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Article ; Online: Development of the next-generation functional neuro-cognitive imaging protocol - Part 1: A 3D sliding-window convolutional neural net for automated brain parcellation.

Lorzel, Heath M / Allen, Mark D

2024 Volume 286, Page(s) 120505

Abstract: Functional MRI has emerged as a powerful tool to assess the severity of Post-concussion syndrome (PCS) and to provide guidance for neuro-cognitive therapists during treatment. The next-generation functional neuro-cognitive imaging protocol (fNCI2) has ... ...

Abstract	Functional MRI has emerged as a powerful tool to assess the severity of Post-concussion syndrome (PCS) and to provide guidance for neuro-cognitive therapists during treatment. The next-generation functional neuro-cognitive imaging protocol (fNCI2) has been developed to provide this assessment. This paper covers the first step in the analysis process, the development of a rapidly re-trainable, machine-learning, brain parcellation tool. The use of a sufficiently deep U-Net architecture encompassing a small (39 × 39 × 39 voxel input, 27 × 27 × 27 voxel output) sliding window to sample the entirety of the 3D image allows for the prediction of the entire image using only a single trained network. A large number of training, validating, and testing windows are thus generated from the 101 manually-labeled Mindboggle images, and full-image prediction is provided via a voxel-vote method using overlapping windows. Our method produces parcellated images that are highly consistent with standard atlas-based methods in under 3 min on a modern GPU, and the single network architecture allows for rapid retraining (<36 hr) as needed.
MeSH term(s)	Humans ; Neural Networks, Computer ; Brain ; Imaging, Three-Dimensional/methods ; Magnetic Resonance Imaging/methods ; Cognition ; Image Processing, Computer-Assisted/methods
Language	English
Publishing date	2024-01-14
Publishing country	United States
Document type	Journal Article
ZDB-ID	1147767-2
ISSN	1095-9572 ; 1053-8119
ISSN (online)	1095-9572
ISSN	1053-8119
DOI	10.1016/j.neuroimage.2023.120505
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Zs.A 3664: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: Structure of the BRK domain of the SWI/SNF chromatin remodeling complex subunit BRG1 reveals a potential role in protein-protein interactions.

Allen, Mark D / Bycroft, Mark / Zinzalla, Giovanna

Protein science : a publication of the Protein Society

2020 Volume 29, Issue 4, Page(s) 1047–1053

Abstract: BRG1/SMARCA4 and its paralog BRM/SMARCA2 are the ATPase subunits of human SWI/SNF chromatin remodeling complexes. These multisubunit assemblies can act as either tumor suppressors or drivers of cancer, and inhibiting both BRG1 and BRM, is emerging as an ... ...

Abstract	BRG1/SMARCA4 and its paralog BRM/SMARCA2 are the ATPase subunits of human SWI/SNF chromatin remodeling complexes. These multisubunit assemblies can act as either tumor suppressors or drivers of cancer, and inhibiting both BRG1 and BRM, is emerging as an effective therapeutic strategy in diverse cancers. BRG1 and BRM contain a BRK domain. The function of this domain is unknown, but it is often found in proteins involved in transcription and developmental signaling in higher eukaryotes, in particular in proteins that remodel chromatin. We report the NMR structure of the BRG1 BRK domain. It shows similarity to the glycine-tyrosine-phenylalanine (GYF) domain, an established protein-protein interaction module. Computational peptide-binding-site analysis of the BRK domain identifies a binding site that coincides with a highly conserved groove on the surface of the protein. This sets the scene for experiments to elucidate the role of this domain, and evaluate the potential of targeting it for cancer therapy.
MeSH term(s)	Chromatin/chemistry ; Chromatin/metabolism ; Chromatin Assembly and Disassembly ; DNA Helicases/chemistry ; DNA Helicases/genetics ; DNA Helicases/isolation & purification ; Humans ; Models, Molecular ; Nuclear Proteins/chemistry ; Nuclear Proteins/genetics ; Nuclear Proteins/isolation & purification ; Protein Binding ; Protein Conformation ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors/isolation & purification ; src Homology Domains
Chemical Substances	Chromatin ; Nuclear Proteins ; SMARCA2 protein, human ; Transcription Factors ; SMARCA4 protein, human (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2020-01-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1106283-6
ISSN	1469-896X ; 0961-8368
ISSN (online)	1469-896X
ISSN	0961-8368
DOI	10.1002/pro.3820
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Zs.A 3407: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (2.OG) ab Jg. 2022: Lesesaal (EG)
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Article ; Online: SWI/SNF subunit BAF155 N-terminus structure informs the impact of cancer-associated mutations and reveals a potential drug binding site.

