID: PMC3643596 DOI: 10.1093/nar/gkt184] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells. Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown. We study the effects of RyhB, a small-RNA of Escherichia coli produced on iron stress, on the phenotypic variability of two of its downregulated target proteins, using dual chromosomal fusions to fluorescent reporters and measurements in live individual cells. The total noise of each of the target proteins is remarkably constant over a wide range of RyhB production rates despite cells being in stress. In fact, coordinate downregulation of the two target proteins by RyhB reduces the correlation between their levels. Hence, an increase in phenotypic variability under stress is achieved by decoupling the expression of different target proteins in the same cell, rather than by an increase in the total noise of each. Extrinsic noise provides the dominant contribution to the total protein noise over the total range of RyhB production rates. Stochastic simulations reproduce qualitatively key features of our observations and show that a feed-forward loop formed by transcriptional extrinsic noise, an sRNA and its target genes exhibits strong noise filtration capabilities.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
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Friedlander T, Ngo V, Doty S, Zhao Q, Dong H, Ryan C, Chen W, Paris P. 490 Detection and Genomic Interrogation of Circulating Tumor Cells (CTCs) and Circulating Tumor Stem Cells (CTSCs) From Men with Metastatic Castration-resistant Prostate Cancer (mCRPC). Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)72288-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Abstract
Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus, often supported by protein activity-dependent inactivation. Adaptive response is thought to be related to various cellular functions such as homeostasis and enlargement of dynamic range by background compensation. Here we study the quantitative relation between adaptive response and background compensation within a modeling framework. We show that any particular type of adaptive response is neither sufficient nor necessary for adaptive enlargement of dynamic range. In particular a precise adaptive response, where system activity is maintained at a constant level at steady state, does not ensure a large dynamic range neither in input signal nor in system output. A general mechanism for input dynamic range enlargement can come about from the activity-dependent modulation of protein responsiveness by multiple biochemical modification, regardless of the type of adaptive response it induces. Therefore hierarchical biochemical processes such as methylation and phosphorylation are natural candidates to induce this property in signaling systems.
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Affiliation(s)
- Tamar Friedlander
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel.
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Abstract
Proliferating cell populations at steady-state growth often exhibit broad protein distributions with exponential tails. The sources of this variation and its universality are of much theoretical interest. Here we address the problem by asymptotic analysis of the population balance equation. We show that the steady-state distribution tail is determined by a combination of protein production and cell division and is insensitive to other model details. Under general conditions this tail is exponential with a dependence on parameters consistent with experiment. We discuss the conditions for this effect to be dominant over other sources of variation and the relation to experiments.
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Affiliation(s)
- Tamar Friedlander
- Department of Physics, Technion-Israel Institute of Technology, Haifa 32000, Israel
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Friedlander T. A new technique and device for 3D imaging of crystals while still in solution. Acta Crystallogr A 2006. [DOI: 10.1107/s0108767306099764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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