Rationale and design of a multisite randomized clinical trial examining an integrated behavioral treatment for veterans with co-occurring chronic pain and opioid use disorder: The pain and opioids integrated treatment in veterans (POSITIVE) trial.

BACKGROUND: Chronic pain and opioid use disorder (OUD) individually represent a risk to health and well-being. Concerningly, there is evidence that they are frequently co-morbid. While few treatments exist that simultaneously target both conditions, preliminary work has supported the feasibility of an integrated behavioral treatment targeting pain interference and opioid misuse. This treatment combined Acceptance and Commitment Therapy (ACT) and Mindfulness-Based Relapse Prevention (ACT+MBRP). This paper describes the protocol for the adequately powered efficacy study of this integrated treatment. METHODS: A multisite randomized controlled trial will examine the efficacy of ACT+MBRP in comparison to a parallel education control condition, focusing on opioid safety and pain education. Participants include veterans (n = 160; 21-75 years old) recruited from three Veterans Administration (VA) Healthcare Systems with chronic pain who are on a stable dose of buprenorphine. Both conditions include twelve weekly 90 min group sessions delivered via telehealth. Primary outcomes include pain interference (Patient Reported Outcome Measurement Information System - Pain Interference) and hazardous opioid use (Current Opioid Misuse Measure), which will be examined at the end of the active treatment phase and through 12 months post-intervention. Secondary analyses will evaluate outcomes including pain intensity, depression, pain-related fear, and substance use, as well as treatment mechanisms. CONCLUSION: This study will determine the efficacy of an integrated behavioral treatment program for pain interference and hazardous opioid use among veterans with chronic pain and OUD who are prescribed buprenorphine, addressing a critical need for more integrated treatments for chronic pain and OUD. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04648228.

ChemInformatics Model Explorer (CIME): exploratory analysis of chemical model explanations.

The introduction of machine learning to small molecule research- an inherently multidisciplinary field in which chemists and data scientists combine their expertise and collaborate - has been vital to making screening processes more efficient. In recent years, numerous models that predict pharmacokinetic properties or bioactivity have been published, and these are used on a daily basis by chemists to make decisions and prioritize ideas. The emerging field of explainable artificial intelligence is opening up new possibilities for understanding the reasoning that underlies a model. In small molecule research, this means relating contributions of substructures of compounds to their predicted properties, which in turn also allows the areas of the compounds that have the greatest influence on the outcome to be identified. However, there is no interactive visualization tool that facilitates such interdisciplinary collaborations towards interpretability of machine learning models for small molecules. To fill this gap, we present CIME (ChemInformatics Model Explorer), an interactive web-based system that allows users to inspect chemical data sets, visualize model explanations, compare interpretability techniques, and explore subgroups of compounds. The tool is model-agnostic and can be run on a server or a workstation.

Energy coupling of membrane transport and efficiency of sucrose dissimilation in yeast.

Proton coupled transport of α-glucosides via Mal11 into Saccharomyces cerevisiae costs one ATP per imported molecule. Targeted mutation of all three acidic residues in the active site resulted in sugar uniport, but expression of these mutant transporters in yeast did not enable growth on sucrose. We then isolated six unique transporter variants of these mutants by directed evolution of yeast for growth on sucrose. In three variants, new acidic residues emerged near the active site that restored proton-coupled sucrose transport, whereas the other evolved transporters still catalysed sucrose uniport. The localization of mutations and transport properties of the mutants enabled us to propose a mechanistic model of proton-coupled sugar transport by Mal11. Cultivation of yeast strains expressing one of the sucrose uniporters in anaerobic, sucrose-limited chemostat cultures indicated an increase in the efficiency of sucrose dissimilation by 21% when additional changes in strain physiology were taken into account. We thus show that a combination of directed and evolutionary engineering results in more energy efficient sucrose transport, as a starting point to engineer yeast strains with increased yields for industrially relevant products.

Weak Acid Permeation in Synthetic Lipid Vesicles and Across the Yeast Plasma Membrane.

We present a fluorescence-based approach for determination of the permeability of small molecules across the membranes of lipid vesicles and living cells. With properly designed experiments, the method allows us to assess the membrane physical properties both in vitro and in vivo. We find that the permeability of weak acids increases in the order of benzoic > acetic > formic > lactic, both in synthetic lipid vesicles and the plasma membrane of Saccharomyces cerevisiae, but the permeability is much lower in yeast (one to two orders of magnitude). We observe a relation between the molecule permeability and the saturation of the lipid acyl chain (i.e., lipid packing) in the synthetic lipid vesicles. By analyzing wild-type yeast and a manifold knockout strain lacking all putative lactic acid transporters, we conclude that the yeast plasma membrane is impermeable to lactic acid on timescales up to ∼2.5 h.