Allen, Mark D / Freund, Stefan M V / Bycroft, Mark / Zinzalla, Giovanna

Communications biology

2021 Volume 4, Issue 1, Page(s) 528

Abstract: SWI/SNF (BAF) chromatin remodelling complexes are key regulators of gene expression programs, and attractive drug targets for cancer therapies. Here we show that the N-terminus of the BAF155/SMARCC1 subunit contains a putative DNA-binding MarR-like ... ...

Abstract	SWI/SNF (BAF) chromatin remodelling complexes are key regulators of gene expression programs, and attractive drug targets for cancer therapies. Here we show that the N-terminus of the BAF155/SMARCC1 subunit contains a putative DNA-binding MarR-like domain, a chromodomain and a BRCT domain that are interconnected to each other to form a distinct module. In this structure the chromodomain makes interdomain interactions and has lost its canonical function to bind to methylated lysines. The structure provides new insights into the missense mutations that target this module in cancer. This study also reveals two adjacent, highly-conserved pockets in a cleft between the domains that form a potential binding site, which can be targeted with small molecules, offering a new strategy to target SWI/SNF complexes.
MeSH term(s)	Binding Sites ; Humans ; Models, Molecular ; Mutation ; Neoplasms/genetics ; Pharmaceutical Preparations/metabolism ; Protein Conformation ; Transcription Factors/chemistry ; Transcription Factors/genetics ; Transcription Factors/metabolism
Chemical Substances	Pharmaceutical Preparations ; SMARCC1 protein, human ; Transcription Factors
Language	English
Publishing date	2021-05-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-021-02050-z
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Article ; Online: An fMRI investigation of emotional processing of body shape in bulimia nervosa.

Spangler, Diane L / Allen, Mark D

The International journal of eating disorders

2012 Volume 45, Issue 1, Page(s) 17–25

Abstract: Objective: Cognitive-behavioral theories of eating disorder etiology emphasize the role of body-oriented self-schemas. Examination of brain regions associated with self-referencing, such as medial prefrontal cortex (mPFC), during processing of body- ... ...

Abstract	Objective: Cognitive-behavioral theories of eating disorder etiology emphasize the role of body-oriented self-schemas. Examination of brain regions associated with self-referencing, such as medial prefrontal cortex (mPFC), during processing of body-related stimuli can thus be utilized to evaluate such theories. Method: Twelve women with bulima nervosa (BN) and 12 comparison women underwent functional brain imaging while viewing images of women with either thin or overweight bodies in a self-referencing context. Results: For thin bodies, there was no significant mPFC activation for either group. For overweight bodies, mPFC activation was significantly greater for BN patients, with a focus in subregions associated with emotional processing. Discussion: These findings are consistent with cognitive models of eating disorders which posit that negative body-related stimuli are more central to self-schemas and more emotionally provocative in persons with eating disorders, lending support to treatment and prevention interventions that emphasize body overvaluation as a primary target of change.
MeSH term(s)	Adolescent ; Adult ; Body Image ; Brain Mapping ; Bulimia Nervosa/physiopathology ; Emotions/physiology ; Female ; Humans ; Magnetic Resonance Imaging ; Overweight ; Photic Stimulation ; Prefrontal Cortex/physiopathology
Language	English
Publishing date	2012-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	603170-5
ISSN	1098-108X ; 0276-3478
ISSN (online)	1098-108X
ISSN	0276-3478
DOI	10.1002/eat.20899
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Zs.A 1749: Show issues

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Article: Developing the Standard of Care for Post-Concussion Treatment: Neuroimaging-Guided Rehabilitation of Neurovascular Coupling.

