Performance of artificial intelligence chatbots in sleep medicine certification board exams: ChatGPT versus Google Bard.

PURPOSE: To conduct a comparative performance evaluation of GPT-3.5, GPT-4 and Google Bard in self-assessment questions at the level of the American Sleep Medicine Certification Board Exam. METHODS: A total of 301 text-based single-best-answer multiple choice questions with four answer options each, across 10 categories, were included in the study and transcribed as inputs for GPT-3.5, GPT-4 and Google Bard. The first output responses generated were selected and matched for answer accuracy against the gold-standard answer provided by the American Academy of Sleep Medicine for each question. A global score of 80% and above is required by human sleep medicine specialists to pass each exam category. RESULTS: GPT-4 successfully achieved the pass mark of 80% or above in five of the 10 exam categories, including the Normal Sleep and Variants Self-Assessment Exam (2021), Circadian Rhythm Sleep-Wake Disorders Self-Assessment Exam (2021), Insomnia Self-Assessment Exam (2022), Parasomnias Self-Assessment Exam (2022) and the Sleep-Related Movements Self-Assessment Exam (2023). GPT-4 demonstrated superior performance in all exam categories and achieved a higher overall score of 68.1% when compared against both GPT-3.5 (46.8%) and Google Bard (45.5%), which was statistically significant (p value < 0.001). There was no significant difference in the overall score performance between GPT-3.5 and Google Bard. CONCLUSIONS: Otolaryngologists and sleep medicine physicians have a crucial role through agile and robust research to ensure the next generation AI chatbots are built safely and responsibly.

Assessment of Reversibility for Covalent Cysteine Protease Inhibitors Using Quantum Mechanics/Molecular Mechanics Free Energy Surfaces.

We have used molecular dynamics (MD) simulations with hybrid quantum mechanics/molecular mechanics (QM/MM) potentials to investigate the reaction mechanism for covalent inhibition of cathepsin K and assess the reversibility of inhibition. The computed free energy profiles suggest that a nucleophilic attack by the catalytic cysteine on the inhibitor warhead and proton transfer from the catalytic histidine occur in a concerted manner. The results indicate that the reaction is more strongly exergonic for the alkyne-based inhibitors, which bind irreversibly to cathepsin K, than for the nitrile-based inhibitor odanacatib, which binds reversibly. Gas-phase energies were also calculated for the addition of methanethiol to structural prototypes for a number of warheads of interest in cysteine protease inhibitor design in order to assess electrophilicity. The approaches presented in this study are particularly applicable to assessment of novel warheads, and computed transition state geometries can be incorporated into molecular models for covalent docking.

Crystal structure of Leishmania mexicana cysteine protease B in complex with a high-affinity azadipeptide nitrile inhibitor.

Leishmania mexicana is an obligate intracellular protozoan parasite that causes the cutaneous form of leishmaniasis affecting South America and Mexico. The cysteine protease LmCPB is essential for the virulence of the parasite and therefore, it is an appealing target for antiparasitic therapy. A library of nitrile-based cysteine protease inhibitors was screened against LmCPB to develop a treatment of cutaneous leishmaniasis. Several compounds are sufficiently high-affinity LmCPB inhibitors to serve both as starting points for drug discovery projects and as probes for target validation. A 1.4 Å X ray crystal structure, the first to be reported for LmCPB, was determined for the complex of this enzyme covalently bound to an azadipeptide nitrile ligand. Mapping the structure-activity relationships for LmCPB inhibition revealed superadditive effects for two pairs of structural transformations. Therefore, this work advances our understanding of azadipeptidyl and dipeptidyl nitrile structure-activity relationships for LmCPB structure-based inhibitor design. We also tested the same series of inhibitors on related cysteine proteases cathepsin L and Trypanosoma cruzi cruzain. The modulation of these mammalian and protozoan proteases represents a new framework for targeting papain-like cysteine proteases.

Synthesis and structure-activity relationship of nitrile-based cruzain inhibitors incorporating a trifluoroethylamine-based P2 amide replacement.

