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Article ; Online: Spontaneous Breathing Trials and Conservative Sedation Practices Reduce Mechanical Ventilation Duration in Subjects With ARDS.

Kallet, Richard H / Zhuo, Hanjing / Yip, Vivian / Gomez, Antonio / Lipnick, Michael S

2018 Volume 63, Issue 1, Page(s) 1–10

Abstract: Background: Spontaneous breathing trials (SBTs) and daily sedation interruptions (DSIs) reduce both the duration of mechanical ventilation and ICU length of stay (LOS). The impact of these practices in patients with ARDS has not previously been reported. ...

Abstract	Background: Spontaneous breathing trials (SBTs) and daily sedation interruptions (DSIs) reduce both the duration of mechanical ventilation and ICU length of stay (LOS). The impact of these practices in patients with ARDS has not previously been reported. We examined whether implementation of SBT/DSI protocols reduce duration of mechanical ventilation and ICU LOS in a retrospective group of subjects with ARDS at a large, urban, level-1 trauma center. Methods: All ARDS survivors from 2002 to 2016 ( Results: Compared to the pre-protocol group, subjects with ARDS managed with SBT/DSI protocols experienced pronounced reductions both in median (IQR) mechanical ventilation duration (14 [6-29] vs 9 [4-17] d, respectively, Conclusion: Evidenced-based protocols governing weaning and sedation practices were associated with both reduced mechanical ventilation duration and ICU LOS in subjects with ARDS. However, higher respiratory system compliance in the SBT/DSI cohort also contributed to these improved outcomes.
MeSH term(s)	Adult ; Clinical Protocols ; Conscious Sedation/methods ; Female ; Humans ; Intensive Care Units ; Length of Stay ; Male ; Middle Aged ; Respiration, Artificial/methods ; Respiration, Artificial/statistics & numerical data ; Respiratory Distress Syndrome, Adult/therapy ; Retrospective Studies ; Time Factors ; Treatment Outcome ; Ventilator Weaning/methods
Language	English
Publishing date	2018-01
Publishing country	United States
Document type	Comparative Study ; Editorial
ZDB-ID	603252-7
ISSN	1943-3654 ; 0098-9142 ; 0020-1324
ISSN (online)	1943-3654
ISSN	0098-9142 ; 0020-1324
DOI	10.4187/respcare.05270
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Article: A Text Messaging Intervention for Coping With Social Distancing During COVID-19 (StayWell at Home): Protocol for a Randomized Controlled Trial.

Figueroa, Caroline Astrid / Hernandez-Ramos, Rosa / Boone, Claire Elizabeth / Gómez-Pathak, Laura / Yip, Vivian / Luo, Tiffany / Sierra, Valentín / Xu, Jing / Chakraborty, Bibhas / Darrow, Sabrina / Aguilera, Adrian

JMIR research protocols

2021 Volume 10, Issue 1, Page(s) e23592

Abstract: Background: Social distancing is a crucial intervention to slow down person-to-person transmission of COVID-19. However, social distancing has negative consequences, including increases in depression and anxiety. Digital interventions, such as text ... ...

Abstract	Background: Social distancing is a crucial intervention to slow down person-to-person transmission of COVID-19. However, social distancing has negative consequences, including increases in depression and anxiety. Digital interventions, such as text messaging, can provide accessible support on a population-wide scale. We developed text messages in English and Spanish to help individuals manage their depressive mood and anxiety during the COVID-19 pandemic. Objective: In a two-arm randomized controlled trial, we aim to examine the effect of our 60-day text messaging intervention. Additionally, we aim to assess whether the use of machine learning to adapt the messaging frequency and content improves the effectiveness of the intervention. Finally, we will examine the differences in daily mood ratings between the message categories and time windows. Methods: The messages were designed within two different categories: behavioral activation and coping skills. Participants will be randomized into (1) a random messaging arm, where message category and timing will be chosen with equal probabilities, and (2) a reinforcement learning arm, with a learned decision mechanism for choosing the messages. Participants in both arms will receive one message per day within three different time windows and will be asked to provide their mood rating 3 hours later. We will compare self-reported daily mood ratings; self-reported depression, using the 8-item Patient Health Questionnaire; and self-reported anxiety, using the 7-item Generalized Anxiety Disorder scale at baseline and at intervention completion. Results: The Committee for the Protection of Human Subjects at the University of California Berkeley approved this study in April 2020 (No. 2020-04-13162). Data collection began in April 2020 and will run to April 2021. As of August 24, 2020, we have enrolled 229 participants. We plan to submit manuscripts describing the main results of the trial and results from the microrandomized trial for publication in peer-reviewed journals and for presentations at national and international scientific meetings. Conclusions: Results will contribute to our knowledge of effective psychological tools to alleviate the negative effects of social distancing and the benefit of using machine learning to personalize digital mental health interventions. Trial registration: ClinicalTrials.gov NCT04473599; https://clinicaltrials.gov/ct2/show/NCT04473599. International registered report identifier (irrid): DERR1-10.2196/23592.
Language	English
Publishing date	2021-01-14
Publishing country	Canada
Document type	Journal Article
ZDB-ID	2719222-2
ISSN	1929-0748
ISSN	1929-0748
DOI	10.2196/23592
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Article ; Online: Identification of Tyr241 as a key catalytic base in the family 4 glycoside hydrolase BglT from Thermotoga maritima.

