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Book ; Online: Integrating Graceful Degradation and Recovery through Requirement-driven Adaptation

Chu, Simon / Koe, Justin / Garlan, David / Kang, Eunsuk

2024

Abstract: ... adaptation tasks: Degradation can be thought of as temporarily weakening an original (i.e., ideal) system ...

Abstract	Cyber-physical systems (CPS) are subject to environmental uncertainties such as adverse operating conditions, malicious attacks, and hardware degradation. These uncertainties may lead to failures that put the system in a sub-optimal or unsafe state. Systems that are resilient to such uncertainties rely on two types of operations: (1) graceful degradation, to ensure that the system maintains an acceptable level of safety during unexpected environmental conditions and (2) recovery, to facilitate the resumption of normal system functions. Typically, mechanisms for degradation and recovery are developed independently from each other, and later integrated into a system, requiring the designer to develop an additional, ad-hoc logic for activating and coordinating between the two operations. In this paper, we propose a self-adaptation approach for improving system resiliency through automated triggering and coordination of graceful degradation and recovery.The key idea behind our approach is to treat degradation and recovery as requirement-driven adaptation tasks: Degradation can be thought of as temporarily weakening an original (i.e., ideal) system requirement to be achieved by the system, and recovery as strengthening the weakened requirement when the environment returns within an expected operating boundary. Furthermore, by treating weakening and strengthening as dual operations, we argue that a single requirement-based adaptation method is sufficient to enable coordination between degradation and recovery. Given system requirements specified in signal temporal logic (STL), we propose a run-time adaptation framework that automatically performs degradation and recovery in response to environmental changes. We describe a prototype implementation of our framework and demonstrate the feasibility of the proposed approach using a case study in unmanned underwater vehicles (UUVs). Comment: Pre-print for the SEAMS '24 conference
Keywords	Computer Science - Software Engineering ; Computer Science - Formal Languages and Automata Theory ; Computer Science - Logic in Computer Science ; Electrical Engineering and Systems Science - Systems and Control
Subject code	005
Publishing date	2024-01-17
Publishing country	us
Document type	Book ; Online
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Article ; Online: BCI-Utility Metric for Asynchronous P300 Brain-Computer Interface Systems.

Ma, Guoxuan / Kang, Jian / Thompson, David E / Huggins, Jane E

IEEE transactions on neural systems and rehabilitation engineering : a publication of the IEEE Engineering in Medicine and Biology Society

2023 Volume 31, Page(s) 3968–3977

Abstract: The Brain-Computer Interface (BCI) was envisioned as an assistive technology option for people with severe movement impairments. The traditional synchronous event-related potential (ERP) BCI design uses a fixed communication speed and is vulnerable to ... ...

Abstract	The Brain-Computer Interface (BCI) was envisioned as an assistive technology option for people with severe movement impairments. The traditional synchronous event-related potential (ERP) BCI design uses a fixed communication speed and is vulnerable to variations in attention. Recent ERP BCI designs have added asynchronous features, including abstention and dynamic stopping, but it remains a open question of how to evaluate asynchronous BCI performance. In this work, we build on the BCI-Utility metric to create the first evaluation metric with special consideration of the asynchronous features of self-paced BCIs. This metric considers accuracy as all of the following three - probability of a correct selection when a selection was intended, probability of making a selection when a selection was intended, and probability of an abstention when an abstention was intended. Further, it considers the average time required for a selection when using dynamic stopping and the proportion of intended selections versus abstentions. We establish the validity of the derived metric via extensive simulations, and illustrate and discuss its practical usage on real-world BCI data. We describe the relative contribution of different inputs with plots of BCI-Utility curves under different parameter settings. Generally, the BCI-Utility metric increases as any of the accuracy values increase and decreases as the expected time for an intended selection increases. Furthermore, in many situations, we find shortening the expected time of an intended selection is the most effective way to improve the BCI-Utility, which necessitates the advancement of asynchronous BCI systems capable of accurate abstention and dynamic stopping.
MeSH term(s)	Humans ; Electroencephalography ; Brain-Computer Interfaces ; Event-Related Potentials, P300 ; Evoked Potentials ; Movement
Language	English
Publishing date	2023-10-16
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1166307-8
ISSN	1558-0210 ; 1063-6528 ; 1534-4320
ISSN (online)	1558-0210
ISSN	1063-6528 ; 1534-4320
DOI	10.1109/TNSRE.2023.3322125
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Zs.A 4726: Show issues

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Article ; Online: Change in Weight Status Among Children Who Do and Do Not Participate in Intensive Health Behavior and Lifestyle Treatment for Obesity.

