Synergy of machine learning and density functional theory calculations for predicting experimental Lewis base affinity and Lewis polybase binding atoms

Investigation of Lewis acid-base interactions has been conducted by ab initio calculations and machine learning (ML) models. This study aims to resolve two critical tasks that have not been quantitatively investigated. First, ML models developed from density functional theory (DFT) calculations predict experimental BF3 affinity with Pearson correlation coefficients around 0.9 and mean absolute errors around 10 kJ mol-1. The ML models are trained by DFT-calculated BF3 affinity of more than 3000 adducts, with input features readily obtained by rdkit. Second, the ML models have the capability of predicting the relative strength of Lewis base binding atoms in Lewis polybases, which is either an extremely challenging task to conduct experimentally or a computationally expensive task for ab initio methods. The study demonstrates and solidifies the potential of combining DFT calculations and ML models to predict experimental properties, especially those that are scarce and impractical to empirically acquire.

IP6 and PF74 affect HIV-1 Capsid Stability through Modulation of Hexamer-Hexamer Tilt Angle Preference

The HIV-1 capsid is an irregularly shaped complex of about 1200 protein chains containing the viral genome and several viral proteins. Together, these components are the key to unlocking passage into the nucleus, allowing for permanent integration of the viral genome into the host cell genome. Recent interest into the role of the capsid in viral replication has been driven by the approval of the first-in-class drug lenacapavir, which marks the first drug approved to target a non-enzymatic HIV-1 viral protein. In addition to lenacapavir, other small molecules such as the drug-like compound PF74, and the anionic sugar inositolhexakisphosphate (IP6), are known to impact capsid stability, and although this is widely accepted as a therapeutic effect, the mechanisms through which they do so remain unknown. In this study, we employed a systematic atomistic simulation approach to study the impact of molecules bound to hexamers at the central pore (IP6) and the FG-binding site (PF74) on capsid oligomer dynamics, compared to apo hexamers and pentamers. We found that neither small molecule had a sizeable impact on the free energy of binding of the interface between neighboring hexamers but that both had impacts on the free energy profiles of performing angular deformations to the pair of oligomers akin to the variations in curvature along the irregular surface of the capsid. The IP6 cofactor, on one hand, stabilizes a pair of neighboring hexamers in their flattest configurations, whereas without IP6, the hexamers prefer a high tilt angle between them. On the other hand, having PF74 bound introduces a strong preference for intermediate tilt angles. These results suggest that structural instability is a natural feature of the HIV-1 capsid which is modulated by molecules bound in either the central pore or the FG-binding site. Such modulators, despite sharing many of the same effects on non-bonded interactions at the various protein-protein interfaces, have decidedly different effects on the flexibility of the complex. This study provides a detailed model of the HIV-1 capsid and its interactions with small molecules, informing structure-based drug design, as well as experimental design and interpretation.

Reactive Docking: A Computational Method for High-Throughput Virtual Screenings of Reactive Species

We describe the formalization of the reactive docking protocol, a method developed to model and predict reactions between small molecules and biological macromolecules. The method has been successfully used in a number of applications already, including recapitulating large proteomics data sets, performing structure-reactivity target optimizations, and prospective virtual screenings. By modeling a near-attack conformation-like state, no QM calculations are required to model the ligand and receptor geometries. Here, we present its generalization using a large data set containing more than 400 ligand-target complexes, 8 nucleophilic modifiable residue types, and more than 30 warheads. The method correctly predicts the modified residue in ∼85% of complexes and shows enrichments comparable to standard focused virtual screenings in ranking ligands. This performance supports this approach for the docking and screening of reactive ligands in virtual chemoproteomics and drug design campaigns.

Stretching Peptides to Generate Small Molecule β-Strand Mimics

Advances in the modulation of protein-protein interactions (PPIs) enable both characterization of PPI networks that govern diseases and design of therapeutics and probes. The shallow protein surfaces that dominate PPIs are challenging to target using standard methods, and approaches for accessing extended backbone structures are limited. Here, we incorporate a rigid, linear, diyne brace between side chains at the i to i+2 positions to generate a family of low-molecular-weight, extended-backbone peptide macrocycles. NMR and density functional theory studies show that these stretched peptides adopt stable, rigid conformations in solution and can be tuned to explore extended peptide conformational space. The diyne brace is formed in excellent conversions (>95%) and amenable to high-throughput synthesis. The minimalist structure-inducing tripeptide core (<300 Da) is amenable to further synthetic elaboration. Diyne-braced inhibitors of bacterial type 1 signal peptidase demonstrate the utility of the technique.

Ringtail: A Python Tool for Efficient Management and Storage of Virtual Screening Results

Virtual screening using molecular docking is now routinely used for the rapid evaluation of very large ligand libraries in early stage drug discovery. As the size of compound libraries which can feasibly be screened grows, so do the challenges in result management and storage. Here we introduce Ringtail, a new Python tool in the AutoDock Suite for efficient storage and analysis of virtual screening data based on portable SQLite databases. Ringtail is designed to work with AutoDock-GPU and AutoDock Vina out-of-the-box. Its modular design also allows for easy extension to support input file types from other docking software, different storage solutions, and incorporation into other applications. Ringtail's SQLite database output can dramatically reduce the required disk storage (36-46 fold) by selecting individual poses to store and by taking advantage of the relational database format. Filtering times are also dramatically reduced, requiring minutes to filter millions of ligands. Thus, Ringtail is a tool that can immediately integrate into existing virtual screening pipelines using AutoDock-GPU and Vina, and is scriptable and modifiable to fit specific user needs.

Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR

Glycine is a major neurotransmitter involved in several fundamental neuronal processes. The identity of the metabotropic receptor mediating slow neuromodulatory effects of glycine is unknown. We identified an orphan G protein-coupled receptor, GPR158, as a metabotropic glycine receptor (mGlyR). Glycine and a related modulator, taurine, directly bind to a Cache domain of GPR158, and this event inhibits the activity of the intracellular signaling complex regulator of G protein signaling 7-G protein β5 (RGS7-Gβ5), which is associated with the receptor. Glycine signals through mGlyR to inhibit production of the second messenger adenosine 3',5'-monophosphate. We further show that glycine, but not taurine, acts through mGlyR to regulate neuronal excitability in cortical neurons. These results identify a major neuromodulatory system involved in mediating metabotropic effects of glycine, with implications for understanding cognition and affective states.

Logical memory, visual reproduction, and verbal paired associates are effective embedded validity indicators in patients with traumatic brain injury

OBJECTIVE

This study was design to evaluate the potential of the recognition trials for the Logical Memory (LM), Visual Reproduction (VR), and Verbal Paired Associates (VPA) subtests of the Wechsler Memory Scales-Fourth Edition (WMS-IV) to serve as embedded performance validity tests (PVTs).

METHOD

The classification accuracy of the three WMS-IV subtests was computed against three different criterion PVTs in a sample of 103 adults with traumatic brain injury (TBI).

RESULTS

The optimal cutoffs (LM ≤ 20, VR ≤ 3, VPA ≤ 36) produced good combinations of sensitivity (.33-.87) and specificity (.92-.98). An age-corrected scaled score of ≤5 on either of the free recall trials on the VPA was specific (.91-.92) and relatively sensitive (.48-.57) to psychometrically defined invalid performance. A VR I ≤ 5 or VR II ≤ 4 had comparable specificity, but lower sensitivity (.25-.42). There was no difference in failure rate as a function of TBI severity.

CONCLUSIONS

In addition to LM, VR, and VPA can also function as embedded PVTs. Failing validity cutoffs on these subtests signals an increased risk of non-credible presentation and is robust to genuine neurocognitive impairment. However, they should not be used in isolation to determine the validity of an overall neurocognitive profile.

Evaluation of AlphaFold2 structures as docking targets

AlphaFold2 is a promising new tool for researchers to predict protein structures and generate high-quality models, with low backbone and global root-mean-square deviation (RMSD) when compared with experimental structures. However, it is unclear if the structures predicted by AlphaFold2 will be valuable targets of docking. To address this question, we redocked ligands in the PDBbind datasets against the experimental co-crystallized receptor structures and against the AlphaFold2 structures using AutoDock-GPU. We find that the quality measure provided during structure prediction is not a good predictor of docking performance, despite accurately reflecting the quality of the alpha carbon alignment with experimental structures. Removing low-confidence regions of the predicted structure and making side chains flexible improves the docking outcomes. Overall, despite high-quality prediction of backbone conformation, fine structural details limit the naive application of AlphaFold2 models as docking targets.

BNT-15: Revised Performance Validity Cutoffs and Proposed Clinical Classification Ranges

BACKGROUND

Abbreviated neurocognitive tests offer a practical alternative to full-length versions but often lack clear interpretive guidelines, thereby limiting their clinical utility.

OBJECTIVE

To replicate validity cutoffs for the Boston Naming Test-Short Form (BNT-15) and to introduce a clinical classification system for the BNT-15 as a measure of object-naming skills.

METHOD

We collected data from 43 university students and 46 clinical patients. Classification accuracy was computed against psychometrically defined criterion groups. Clinical classification ranges were developed using a z -score transformation.

RESULTS

Previously suggested validity cutoffs (≤11 and ≤12) produced comparable classification accuracy among the university students. However, a more conservative cutoff (≤10) was needed with the clinical patients to contain the false-positive rate (0.20-0.38 sensitivity at 0.92-0.96 specificity). As a measure of cognitive ability, a perfect BNT-15 score suggests above average performance; ≤11 suggests clinically significant deficits. Demographically adjusted prorated BNT-15 T-scores correlated strongly (0.86) with the newly developed z -scores.

CONCLUSION

Given its brevity (<5 minutes), ease of administration and scoring, the BNT-15 can function as a useful and cost-effective screening measure for both object-naming/English proficiency and performance validity. The proposed clinical classification ranges provide useful guidelines for practitioners.