The structure-activity relationship for nitrile-based cruzain inhibitors incorporating a P2 amide replacement based on trifluoroethylamine was explored by deconstruction of a published series of inhibitors. It was demonstrated that the P3 biphenyl substituent present in the published inhibitor structures could be truncated to phenyl with only a small loss of affinity. The effects of inverting the configuration of the P2 amide replacement and linking a benzyl substituent at P1 were observed to be strongly nonadditive. We show that plotting affinity against molecular size provides a means to visualize both the molecular size efficiency of structural transformations and the nonadditivity in the structure-activity relationship. We also show how the relationship between affinity and lipophilicity, measured by high-performance liquid chromatography with an immobilized artificial membrane stationary phase, may be used to normalize affinity with respect to lipophilicity.

Palate surgery for obstructive sleep apnea: a 17-year meta-analysis.

OBJECTIVES: Systematic review of palate surgery for the treatment of OSA. METHODS: Independent searches to identify publications relevant to OSA treatment and upper airway palate surgery. All relevant studies published between January 2001 and February 2018 were included. Inclusion criteria were adult patients, documented airway evaluation methods and absent hypopharyngeal collapse. Outcomes included success rates of treatment, AHI, Epworth scale, QOL and snoring VAS. RESULTS: Fifty-nine papers with a total of 2715 patients, UPPP accounted for 16.7% of all the procedures. Evident differentiation progressing from 2001 to 2018, from 2001 to 2010, the percentage of UPPP procedures were 25.67%, from 2011 to 2018, there were only 12.6% of UPPP procedures. The average follow up was 8.18 months. Meta-analysis on the AHI change for all procedures, showed the fixed effect AHI per follow-up (FU) month change was 1.45 (95% CI 1.33, 1.8), p < 0.001; while for ESS, the fixed effect AHI per FU month change was 0.61 (95% CI 0.56, 0.66), p < 0.001. The mean decrease in AHI was from 35.66 to 13.91 (p < 0.001). The mean decrease in ESS was from 11.65 to 5.08 (p < 0.001). The mean AHI change was 19.9 (p < 0.001). The mean ESS change was 5.8 (p < 0.001). The overall pooled success rate was 67.5%. Meta-analysis of the procedures, showed that the respective mean AHI reduction was 24.7 for the anterior palatoplasty (p = 0.015), 19.8 for the lateral/expansion pharyngoplasty (p = 0.046), and 17.2 for the uvulopalatopharyngoplasty (p = 0.360). CONCLUSIONS: Better understanding of the upper airway and objective airway evaluation diagnostic techniques and innovative palate surgeries have improved success rates of OSA surgery.

A comparative study of warheads for design of cysteine protease inhibitors.

The effects on potency of cruzain inhibition of replacing a nitrile group with alternative warheads were explored. The oxime was almost an order of magnitude more potent than the corresponding nitrile and has the potential to provide access to the prime side of the catalytic site. Dipeptide aldehydes and azadipeptide nitriles were found to be two orders of magnitude more potent cruzain inhibitors than the corresponding dipeptide nitriles although potency differences were modulated by substitution at P1 and P3. Replacement of the α methylene of a dipeptide aldehyde with cyclopropane led to a loss of potency of almost three orders of magnitude. The vinyl esters and amides that were characterized as reversible inhibitors were less potent than the corresponding nitrile by between one and two orders of magnitude.

Comment on The Ecstasy and Agony of Assay Interference Compounds.

A recent editorial (Aldrich et al. The Ecstasy and Agony of Assay Interference Compounds . J. Chem. Inf. MODEL: 2017 , 57 , 387 - 390 ) is examined critically. When assessing assay hits from screening, it is important to draw a distinction between false positives, that have no effect on target function, and compounds that affect target function through an undesirable mechanism of action. Observation of frequent-hitter behavior for a compound should be regarded as circumstantial evidence, rather than definitive proof, that the compound has interfered with assay readouts or acted through an undesirable mechanism of action. The applicability domain of published (Baell and Holloway J. Med. Chem. 2010 , 53 , 2719 - 2740 ) Pan Assay INterference compoundS (PAINS) filters is limited by the narrow scope of the proprietary data used to derive them. It is suggested that journal guidelines for authors should not prescribe, as those for the Journal of Medicinal Chemistry appear to do, that activity in assays reported for compounds that match PAINS filters be treated any differently from that for compounds that do not match PAINS filters. It is argued that use of models based on proprietary data in the evaluation of manuscripts would contradict the editorial policy of any journal that deemed the use of proprietary data to be unacceptable in modeling studies.