Wing, Benjamin H / Tucker, Braden J / Fong, Alina K / Allen, Mark D

The open neuroimaging journal

2017 Volume 11, Page(s) 58–71

Abstract: Background: Emerging research proposes the imbalance between microvascular supply and metabolic demand as a contributing factor in the pathophysiology of mild traumatic brain injury. Prolonged effects on the dysregulation of neurovascular coupling may ... ...

Abstract	Background: Emerging research proposes the imbalance between microvascular supply and metabolic demand as a contributing factor in the pathophysiology of mild traumatic brain injury. Prolonged effects on the dysregulation of neurovascular coupling may explain persistent symptomatic models such as Post-Concussion Syndrome. Objective: Increased knowledge of what we refer to as neurovascular uncoupling provides a template for establishing a new concussion treatment standard in the assessment and therapeutic guidance of concussion. Methods: The degree and localization of neurovascular uncoupling were statistically contextualized against a normative-based atlas in 270 concussed patients. Functional NeuroCognitive Imaging Results: Functional neurocognitive imaging was successful in identifying regions of Neurovascular uncoupling unique to each patient's brain and concussion profile. Longitudinal objective outcome measures demonstrated timely and lasting improvement of neurovascular coupling functioning in a significant majority of patients. Conclusion: We present practice-based evidence supporting the clinical administration of functional neurocognitive imaging with particular efficacy in the neurorehabilitation of concussion. We advocate the reliability of functional neurocognitive imaging in assessing severity and localization of neurovascular uncoupling, and promote its use in the therapeutic guidance and neurorehabilitation of mild traumatic brain injury. We further support the continual exploration of other potential pathophysiological alterations resulting from concussion.
Language	English
Publishing date	2017-10-24
Publishing country	United Arab Emirates
Document type	Journal Article
ZDB-ID	2395976-9
ISSN	1874-4400
ISSN	1874-4400
DOI	10.2174/1874440001711010058
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Article: The preservation of verb subcategory knowledge in a spoken language comprehension deficit.

Allen, Mark D

Brain and language

2005 Volume 95, Issue 2, Page(s) 255–264

Abstract: Patient WBN has a lexical-semantic deficit resulting in impaired performance on language comprehension tasks that require access to verb meanings in both single-word and sentence contexts. However, WBN shows no such comprehension impairment with respect ... ...

Abstract	Patient WBN has a lexical-semantic deficit resulting in impaired performance on language comprehension tasks that require access to verb meanings in both single-word and sentence contexts. However, WBN shows no such comprehension impairment with respect to lexical syntax. Specifically, he performs without error on comprehension tasks that rely on knowledge of lexical-specific verb subcategory requirements. This performance pattern supports theories of lexical representation and processing in which lexical syntactic information may be encoded and retrieved independently from lexical semantic information.
MeSH term(s)	Aged, 80 and over ; Aphasia/pathology ; Aphasia/physiopathology ; Dominance, Cerebral ; Humans ; Male ; Semantics ; Speech Perception ; Stroke/pathology ; Stroke/physiopathology ; Temporal Lobe/pathology
Language	English
Publishing date	2005-11
Publishing country	Netherlands
Document type	Case Reports ; Journal Article
ZDB-ID	7448-2
ISSN	1090-2155 ; 0093-934X
ISSN (online)	1090-2155
ISSN	0093-934X
DOI	10.1016/j.bandl.2004.10.005
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Zs.A 1063: Show issues

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Article ; Online: Concentration-Dependent Inhibition of Mesophilic PETases on Poly(ethylene terephthalate) Can Be Eliminated by Enzyme Engineering.

