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Folds induced by multiple parallel or antiparallel double-helices: (pseudo)knotting of single-stranded RNA [article]

Stephen T Hyde
2021 bioRxiv   pre-print
Those circular folds lead to pseudoknotted folds for linear ssRNA strands.  ...  The fold topology is captured by a 'contracted fold' which merges helices separated by bulges and removes hairpin loops. Contracted folds are either trivial or pseudoknotted.  ...  Table 14 identified the fold {1 e 2 e 123 e 4 e 34} with t 1 , t 2 , t 3 , t 4 = 0, 2, 2, 4 as knotted, forming the 5 2 knot. • {1 o 2 o 3 o 123} L ⌦ ⇧ t 1 t 2 t 3 t 4 pseudoknot knot knot ID {1 e 2 e  ... 
doi:10.1101/2021.03.12.435210 fatcat:esleaxuj3jgtdbkmpjv3fqw77i

Amino acid torsion angles enable prediction of protein fold classification

Kun Tian, Xin Zhao, Xiaogeng Wan, Stephen S.-T. Yau
2020 Scientific Reports  
B 1 ) stands for the Hausdorff distance between A 1 and B 1 after shifting A 1 by t.  ...  Our results demonstrate that this new approach is efficient and reliable on protein structure prediction, and can obtain multiple different structures for the same sequence, improve protein-folding recognition  ... 
doi:10.1038/s41598-020-78465-1 pmid:33303802 fatcat:twnsd5xov5gbrkwwps76qgvzny

Assembly of a M4L4 "folded-cube" using a T-shaped, right-angled ligand

Ismail Elguraish, Kelong Zhu, Leslie A. Hernandez, Hazem Amarne, Jingwei Luo, V. Nicholas Vukotic, Stephen J. Loeb
2015 Dalton Transactions  
A new bipyridine ligand based on a T-shaped 2,4,7-trisubstituted benzimidazole framework was synthesised.  ...  When combined with [Pt(dppp)]2+ corners, eight right angles (four metal and four ligand) combine to form a M4L4 cluster with an unusual folded-cube structure.  ...  The T-shaped, bipyridine ligand with a benzimidazole core was prepared as outlined in Scheme 1.  ... 
doi:10.1039/c4dt03198a pmid:25462831 fatcat:tvrhtery3ndmtbdwspfam6ep7y

MEG-based neurofeedback for hand rehabilitation

Stephen T. Foldes, Douglas J. Weber, Jennifer L. Collinger
2015 Journal of NeuroEngineering and Rehabilitation  
Success rate was also significant for each subject when considering grasp-only and restonly trials (p < 0.001, t-test).  ...  Success rate was significantly better than chance for each participant (p < 0.001, t-test) with chance levels ranging from 12 to 31 %.  ... 
doi:10.1186/s12984-015-0076-7 pmid:26392353 pmcid:PMC4578759 fatcat:p4oqzhyik5arnhuy2sflalse5e

Altered modulation of sensorimotor rhythms with chronic paralysis

Stephen T. Foldes, Douglas J. Weber, Jennifer L. Collinger
2017 Journal of Neurophysiology  
Foldes ST, Weber DJ, Collinger JL. Altered modulation of sensorimotor rhythms with chronic paralysis.  ...  Time-frequency representations span the grasp/release cycle with the cue to grasp at t ϭ 0.  ...  A new approach to MI therapy is to supplement MI practice with real-time neurofeedback of the patient's brain activity (Foldes et al. 2015; Ramos-Murguialday et al. 2013 ).  ... 
doi:10.1152/jn.00878.2016 pmid:28768745 fatcat:ihglvmvk2bf7ll5bqsh57rdoz4

POEMS neuropathy: optimising diagnosis and management

Stephen Keddie, Shirley D'Sa, David Foldes, Aisling S Carr, Mary M Reilly, Michael P T Lunn
2018 Practical Neurology  
Ethics: All patients signed consent forms to allow for their case histories and clinical images to be published. Abstract POEMS syndrome is a rare and disabling autoinflammatory condition, typified by a typical peripheral neuropathy and the presence of a monoclonal plasma cell disorder. The acronym 'POEMS' represents the complex and multi-system features of the disease, including polyneuropathy, organomegaly, endocrinopathy, a monoclonal plasma cell disorder, and skin disease. The diagnosis of
more » ... OEMS is a significant challenge because of the heterogeneity of clinical presentations and variation of POEMS features. Patients are often misdiagnosed with another cause of inflammatory neuropathy and receive one or more ineffective immunomodulatory medications resulting in delayed diagnosis and further clinical deterioration before a diagnosis is made. University College London Hospital sees one of the largest reported POEMS cohorts in Europe, and runs a multi-specialist clinic to assist with diagnosis, treatment and ongoing support. This review draws upon our experience to present the typical features of POEMS syndrome, and highlight diagnostic conundrums commonly experienced supplemented with clinical cases. We will provide an investigative guide for clinicians when considering POEMS as the diagnosis, and propose a treatment algorithm which centres on the site and degree of monoclonal cell proliferation.
doi:10.1136/practneurol-2017-001792 pmid:29511110 fatcat:6viylhnrpjg4plulzdytffzrze