Chen, Cathy / Eichen, Dawn / Kang Sim, D Eastern / Strong, David / Boutelle, Kerri N / Rhee, Kyung E

Childhood obesity (Print)

2024

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2639910-6
ISSN	2153-2176 ; 2153-2168
ISSN (online)	2153-2176
ISSN	2153-2168
DOI	10.1089/chi.2023.0114
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Article ; Online: Functional traits of the gut microbiome correlated with host lipid content in a natural population of

Kang, David / Douglas, Angela E

Biology letters

2020 Volume 16, Issue 2, Page(s) 20190803

Abstract: Most research on the nutritional significance of the gut microbiome is conducted on laboratory animals, and its relevance to wild animals is largely unknown. This study investigated the microbiome correlates of lipid content in individual wild fruit ... ...

Abstract	Most research on the nutritional significance of the gut microbiome is conducted on laboratory animals, and its relevance to wild animals is largely unknown. This study investigated the microbiome correlates of lipid content in individual wild fruit flies,
MeSH term(s)	Animals ; Drosophila melanogaster ; Gastrointestinal Microbiome ; Gastrointestinal Tract ; Lipids ; Phenotype
Chemical Substances	Lipids
Language	English
Publishing date	2020-02-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2135022-X
ISSN	1744-957X ; 1744-9561
ISSN (online)	1744-957X
ISSN	1744-9561
DOI	10.1098/rsbl.2019.0803
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Zs.A 1364 -Letters-: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.A 6024: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Treatment of venous malformations with tumescent-assisted sclero-embolic and ablative lasers (SEALs): Safe and effective long-term outcomes.

Kang, Mina / Connor, David E / Parsi, Kurosh

Phlebology

2022 Volume 37, Issue 5, Page(s) 367–380

Abstract: Background: Perivascular infiltration of tumescent anaesthesia (TA) is an essential element of endovenous thermal ablative procedures employed to treat superficial venous disease. In addition to anaesthesia, TA is administered to achieve vessel wall ... ...

Abstract	Background: Perivascular infiltration of tumescent anaesthesia (TA) is an essential element of endovenous thermal ablative procedures employed to treat superficial venous disease. In addition to anaesthesia, TA is administered to achieve vessel wall approximation and to protect surrounding structures from thermal damage. However, its role in the treatment of venous malformations (VMs) has not been established. Objectives: To assess the safety and efficacy of tumescent-assisted thermal and chemical ablative methods in the treatment of VMs. Methods: Adult and paediatric patients presenting with VMs were treated using a combination of endovenous laser ablation, foam embolo-sclerotherapy and liquid embolisation using n-BCA. All procedures were ultrasound-guided. Treatment outcomes were assessed in early and late follow-ups. To assess the efficacy of TA in achieving vessel wall approximation, cross-sectional lesional diameters were measured by ultrasound, before and after the administration of TA during endovenous procedures. Results: In a 12 month period, 22 patients recruited in the study presented with 27 VMs which included 23 extra-truncular lesions (16 subcutaneous and seven intramuscular) and four truncular anomalies. On average the subcutaneous lesions measured 5.5 mm (1.9-24.5 mm) in diameter, intramuscular lesions measured 9.2 mm (5.9-15.1 mm) and truncular anomalies measured 4.9 mm (1.2-12 mm) in diameter. Perivascular infiltration of TA resulted in a significant reduction in vessel calibre (90% reduction on average). Intramuscular VMs were less compressible with TA (69.2% reduction) compared to subcutaneous lesions (98% reduction). Truncular anomalies such as the embryonic marginal vein achieved complete approximation (100% reduction). Procedures were safely tolerated with no major complications such as thromboembolism, stroke, nerve damage or tissue necrosis. Most patients had significant clinical as well as ultrasonographic improvement. Conclusion: Tumescent-assisted endovenous laser ablation and foam sclerotherapy provides safe and effective outcomes in patients with a variety of VMs.
MeSH term(s)	Adult ; Child ; Cross-Sectional Studies ; Humans ; Laser Therapy/adverse effects ; Lasers ; Saphenous Vein/surgery ; Sclerotherapy/adverse effects ; Treatment Outcome ; Vascular Diseases/surgery ; Vascular Malformations/diagnostic imaging ; Vascular Malformations/therapy ; Venous Insufficiency/therapy
Language	English
Publishing date	2022-03-28
Publishing country	England
Document type	Journal Article
ZDB-ID	645172-x
ISSN	1758-1125 ; 0268-3555
ISSN (online)	1758-1125
ISSN	0268-3555
DOI	10.1177/02683555221080045
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Zs.A 2538: Show issues