Yip, Vivian L Y / Withers, Stephen G

Biochemistry

2012 Volume 51, Issue 42, Page(s) 8464–8474

Abstract: While the vast majority of glycosidases catalyze glycoside hydrolysis via oxocarbenium ion-like transition states and typically employ carboxylic acid residues as acid/base or nucleophile catalysts, two subfamilies of these enzymes (GH4 and GH109 in the ... ...

Abstract	While the vast majority of glycosidases catalyze glycoside hydrolysis via oxocarbenium ion-like transition states and typically employ carboxylic acid residues as acid/base or nucleophile catalysts, two subfamilies of these enzymes (GH4 and GH109 in the CAZY classification) conduct hydrolysis via a redox-assisted mechanism involving anionic transition states. While good evidence of this mechanism has been obtained, the identities of the catalytic residues involved have not yet been confirmed. Mechanistic analyses of mutants of the 6-phospho-β-glucosidase from Thermotoga maritima (BglT), in which the active site tyrosine residue (Tyr 241) has been replaced with Phe and Ala, provide support for its role as a catalytic base. The pH dependence of k(cat) and k(cat)/K(m), particularly of the acidic limb corresponding to the base, is shifted relative to that of the wild-type enzyme. Kinetic isotope effects for hydrolysis of substrates deuterated at C1, C2, and C3 by the Tyr 241 mutants are strongly pH-dependent, with essentially full primary kinetic isotope effects being observed for the 2-deutero substrate at low pH with the Tyr241Ala mutant. This is consistent with a slowing of the deprotonation step upon removal of the base.
MeSH term(s)	Amino Acid Substitution ; Catalysis ; Glucosidases/chemistry ; Glucosidases/genetics ; Hydrogen-Ion Concentration ; Kinetics ; NAD/metabolism ; Thermotoga maritima/enzymology ; Tyrosine/genetics ; Tyrosine/metabolism
Chemical Substances	NAD (0U46U6E8UK) ; Tyrosine (42HK56048U) ; Glucosidases (EC 3.2.1.-) ; 6-phospho-beta-glucosidase (EC 3.2.1.86)
Language	English
Publishing date	2012-10-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi301021u
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Article: Identification of Tyr241 as a Key Catalytic Base in the Family 4 Glycoside Hydrolase BglT from Thermotoga maritima

Yip, Vivian L. Y / Withers Stephen G

Biochemistry. 2012 Oct. 23, v. 51, no. 42

2012

Abstract	While the vast majority of glycosidases catalyze glycoside hydrolysis via oxocarbenium ion-like transition states and typically employ carboxylic acid residues as acid/base or nucleophile catalysts, two subfamilies of these enzymes (GH4 and GH109 in the CAZY classification) conduct hydrolysis via a redox-assisted mechanism involving anionic transition states. While good evidence of this mechanism has been obtained, the identities of the catalytic residues involved have not yet been confirmed. Mechanistic analyses of mutants of the 6-phospho-Î²-glucosidase from Thermotoga maritima (BglT), in which the active site tyrosine residue (Tyr 241) has been replaced with Phe and Ala, provide support for its role as a catalytic base. The pH dependence of kcââ and kcââ/Kâ, particularly of the acidic limb corresponding to the base, is shifted relative to that of the wild-type enzyme. Kinetic isotope effects for hydrolysis of substrates deuterated at C1, C2, and C3 by the Tyr 241 mutants are strongly pH-dependent, with essentially full primary kinetic isotope effects being observed for the 2-deutero substrate at low pH with the Tyr241Ala mutant. This is consistent with a slowing of the deprotonation step upon removal of the base.
Keywords	Thermotoga maritima ; active sites ; catalysts ; glycosidases ; glycosides ; hydrolysis ; isotopes ; mutants ; pH ; tyrosine
Language	English
Dates of publication	2012-1023
Size	p. 8464-8474.
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%2Fbi301021u
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Severity of Hypoxemia and Other Factors That Influence the Response to Aerosolized Prostacyclin in ARDS.