The influence of hydrogen bonding on partition coefficients.

This Perspective explores how consideration of hydrogen bonding can be used to both predict and better understand partition coefficients. It is shown how polarity of both compounds and substructures can be estimated from measured alkane/water partition coefficients. When polarity is defined in this manner, hydrogen bond donors are typically less polar than hydrogen bond acceptors. Analysis of alkane/water partition coefficients in conjunction with molecular electrostatic potential calculations suggests that aromatic chloro substituents may be less lipophilic than is generally believed and that some of the effect of chloro-substitution stems from making the aromatic π-cloud less available to hydrogen bond donors. Relationships between polarity and calculated hydrogen bond basicity are derived for aromatic nitrogen and carbonyl oxygen. Aligned hydrogen bond acceptors appear to present special challenges for prediction of alkane/water partition coefficients and this may reflect 'frustration' of solvation resulting from overlapping hydration spheres. It is also shown how calculated hydrogen bond basicity can be used to model the effect of aromatic aza-substitution on octanol/water partition coefficients.

Nitrate in the active site of protein tyrosine phosphatase 1B is a putative mimetic of the transition state.

The X-ray crystal structure of the complex of protein tyrosine phosphatase 1B with nitrate anion has been determined and modelled quantum-mechanically. Two protomers were present in the structure, one with the mechanistically important WPD loop closed and the other with this loop open. Nitrate was observed bound to each protomer, making close contacts with the S atom of the catalytic cysteine and a tyrosine residue from a crystallographically related protomer.

Ligand efficiency metrics considered harmful.

Ligand efficiency metrics are used in drug discovery to normalize biological activity or affinity with respect to physicochemical properties such as lipophilicity and molecular size. This Perspective provides an overview of ligand efficiency metrics and summarizes thermodynamics of protein-ligand binding. Different classes of ligand efficiency metric are critically examined and the study concludes with suggestions for alternative ways to account for physicochemical properties when prioritizing and optimizing leads.

Effect of spherical aberration on visual acuity and depth of focus in pseudophakic eyes.

PURPOSE: To assess the performance of 4 intraocular lenses (IOLs) in various spherical aberration (SA) conditions, using the VAO adaptive optics simulator. SETTING: Cullen Eye Institute, Baylor College of Medicine, Houston, Texas. DESIGN: Prospective case series. METHODS: Distance-corrected visual acuities at distance (CDVA), intermediate (DCIVA), and near (DCNVA) were measured in 42 dilated pseudophakic eyes at baseline and with ocular SA ranging from -0.4 to +0.4 µm in increments of 0.2 µm (6.0-mm pupil). 4 IOL types were assessed: monofocal IOLs with zero-SA, enhanced-monofocal, extended depth-of-focus (EDOF), and continuous range-of-vision. RESULTS: Compared with SA = 0 µm, significant changes (all P < .05) were: (1) zero-SA monofocal IOLs' DCNVA at high contrast improved by 0.13 logMAR with SA = -0.4 µm and worsened by 0.09 and 0.10 logMAR with SA = +0.2 and +0.4 µm, respectively. DCNVA at low contrast worsened by 0.09 logMAR with SA = +0.4 µm; and (2) with SA = -0.4 µm, the enhanced monofocal IOL lost 0.06 logMAR of CDVA at high contrast and gained 0.09 logMAR of DCNVA at low contrast. There were no significant changes from SA = 0 µm for EDOF and continuous range-of-vision IOLs. CONCLUSIONS: Zero-SA and EDOF IOLs were the most and least sensitive to SA modulation, respectively. In perfect optical systems where all the optical elements are aligned, induction of targeted amounts of negative SA improved the depth of focus of some IOL types. No benefit was found with positive SA.