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Book ; Online: "Is the Pope Catholic?" Applying Chain-of-Thought Reasoning to Understanding Conversational Implicatures

Kim, Zae Myung / Taylor, David E. / Kang, Dongyeop

2023

Abstract: Conversational implicatures are pragmatic inferences that require listeners to deduce the intended meaning conveyed by a speaker from their explicit utterances. Although such inferential reasoning is fundamental to human communication, recent research ... ...

Abstract	Conversational implicatures are pragmatic inferences that require listeners to deduce the intended meaning conveyed by a speaker from their explicit utterances. Although such inferential reasoning is fundamental to human communication, recent research indicates that large language models struggle to comprehend these implicatures as effectively as the average human. This paper demonstrates that by incorporating Grice's Four Maxims into the model through chain-of-thought prompting, we can significantly enhance its performance, surpassing even the average human performance on this task.
Keywords	Computer Science - Computation and Language
Publishing date	2023-05-23
Publishing country	us
Document type	Book ; Online
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Article ; Online: The impacts of the mitochondrial myopathy-associated G58R mutation on the dynamic structural properties of CHCHD10.

Alici, Hakan / Uversky, Vladimir N / Kang, David E / Woo, Junga Alexa / Coskuner-Weber, Orkid

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–10

Abstract: The mitochondria are responsible for producing energy within the cell, and in mitochondrial myopathy, there is a defect in the energy production process. The CHCHD10 gene codes for a protein called coiled-coil-helix-coiled-coil-helix domain-containing ... ...

Abstract	The mitochondria are responsible for producing energy within the cell, and in mitochondrial myopathy, there is a defect in the energy production process. The CHCHD10 gene codes for a protein called coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), which is found in the mitochondria and is involved in the regulation of mitochondrial function. G58R mutation has been shown to disrupt the normal function of CHCHD10, leading to mitochondrial dysfunction and ultimately to the development of mitochondrial myopathy. The structures of G58R mutant CHCHD10 and how G58R mutation impacts the wild-type CHCHD10 protein at the monomeric level are unknown. To address this problem, we conducted homology modeling, multiple run molecular dynamics simulations and bioinformatics calculations. We represent herein the structural ensemble properties of the G58R mutant CHCHD10 (CHCHD10
Language	English
Publishing date	2023-06-22
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2227713
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Zs.A 2093: Show issues

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Article ; Online: Effects of the Jokela type of spinal muscular atrophy-related G66V mutation on the structural ensemble characteristics of CHCHD10.

Alici, Hakan / Uversky, Vladimir N / Kang, David E / Woo, Junga Alexa / Coskuner-Weber, Orkid

Proteins

2023 Volume 91, Issue 6, Page(s) 739–749

Abstract: The G66V pathological variant of the coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), mitochondrial, plays a role in Jokela type spinal muscular atrophy. The wild-type and G66V mutant-type CHCHD10 proteins contain intrinsically ...

Abstract	The G66V pathological variant of the coiled-coil-helix-coiled-coil-helix domain-containing protein 10 (CHCHD10), mitochondrial, plays a role in Jokela type spinal muscular atrophy. The wild-type and G66V mutant-type CHCHD10 proteins contain intrinsically disordered regions, and therefore, their structural ensemble studies have been experiencing difficulties using conventional tools. Here, we show our results regarding the first characterization of the structural ensemble characteristics of the G66V mutant form of CHCHD10 and the first comparison of these characteristics with the structural ensemble properties of wild-type CHCHD10. We find that the structural properties, potential of mean force surfaces, and principal component analysis show stark differences between these two proteins. These results are important for a better pathology, biochemistry and structural biology understanding of CHCHD10 and its G66V genetic variant and it is likely that these reported structural properties are important for designing more efficient treatments for the Jokela type of spinal muscular atrophy disease.
MeSH term(s)	Humans ; Mitochondrial Proteins/chemistry ; Mutation ; Mitochondria/genetics ; Muscular Atrophy, Spinal/genetics ; Muscular Atrophy, Spinal/metabolism ; Muscular Atrophy, Spinal/pathology ; HeLa Cells
Chemical Substances	Mitochondrial Proteins ; CHCHD10 protein, human
Language	English
Publishing date	2023-01-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	806683-8
ISSN	1097-0134 ; 0887-3585
ISSN (online)	1097-0134
ISSN	0887-3585
DOI	10.1002/prot.26463
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Zs.A 2291: Show issues