Kallet, Richard H / Burns, Gregory / Zhuo, Hanjing / Ho, Kelly / Phillips, Justin S / Pangilinan, Lance P / Yip, Vivian / Gomez, Antonio / Lipnick, Michael S

Respiratory care

2017 Volume 62, Issue 8, Page(s) 1014–1022

Abstract: Background: ARDS is characterized by decreased functional residual capacity (FRC), heterogeneous lung injury, and severe hypoxemia. Tidal ventilation is preferentially distributed to ventilated alveoli. Aerosolized prostaglandin I: Methods: We ... ...

Abstract	Background: ARDS is characterized by decreased functional residual capacity (FRC), heterogeneous lung injury, and severe hypoxemia. Tidal ventilation is preferentially distributed to ventilated alveoli. Aerosolized prostaglandin I Methods: We reviewed the records of 208 ARDS subjects who received aerosolized prostaglandin I Results: Mean P Conclusions: Aerosolized prostaglandin I
Language	English
Publishing date	2017-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	603252-7
ISSN	1943-3654 ; 0098-9142 ; 0020-1324
ISSN (online)	1943-3654
ISSN	0098-9142 ; 0020-1324
DOI	10.4187/respcare.05268
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Article ; Online: A Text Messaging Intervention for Coping With Social Distancing During COVID-19 (StayWell at Home)

JMIR Research Protocols, Vol 10, Iss 1, p e

Protocol for a Randomized Controlled Trial

2021 Volume 23592

Abstract: BackgroundSocial distancing is a crucial intervention to slow down person-to-person transmission of COVID-19. However, social distancing has negative consequences, including increases in depression and anxiety. Digital interventions, such as text ... ...

Abstract	BackgroundSocial distancing is a crucial intervention to slow down person-to-person transmission of COVID-19. However, social distancing has negative consequences, including increases in depression and anxiety. Digital interventions, such as text messaging, can provide accessible support on a population-wide scale. We developed text messages in English and Spanish to help individuals manage their depressive mood and anxiety during the COVID-19 pandemic. ObjectiveIn a two-arm randomized controlled trial, we aim to examine the effect of our 60-day text messaging intervention. Additionally, we aim to assess whether the use of machine learning to adapt the messaging frequency and content improves the effectiveness of the intervention. Finally, we will examine the differences in daily mood ratings between the message categories and time windows. MethodsThe messages were designed within two different categories: behavioral activation and coping skills. Participants will be randomized into (1) a random messaging arm, where message category and timing will be chosen with equal probabilities, and (2) a reinforcement learning arm, with a learned decision mechanism for choosing the messages. Participants in both arms will receive one message per day within three different time windows and will be asked to provide their mood rating 3 hours later. We will compare self-reported daily mood ratings; self-reported depression, using the 8-item Patient Health Questionnaire; and self-reported anxiety, using the 7-item Generalized Anxiety Disorder scale at baseline and at intervention completion. ResultsThe Committee for the Protection of Human Subjects at the University of California Berkeley approved this study in April 2020 (No. 2020-04-13162). Data collection began in April 2020 and will run to April 2021. As of August 24, 2020, we have enrolled 229 participants. We plan to submit manuscripts describing the main results of the trial and results from the microrandomized trial for publication in peer-reviewed journals and for ...
Keywords	Medicine ; R ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	150
Language	English
Publishing date	2021-01-01T00:00:00Z
Publisher	JMIR Publications
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Mechanism of GlvA from Bacillus subtilis: a detailed kinetic analysis of a 6-phospho-alpha-glucosidase from glycoside hydrolase family 4.

Yip, Vivian L Y / Thompson, John / Withers, Stephen G

Biochemistry

2007 Volume 46, Issue 34, Page(s) 9840–9852

Abstract: GlvA, a 6-phospho-alpha-glucosidase from Bacillus subtilis assigned to glycoside hydrolase family 4, catalyzes the hydrolysis of maltose 6'-phosphate via a redox-elimination-addition mechanism requiring NAD+ as cofactor. In contrast to previous reports ... ...