Avilan, Luisana / Lichtenstein, Bruce R / König, Gerhard / Zahn, Michael / Allen, Mark D / Oliveira, Liliana / Clark, Matilda / Bemmer, Victoria / Graham, Rosie / Austin, Harry P / Dominick, Graham / Johnson, Christopher W / Beckham, Gregg T / McGeehan, John E / Pickford, Andrew R

ChemSusChem

2023 Volume 16, Issue 8, Page(s) e202202277

Abstract: Enzyme-based depolymerization is a viable approach for recycling of poly(ethylene terephthalate) (PET). PETase from Ideonella sakaiensis (IsPETase) is capable of PET hydrolysis under mild conditions but suffers from concentration-dependent inhibition. In ...

Abstract	Enzyme-based depolymerization is a viable approach for recycling of poly(ethylene terephthalate) (PET). PETase from Ideonella sakaiensis (IsPETase) is capable of PET hydrolysis under mild conditions but suffers from concentration-dependent inhibition. In this study, this inhibition is found to be dependent on incubation time, the solution conditions, and PET surface area. Furthermore, this inhibition is evident in other mesophilic PET-degrading enzymes to varying degrees, independent of the level of PET depolymerization activity. The inhibition has no clear structural basis, but moderately thermostable IsPETase variants exhibit reduced inhibition, and the property is completely absent in the highly thermostable HotPETase, previously engineered by directed evolution, which simulations suggest results from reduced flexibility around the active site. This work highlights a limitation in applying natural mesophilic hydrolases for PET hydrolysis and reveals an unexpected positive outcome of engineering these enzymes for enhanced thermostability.
MeSH term(s)	Polyethylene Terephthalates/chemistry ; Hydrolases ; Phthalic Acids/chemistry ; Ethylenes
Chemical Substances	terephthalic acid (6S7NKZ40BQ) ; Polyethylene Terephthalates ; Hydrolases (EC 3.-) ; Phthalic Acids ; Ethylenes
Language	English
Publishing date	2023-03-23
Publishing country	Germany
Document type	Journal Article
ISSN	1864-564X
ISSN (online)	1864-564X
DOI	10.1002/cssc.202202277
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Article: The structure of INI1/hSNF5 RPT1 and its interactions with the c‐MYC:MAX heterodimer provide insights into the interplay between MYC and the SWI/SNF chromatin remodeling complex

Sammak, Susan / Allen, Mark D / Hamdani, Najoua / Bycroft, Mark / Zinzalla, Giovanna

FEBS journal. 2018 Nov., v. 285, no. 22

2018

Abstract: c‐MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the ... ...

Abstract	c‐MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the structure of the RPT1 region of the INI1/hSNF5/BAF47/SMARCB1 subunit of the SWI/SNF complex that acts as a c‐MYC‐binding domain, and have localized the interaction regions on both INI1 and on the c‐MYC:MAX heterodimer. c‐MYC interacts with a highly conserved groove on INI1, while INI1 binds to the c‐MYC helix‐loop‐helix region. The binding site overlaps with the c‐MYC DNA‐binding region, and we show that binding of INI1 and E‐box DNA to c‐MYC:MAX are mutually exclusive.
Keywords	DNA ; binding sites ; chromatin ; humans ; neoplasms
Language	English
Dates of publication	2018-11
Size	p. 4165-4180.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.14660
Database	NAL-Catalogue (AGRICOLA)

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Article: Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA

Sammak, Susan / Hamdani, Najoua / Gorrec, Fabrice / Allen, Mark D / Freund, Stefan M. V / Bycroft, Mark / Zinzalla, Giovanna

Biochemistry. 2019 July 01, v. 58, no. 29

2019

Abstract: The c-MYC transcription factor is a master regulator of cell growth and proliferation and is an established target for cancer therapy. This basic helix–loop–helix Zip protein forms a heterodimer with its obligatory partner MAX, which binds to DNA via the ...