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Article: Cell cycle perturbation uncouples mitotic progression and invasive behavior in a post-mitotic cell.

Martinez, Michael A Q / Zhao, Chris Z / Moore, Frances E Q / Yee, Callista / Zhang, Wan / Shen, Kang / Martin, Benjamin L / Matus, David Q

bioRxiv : the preprint server for biology

2024

Abstract: The acquisition of the post-mitotic state is crucial for the execution of many terminally differentiated cell behaviors during organismal development. However, the mechanisms that maintain the post-mitotic state in this context remain poorly understood. ... ...

Abstract	The acquisition of the post-mitotic state is crucial for the execution of many terminally differentiated cell behaviors during organismal development. However, the mechanisms that maintain the post-mitotic state in this context remain poorly understood. To gain insight into these mechanisms, we used the genetically and visually accessible model of
Language	English
Publishing date	2024-02-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.03.16.533034
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Article ; Online: Cofilin, a Master Node Regulating Cytoskeletal Pathogenesis in Alzheimer's Disease.

Kang, David E / Woo, Jung A

Journal of Alzheimer's disease : JAD

2019 Volume 72, Issue s1, Page(s) S131–S144

Abstract: The defining pathological hallmarks of Alzheimer's disease (AD) are proteinopathies marked by the amyloid-β (Aβ) peptide and hyperphosphorylated tau. In addition, Hirano bodies and cofilin-actin rods are extensively found in AD brains, both of which are ... ...

Abstract	The defining pathological hallmarks of Alzheimer's disease (AD) are proteinopathies marked by the amyloid-β (Aβ) peptide and hyperphosphorylated tau. In addition, Hirano bodies and cofilin-actin rods are extensively found in AD brains, both of which are associated with the actin cytoskeleton. The actin-binding protein cofilin known for its actin filament severing, depolymerizing, nucleating, and bundling activities has emerged as a significant player in AD pathogenesis. In this review, we discuss the regulation of cofilin by multiple signaling events impinging on LIM kinase-1 (LIMK1) and/or Slingshot homolog-1 (SSH1) downstream of Aβ. Such pathophysiological signaling pathways impact actin dynamics to regulate synaptic integrity, mitochondrial translocation of cofilin to promote neurotoxicity, and formation of cofilin-actin pathology. Other intracellular signaling proteins, such as β-arrestin, RanBP9, Chronophin, PLD1, and 14-3-3 also impinge on the regulation of cofilin downstream of Aβ. Finally, we discuss the role of activated cofilin as a bridge between actin and microtubule dynamics by displacing tau from microtubules, thereby destabilizing tau-induced microtubule assembly, missorting tau, and promoting tauopathy.
MeSH term(s)	Alzheimer Disease/metabolism ; Alzheimer Disease/pathology ; Animals ; Brain/metabolism ; Brain/pathology ; Cofilin 1/metabolism ; Cytoskeleton/metabolism ; Cytoskeleton/pathology ; Humans ; Lim Kinases/metabolism ; Phosphoprotein Phosphatases/metabolism ; Tauopathies/metabolism ; Tauopathies/pathology
Chemical Substances	Cofilin 1 ; LIMK1 protein, human (EC 2.7.11.1) ; Lim Kinases (EC 2.7.11.1) ; Phosphoprotein Phosphatases (EC 3.1.3.16) ; SSH1 protein, human (EC 3.1.3.16)
Language	English
Publishing date	2019-10-08
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	1440127-7
ISSN	1875-8908 ; 1387-2877
ISSN (online)	1875-8908
ISSN	1387-2877
DOI	10.3233/JAD-190585
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