Abstract	GlvA, a 6-phospho-alpha-glucosidase from Bacillus subtilis assigned to glycoside hydrolase family 4, catalyzes the hydrolysis of maltose 6'-phosphate via a redox-elimination-addition mechanism requiring NAD+ as cofactor. In contrast to previous reports and consistent with the proposed mechanism, GlvA is only activated in the presence of the nicotinamide cofactor in its oxidized, and not the reduced NADH, form. Significantly, GlvA catalyzes the hydrolysis of both 6-phospho-alpha- and 6-phospho-beta-glucosides containing activated leaving groups such as p-nitrophenol and does so with retention and inversion, respectively, of anomeric configuration. Mechanistic details of the individual bond cleaving and forming steps were probed using a series of 6-phospho-alpha- and 6-phospho-beta-glucosides. Primary deuterium kinetic isotope effects (KIEs) were measured for both classes of substrates in which either the C2 or the C3 protons have been substituted with a deuterium, consistent with C-H bond cleavage at each center being partially rate-limiting. Kinetic parameters were also determined for 1-[2H]-substituted substrates, and depending on the substrates and the reaction conditions, the measurements of kcat and kcat/KM produced either no KIEs or inverse KIEs. In conjunction with results of Brønsted analyses with both aryl 6-phospho-alpha- and beta-glucosides, the kinetic data suggest that GlvA utilizes an E1cb mechanism analogous to that proposed for the Thermotoga maritima BglT, a 6-phospho-beta-glucosidase in glycoside hydrolase family 4 (Yip, V.L.Y et al. (2006) Biochemistry 45, 571-580). The pattern of isotope effects measured and the observation of very similar kcat values for all substrates, including unactivated and natural substrates, indicate that the oxidation and deprotonation steps are rate-limiting steps in essentially all cases. This mechanism permits the cleavage of both alpha- and beta-glycosides within the same active site motif and, for activated substrates that do not require acid catalysis for cleavage, within the same active site, yielding the product sugar-6-phosphate in the same anomeric form in the two cases.
MeSH term(s)	Bacillus subtilis/enzymology ; Binding Sites ; Catalysis ; Deuterium Exchange Measurement ; Deuterium Oxide ; Glycosides ; Hydrogen-Ion Concentration ; Hydrolysis ; Kinetics ; NAD/metabolism ; Oxidation-Reduction ; Substrate Specificity ; alpha-Glucosidases/chemistry ; alpha-Glucosidases/metabolism
Chemical Substances	Glycosides ; NAD (0U46U6E8UK) ; maltose-6'-phosphate glucosidase (EC 3.2.1.122) ; alpha-Glucosidases (EC 3.2.1.20) ; Deuterium Oxide (J65BV539M3)
Language	English
Publishing date	2007-08-28
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi700536p
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Article: Mechanistic analysis of the unusual redox-elimination sequence employed by Thermotoga maritima BglT: a 6-phospho-beta-glucosidase from glycoside hydrolase family 4.

Yip, Vivian L Y / Withers, Stephen G

Biochemistry

2006 Volume 45, Issue 2, Page(s) 571–580

Abstract: Classical" glycosidases utilize either direct or double-displacement mechanisms involving oxocarbenium ion-like transition states to catalyze the hydrolysis of glycosidic bonds. By contrast, the mechanism of the glycosidases in glycoside hydrolase ... ...