Approaches to Multimodality Monitoring in Pediatric Traumatic Brain Injury

Brian Appavu, Brian T Burrows, Stephen Foldes, P David Adelson
2019 Frontiers in Neurology  
Copyright © 2019 Appavu, Burrows, Foldes and Adelson. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY).  ... 
doi:10.3389/fneur.2019.01261 pmid:32038449 pmcid:PMC6988791 fatcat:scdhwdnjzjfwvpdftlm2sqmbku

High surface area and Z′ in a thermally stable 8-fold polycatenated hydrogen-bonded framework

Cassandra A. Zentner, Holden W. H. Lai, Joshua T. Greenfield, Ren A. Wiscons, Matthias Zeller, Charles F. Campana, Orhan Talu, Stephen A. FitzGerald, Jesse L. C. Rowsell
2015 Chemical Communications  
Permanent porosity, a large surface area, and unprecedented Z′ was exhibited in an 8-fold polycatenated hydrogen-bonded organic framework.  ...  polycatenation; (e) extended view of the 8-fold polycatenation of hexagonal layers.  ...  The polycatenating hexagonal sheets are created through the two-fold rotation axis (Fig. 4a) .  ... 
doi:10.1039/c5cc04219d pmid:26099041 fatcat:6qfbo2kmvzfdrkllbhyybt7euu

Carboxyl pKa Values, Ion Pairs, Hydrogen Bonding, and the pH-dependence of Folding the Hyperthermophile Proteins Sac7d and Sso7d

Andrew T. Clark, Kelley Smith, Ranjith Muhandiram, Stephen P. Edmondson, John W. Shriver
2007 Journal of Molecular Biology  
The linkage of the ionization of two or more side chains to protein folding leads to apparent cooperativity in the pH dependence of folding, although each group titrates independently with a Hill coefficient  ...  The small number (3) of significantly altered pK a values was in good agreement with a linkage analysis of the temperature, pH, and salt dependence of folding.  ...  The stabilities of Sac7d and Sso7d are some of the best characterized of any protein. 63, 64 This is the result of the fact that not only are these thermophile proteins with T m values that approach  ... 
doi:10.1016/j.jmb.2007.06.089 pmid:17692336 pmcid:PMC2083566 fatcat:g7yjusznpfay3lat6mspj7mwdm

Contribution of Residue B5 to the Folding and Function of Insulin and IGF-I

Youhei Sohma, Qing-xin Hua, Ming Liu, Nelson B. Phillips, Shi-Quan Hu, Jonathan Whittaker, Linda J. Whittaker, Aubree Ng, Charles T. Roberts, Peter Arvan, Stephen B. H. Kent, Michael A. Weiss
2009 Journal of Biological Chemistry  
denaturation studies indicate that His B5 does not significantly enhance thermodynamic stability (ΔΔG u 0.2 ± 0.2 kcal/mole), implying that the substitution favors canonical pairing by destabilizing competing folds  ...  Paired Student's t tests were used for all statistical analyses. Significance was accepted at P < 0.05.  ...  (B) Ribbon model of human insulin (T-state protomer; PDB accession code 4INS). The coloring scheme is as in panel A. His B5 is shown in green.  ... 
doi:10.1074/jbc.m109.062992 pmid:19959476 pmcid:PMC2836107 fatcat:xtuu4tncivbblp5beltubesg5q

Transdermal Electrical Neuromodulation for Anxiety and Sleep Problems in High-Functioning Autism Spectrum Disorder: Feasibility and Preliminary Findings

