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Article: The preferred conformations of protected homodito homoheptamethionine peptides. A1 H n.m.r. study in deuterochloroform medium.

Ribeiro, A A / Goodman, M / Naider, F

International journal of peptide and protein research

1979 Volume 14, Issue 5, Page(s) 414–436

Abstract: ... in deuterochloroform have been carried out with proton n.m.r. and IR spectroscopy. Well-resolved high field n.m.r ... presented. Extensive n.m.r. concentration-dependent chemical shift studies are combined with IR results ... hydrogen bonding. N.m.r. chemical shift dependencies with temperature and solvent, DMSO-d6, are used to explore ...

Abstract	Detailed analyses of the conformations of the homo-oligopeptide series, Boc-(L-Met)n-OME n = 2--7, in deuterochloroform have been carried out with proton n.m.r. and IR spectroscopy. Well-resolved high field n.m.r. spectra with assignments for the NH and alpha-CH resonances of these homo-methionine peptides are presented. Extensive n.m.r. concentration-dependent chemical shift studies are combined with IR results to delineate the involvement of the various methionine NH protons in intra- and/or intermolecular hydrogen bonding. N.m.r. chemical shift dependencies with temperature and solvent, DMSO-d6, are used to explore the strength of the hydrogen bonds for the various oligopeptides. At low concentrations, where peptide aggregation is absent, the dipeptide is found to be disordered. The tetra- to heptapeptides possess intramolecular hydrogen bonded seven-membered rings at internal residues. The number of internal rings and the oligopeptide self-association increase with increasing peptide chainlength. At intermediate concentrations associations of peptide molecules with folded structures occur with initial association at the C-terminal region. At high concentrations, "in-register" associated extended beta structures are formed.
MeSH term(s)	Amino Acid Sequence ; Dimethyl Sulfoxide ; Hydrogen Bonding ; Magnetic Resonance Spectroscopy ; Methionine/analogs & derivatives ; Peptides ; Protein Conformation ; Spectrophotometry, Infrared
Chemical Substances	Peptides ; Methionine (AE28F7PNPL) ; Dimethyl Sulfoxide (YOW8V9698H)
Language	English
Publishing date	1979
Publishing country	Denmark
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	121895-5
ISSN	0367-8377 ; 0300-9769
ISSN	0367-8377 ; 0300-9769
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Zs.A 703: Show issues

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Article ; Online: Optimal control approach to gradient-index design for beam reshaping.

Adriazola, J / Goodman, R H

Journal of the Optical Society of America. A, Optics, image science, and vision

2022 Volume 39, Issue 5, Page(s) 907–915

Abstract: We address the problem of reshaping light in the Schrödinger optics regime from the perspective of the optimal control theory. In technological applications, Schrödinger optics is often used to model a slowly varying amplitude of a para-axially ... ...

Abstract	We address the problem of reshaping light in the Schrödinger optics regime from the perspective of the optimal control theory. In technological applications, Schrödinger optics is often used to model a slowly varying amplitude of a para-axially propagating electric field where the square of the waveguide's index of refraction is treated as the potential. The objective of the optimal control problem is to find the controlling potential which, together with the constraining Schrödinger dynamics, optimally reshapes the intensity distribution of Schrödinger eigenfunctions from one end of the waveguide to the other. This work considers reshaping problems found in work by Kunkel and Leger, and addresses computational needs by adopting tools from the quantum control literature. The success of the optimal control approach is demonstrated numerically.
Language	English
Publishing date	2022-10-10
Publishing country	United States
Document type	Journal Article
ZDB-ID	283633-6
ISSN	1520-8532 ; 1084-7529 ; 0740-3232
ISSN (online)	1520-8532
ISSN	1084-7529 ; 0740-3232
DOI	10.1364/JOSAA.450257
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Article ; Online: Reduction-based strategy for optimal control of Bose-Einstein condensates.

Adriazola, J / Goodman, R H

Physical review. E

2022 Volume 105, Issue 2-2, Page(s) 25311

Abstract: Applications of Bose-Einstein condensates (BEC) often require that the condensate be prepared in a specific complex state. Optimal control is a reliable framework to prepare such a state while avoiding undesirable excitations, and, when applied to the ... ...