Coupling efficiency of secondary active transporters.

Secondary active transporters are fundamental to a myriad of biological processes. They use the electrochemical gradient of one solute to drive transport of another solute against its concentration gradient. Central to this mechanism is that the transport of one does not occur in the absence of the other. However, like in most of biology, imperfections in the coupling mechanism exist and we argue that these are innocuous and may even be beneficial for the cell. We discuss the energetics and kinetics of alternating-access in secondary transport and focus on the mechanistic aspects of imperfect coupling that give rise to leak pathways. Additionally, inspection of available transporter structures gives valuable insight into coupling mechanics, and we review literature where proteins have been altered to change their coupling efficiency.

Combined engineering of disaccharide transport and phosphorolysis for enhanced ATP yield from sucrose fermentation in Saccharomyces cerevisiae.

Anaerobic industrial fermentation processes do not require aeration and intensive mixing and the accompanying cost savings are beneficial for production of chemicals and fuels. However, the free-energy conservation of fermentative pathways is often insufficient for the production and export of the desired compounds and/or for cellular growth and maintenance. To increase free-energy conservation during fermentation of the industrially relevant disaccharide sucrose by Saccharomyces cerevisiae, we first replaced the native yeast α-glucosidases by an intracellular sucrose phosphorylase from Leuconostoc mesenteroides (LmSPase). Subsequently, we replaced the native proton-coupled sucrose uptake system by a putative sucrose facilitator from Phaseolus vulgaris (PvSUF1). The resulting strains grew anaerobically on sucrose at specific growth rates of 0.09 ± 0.02h-1 (LmSPase) and 0.06 ± 0.01h-1 (PvSUF1, LmSPase). Overexpression of the yeast PGM2 gene, which encodes phosphoglucomutase, increased anaerobic growth rates on sucrose of these strains to 0.23 ± 0.01h-1 and 0.08 ± 0.00h-1, respectively. Determination of the biomass yield in anaerobic sucrose-limited chemostat cultures was used to assess the free-energy conservation of the engineered strains. Replacement of intracellular hydrolase with a phosphorylase increased the biomass yield on sucrose by 31%. Additional replacement of the native proton-coupled sucrose uptake system by PvSUF1 increased the anaerobic biomass yield by a further 8%, resulting in an overall increase of 41%. By experimentally demonstrating an energetic benefit of the combined engineering of disaccharide uptake and cleavage, this study represents a first step towards anaerobic production of compounds whose metabolic pathways currently do not conserve sufficient free-energy.

Proton-solute coupling mechanism of the maltose transporter from Saccharomyces cerevisiae.

Mal11 catalyzes proton-coupled maltose transport across the plasma membrane of Saccharomyces cerevisiae. We used structure-based design of mutants and a kinetic analysis of maltose transport to determine the energy coupling mechanism of transport. We find that wildtype Mal11 is extremely well coupled and allows yeast to rapidly accumulate maltose to dangerous levels, resulting under some conditions in self-lysis. Three protonatable residues lining the central membrane-embedded cavity of Mal11 were identified as having potential roles in proton translocation. We probed the mechanistic basis for proton coupling with uphill and downhill transport assays and found that single mutants can still accumulate maltose but with a lower coupling efficiency than the wildtype. Next, we combined the individual mutations and created double and triple mutants. We found some redundancy in the functions of the acidic residues in proton coupling and that no single residue is most critical for proton coupling to maltose uptake, unlike what is usually observed in related transporters. Importantly, the triple mutants were completely uncoupled but still fully active in downhill efflux and equilibrium exchange. Together, these results depict a concerted mechanism of proton transport in Mal11 involving multiple charged residues.

Pseudo-fivefold diffraction symmetries in tetrahedral packing.