Abstract	"Classical" glycosidases utilize either direct or double-displacement mechanisms involving oxocarbenium ion-like transition states to catalyze the hydrolysis of glycosidic bonds. By contrast, the mechanism of the glycosidases in glycoside hydrolase family 4 has been recently proposed to involve NAD+-mediated redox steps along with alpha,beta-elimination and addition steps via anionic intermediates. Support for this mechanism in BglT, a 6-phospho-beta-glucosidase in family 4, has been provided through mechanistic and X-ray crystallographic analyses [Yip, V. L.Y., et al. (2004) J. Am. Chem. Soc. 126, 8354-8355] in which primary deuterium kinetic isotope effects for the hydride abstraction at C3 and for the alpha-proton abstraction at C2 indicate that these two steps are both partially rate-limiting. Current data reveal that there is no secondary deuterium kinetic isotope effect associated with the rehybridization of the C1 sp3 center to a sp2 center. Furthermore, a flat linear free energy relationship was established with a series of aryl 6-phospho-beta-D-glucosides of varying leaving group abilities. Taken together, these data indicate that cleavage of the C1-O1 linkage does not occur during a rate-limiting step. Since the deprotonation at C2 is slow and partially rate-limiting while the departure of the leaving group is not, a stepwise E1(cb)-type mechanism rather than an E1 or a concerted E2-syn mechanism is proposed. Direct evidence for the role of NAD+ was obtained by reduction in situ using NaBH4 leading to an inactive enzyme that could be reactivated by the addition of excess NAD+. This was accompanied by the expected UV-vis spectrophotometric changes.
MeSH term(s)	Catalysis ; Deuterium Exchange Measurement ; Deuterium Oxide ; Glucose-6-Phosphate/analogs & derivatives ; Glucosephosphate Dehydrogenase/chemistry ; Glucosidases/chemistry ; Glucosidases/metabolism ; Glycoside Hydrolases/chemistry ; Glycoside Hydrolases/metabolism ; Kinetics ; Multigene Family ; NAD/metabolism ; Oxidation-Reduction ; Spectrophotometry, Ultraviolet ; Thermodynamics ; Thermotoga maritima/enzymology ; alpha-Glucosidases/chemistry
Chemical Substances	NAD (0U46U6E8UK) ; Glucose-6-Phosphate (56-73-5) ; Glucosephosphate Dehydrogenase (EC 1.1.1.49) ; Glucosidases (EC 3.2.1.-) ; Glycoside Hydrolases (EC 3.2.1.-) ; maltose-6'-phosphate glucosidase (EC 3.2.1.122) ; alpha-Glucosidases (EC 3.2.1.20) ; 6-phospho-beta-glucosidase (EC 3.2.1.86) ; Deuterium Oxide (J65BV539M3)
Language	English
Publishing date	2006-01-17
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/bi052054x
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Article: Family 4 glycosidases carry out efficient hydrolysis of thioglycosides by an alpha,beta-elimination mechanism.

Yip, Vivian L Y / Withers, Stephen G

Angewandte Chemie (International ed. in English)

2006 Volume 45, Issue 37, Page(s) 6179–6182

MeSH term(s)	Catalysis ; Disaccharides/chemistry ; Glycoside Hydrolases/metabolism ; Hydrolysis ; Thermotoga maritima/enzymology ; Thioglycosides/chemistry ; Thioglycosides/metabolism
Chemical Substances	Disaccharides ; Thioglycosides ; Glycoside Hydrolases (EC 3.2.1.-) ; 6-phospho-beta-galactosidase (EC 3.2.1.85)
Language	English
Publishing date	2006-09-18
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.200601421
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Article: Breakdown of oligosaccharides by the process of elimination.

Yip, Vivian L Y / Withers, Stephen G

Current opinion in chemical biology

2006 Volume 10, Issue 2, Page(s) 147–155

Abstract: Several new mechanisms for enzyme-catalyzed breakdown of oligosaccharides have been uncovered in recent years. A common feature is the recruitment of elimination steps rather than direct displacements. Bond cleavage can proceed via E1 mechanisms with ... ...

Abstract	Several new mechanisms for enzyme-catalyzed breakdown of oligosaccharides have been uncovered in recent years. A common feature is the recruitment of elimination steps rather than direct displacements. Bond cleavage can proceed via E1 mechanisms with cationic transition states or E1(cb) mechanisms with anionic transition states, and can even involve NAD(+)-mediated redox steps. A common feature emerging from studies on disparate syn-eliminating enzymes is the use of a single catalytic residue, often tyrosine, as both general acid and base.
MeSH term(s)	DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Glycoside Hydrolases/metabolism ; Oligosaccharides/metabolism ; Polysaccharide-Lyases/metabolism
Chemical Substances	Oligosaccharides ; Glycoside Hydrolases (EC 3.2.1.-) ; Polysaccharide-Lyases (EC 4.2.2.-) ; alpha-1,4-glucan lyase (EC 4.2.2.13) ; DNA-(Apurinic or Apyrimidinic Site) Lyase (EC 4.2.99.18)
Language	English
Publishing date	2006-04
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1439176-4
ISSN	1879-0402 ; 1367-5931
ISSN (online)	1879-0402
ISSN	1367-5931
DOI	10.1016/j.cbpa.2006.02.005
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