Performance of IOL calculation formulas that use measured posterior corneal power in eyes following myopic laser vision correction.

PURPOSE: To compare the predictive accuracy of the biometer-embedded Barrett True-K TK and new total corneal power methods of intraocular lens (IOL) power calculation in eyes with prior laser vision correction (LVC) for myopia. SETTING: Academic clinical practice. DESIGN: Retrospective case series. METHODS: IOL power formulas were assessed using measurements from a swept-source optical coherence biometer. Refractive prediction errors were calculated for the Barrett True-K TK, EVO 2.0, Pearl-DGS, and HofferQST, which use both anterior and posterior corneal curvature measurements. These were compared with the Shammas, Haigis-L, Barrett True-K No History (NH), optical coherence tomography, and 4-formula average (AVG-4) on the ASCRS postrefractive calculator, and to the Holladay 1 and 2 with non linear axial length regressions (H1- and H2-NLR). RESULTS: The study comprised 85 eyes from 85 patients. Only the Barrett True-K TK and EVO 2.0 had mean numerical errors that were not significantly different from 0. The EVO 2.0, Barrett True-K TK, Pearl-DGS, AVG-4, H2-NLR, and Barrett True-K NH were selected for further pairwise analysis. The Barrett True-K TK and EVO 2.0 demonstrated smaller root-mean-square absolute error compared with the Pearl-DGS, and the Barrett True-K TK also had a smaller mean absolute error than the Pearl-DGS. CONCLUSIONS: The Barrett True-K TK and EVO 2.0 formulas had comparable performance to existing formulas in eyes with prior myopic LVC.

Food, nutrition and the dining experience in aged care settings: Findings of a nationwide survey.

OBJECTIVE: Previous research on food, nutrition and dining practices in Australian residential aged care (RAC) homes has been based on a limited sample of single-home or multiple-home providers, but a nationwide study has not been conducted. The aim of this study was to provide a preliminary overview of current food, nutrition and dining practices across Australian RAC facilities using a nationwide survey. METHODS: A survey was distributed to Australian RAC homes in August-September 2020, as part of the National Congress on Food, Nutrition and the Dining Experience in Aged Care (February 2021). The survey, administered via an online portal, consisted of 38 semistructured questions including yes/no or multiple-choice responses, free text, frequency scales and number entry. Six key topics were explored, including 'food service system and environment', 'catering style', 'menu planning and evaluation', 'nutrition planning and requirements', 'nutrition-related screening and assessment' and 'training and additional information', which were informed by the Australian Government Department of Health and reflected the interests of the Congress. RESULTS: The final sample included 292 respondents (204 individual homes and 88 multiple-home proprietors) representing 1152 homes and 125,393 residents, encompassing approximately 43% of RAC homes (of a possible 2671) and 57% of residents (of a possible 219,965) in Australia. Survey respondents representing RAC homes included service managers, catering managers, Chief Executive Officers, cooks, chefs, dietitians or staff from other roles within homes. A number of potential areas of need were identified, included increasing the autonomy of residents to select the foods they desire, increasing the variety and choice (including timing) of meals, enhancing the dining environments in homes to stimulate food intake and increasing staff training and the number of trained chefs in homes, so that meals are prepared which address diverse nutritional needs of residents. CONCLUSIONS: This study provides insight into the food service and mealtime practices of over a third of Australian RAC homes. The findings of this survey may help to identify key targets for intervention to improve the food, nutrition and quality of life of aged care residents.

Inflation of correlation in the pursuit of drug-likeness.

Drug-likeness is a frequently invoked, although not always precisely defined, concept in drug discovery. Opinions on drug-likeness are to a large extent shaped by the relationships that are observed between surrogate measures of drug-likeness (e.g. aqueous solubility; permeability; pharmacological promiscuity) and fundamental physicochemical properties (e.g. lipophilicity; molecular size). This article draws on examples from the literature to highlight approaches to data analysis that exaggerate trends in data and the term correlation inflation is introduced in the context of drug discovery. Averaging groups of data points prior to analysis is a common cause of correlation inflation and results from analysis of binned continuous data should always be treated with caution.

