Mass Dynamics 1.0: A Streamlined, Web-Based Environment for Analyzing, Sharing, and Integrating Label-Free Data.

Label-free quantification (LFQ) of shotgun proteomics data is a popular and robust method for the characterization of relative protein abundance between samples. Many analytical pipelines exist for the automation of this analysis, and some tools exist for the subsequent representation and inspection of the results of these pipelines. Mass Dynamics 1.0 (MD 1.0) is a web-based analysis environment that can analyze and visualize LFQ data produced by software such as MaxQuant. Unlike other tools, MD 1.0 utilizes a cloud-based architecture to enable researchers to store their data, enabling researchers to not only automatically process and visualize their LFQ data but also annotate and share their findings with collaborators and, if chosen, to easily publish results to the community. With a view toward increased reproducibility and standardization in proteomics data analysis and streamlining collaboration between researchers, MD 1.0 requires minimal parameter choices and automatically generates quality control reports to verify experiment integrity. Here, we demonstrate that MD 1.0 provides reliable results for protein expression quantification, emulating Perseus on benchmark datasets over a wide dynamic range. The MD 1.0 platform is available globally via: https://app.massdynamics.com/.

Impact of HLA-DR Antigen Binding Cleft Rigidity on T Cell Recognition.

The interaction between T cell receptor (TCR) and peptide (p)-Human Leukocyte Antigen (HLA) complexes is the critical first step in determining T cell responses. X-ray crystallographic studies of pHLA in TCR-bound and free states provide a structural perspective that can help understand T cell activation. These structures represent a static "snapshot", yet the nature of pHLAs and their interactions with TCRs are highly dynamic. This has been demonstrated for HLA class I molecules with in silico techniques showing that some interactions, thought to stabilise pHLA-I, are only transient and prone to high flexibility. Here, we investigated the dynamics of HLA class II molecules by focusing on three allomorphs (HLA-DR1, -DR11 and -DR15) that are able to present the same epitope and activate CD4+ T cells. A single TCR (F24) has been shown to recognise all three HLA-DR molecules, albeit with different affinities. Using molecular dynamics and crystallographic ensemble refinement, we investigate the molecular basis of these different affinities and uncover hidden roles for HLA polymorphic residues. These polymorphisms were responsible for the widening of the antigen binding cleft and disruption of pHLA-TCR interactions, underpinning the hierarchy of F24 TCR binding affinity, and ultimately T cell activation. We expanded this approach to all available pHLA-DR structures and discovered that all HLA-DR molecules were inherently rigid. Together with in vitro protein stability and peptide affinity measurements, our results suggest that HLA-DR1 possesses inherently high protein stability, and low HLA-DM susceptibility.

Synthesis, Anti-Cancer and Anti-Migratory Evaluation of 3,6-Dibromocarbazole and 5-Bromoindole Derivatives.

In this study, a new series of N-alkyl-3,6-dibromocarbazole and N-alkyl-5-bromoindole derivatives have been synthesized and evaluated in vitro as anti-cancer and anti-migration agents. Cytotoxic and anti-migratory effects of these compounds were evaluated in MCF-7 and MDA-MB-231 breast cancer cell lines and an insight on the structure-activity relationship was developed. Preliminary investigations of their anti-cancer activity demonstrated that several compounds have moderate antiproliferative effects on cancer cell lines with GI50 values in the range of 4.7-32.2 µM. Moreover, carbazole derivatives 10, 14, 15, 23, and 24 inhibit migration activity of metastatic cell line MDA-MB-231 in the range of 18-20%. The effect of compounds 10, 14, and 15 in extension of invadopodia and filopodia was evaluated by fluorescence microscopy and results demonstrated a reduction in actin-based cell extensions by compounds 10 and 15.

CYP2A6 metabolism in the development of smoking behaviors in young adults.