We review the way in which atomic tetrahedra composed of metallic elements pack naturally into fused icosahedra. Orthorhombic, hexagonal, and cubic intermetallic crystals based on this packing are all shown to be united in having pseudo-fivefold rotational diffraction symmetry. A unified geometric model involving the 600-cell is presented: the model accounts for the observed pseudo-fivefold symmetries among the different Bravais lattice types. The model accounts for vertex-, edge-, polygon-, and cell-centered fused-icosahedral clusters. Vertex-centered and edge-centered types correspond to the well-known pseudo-fivefold symmetries in Ih and D5h quasicrystalline approximants. The concept of a tetrahedrally-packed reciprocal space cluster is introduced, the vectors between sites in this cluster corresponding to the principal diffraction peaks of fused-icosahedrally-packed crystals. This reciprocal-space cluster is a direct result of the pseudosymmetry and, just as the real-space clusters, can be rationalized by the 600-cell. The reciprocal space cluster provides insights for the Jones model of metal stability. For tetrahedrally-packed crystals, Jones zone faces prove to be pseudosymmetric with one another. Lower and upper electron per atom bounds calculated for this pseudosymmetry-based Jones model are shown to accord with the observed electron counts for a variety of Group 10-12 tetrahedrally-packed structures, among which are the four known Cu/Cd intermetallic compounds: CdCu2, Cd3Cu4, Cu5Cd8, and Cu3Cd10. The rationale behind the Jones lower and upper bounds is reviewed. The crystal structure of Zn11Au15Cd23, an example of a 1:1 MacKay cubic quasicrystalline approximant based solely on Groups 10-12 elements is presented. This compound crystallizes in Im3 (space group no. 204) with a = 13.842(2) Å. The structure was solved with R1 = 3.53 %, I > 2σ; = 5.33 %, all data with 1282/0/38 data/restraints/parameters.

Site preference and ordering induced by Au substitution in the γ-brass related complex Au-Cr-Zn phases.

The crystal chemistry of the ternary Au-Cr-Zn alloy was studied by means of synthesis, single crystal X-ray diffraction, and electron structure calculations. While the compound CrZn(∼17) represents the binary end-point of the homogeneity range, the inclusion of Au proves to be very site specific, and at the limiting composition Au10Cr4Zn89 the structure is completely ordered. The crystallographic site occupancy pattern calculated by the Local Density Approximation (LDA)-Density Functional Theory (DFT) parametrized extended Hückel (eH) Mulliken charge populations in Au10Cr4Zn89 agrees very well with the experimentally found site occupancy pattern.

CD4(+) T-cell inhibitory ligands: a tool for characterizing dysfunctional CD4(+) T cells during chronic infection.

Activation of CD4(+) T cells helps to establish and maintain immune responses. During infection with lymphocytic choriomeningitis virus (LCMV) clone 13, the CD4(+) T-cell responses are lost. In this study, we were interested in the nature of the CD4(+) T-cell responses following infection with LCMV clone 13. To pursue this question, we infected C57BL/6 mice with LCMV clone 13. We used a GP66-80 MHC Class II tetramer to determine whether the CD4(+) T cells were present following infection with LCMV clone 13. We determined that the cells were present and antigen specific, but not functional. We attributed their dysfunction to the presence of CD4(+) T-cell inhibitory ligands. We further stained for the presence of CD4(+) T-cell inhibitory ligands. We found that the during chronic infection the number of CD4(+) T cells expressing programmed death-1 and CD160 were greater over the time-course study than the other CD4(+) T-cell inhibitory ligands. These data show that using CD4(+) T-cell inhibitory ligands as a reagent for characterization can help in understanding the complex immune responses associated with persistent infections.

Linker histone H1.0 interacts with an extensive network of proteins found in the nucleolus.

The H1 linker histones are abundant chromatin-associated DNA-binding proteins. Recent evidence suggests that linker histones also may function through protein-protein interactions. To gain a better understanding of the scope of linker histone involvement in protein-protein interactions, we used a proteomics approach to identify H1-binding proteins in human nuclear extracts. Full-length H1.0 and H1.0 lacking its C-terminal domain (CTD) were used for protein pull-downs. A total of 107 candidate H1.0 binding proteins were identified by LC-MS/MS. About one-third of the H1.0-dependent interactions were mediated by the CTD, and two-thirds by the N-terminal domain-globular domain fragment. Many of the proteins pulled down by H1.0 were core splicing factors. Another group of H1-binding proteins functions in rRNA biogenesis. H1.0 also pulled down numerous ribosomal proteins and proteins involved in cellular transport. Strikingly, nearly all of the H1.0-binding proteins are found in the nucleolus. Quantitative biophysical studies with recombinant proteins confirmed that H1.0 directly binds to FACT and the splicing factors SF2/ASF and U2AF65. Our results demonstrate that H1.0 interacts with an extensive network of proteins that function in RNA metabolism in the nucleolus, and suggest that a new paradigm for linker histone action is in order.