ClogP(alk): a method for predicting alkane/water partition coefficient.

Alkane/water partition coefficients (P(alk)) are less familiar to the molecular design community than their 1-octanol/water equivalents and access to both data and prediction tools is much more limited. A method for predicting alkane/water partition coefficient from molecular structure is introduced. The basis for the ClogP(alk) model is the strong (R² = 0.987) relationship between alkane/water partition coefficient and molecular surface area (MSA) that was observed for saturated hydrocarbons. The model treats a molecule as a perturbation of a saturated hydrocarbon molecule with the same MSA and uses increments defined for functional groups to quantify the extent to which logP(alk) is perturbed by the introduction each functional group. Interactions between functional groups, such as intramolecular hydrogen bonds are also parameterized within a perturbation framework. The functional groups and interactions between them are specified substructurally in a transparent and reproducible manner using SMARTS notation. The ClogP(alk) model was parameterized using data measured for structurally prototypical compounds that dominate the literature on alkane/water partition coefficients and then validated using an external test set of 100 alkane/water logP measurements, the majority of which were for drugs.

Automated molecule editing in molecular design.

The ability to modify chemical structures in an automated and controlled manner is useful in molecular design. This Perspective introduces the MUDO molecule editor and shows how automated molecule editing can be used to standardize structures, enumerate tautomeric and ionization states, identify matched molecular pairs. Unlike its predecessor Leatherface, MUDO can also process 3D structures and this capability can be used to link non-covalently docked ligands to proteins.

Efficacy of segmented axial length and artificial intelligence approaches to intraocular lens power calculation in short eyes.

PURPOSE: In short eyes, to compare the predictive accuracy of newer intraocular lens (IOL) power calculation formulas using traditional and segmented axial length (AL) measurements. SETTING: Cullen Eye Institute, Baylor College of Medicine, Houston, Texas and East Valley Ophthalmology, Mesa, Arizona. DESIGN: Multi-center retrospective case series. METHODS: Measurements from an optical biometer were collected in eyes with AL <22 mm. IOL power calculations were performed with 15 formulas using 2 AL values: (1) machine-reported traditional AL (Td-AL) and (2) segmented AL calculated with the Cooke-modified AL nomogram (CMAL). 1 AL method and 7 formulas were selected for pairwise analysis of mean absolute error (MAE) and root mean square absolute error (RMSAE). RESULTS: The study comprised 278 eyes. Compared with the Td-AL, the CMAL produced hyperopic shifts without differences in RMSAE. The ZEISS AI IOL Calculator (ZEISS AI), K6, Kane, Hill-RBF, Pearl-DGS, EVO, and Barrett Universal II (Barrett) formulas with Td-AL were compared pairwise. The ZEISS AI demonstrated smaller MAE and RMSAE than the Barrett, Pearl-DGS, and Kane. K6 had a smaller RMSAE than the Barrett formula. In 73 eyes with shallow anterior chamber depth, the ZEISS AI and Kane had a smaller RMSAE than the Barrett. CONCLUSIONS: ZEISS AI outperformed Barrett, Pearl-DGS, and Kane. The K6 formula outperformed some formulas in selected parameters. Across all formulas, use of a segmented AL did not improve refractive predictions.

Comparison of Keratoconus Specific to Standard IOL Formulas in Patients With Keratoconus Undergoing Cataract Surgery.