Cytochrome P450 2A6 (CYP2A6) encodes the enzyme responsible for the majority of nicotine metabolism. Previous studies support that slow metabolizers smoke fewer cigarettes once nicotine dependent but provide conflicting results on the role of CYP2A6 in the development of dependence. By focusing on the critical period of young adulthood, this study examines the relationship of CYP2A6 variation and smoking milestones. A total of 1209 European American young adults enrolled in the Collaborative Study on the Genetics of Alcoholism were genotyped for CYP2A6 variants to calculate a previously well-validated metric that estimates nicotine metabolism. This metric was not associated with the transition from never smoking to smoking initiation nor with the transition from initiation to daily smoking (P > 0.4). But among young adults who had become daily smokers (n = 506), decreased metabolism was associated with increased risk of nicotine dependence (P = 0.03) (defined as Fagerström Test for Nicotine Dependence score ≥4). This finding was replicated in the Collaborative Genetic Study of Nicotine Dependence with 335 young adult daily smokers (P = 0.02). Secondary meta-analysis indicated that slow metabolizers had a 53 percent increased odds (OR = 1.53, 95 percent CI 1.11-2.11, P = 0.009) of developing nicotine dependence compared with normal metabolizers. Furthermore, secondary analyses examining four-level response of time to first cigarette after waking (>60, 31-60, 6-30, ≤5 minutes) demonstrated a robust effect of the metabolism metric in Collaborative Study on the Genetics of Alcoholism (P = 0.03) and Collaborative Genetic Study of Nicotine Dependence (P = 0.004), illustrating the important role of this measure of dependence. These findings highlight the complex role of CYP2A6 variation across different developmental stages of smoking behaviors.

Conditional Release Placements of Insanity Acquittees in Oregon: 2012-2014.

Between January 1, 2012 and December 31, 2014, there was a large population (N = 200) of insanity acquittees placed on conditional release (CR) in the state of Oregon. This article looks at the demographic and system characteristics of this large group of individuals. The authors then focus on the initial housing placement and what happens to individuals after their release in relation to their housing placement. In Oregon, insanity acquittees are either conditionally released directly by the court or placed in the hospital prior to potential CR by a supervising board. In general, once CR occurs, individuals tend to stay in their initial placement without moving to less structured levels of care, raising concerns about transinstitutionalization. This is especially true for individuals released to the most structured living arrangement (secure residential treatment facility). Those individuals who are conditionally released to less structured settings have a higher rate of revocation back to the hospital. Those individuals who do move to less structured levels of care usually have longer hospital stays and start off in more structured levels of care to start their CR. Copyright © 2016 John Wiley & Sons, Ltd.

Oregon's Gun Relief Program for Adjudicated Mentally Ill Persons: The Psychiatric Security Review Board.

This article describes the State of Oregon's implementation of two programs designed to comply with federal gun laws regarding reporting individuals who have received mental health adjudications in criminal and civil courts. One mandate requires that states submit names of adjudicated individuals to the National Instant Criminal Background Check System (NICS) while the second requires that the state establish a qualifying gun restoration program for those disqualified from gun ownership. In 2009, Oregon's Legislature developed an administrative approach to gun restoration and assigned the responsibility for conducting these hearing to the Oregon Psychiatric Security Review Board (PSRB). The PSRB is a state administrative board that has existed since 1977 and has been primarily focused on the supervision and treatment of adult and juvenile insanity acquittees. The gun restoration program began in 2010, but to date has only received three completed petitions requesting restoration of firearm rights. The article concludes with a discussion that surmises why very few of the Oregonians who are listed in NICS have submitted petitions for relief.

Statewide survey of living arrangements for conditionally released insanity acquittees.

There is a large population (n =389) of insanity acquittees on monitored conditional release in Oregon. This article focuses on the living situation for these individuals, which can range from a secure residential treatment facility to independent living. This article will define all the different placement options available and then review the current living situation for all conditionally released insanity acquittees in the state of Oregon on a single day, February 1, 2014. This article shows that the majority of individuals on conditional release live in the most highly structured settings available. The article then ends with a discussion of these findings, including a comparison of current placement options, with previous descriptions in the literature demonstrating that current community options offer more structure and more individuals reside in structured settings than was previously the case. Current findings will be related to inpatient psychiatric bed reduction strategies and the question of possible transinstitutionalization.

COVID-19, Mink-Bowman, and Court-Ordered Psychiatric Services in Oregon.

COVID-19 strongly affected referral of individuals from Oregon's courts and the ability of Oregon State Hospital (OSH) to accept patients. Despite acceleration in the decline in civil commitment, competency to stand trial (CST) admissions increased, causing a bed crisis at OSH, which in turn affected community hospitals and jails. In 1993, the Ninth Circuit Court of Appeals mandated admission of jail detainees to OSH within seven days after a judicial order for CST evaluation or restoration. During COVID, as the number of such patients increased to crisis proportions, average jail detention times exceeded seven days. An inevitable judicial process intensified in the U.S. District Court of Oregon after OSH requested a COVID-related modification of the seven-day limit. This commentary demonstrates more clearly than in the past that there is a negative correlation between civil commitment and competency restoration as components of an interrelated system. After updating the situation in Oregon, this article ends with suggested interventions to improve Oregon's civil and criminal commitment processes, hoping for better care of patients and improved administration of justice.