Abstract	Applications of Bose-Einstein condensates (BEC) often require that the condensate be prepared in a specific complex state. Optimal control is a reliable framework to prepare such a state while avoiding undesirable excitations, and, when applied to the time-dependent Gross-Pitaevskii equation (GPE) model of BEC in multiple space dimensions, results in a large computational problem. We propose a control method based on first reducing the problem, using a Galerkin expansion, from a partial differential equation to a low-dimensional Hamiltonian ordinary differential equation system. We then apply a two-stage hybrid control strategy. At the first stage, we approximate the control using a second Galerkin-like method known as the chopped random basis to derive a finite-dimensional nonlinear programing problem, which we solve with a differential evolution algorithm. This search method then yields a candidate local minimum which we further refine using a variant of gradient descent. This hybrid strategy allows us to greatly reduce excitations both in the reduced model and the full GPE system.
Language	English
Publishing date	2022-03-15
Publishing country	United States
Document type	Journal Article
ZDB-ID	2844562-4
ISSN	2470-0053 ; 2470-0045
ISSN (online)	2470-0053
ISSN	2470-0045
DOI	10.1103/PhysRevE.105.025311
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Book ; Online: Apodizer Design to Efficiently Couple Light into a Fiber Bragg Grating

Adriazola, J. / Goodman, R. H.

2022

Abstract: We provide an optimal control framework for efficiently coupling light in a bare fiber into Bragg gratings with a cubic nonlinearity. The light-grating interaction excites gap solitons, a type of localized nonlinear coherent state which propagates with a ...

Abstract	We provide an optimal control framework for efficiently coupling light in a bare fiber into Bragg gratings with a cubic nonlinearity. The light-grating interaction excites gap solitons, a type of localized nonlinear coherent state which propagates with a central frequency in the forbidden band gap, resulting in a dramatically slower group velocity. Due to the nature of the band gap, a substantial amount of light is back-reflected by the grating's strong reflective properties. We optimize, via a projected gradient descent method, the transmission efficiency of previously designed nonuniform grating structures in order to couple more slow light into the grating. We further explore the space of possible grating designs, using genetic algorithms, along with a previously unexplored design parameter: the grating chirp. Through these methods, we find structures that couple a greater fraction of light into the grating with the added bonus of creating slower pulses.
Keywords	Physics - Optics ; Mathematics - Optimization and Control ; Nonlinear Sciences - Pattern Formation and Solitons
Subject code	621
Publishing date	2022-06-06
Publishing country	us
Document type	Book ; Online
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Article ; Online: Rapid volume pulsations of the extracellular space accompany epileptiform activity in trauma-injured neocortex and depend on the sodium-bicarbonate cotransporter NBCe1.

Fringuello, Anthony R / Colbourn, Robert / Goodman, Jeffrey H / Michelson, Hillary B / Ling, Douglas S F / Hrabetova, Sabina

Epilepsy research

2024 Volume 201, Page(s) 107337

Abstract: Post traumatic epilepsy (PTE) is a treatment-resistant consequence of traumatic brain injury (TBI). Recently, it has been revealed that epileptiform activity in acute chemoconvulsant seizure models is accompanied by transient shrinkages of extracellular ... ...

Abstract	Post traumatic epilepsy (PTE) is a treatment-resistant consequence of traumatic brain injury (TBI). Recently, it has been revealed that epileptiform activity in acute chemoconvulsant seizure models is accompanied by transient shrinkages of extracellular space (ECS) called rapid volume pulsations (RVPs). Shrinkage of the ECS surrounding neurons and glia may contribute to ictogenic hyperexcitability and hypersynchrony during the chronic phase of TBI. Here, we identify the phenomenon of RVPs occurring spontaneously in rat neocortex at ≥ 3 weeks after injury in the controlled cortical impact (CCI) model for PTE. We further report that blocking the electrogenic action of the astrocytic cotransporter NBCe1 with 4,4'-diisothiocyano-2,2'-stilbenedisulfonic acid (DIDS) eliminates both RVPs and epileptiform activity in ex-vivo CCI neocortical brain slices. We conclude that NBCe1-mediated extracellular volume shrinkage may represent a new target for therapeutic intervention in PTE.
MeSH term(s)	Rats ; Animals ; Sodium-Bicarbonate Symporters/metabolism ; Extracellular Space/metabolism ; Neocortex/metabolism ; Brain Injuries, Traumatic ; Epilepsy, Post-Traumatic
Chemical Substances	Sodium-Bicarbonate Symporters
Language	English
Publishing date	2024-03-02
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	632939-1
ISSN	1872-6844 ; 0920-1211
ISSN (online)	1872-6844
ISSN	0920-1211
DOI	10.1016/j.eplepsyres.2024.107337
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Article ; Online: Psychological well-being in US veterans with non-fatal suicide attempts: A multi-cohort population-based study.

Brown, Bradley A / Goodman, Fallon R / Pietrzak, Robert H / Rottenberg, Jonathan

Journal of affective disorders

2022 Volume 314, Page(s) 34–43

Abstract: Background: Most people who survive suicide attempts neither re-attempt suicide nor die by suicide. Research on suicide attempt survivors has primarily focused on negative endpoints (e.g., increased suicide risk) rather than positive outcomes. One ... ...