PURPOSE: To assess the performance of multiple intraocular lens (IOL) formulas in eyes with keratoconus. METHODS: Eyes with stable keratoconus scheduled for cataract surgery with biometry measurements on the Lenstar LS900 (Haag-Streit) were included. Prediction errors were calculated using 11 different formulas, including two with keratoconus modifiers. Primary outcomes compared standard deviations, mean and median numerical errors, and percentage of eyes within diopter (D) ranges across all eyes with subgroup analysis according to anterior keratometric values. RESULTS: Sixty-eight eyes from 44 patients were identified. In eyes with keratometric values less than 50.00 D, prediction error standard deviations ranged from 0.680 to 0.857 D. Percentages of eyes within ±0.50 D of target ranged from 57.89% to 73.68% with no statistical differences among formulas. In eyes with a keratometric value of more than 50.00 D, prediction error standard deviations ranged from 1.849 to 2.349 D and were not statistically different with heteroscedastic analysis; percentages of eyes within ±0.50 D of target ranged from 0% to 18.18% with no statistical differences among formulas. Only keratoconus-specific formulas (Barrett-KC and Kane-KC) and the Wang-Koch axial length adjustment version of SRK/T resulted in median numerical errors not significantly different than 0, regardless of keratometric values. CONCLUSIONS: In keratoconic eyes, IOL formulas are less accurate than in normal eyes and result in hyperopic refractive outcomes that increase with steeper keratometric values. Using keratoconus-specific formulas and the Wang-Koch axial length adjustment version of SRK/T for axial lengths of 25.2 mm or greater improved IOL power prediction accuracy compared to other formulas. [J Refract Surg. 2023;39(4):242-248.].

Hydrogen-Bond Donors in Drug Design.

Hydrogen-bond donors are seen to cause more problems for drug designers than hydrogen-bond acceptors. Most of the polarity in drug-like compounds comes from hydrogen-bond acceptors since they typically exceed the hydrogen-bond donors in number and are more heavily solvated on an individual basis. The implications of this polarity imbalance for optimization of permeability and aqueous solubility are discussed. A factor that should be considered in optimization of ligand recognition by targets is that the presence of a hydrogen-bond donor generally implies that a hydrogen-bond acceptor is also present (but not vice versa). Frustrated solvation and secondary electrostatic interactions result from aligned hydrogen-bond donors and acceptors, and the design opportunities presented by these phenomena are discussed. Hydrogen-bond donors based on oxygen, nitrogen and carbon are compared as target recognition elements, and halogen- and chalcogen-bond donors are discussed as hydrogen-bond donor equivalents.

A tandem mass spectrometric investigation of N-(3-ferrocenyl-2-naphthoyl) dipeptide ethyl esters and N-(6-ferrocenyl-2-naphthoyl) dipeptide ethyl esters.

N-(3-Ferrocenyl-2-naphthoyl) dipeptide ethyl esters 1-4 and N-(6-ferrocenyl-2-naphthoyl) dipeptide ethyl esters 5-8 were prepared by coupling either 3-ferrocenylnaphthalene-2-carboxylic acid or 6-ferrocenylnaphthalene-2-carboxylic acid to the dipeptide ethyl esters GlyGly(OEt) (1, 5), AlaGly(OEt) (2, 6), GlyPhe(OEt) (3, 7) and GlyLeu(OEt) (4, 8), using the standard N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride, 1-hydroxybenzotriazole protocol. Electrospray ionization mass spectrometry (ESI-MS) and laser desorption ionization mass spectrometry (LDI-MS) were employed in conjunction with tandem mass spectrometry in the analysis of N-(3-ferrocenyl-2-naphthoyl) dipeptide ethyl esters 1-4 and N-(6-ferrocenyl-2-naphthoyl) dipeptide ethyl esters 5-8. Radical cations, [M](+•) and [M + H](+) species were both observed in the mass spectra. Intense sodium [M + Na](+) and potassium [M + K](+) adducts were also present. An important diagnostic ion at m/z [M-65](+) was observed in both the MS and MS/MS spectra of the N-(3-ferrocenyl-2-naphthoyl) dipeptide derivatives. Sequence-specific ions were generally not observed in the MS/MS spectra of the N-(3-ferrocenyl-2-naphthoyl) series due to formation of the diagnostic [M-65](+) ion. Sequence-specific ions were observed in the MS/MS spectra of the N-(6-ferrocenyl-2-naphthoyl) dipeptide esters with charge retention on the derivatized N-terminal of the dipeptide. Both series of compounds could be successfully analyzed by MALDI without the use of a matrix (LDI).