Memory T cells in latent Mycobacterium tuberculosis infection are directed against three antigenic islands and largely contained in a CXCR3+CCR6+ Th1 subset.

An understanding of the immunological footprint of Mycobacterium tuberculosis (MTB) CD4 T cell recognition is still incomplete. Here we report that human Th1 cells specific for MTB are largely contained in a CXCR3(+)CCR6(+) memory subset and highly focused on three broadly immunodominant antigenic islands, all related to bacterial secretion systems. Our results refute the notion that secreted antigens act as a decoy, since both secreted proteins and proteins comprising the secretion system itself are targeted by a fully functional T cell response. In addition, several novel T cell antigens were identified which can be of potential diagnostic use, or as vaccine antigens. These results underline the power of a truly unbiased, genome-wide, analysis of CD4 MTB recognition based on the combined use of epitope predictions, high throughput ELISPOT, and T cell libraries using PBMCs from individuals latently infected with MTB.

Next steps in addressing the prevention, screening, and treatment of substance use disorder in active duty and veteran Operation Enduring Freedom and Operation Iraqi Freedom populations.

The two articles presented previously in this volume provide state-of-the-art reviews of the etiology, epidemiology, screening and treatment of substance use disorder (SUD). This article identifies next steps in research and development for understanding and treating SUD in Operation Enduring Freedom/Operation Iraqi Freedom service members and veterans. Four promising areas are reviewed: advances in psychopharmacological treatment of SUD, innovations in behavioral treatments, the use of technological advances for the screening and treatment of SUD, and integration of treatment services. Future directions are explored and suggestions for research, development and implementation of each of these trends are discussed.

Dissecting mechanisms of immunodominance to the common tuberculosis antigens ESAT-6, CFP10, Rv2031c (hspX), Rv2654c (TB7.7), and Rv1038c (EsxJ).

Diagnosis of tuberculosis often relies on the ex vivo IFN-γ release assays QuantiFERON-TB Gold In-Tube and T-SPOT.TB. However, understanding of the immunological mechanisms underlying their diagnostic use is still incomplete. Accordingly, we investigated T cell responses for the TB Ags included in the these assays and other commonly studied Ags: early secreted antigenic target 6 kDa, culture filtrate protein 10 kDa, Rv2031c, Rv2654c, and Rv1038c. PBMC from latently infected individuals were tested in ex vivo ELISPOT assays with overlapping peptides spanning the entirety of these Ags. We found striking variations in prevalence and magnitude of ex vivo reactivity, with culture filtrate protein 10 kDa being most dominant, followed by early secreted antigenic target 6 kDa and Rv2654c being virtually inactive. Rv2031c and Rv1038c were associated with intermediate patterns of reactivity. Further studies showed that low reactivity was not due to lack of HLA binding peptides, and high reactivity was associated with recognition of a few discrete dominant antigenic regions. Different donors recognized the same core sequence in a given epitope. In some cases, the identified epitopes were restricted by a single specific common HLA molecule (selective restriction), whereas in other cases, promiscuous restriction of the same epitope by multiple HLA molecules was apparent. Definition of the specific restricting HLA allowed to produce tetrameric reagents and showed that epitope-specific T cells recognizing either selectively or promiscuously restricted epitopes were predominantly T effector memory. In conclusion, these results highlight the feasibility of more clearly defined TB diagnostic reagent.

Who spares the rod? Religious orientation, social conformity, and child abuse potential.

OBJECTIVE: Relatively little research has investigated the connection between religiosity and physical child abuse risk. Certain aspects, such as specific religious orientation or beliefs, and cognitive schema, such as socially conformist beliefs, may account for the connection that some have claimed increase religious parents' abuse potential. The current study examined whether greater Extrinsic religiosity, but not Intrinsic religiosity, was associated with elevated physical abuse potential. Those who hold a literal interpretation of the Bible and attend church more frequently were also expected to evidence increased abuse risk. Additionally, the role of social conformity in mediating or moderating the association between religiosity and abuse potential was investigated. METHODS: Two hundred and seven regularly attending Christians of various denominations completed self-report measures of religiosity, social conformity, and child abuse potential. RESULTS: Findings indicate that Extrinsic religiosity was associated with increased physical abuse potential, with greater social conformity further moderating this association. Intrinsic religious orientation was not associated with abuse risk. Further, those who consider the Bible to be literally true were more socially conformist and evidenced greater abuse risk. CONCLUSIONS: For those working with religious parents, the particular nature of religiosity needs to be considered when interpreting a connection between religiosity and abuse risk, as well as the potential attitudes the parent holds regarding the need for conformity. Given the complexity of religiosity, future research should explore other potential mediating and moderating factors that could further clarify its connection to physical abuse risk. PRACTICE IMPLICATIONS: Clarifying how religiosity relates to child abuse risk has implications for professionals working with the vast numbers of parents for whom religion is a visible force in their daily lives. Findings from the present study suggest that professionals should consider the underlying motivation for an individual's religion as well as the importance the individual places on conformity. Religiosity per se may not be as critical to predicting physical abuse risk as selected approaches to religion or particular attitudes the religious individual assumes in their daily life.