Abstract	Background: Most people who survive suicide attempts neither re-attempt suicide nor die by suicide. Research on suicide attempt survivors has primarily focused on negative endpoints (e.g., increased suicide risk) rather than positive outcomes. One important outcome is psychological well-being (PWB), defined as positive functioning across emotional, intrapersonal, and interpersonal domains. We compared PWB among US military veterans with (i.e., attempt survivors) and without (i.e., non-attempters) a history of suicide attempt(s) using data from three nationally representative cohorts. Methods: Each US veteran cohort (Cohort1: N = 3148; Cohort2: N = 1474; Cohort3: N = 4042) completed measures of suicidality (e.g., attempt history), character strengths (e.g., curiosity, optimism), psychological symptoms (e.g., depression), and indicators of PWB (e.g., happiness). t-Tests were conducted to examine group differences in PWB; hierarchical regressions were conducted to examine suicide attempt status as a predictor of PWB controlling for symptoms and demographics. Multivariable regressions were conducted to identify predictors of PWB among attempt survivors. Results: In each cohort, reported PWB was markedly lower among suicide attempt survivors than non-attempters (ds = 0.9-1.2), even after adjusting for mental health symptoms. Individual differences in PWB were observed, with a subset of suicide attempt survivors reporting higher PWB levels than non-attempters (1.4-7.4 %). Curiosity and optimism were positively associated with PWB among suicide attempt survivors (rs = 0.60-0.78). Limitations: Data were cross-sectional, limiting inferences about causation and directionality of associations. Conclusions: Findings highlight diminished PWB as an important and understudied concern among veteran attempt survivors. Collectively, our findings underscore the importance of considering PWB in the research, assessment, and treatment of suicidality.
MeSH term(s)	Emotions ; Humans ; Risk Factors ; Suicidal Ideation ; Suicide, Attempted/psychology ; Survivors ; Veterans/psychology
Language	English
Publishing date	2022-07-06
Publishing country	Netherlands
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	135449-8
ISSN	1573-2517 ; 0165-0327
ISSN (online)	1573-2517
ISSN	0165-0327
DOI	10.1016/j.jad.2022.07.003
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Article: Real-World Implementation Challenges Associated with a Digital Pill System to Measure Adherence to HIV Pre-Exposure Prophylaxis from Two Studies of Men Who Have Sex With Men.

Goodman, Georgia R / Carnes, T Chris / Albrechta, Hannah / Alpert, Pamela / Hokayem, Joanne / Goldfine, Charlotte / Lee, Jasper S / Boyer, Edward W / Rosen, Rochelle / Mayer, Kenneth H / O'Cleirigh, Conall / Chai, Peter R

Proceedings of the ... Annual Hawaii International Conference on System Sciences. Annual Hawaii International Conference on System Sciences

2024 Volume 57, Page(s) 3211–3221

Abstract: Once-daily oral pre-exposure prophylaxis (PrEP) is highly effective for HIV prevention, but its efficacy is dependent on adherence, which can be challenging for men who have sex with men (MSM) with substance use. Digital pill systems (DPS) represent a ... ...

Abstract	Once-daily oral pre-exposure prophylaxis (PrEP) is highly effective for HIV prevention, but its efficacy is dependent on adherence, which can be challenging for men who have sex with men (MSM) with substance use. Digital pill systems (DPS) represent a novel tool for directly measuring adherence through ingestible radiofrequency sensors that confirm ingestions in real-time. We examined operational challenges across two studies involving DPS to measure PrEP adherence. While most participants successfully operated the system, a number of technological and sociobehavioral challenges requiring intervention were identified across both studies. Technological issues were both system- and participant-related, and were primarily addressed with technical updates and participant re-education, while sociobehavioral issues, including health and housing changes and issues with technology access, warranted innovative solutions. Future research leveraging DPS technology should develop robust supportive infrastructure and mitigation procedures to promptly identify and resolve operational issues to optimize the potential benefits of DPS use.
Language	English
Publishing date	2024-01-03
Publishing country	United States
Document type	Journal Article
ISSN	1530-1605
ISSN	1530-1605
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Article ; Online: Acceptance of digital phenotyping linked to a digital pill system to measure PrEP adherence among men who have sex with men with substance use.

Albrechta, Hannah / Goodman, Georgia R / Oginni, Elizabeth / Mohamed, Yassir / Venkatasubramanian, Krishna / Dumas, Arlen / Carreiro, Stephanie / Lee, Jasper S / Glynn, Tiffany R / O'Cleirigh, Conall / Mayer, Kenneth H / Fisher, Celia B / Chai, Peter R

PLOS digital health

2024 Volume 3, Issue 2, Page(s) e0000457

Abstract: Once-daily oral HIV pre-exposure prophylaxis (PrEP) is an effective strategy to prevent HIV, but is highly dependent on adherence. Men who have sex with men (MSM) who use substances face unique challenges maintaining PrEP adherence. Digital pill systems ( ...