Stephen T. Foldes, Amanda R. Jensen, Austin Jacobson, Sarah Vassall, Emily Foldes, Ann Guthery, Danni Brown, Todd Levine, William James Tyler, Richard E. Frye
2021 Journal of Personalized Medicine  
Autism spectrum disorder (ASD) is associated with anxiety and sleep problems. We investigated transdermal electrical neuromodulation (TEN) of the cervical nerves in the neck as a safe, effective, comfortable and non-pharmacological therapy for decreasing anxiety and enhancing sleep quality in ASD. Methods: In this blinded, sham-controlled study, seven adolescents and young adults with high-functioning ASD underwent five consecutive treatment days, one day of the sham followed by four days of
more » ... threshold TEN for 20 min. Anxiety-provoking cognitive tasks were performed after the sham/TEN. Measures of autonomic nervous system activity, including saliva α-amylase and cortisol, electrodermal activity, and heart rate variability, were collected from six participants. Results: Self-rated and caretaker-rated measures of anxiety were significantly improved with TEN treatment as compared to the sham, with effect sizes ranging from medium to large depending on the rating scale. Sleep scores from caretaker questionnaires also improved, but not significantly. Performance on two of the three anxiety-provoking cognitive tasks and heart rate variability significantly improved with TEN stimulation as compared to the sham. Four of the seven (57%) participants were responders, defined as a ≥ 30% improvement in self-reported anxiety. Salivary α-amylase decreased with more TEN sessions and decreased from the beginning to the end of the session on TEN days for responders. TEN was well-tolerated without significant adverse events. Conclusions: This study provides preliminary evidence that TEN is well-tolerated in individuals with ASD and can improve anxiety.
doi:10.3390/jpm11121307 pmid:34945779 pmcid:PMC8704341 fatcat:lq4shzzakbbgjevmp7zokrlq4u

Speaking and cognitive distractions during EEG-based brain control of a virtual neuroprosthesis-arm

Stephen T Foldes, Dawn M Taylor
2013 Journal of NeuroEngineering and Rehabilitation  
On average, all metrics showed a decline in control performance with increased cognitive load, although this decline was not significant in the more variable movement-time metric (paired t-test).  ... 
doi:10.1186/1743-0003-10-116 pmid:24359452 pmcid:PMC3878059 fatcat:6ieex4afd5cdvmsjgtuszawepi

Smoothing a rugged protein folding landscape by sequence-based redesign

Benjamin T. Porebski, Shani Keleher, Jeffrey J. Hollins, Adrian A. Nickson, Emilia M. Marijanovic, Natalie A. Borg, Mauricio G. S. Costa, Mary A. Pearce, Weiwen Dai, Liguang Zhu, James A. Irving, David E. Hoke (+6 others)
2016 Scientific Reports  
Characterization of its structure, folding and dynamics suggest that consensus design has remodeled the folding landscape to reconcile competing requirements for stability and function.  ...  To investigate how serpins balance function and folding, we used consensus design to create conserpin, a synthetic serpin that folds reversibly, is functional, thermostable, and polymerization resistant  ...  Variable-temperature far-UV CD melting curves in 2 M GuHCl gave a T m of 60.7 °C (conserpin T m = 72.5 °C; (Fig. S7F) ).  ... 
doi:10.1038/srep33958 pmid:27667094 pmcid:PMC5036219 fatcat:ykgt5exnovbnjgn7vfgfs5hf54

Decoding Brain States Based on Magnetoencephalography From Prespecified Cortical Regions

Jinyin Zhang, Xin Li, Stephen T. Foldes, Wei Wang, Jennifer L. Collinger, Douglas J. Weber, Anto Bagic
2016 IEEE Transactions on Biomedical Engineering  
Hence, we evaluate the decoding accuracy by using six-fold cross-validation [19] and assess the ROI selectivity by using the discriminant pattern source localization (DPSL) method [29] .  ...  The power of y Φ and yΦ can be calculated as p Φ = y Φ y T Φ = w T · m ∈Φ n ∈Φ A m · q m · q T n · A T n · w (10) pΦ = yΦ y T Φ = w T · m / ∈Φ n / ∈Φ A m · q m · q T n · A T n · w. (11) We use the ratio  ...  Based on this observation, we define w = w 1 w 2 · · · w M −1 1 T = v T 1 T , (28) where v = [w 1 w 2 ... w M −1 ] T .  ... 
doi:10.1109/tbme.2015.2439216 pmid:26699648 fatcat:ksjfgxb5z5fijcijpytsrayxbi

Hereditary transthyretin amyloidosis: baseline characteristics of patients in the NEURO-TTR trial

Marcia Waddington-Cruz, Elizabeth J. Ackermann, Michael Polydefkis, Stephen B. Heitner, Peter J. Dyck, Fabio A. Barroso, Annabel K. Wang, John L. Berk, P. James B. Dyck, Brett P. Monia, Steven G. Hughes, Li Tai (+5 others)
2018 Amyloid: Journal of Protein Folding Disorders  
Statistical significance was determined by analysis of variance (ANOVA) and two-sample t-test with two-sided significance level of 0.05.  ... 
doi:10.1080/13506129.2018.1503593 pmid:30169969 fatcat:dsy5sibheja4zjvi65ikqttkve
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