Take Their Word for It: The Inventory of Problems Provides Valuable Information on Both Symptom and Performance Validity

This study was designed to compare the validity of the Inventory of Problems (IOP-29) and its newly developed memory module (IOP-M) in 150 patients clinically referred for neuropsychological assessment. Criterion groups were psychometrically derived based on established performance and symptom validity tests (PVTs and SVTs). The criterion-related validity of the IOP-29 was compared to that of the Negative Impression Management scale of the Personality Assessment Inventory (NIM_PAI) and the criterion-related validity of the IOP-M was compared to that of Trial-1 on the Test of Memory Malingering (TOMM-1). The IOP-29 correlated significantly more strongly (z = 2.50, p = .01) with criterion PVTs than the NIM_PAI (r_IOP-29 = .34; r_NIM-PAI = .06), generating similar overall correct classification values (OCC_IOP-29: 79-81%; OCC_NIM-PAI: 71-79%). Similarly, the IOP-M correlated significantly more strongly (z = 2.26, p = .02) with criterion PVTs than the TOMM-1 (r_IOP-M = .79; r_TOMM-1 = .59), generating similar overall correct classification values (OCC_IOP-M: 89-91%; OCC_TOMM-1: 84-86%). Findings converge with the cumulative evidence that the IOP-29 and IOP-M are valuable additions to comprehensive neuropsychological batteries. Results also confirm that symptom and performance validity are distinct clinical constructs, and domain specificity should be considered while calibrating instruments.

Direct observation of peptide hydrogel self-assembly

The characterization of self-assembling molecules presents significant experimental challenges, especially when associated with phase separation or precipitation. Transparent window infrared (IR) spectroscopy leverages site-specific probes that absorb in the “transparent window” region of the biomolecular IR spectrum. Carbon–deuterium (C–D) bonds are especially compelling transparent window probes since they are non-perturbative, can be readily introduced site selectively into peptides and proteins, and their stretch frequencies are sensitive to changes in the local molecular environment. Importantly, IR spectroscopy can be applied to a wide range of molecular samples regardless of solubility or physical state, making it an ideal technique for addressing the solubility challenges presented by self-assembling molecules. Here, we present the first continuous observation of transparent window probes following stopped-flow initiation. To demonstrate utility in a self-assembling system, we selected the MAX1 peptide hydrogel, a biocompatible material that has significant promise for use in drug delivery and medical applications. C–D labeled valine was synthetically introduced into five distinct positions of the twenty-residue MAX1 β-hairpin peptide. Consistent with current structural models, steady-state IR absorption frequencies and linewidths of C–D bonds at all labeled positions indicate that these side chains occupy a hydrophobic region of the hydrogel and that the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. Following a rapid change in ionic strength to initiate self-assembly, the peptide absorption spectra were monitored as function of time, allowing determination of site-specific time constants. We find that within the experimental resolution, MAX1 self-assembly occurs as a cooperative process. These studies suggest that stopped-flow transparent window FTIR can be extended to other time-resolved applications, such as protein folding and enzyme kinetics.

To facilitate the characterization of phase-transitioning molecules, site-specific non-perturbative infrared probes are leveraged for continuous observation of the self-assembly of fibrils in a peptide hydrogel following stopped-flow initiation.

The emotion word fluency test as an embedded performance validity indicator - Alone and in a multivariate validity composite

OBJECTIVE

This project was designed to cross-validate existing performance validity cutoffs embedded within measures of verbal fluency (FAS and animals) and develop new ones for the Emotion Word Fluency Test (EWFT), a novel measure of category fluency.

METHOD

The classification accuracy of the verbal fluency tests was examined in two samples (70 cognitively healthy university students and 52 clinical patients) against psychometrically defined criterion measures.

RESULTS

A demographically adjusted T-score of ≤31 on the FAS was specific (.88-.97) to noncredible responding in both samples. Animals T ≤ 29 achieved high specificity (.90-.93) among students at .27-.38 sensitivity. A more conservative cutoff (T ≤ 27) was needed in the patient sample for a similar combination of sensitivity (.24-.45) and specificity (.87-.93). An EWFT raw score ≤5 was highly specific (.94-.97) but insensitive (.10-.18) to invalid performance. Failing multiple cutoffs improved specificity (.90-1.00) at variable sensitivity (.19-.45).

CONCLUSIONS

Results help resolve the inconsistency in previous reports, and confirm the overall utility of existing verbal fluency tests as embedded validity indicators. Multivariate models of performance validity assessment are superior to single indicators. The clinical utility and limitations of the EWFT as a novel measure are discussed.

This will only take a minute: Time cutoffs are superior to accuracy cutoffs on the forced choice recognition trial of the Hopkins Verbal Learning Test - Revised

OBJECTIVE

This study was designed to evaluate the classification accuracy of the recently introduced forced-choice recognition trial to the Hopkins Verbal Learning Test - Revised (FCR_HVLT-R) as a performance validity test (PVT) in a clinical sample. Time-to-completion (T2C) for FCR_HVLT-R was also examined.

METHOD

Forty-three students were assigned to either the control or the experimental malingering (expMAL) condition. Archival data were collected from 52 adults clinically referred for neuropsychological assessment. Invalid performance was defined using expMAL status, two free-standing PVTs and two validity composites.

RESULTS

Among students, FCR_HVLT-R ≤11 or T2C ≥45 seconds was specific (0.86-0.93) to invalid performance. Among patients, an FCR_HVLT-R ≤11 was specific (0.94-1.00), but relatively insensitive (0.38-0.60) to non-credible responding0. T2C ≥35 s produced notably higher sensitivity (0.71-0.89), but variable specificity (0.83-0.96). The T2C achieved superior overall correct classification (81-86%) compared to the accuracy score (68-77%). The FCR_HVLT-R provided incremental utility in performance validity assessment compared to previously introduced validity cutoffs on Recognition Discrimination.