Haptoglobin inhibits phospholipid transfer protein activity in hyperlipidemic human plasma.

BACKGROUND: Haptoglobin is a plasma protein that scavenges haemoglobin during haemolysis. Phospholipid Transfer Protein (PLTP) transfers lipids from Low Density Lipoproteins (LDL) to High Density Lipoproteins (HDL). PLTP is involved in the pathogenesis of atherosclerosis which causes coronary artery disease, the leading cause of death in North America. It has been shown that Apolipoprotein-A1 (Apo-A1) binds and regulates PLTP activity. Haptoglobin can also bind to Apo-A1, affecting the ability of Apo-A1 to induce enzymatic activities. Thus we hypothesize that haptoglobin inhibits PLTP activity. This work tested the effect of Haptoglobin and Apo-A1 addition on PLTP activity in human plasma samples. The results will contribute to our understanding of the role of haptoglobin on modulating reverse cholesterol transport. RESULTS: We analyzed the PLTP activity and Apo-A1 and Haptoglobin content in six hyperlipidemic and six normolipidemic plasmas. We found that Apo-A1 levels are proportional to PLTP activity in hyperlipidemic (R2 = 0.66, p < 0.05) but not in normolipidemic human plasma. Haptoglobin levels and PLTP activity are inversely proportional in hyperlipidemic plasmas (R2 = 0.57, p > 0.05). When the PLTP activity was graphed versus the Hp/Apo-A1 ratio in hyperlipidemic plasma there was a significant correlation (R2 = 0.69, p < 0.05) suggesting that PLTP activity is affected by the combined effect of Apo-A1 and haptoglobin. When haptoglobin was added to individual hyperlipidemic plasma samples there was a dose dependent decrease in PLTP activity. In these samples we also found a negative correlation (-0.59, p < 0.05) between PLTP activity and Hp/Apo-A1. When we added an amount of haptoglobin equivalent to 100% of the basal levels, we found a 64 +/- 23% decrease (p < 0.05) in PLTP activity compared to basal PLTP activity. We tested the hypothesis that additional Apo-A1 would induce PLTP activity. Interestingly we found a dose dependent decrease in PLTP activity upon Apo-A1 addition. When both Apo-A1 and Hpt were added to the plasma samples there was no further reduction in PLTP activity suggesting that they act through a common pathway. CONCLUSION: These findings suggest an inhibitory effect of Haptoglobin over PLTP activity in hyperlipidemic plasma that may contribute to the regulation of reverse cholesterol transport.

Differences in human phospholipid transfer protein activity following incubation of Fungizone compared to lipid-based Amphotericin-B formulations in normolipidemic and hyperlipidemic plasma.

AIM: To investigate how different formulations of Amphotericin-B (Amp-B) affect the activity of phospholipid transfer protein (PLTP) when incubated with hyperlipidemic and normolipidemic plasma at physiological temperature (37 degrees C). METHODS: Six hyperlipidemic and six normolipidemic plasma samples were collected and tested for protein concentration. Equivalent protein levels (25 microg) were then tested for PLTP activity using an in vitro established kit at physiological temperature (37 degrees C). Increasing concentrations of different Amp-B formulations (1, 2, and 5 microg/mL) in the pharmacological range were then added to the plasma and tested for activity from 5 to 90 minutes. The Amp-B formulations used in the study were Fungizone, Abelcet, and AmBisome. RESULTS: In normolipidemic plasma, PLTP activity was found to be increased by Abelcet and AmBisome but inhibited by Fungizone. In hyperlipidemic plasma, PLTP activity was found to be increased by Abelcet and AmBisome but not changed by Fungizone. The Vm value for Abelcet and AmBisome was higher than Fungizone(; although, no difference was observed in the Km values between formulations. CONCLUSIONS: Findings suggest that lipid-based formulations of Amp-B promote the transfer of Amp-B into high-density lipoprotein fractions at a degree of increase inversely proportional to the lipid levels in the plasma.