Abstract	Once-daily oral HIV pre-exposure prophylaxis (PrEP) is an effective strategy to prevent HIV, but is highly dependent on adherence. Men who have sex with men (MSM) who use substances face unique challenges maintaining PrEP adherence. Digital pill systems (DPS) allow for real-time adherence measurement through ingestible sensors. Integration of DPS technology with other digital health tools, such as digital phenotyping, may improve understanding of nonadherence triggers and development of personalized adherence interventions based on ingestion behavior. This study explored the willingness of MSM with substance use to share digital phenotypic data and interact with ancillary systems in the context of DPS-measured PrEP adherence. Adult MSM on PrEP with substance use were recruited through a social networking app. Participants were introduced to DPS technology and completed an assessment to measure willingness to participate in DPS-based PrEP adherence research, contribute digital phenotyping data, and interact with ancillary systems in the context of DPS-based research. Medical mistrust, daily worry about PrEP adherence, and substance use were also assessed. Participants who identified as cisgender male and were willing to participate in DPS-based research (N = 131) were included in this subsample analysis. Most were White (76.3%) and non-Hispanic (77.9%). Participants who reported daily PrEP adherence worry had 3.7 times greater odds (95% CI: 1.03, 13.4) of willingness to share biometric data via a wearable device paired to the DPS. Participants with daily PrEP adherence worry were more likely to be willing to share smartphone data (p = 0.006) and receive text messages surrounding their daily activities (p = 0.003), compared to those with less worry. MSM with substance use disorder, who worried about PrEP adherence, were willing to use DPS technology and share data required for digital phenotyping in the context of PrEP adherence measurement. Efforts to address medical mistrust can increase advantages of this technology for HIV prevention.
Language	English
Publishing date	2024-02-22
Publishing country	United States
Document type	Journal Article
ISSN	2767-3170
ISSN (online)	2767-3170
DOI	10.1371/journal.pdig.0000457
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Promising Connection Between Data Science and Evolutionary Theory in Oncology.

Goodman, Jonathan R / Ashrafian, Hutan

Frontiers in oncology

2020 Volume 9, Page(s) 1527

Abstract: Theoretical and empirical work over the past several decades suggests that oncogenesis and disease progression represents an evolutionary story. Despite this knowledge, current anti-resistance strategies to drugs are often managed through treating ... ...

Abstract	Theoretical and empirical work over the past several decades suggests that oncogenesis and disease progression represents an evolutionary story. Despite this knowledge, current anti-resistance strategies to drugs are often managed through treating cancers as independent biological agents divorced from human activity. Yet once drug resistance to cancer treatment is understood as a product of artificial or anthropogenic rather than unconscious selection, oncologists could improve outcomes for their patients by consulting evolutionary studies of oncology prior to clinical trial and treatment plan design. In the setting of multiple cancer types, for example, a machine learning algorithm can predict the genetic changes known to be related to drug resistance. In this way, a unity between technology and theory might have practical clinical implications-and may pave the way for a new paradigm shift in medicine.
Language	English
Publishing date	2020-01-20
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2019.01527
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Article ; Online: Insulin-mediated endothelin signaling is antiviral during West Nile virus infection.

Trammell, Chasity E / Rowe, Evelyn H / Char, Aditya B / Jones, Brianne J / Fawcett, Stephen / Ahlers, Laura R H / Goodman, Alan G

Journal of virology

2023 Volume 97, Issue 10, Page(s) e0111223

Abstract: Importance: Arboviruses, particularly those transmitted by mosquitoes, pose a significant threat to humans and are an increasing concern because of climate change, human activity, and expanding vector-competent populations. West Nile virus is of ... ...

Abstract	Importance: Arboviruses, particularly those transmitted by mosquitoes, pose a significant threat to humans and are an increasing concern because of climate change, human activity, and expanding vector-competent populations. West Nile virus is of significant concern as the most frequent mosquito-borne disease transmitted annually within the continental United States. Here, we identify a previously uncharacterized signaling pathway that impacts West Nile virus infection, namely endothelin signaling. Additionally, we demonstrate that we can successfully translate results obtained from
MeSH term(s)	Animals ; Humans ; Drosophila melanogaster/immunology ; Drosophila melanogaster/metabolism ; Drosophila melanogaster/virology ; Insulin/metabolism ; Signal Transduction ; West Nile Fever/immunology ; West Nile Fever/metabolism ; West Nile Fever/virology ; West Nile virus/immunology ; West Nile virus/physiology ; Endothelins/immunology ; Endothelins/metabolism
Chemical Substances	Insulin ; Endothelins
Language	English
Publishing date	2023-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/jvi.01112-23
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