CONCLUSIONS

Combined with T2C, the FCR_HVLT-R has the potential to function as a quick, inexpensive and effective embedded PVT. The time-cutoff effectively attenuated the low ceiling of the accuracy scores, increasing sensitivity by 19%. Replication in larger and more geographically and demographically diverse samples is needed before the FCR_HVLT-R can be endorsed for routine clinical application.

Assessing the Perturbing Effects of Drugs on Lipid Bilayers Using Gramicidin Channel-Based In Silico and In Vitro Assays

Partitioning of bioactive molecules, including drugs, into cell membranes may produce indiscriminate changes in membrane protein function. As a guide to safe drug development, it therefore becomes important to be able to predict the bilayer-perturbing potency of hydrophobic/amphiphilic drugs candidates. Toward this end, we exploited gramicidin channels as molecular force probes and developed in silico and in vitro assays to measure drugs' bilayer-modifying potency. We examined eight drug-like molecules that were found to enhance or suppress gramicidin channel function in a thick 1,2-dierucoyl-sn-glycero-3-phosphocholine (DC22:1PC) but not in thin 1,2-dioleoyl-sn-glycero-3-phosphocholine (DC18:1PC) lipid bilayer. The mechanism underlying this difference was attributable to the changes in gramicidin dimerization free energy by drug-induced perturbations of lipid bilayer physical properties and bilayer-gramicidin interactions. The combined in silico and in vitro approaches, which allow for predicting the perturbing effects of drug candidates on membrane protein function, have implications for preclinical drug safety assessment.

Initial Analysis of the Arylomycin D Antibiotics

The arylomycins are a class of natural product antibiotics that inhibit bacterial type I signal peptidase and are under development as therapeutics. Four classes of arylomycins are known, arylomycins A-D. Previously, we reported the synthesis and analysis of representatives of the A, B, and C classes and showed that their spectrum of activity has the potential to be much broader than originally assumed. Along with a comparison of the mechanism of acquired and innate resistance, this led us to suggest that the arylomycins are latent antibiotics, antibiotics that once possessed broad-spectrum activity, but which upon examination today, have only narrow spectrum activity due to prior selection for resistance in the course of the competition with other microorganisms that drove their evolution in the first place. Interestingly, actinocarbasin, the only identified member of the arylomycin D class, has been reported to have activity against MRSA. To confirm and understand this activity, several actinocarbasin derivatives were synthesized. We demonstrate that the previously reported structure of actinocarbasin is incorrect, identify what is likely the correct scaffold, confirm that scaffold has activity against MRSA, and determine the origin of this activity.

Examining the relationship between ethnic identity, depression, and alcohol use among students at historically black colleges/universities (HBCUs)

Alcohol abuse among college populations is a serious public health issue and is associated with many negative consequences; however, few studies have examined the drinking behavior of African American students at Historically Black Colleges/Universities (HBCUs). Alcohol abuse, including binge drinking, has historically been lower among African American than Caucasian college students; however, recent studies indicate that HBCU undergraduates are reporting increased rates of alcohol consumption, raising the question of which potential risk and protective factors are associated with alcohol consumption in this population. Ethnic identity has been identified as one protective factor for ethnic minorities, yet the processes that facilitate this relationship are little known. This study sought to further investigate the relationship between ethnic identity, depression, and alcohol use in a sample of 171 African American HBCU students. Participants were tightly clustered toward the desirable end on all measures, which restricted variability and thus attenuated correlational analyses to evaluate the relationships between study variables. There was a consistent pattern of high ethnic identification, minimal mental health distress, and low alcohol and substance use. Results suggest HBCU students are maintaining lower rates of alcohol consumption and binge drinking compared to nationally-stratified samples of undergraduates. Furthermore, these findings suggest African Americans attending HBCUs score highly on ethnic identity and resiliency. Cultural and social norms at HBCUs may help explain low rates of substance and alcohol misuse among HBCU students. Recommendations for culturally-informed alcohol use prevention and intervention strategies and for future research are provided.

pH Method for Determination of Cholinesterase in Whole Blood: Collaborative Study

A collaborative study of an indirect method for determination of cholinesterase activity was conducted with cattle blood. Ten collaborators analyzed 8 samples of varying degrees of cholinesterase inhibition. The sample is diluted with a buffer, and the pH change that results from the hydrolysis of acetylcholine is monitored. Repeatability relative standard deviations (RSDr) ranged from 6.6 to 8.6%, and reproducibility relative standard deviations (RSDR) ranged from 10.7 to 17.3% for mean activities of 0.60-0.40 ΔpH/h. All samples that were completely inhibited were detected. The method was adopted first action by AOAC International for determination of cholinesterase activity in whole bovine blood.

Eight-Letter DNA

Steve Benner and collaborators have recently reported an analysis of DNA containing eight nucleotide letters, the four natural letters (dG, dC, dA, and dT) and four additional letters (dP, dZ, dS, and dB). Their analysis demonstrates that the additional letters do not perturb the structure or stability of the base pairs formed between the natural letters and, remarkably, that the new base pairs, dP-dZ and dS-dB, behave virtually identically to the natural base pairs. This unprecedented result convincingly demonstrates that the thermodynamic and structural behavior previously thought to be the purview of only natural DNA is in fact not unique and can be imparted to suitably designed synthetic components. In addition, the first evidence that the eight-letter DNA can be transcribed into RNA by a mutant RNA polymerase is presented, paving the way for the transfer of more information from one biopolymer to another. Along with others working to develop unnatural DNA base pairs for both in vitro and in vivo applications, this work represents an important step toward the expansion of the genetic alphabet, a central goal of synthetic biology, and has profound implications for our understanding of the molecules and forces that can make life possible.