Abstract	The c-MYC transcription factor is a master regulator of cell growth and proliferation and is an established target for cancer therapy. This basic helix–loop–helix Zip protein forms a heterodimer with its obligatory partner MAX, which binds to DNA via the basic region. Considerable research efforts are focused on targeting the heterodimerization interface and the interaction of the complex with DNA. The only available crystal structure is that of a c-MYC:MAX complex artificially tethered by an engineered disulfide linker and prebound to DNA. We have carried out a detailed structural analysis of the apo form of the c-MYC:MAX complex, with no artificial linker, both in solution using nuclear magnetic resonance (NMR) spectroscopy and by X-ray crystallography. We have obtained crystal structures in three different crystal forms, with resolutions between 1.35 and 2.2 Å, that show extensive helical structure in the basic region. Determination of the α-helical propensity using NMR chemical shift analysis shows that the basic region of c-MYC and, to a lesser extent, that of MAX populate helical conformations. We have also assigned the NMR spectra of the c-MYC basic helix–loop–helix Zip motif in the absence of MAX and showed that the basic region has an intrinsic helical propensity even in the absence of its dimerization partner. The presence of helical structure in the basic regions in the absence of DNA suggests that the molecular recognition occurs via a conformational selection rather than an induced fit. Our work provides both insight into the mechanism of DNA binding and structural information to aid in the development of MYC inhibitors.
Keywords	DNA ; X-ray diffraction ; cell growth ; crystal structure ; dimerization ; disulfides ; neoplasms ; nuclear magnetic resonance spectroscopy ; therapeutics ; transcription factors
Language	English
Dates of publication	2019-0701
Size	p. 3144-3154.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.9b00296
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Article ; Online: The structure of INI1/hSNF5 RPT1 and its interactions with the c-MYC:MAX heterodimer provide insights into the interplay between MYC and the SWI/SNF chromatin remodeling complex.

Sammak, Susan / Allen, Mark D / Hamdani, Najoua / Bycroft, Mark / Zinzalla, Giovanna

The FEBS journal

2018 Volume 285, Issue 22, Page(s) 4165–4180

Abstract: c-MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the ... ...

Abstract	c-MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the structure of the RPT1 region of the INI1/hSNF5/BAF47/SMARCB1 subunit of the SWI/SNF complex that acts as a c-MYC-binding domain, and have localized the interaction regions on both INI1 and on the c-MYC:MAX heterodimer. c-MYC interacts with a highly conserved groove on INI1, while INI1 binds to the c-MYC helix-loop-helix region. The binding site overlaps with the c-MYC DNA-binding region, and we show that binding of INI1 and E-box DNA to c-MYC:MAX are mutually exclusive.
MeSH term(s)	Amino Acid Sequence ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/chemistry ; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism ; Binding Sites ; Chromosomal Proteins, Non-Histone ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Protein Conformation ; Protein Domains ; Protein Multimerization ; Proto-Oncogene Proteins c-myc/chemistry ; Proto-Oncogene Proteins c-myc/metabolism ; SMARCB1 Protein/chemistry ; SMARCB1 Protein/metabolism ; Transcription Factors
Chemical Substances	Basic Helix-Loop-Helix Leucine Zipper Transcription Factors ; Chromosomal Proteins, Non-Histone ; MAX protein, human ; MYC protein, human ; Proto-Oncogene Proteins c-myc ; SMARCB1 Protein ; SMARCB1 protein, human ; SWI-SNF-B chromatin-remodeling complex ; Transcription Factors
Language	English
Publishing date	2018-10-01
Publishing country	England
Document type	Journal Article
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.14660
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