Progress Toward a Semi-Synthetic Organism with an Unrestricted Expanded Genetic Alphabet

We have developed a family of unnatural base pairs (UBPs), exemplified by the pair formed between dNaM and dTPT3, for which pairing is mediated not by complementary hydrogen bonding but by hydrophobic and packing forces. These UBPs enabled the creation of the first semisynthetic organisms (SSOs) that store increased genetic information and use it to produce proteins containing noncanonical amino acids. However, retention of the UBPs was poor in some sequence contexts. Here, to optimize the SSO, we synthesize two novel benzothiophene-based dNaM analogs, dPTMO and dMTMO, and characterize the corresponding UBPs, dPTMO-dTPT3 and dMTMO-dTPT3. We demonstrate that these UBPs perform similarly to, or slightly worse than, dNaM-dTPT3 in vitro. However, in the in vivo environment of an SSO, retention of dMTMO-dTPT3, and especially dPTMO-dTPT3, is significantly higher than that of dNaM-dTPT3. This more optimal in vivo retention results from better replication, as opposed to more efficient import of the requisite unnatural nucleoside triphosphates. Modeling studies suggest that the more optimal replication results from specific internucleobase interactions mediated by the thiophene sulfur atoms. Finally, we show that dMTMO and dPTMO efficiently template the transcription of RNA containing TPT3 and that their improved retention in DNA results in more efficient production of proteins with noncanonical amino acids. This is the first instance of using performance within the SSO as part of the UBP evaluation and optimization process. From a general perspective, the results demonstrate the importance of evaluating synthetic biology "parts" in their in vivo context and further demonstrate the ability of hydrophobic and packing interactions to replace the complementary hydrogen bonding that underlies the replication of natural base pairs. From a more practical perspective, the identification of dMTMO-dTPT3 and especially dPTMO-dTPT3 represents significant progress toward the development of SSOs with an unrestricted ability to store and retrieve increased information.

Copper-Catalyzed Chan-Lam Cyclopropylation of Phenols and Azaheterocycles

Small molecules containing cyclopropane-heteroatom linkages are commonly needed in medicinal chemistry campaigns yet are problematic to prepare using existing methods. To address this issue, a scalable Chan-Lam cyclopropylation reaction using potassium cyclopropyl trifluoroborate has been developed. With phenol nucleophiles, the reaction effects O-cyclopropylation, whereas with 2-pyridones, 2-hydroxybenzimidazoles, and 2-aminopyridines the reaction brings about N-cyclopropylation. The transformation is catalyzed by Cu(OAc)₂ and 1,10-phenanthroline and employs 1 atm of O₂ as the terminal oxidant. This method is operationally convenient to perform and provides a simple, strategic disconnection toward the synthesis of cyclopropyl aryl ethers and cyclopropyl amine derivatives bearing an array of functional groups.

RNA-Sequencing Analysis of Messenger RNA/MicroRNA in a Rabbit Aneurysm Model Identifies Pathways and Genes of Interest

BACKGROUND AND PURPOSE

Rabbit aneurysm models are used for the testing of embolization devices and elucidating the mechanisms of human intracranial aneurysm growth and healing. We used RNA-sequencing technology to identify genes relevant to induced rabbit aneurysm biology and to identify genes and pathways of potential clinical interest. This process included sequencing microRNAs, which are important regulatory noncoding RNAs.

MATERIALS AND METHODS

Elastase-induced saccular aneurysms were created at the origin of the right common carotid artery in 6 rabbits. Messenger RNA and microRNA were isolated from the aneurysm and from the control left common carotid artery at 12 weeks and processed by using RNA-sequencing technology. The results from RNA sequencing were analyzed by using the Ingenuity Pathway Analysis tool.

RESULTS

A total of 9396 genes were analyzed by using RNA sequencing, 648 (6.9%) of which were found to be significantly differentially expressed between the aneurysms and control tissues (P < .05; false-discovery rate, <0.01; fold change, >2 or <.5). Of these genes, 614 were mapped successfully, 143 were down-regulated, and 471 were up-regulated in the aneurysms as compared with controls. Using the same criteria for significance, 3 microRNAs were identified as down-regulated and 5 were identified as up-regulated. Pathway analysis associated these genes with inflammatory response, cellular migration, and coagulation, among other functions and pathologies.

CONCLUSIONS

RNA-sequencing analysis of rabbit aneurysms revealed differential regulation of some key pathways, including inflammation and antigen presentation. ANKRD1 and TACR1 were identified as genes of interest in the regulation of matrix metalloproteinases.

Abstract W MP45: RNA-seq Analysis of mRNA/miRNA in Rabbit Aneurysm Model Reveals Similar Expression Patterns to Human Intracranial Aneurysms

Background and Purpose: Rabbit aneurysm models are used in the testing of embolization devices as well as elucidating the mechanisms human intracranial aneurysm growth and healing. We employed ribonucleic acid sequencing (RNA-seq) technology to identify genes relevant to induced rabbit aneurysm biology and compare these with genes related to human intracranial aneurysms to identify genes of potential clinical interest. This included sequencing micro RNA, which are important regulatory non-coding RNA.

Materials and Methods: Elastase-induced saccular aneurysms were created at the origin of the right common carotid artery (CCA) in 5 rabbits. Messenger ribonucleic acid (mRNA) and micro ribonucleic acid (miRNA) was isolated from the aneurysm and the control unoperated left CCA at 12 weeks and was processed using RNA-seq technology. The results from RNA-seq were analyzed using Ingenuity Pathway Analysis.

Results: 9396 genes were analyzed using RNA-seq, of which 649 (6.9%) were found to be significantly differentially expressed between aneurysm and control tissues (p < 0.05, false discovery rate 2). Of these, 500 were up-regulated in the aneurysm and 149 were down-regulated as compared to controls. Using the same criteria, 3 miRNA were identified as down regulated and 5 were identified as up regulated. Pathway analysis associated these genes with inflammatory response, cellular migration, and coagulation, among other functions and pathologies.

Conclusion: RNA-seq next-gen analysis of rabbit aneurysms shows similarities to human intracranial aneurysms with respect to regulation of some key pathways.

Coral calcifying fluid pH dictates response to ocean acidification

Ocean acidification driven by rising levels of CO₂ impairs calcification, threatening coral reef growth. Predicting how corals respond to CO₂ requires a better understanding of how calcification is controlled. Here we show how spatial variations in the pH of the internal calcifying fluid (pH_cf) in coral (Stylophora pistillata) colonies correlates with differential sensitivity of calcification to acidification. Coral apexes had the highest pH_cf and experienced the smallest changes in pH_cf in response to acidification. Lateral growth was associated with lower pH_cf and greater changes with acidification. Calcification showed a pattern similar to pH_cf, with lateral growth being more strongly affected by acidification than apical. Regulation of pH_cf is therefore spatially variable within a coral and critical to determining the sensitivity of calcification to ocean acidification.

X-ray linear dichroism dependence on ferroelectric polarization

X-ray absorption spectroscopy and photoemission electron microscopy are techniques commonly used to determine the magnetic properties of thin films, crystals, and heterostructures. Recently, these methods have been used in the study of magnetoelectrics and multiferroics. The analysis of such materials has been compromised by the presence of multiple order parameters and the lack of information on how to separate these coupled properties. In this work, we shed light on the manifestation of dichroism from ferroelectric polarization and atomic structure using photoemission electron microscopy and x-ray absorption spectroscopy. Linear dichroism arising from the ferroelectric order in the PbZr0:2Ti0:8O3 thin films was studied as a function of incident x-ray polarization and geometry to unambiguously determine the angular dependence of the ferroelectric contribution to the dichroism. These measurements allow us to examine the contribution of surface charges and ferroelectric polarization as potential mechanisms for linear dichroism. The x-ray linear dichroism from ferroelectric order revealed an angular dependence based on the angle between the ferroelectric polarization direction and the x-ray polarization axis, allowing a formula for linear dichroism in ferroelectric samples to be defined.

Cognitive effects of memantine in postmenopausal women at risk of dementia: a pilot study

BACKGROUND

To determine the effects of memantine on cognition in a normal population of postmenopausal women with putative risk factors for Alzheimer's disease (AD) using a built-in control for the genetic risk factor for AD (apoE-epsilon4 status).

METHODS

A prospective, open-label, 6-month pilot medication trial with memantine and follow-up after discontinuance conducted at the Center for Neuroscience in Women's Health, Stanford University School of Medicine. Neuropsychological data were collected on 22 community-dwelling postmenopausal women (11 apoE-epsilon4 carriers and 11 apoE-epsilon4 non-carriers) with at least one putative risk factor for AD.

RESULTS

ApoE-epsilon4 status was not a significant predictor of change in neuropsychological performance. Changes associated with memantine treatment for entire sample included significant declines in some variables associated with verbal learning and memory that improved upon medication withdrawal. A positive medication effect was noted with executive functions and possibly category fluency. Trend-level improvements were seen in motor dexterity of the non-dominant hand and maintained even after drug discontinuance.

CONCLUSIONS

Treatment with memantine appeared to have differential effects on cognitive performance in a population of women with putative risk factors for AD. ApoE-epsilon4 carrier status did not account for observed changes in cognition.

Telemedicine and telepresence for trauma and emergency care management

The use of telemedicine is long-standing, but only in recent years has it been applied to the specialities of trauma, emergency care, and surgery. Despite being relatively new, the concept of teletrauma, telepresence, and telesurgery is evolving and is being integrated into modern care of trauma and surgical patients. This paper will address the current applications of telemedicine and telepresence to trauma and emergency care as the new frontiers of telemedicine application. The University Medical Center and the Arizona Telemedicine Program (ATP) in Tucson, Arizona have two functional teletrauma and emergency telemedicine programs and one ad-hoc program, the mobile telemedicine program. The Southern Arizona Telemedicine and Telepresence (SATT) program is an inter-hospital telemedicine program, while the Tucson ER-link is a link between prehospital and emergency room system, and both are built upon a successful existing award winning ATP and the technical infrastructure of the city of Tucson. These two programs represent examples of integrated and collaborative community approaches to solving the lack of trauma and emergency care issue in the region. These networks will not only be used by trauma, but also by all other medical disciplines, and as such have become an example of innovation and dedication to trauma care. The first case of trauma managed over the telemedicine trauma program or "teletrauma" was that of an 18-month-old girl who was the only survival of a car crash with three fatalities. The success of this case and the pilot project of SATT that ensued led to the development of a regional teletrauma program serving close to 1.5 million people. The telepresence of the trauma surgeon, through teletrauma, has infused confidence among local doctors and communities and is being used to identify knowledge gaps of rural health care providers and the needs for instituting new outreach educational programs.

Oxygen consumption in unfertilized salmonid eggs: an indicator of egg quality?

A negative correlation between oxygen consumption and fertility was observed in both steelhead and chinook salmon eggs. However, this relationship was attributed to bacterial growth. Elimination of samples with bacterial growth resulted in no significant relationship between the rate of oxygen consumption (VO2) and fertility. VO2 of unfertilized eggs of both steelhead and chinook salmon was measured over a storage period of up to 24 days (d). Despite declines in fertility during storage, VO2 did not significantly change throughout storage. The average respiration rate for steelhead eggs was 3.4 nmol O2 per egg per h, and was 4.3 nmol O2 per egg per h for chinook salmon eggs. Treatment of chinook salmon eggs with uncouplers of mitochondrial respiration, 2,4-dinitrophenol (2,4-DNP) and carbonyl cyanide 4-trifluoro-methoxyphenylhydrazone (FCCP), resulted in an increase in VO2 to 12.9 and 11.5 nmol O2 per egg per h, respectively. Treatment with the putative uncoupler, clove oil, resulted in no change in VO2, while KCN, an inhibitor of oxidative phosphorylation, reduced oxygen consumption to zero. Copper caused an increase in oxygen consumption, even in the absence of eggs, suggesting a need for caution in interpreting changes in respiration rates as a result of metal exposure. Thus, unfertilized salmonid eggs demonstrated submaximal VO2, which was not correlated with fertility.

Carbon dioxide and pH affect sperm motility of white sturgeon(Acipenser transmontanus)

Maintenance of sperm at pH values less than approximately 7.5 inhibited the onset of motility when sperm were subsequently diluted with water; maintenance at pH values above approximately 8.2 was associated with maximal motility upon dilution with water. Within 5∼min of exposure to low pH buffer (pH 6.9),there was a 50% decline in sperm motility upon dilution with water suggesting that exposure to low pH interferes with motility within a time frame that may affect fertilization. In most instances, maintenance of sperm under CO2 at a pressure of 4-5 kPa almost completely blocked their capacity for motility. Furthermore, exposing semen to increasing partial pressures of CO2 up to about 1 kPa resulted in a marked decrease in semen pH. These observations are consistent with the findings that the buffering capacity of semen is particularly low at physiological pH, and that this low buffering capacity corresponds to the highest pH sensitivity of the capacity for sperm motility. The low seminal buffering capacity may represent a physiological adaptation in the control of sperm function. It may also represent a vulnerability to environmental hypercapnia or metabolic acidosis.

Sample preparation for the analysis of flavors and off-flavors in foods

Off-flavors in foods may originate from environmental pollutants, the growth of microorganisms, oxidation of lipids, or endogenous enzymatic decomposition in the foods. The chromatographic analysis of flavors and off-flavors in foods usually requires that the samples first be processed to remove as many interfering compounds as possible. For analysis of foods by gas chromatography (GC), sample preparation may include mincing, homogenation, centrifugation, distillation, simple solvent extraction, supercritical fluid extraction, pressurized-fluid extraction, microwave-assisted extraction, Soxhlet extraction, or methylation. For high-performance liquid chromatography of amines in fish, cheese, sausage and olive oil or aldehydes in fruit juice, sample preparation may include solvent extraction and derivatization. Headspace GC analysis of orange juice, fish, dehydrated potatoes, and milk requires almost no sample preparation. Purge-and-trap GC analysis of dairy products, seafoods, and garlic may require heating, microwave-mediated distillation, purging the sample with inert gases and trapping the analytes with Tenax or C18, thermal desorption, cryofocusing, or elution with ethyl acetate. Solid-phase microextraction GC analysis of spices, milk and fish can involve microwave-mediated distillation, and usually requires adsorption on poly(dimethyl)siloxane or electrodeposition on fibers followed by thermal desorption. For short-path thermal desorption GC analysis of spices, herbs, coffee, peanuts, candy, mushrooms, beverages, olive oil, honey, and milk, samples are placed in a glass-lined stainless steel thermal desorption tube, which is purged with helium and then heated gradually to desorb the volatiles for analysis. Few of the methods that are available for analysis of food flavors and off-flavors can be described simultaneously as cheap, easy and good.

Patterns of use and satisfaction with a university-based teleradiology system

The Radiology Department at the University of Arizona has been operating a teleradiology program for almost 2 years. The goal of this project was to characterize the types of cases reviewed, to assess radiologists' satisfaction with the program, and to examine case turnaround times. On average, about 50 teleradiology cases are interpreted each month. Computed tomography (CT) cases are the most common type of case, constituting 65% of the total case volume. Average turnaround time (to generate a "wet read" once a case is received) is about 1.3 hours. Image quality was rated as generally good to excellent, and the user interface as generally good. Radiologists' confidence in their diagnostic decisions is about the same as reading films in the clinical environment. The most common reason for not being able to read teleradiology images is poor image quality, followed by lack of clinical history and not enough images.

Analysis of fumonisin B1 in rodent feed by CE with fluorescence detection of the FMOC derivative

A fast, simple, and environmentally friendly method has been developed for the analysis of fumonisin B1 (FB1) in rodent feed using CE. FB1 is the major fumonisin metabolite produced by the fungus Fusarium moniliforme and has been implicated in human and animal diseases. FB1 was extracted from rodent feed with acetonitrile/water (50/50) (vol/vol) and cleaned up with a C18 Sep-Pak Vac cartridge (Waters Corp., Milford, MA, U.S.A.). FB1 was quantitated after elution from the column using capillary electrophoresis with a 25-mM sodium borate buffer (pH 9.0) containing 10% acetonitrile and fluorescence detection of the (9-fluorenylmethyl) chloroformate (FMOC) derivative. The minimum detectable amount in rodent feed was 0.5 pmm. Recovery values in spiked rodent feed averaged more than 87% over the 2-20 ppm range.

Fumonisin B1 analysis with capillary electrophoresis-electrospray ionization mass spectrometry

Fumonisin B1, a mycotoxin produced by a common fungal contaminant of corn, Fusarium moniliforme, was analyzed by capillary electrophoresis-electrospray ionization mass spectrometry. System performance was maximal with uncoated columns. System efficiencies of approximately 44,000 plates/m and reproducible analysis times of about 13 min were obtained. System efficiency with methyl-coated columns was approximately 24,000 plates/m. Reproducible analysis times of about 3.5 min were obtained with these columns. With uncoated columns, the concentration limit of detection was 156 ppb with a s/n ratio of approximately 10. The estimated injected mass at 156 ppb was 1.1 pg. Repeated injections of extracts containing constant fumonisin B1 concentrations showed that peak areas were slightly inconsistent, although generally similar to variations encountered with liquid chromatography-electrospray ionization mass spectrometry. The source of this inconsistency was traced to sample solubility, errors inherent in electrophoresis injections, and electrospray instability. Minimizing these problem areas will produce a technique with peak area reproducibilities comparable to liquid chromatography-electrospray ionization mass spectrometry, but with potentially greater resolving power.

Inhibition of 7,12-dimethylbenzanthracene-induced rat mammary tumor growth by 2,3,7,8-tetrachlorodibenzo-p-dioxin

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and related compounds inhibit diverse estrogen-induced responses in the rodent uterus and human breast cancer cells. The effects of a single non-toxic dose of TCDD (10 micrograms/kg) on the development of mammary tumors was investigated in female Sprague-Dawley rats treated with an oral dose of 7,12-dimethylbenzanthracene (DMBA) (20 mg). In rats which developed mammary tumors, subsequent treatment with corn oil (vehicle) resulted in a 3.9-fold increase in mammary tumor volume after 21 days. In contrast, a second group of rats with mammary tumors were treated with a non-toxic dose of TCDD (10 micrograms/kg) and after 21 days, the mean tumor volumes decreased from 89.7 +/- 53 mm3 to 24.9 +/- 28.5 mm3. Moreover, these results demonstrate the antitumorigenic activity of TCDD in female Sprague-Dawley rats.

Determination of aflatoxins in food products by chromatography

Several chromatographic methods for the determination of aflatoxins in agricultural and food products are reviewed. During the past two decades, identification and determination of aflatoxins were done by thin-layer chromatography (TLC) because it was easy, fast and inexpensive. However, high-performance liquid chromatography (HPLC) using fluorescence detection is now the method of choice for determining aflatoxins and is also growing in popularity for their identification. The reasons for selecting HPLC over TLC can be summarized as the ability to analyze for a wide variety of compounds, including compounds that are easily degraded by heat, light or air, the ease of adaptation to confirmatory procedures, the potential for automation and the dramatic improvement in instrumentation, including the development of increasingly sensitive fluorescence and electrochemical detectors and short, high-resolution, reversed-phase columns.

Characterization of iodine derivatives of aflatoxin B1 and G1 by thermospray mass spectrometry

Thermospray mass spectrometry (TSMS) was used to identify the derivatives formed when iodine is reacted with aflatoxins B1 and G1 at approximately 70 degrees C to enhance fluorescence. It was found that stable derivatives were formed by addition of an iodine atom and a methoxy group across the double bond located on the furan ring of the aflatoxin B1 and G1 molecules. TSMS and TSMS/MS daughter spectra of the reaction products of aflatoxin B1 and G1 with iodine provide evidence of the addition of each moiety to produce the iodo-methoxy derivative. The addition of an iodine atom to one carbon and a methoxy group to the other carbon of the furan ring provided molecular weights of 470 and 486 for the products of aflatoxin B1 and G1, respectively.

Effect of electrocautery on wound healing in midline laparotomy incisions

The effect of electrocautery on midline fascial wound healing was studied in 108 Sprague-Dawley rats. Midline wound tensile strength was significantly reduced in fascia incised with the coagulation current compared with the cutting current or scalpel. In addition, tissue necrosis and inflammation as well as adhesion formation between the incision and abdominal viscera were more extensive in animals with incisions made using coagulation current. The results of the study indicate that the use of electrocautery coagulation current is associated with increased tissue damage and a significant reduction in the tensile strength of healing wounds. The contribution of electrocautery to wound complications in patients needs further evaluation.