The Dramatic Decline of Civil Commitment in Oregon, 1972 to 2020.

The rate of civil commitment in Oregon fell from 53.2/100,000 in 1972 to 9.2/100,000 in 2020. The paper discusses this decline in civil commitment as related to statutory and case law changes and complex interactions including bed availability at Oregon State Hospital (OSH). The latter was in turn influenced by the significant increase in the last decade of hospitalization at OSH of competence to stand trial evaluation and restoration (CST) patients. Multnomah County, which contains the city of Portland, was responsible for the largest number of investigations and commitments and led the state in using a 14-day diversion alternative to commitment. This analysis may serve as a model for other states to engage in similar longitudinal research to shed light on the functioning of their involuntary commitment statutes.

Competency to Stand Trial, Civil Commitment, and Oregon State Hospital.

This article examines the explosive growth of individuals referred for competency to stand trial evaluation and restoration services in the state of Oregon and at Oregon State Hospital between the years 2000 and 2020. This paper also examines the links between competency to stand trial and civil commitment statutes. As yearly civil commitments rates have decreased in Oregon, competency to stand trial commitments to Oregon State Hospital have increased, suggesting an inverse relationship between these two important statutes. There is an overlap in the jurisdiction of these statutes, with both needing to function harmoniously for the civil and the criminal justice processes to each work for the benefit of the individuals involved in the criminal justice and mental health systems.

A SARM1-mitochondrial feedback loop drives neuropathogenesis in a Charcot-Marie-Tooth disease type 2A rat model.

Charcot-Marie-Tooth disease type 2A (CMT2A) is an axonal neuropathy caused by mutations in the mitofusin 2 (MFN2) gene. MFN2 mutations result in profound mitochondrial abnormalities, but the mechanism underlying the axonal pathology is unknown. Sterile α and Toll/IL-1 receptor motif-containing 1 (SARM1), the central executioner of axon degeneration, can induce neuropathy and is activated by dysfunctional mitochondria. We tested the role of SARM1 in a rat model carrying a dominant CMT2A mutation (Mfn2H361Y) that exhibits progressive dying-back axonal degeneration, neuromuscular junction (NMJ) abnormalities, muscle atrophy, and mitochondrial abnormalities - all hallmarks of the human disease. We generated Sarm1-KO (Sarm1-/-) and Mfn2H361Y Sarm1 double-mutant rats and found that deletion of Sarm1 rescued axonal, synaptic, muscle, and functional phenotypes, demonstrating that SARM1 was responsible for much of the neuropathology in this model. Despite the presence of mutant MFN2 protein in these double-mutant rats, loss of SARM1 also dramatically suppressed many mitochondrial defects, including the number, size, and cristae density defects of synaptic mitochondria. This surprising finding indicates that dysfunctional mitochondria activated SARM1 and that activated SARM1 fed back on mitochondria to exacerbate the mitochondrial pathology. As such, this work identifies SARM1 inhibition as a therapeutic candidate for the treatment of CMT2A and other neurodegenerative diseases with prominent mitochondrial pathology.

The contribution of common CYP2A6 alleles to variation in nicotine metabolism among European-Americans.

OBJECTIVE: To study the association between cytochrome P450 2A6 (CYP2A6) genotype and metabolism of nicotine to cotinine, identify functional polymorphisms, and develop a predictive genetic model of nicotine metabolism. METHODS: The conversion of deuterated (D2)-nicotine to D2-cotinine was quantified in 189 European-Americans and the contribution of CYP2A6 genotype to variability in first-pass nicotine metabolism was assessed. Specifically, (i) single time point measures of D2-cotinine/(D2-cotinine+D2-nicotine) after oral administration were used as a metric of CYP2A6 activity; (ii) the impact of CYP2A6 haplotype was treated as acting multiplicatively; (iii) parameter estimates were calculated for all haplotypes in the subject pool, defined by a set of polymorphisms previously reported to affect function, including gene copy number; and (iv) a minimum number of predictive polymorphisms were justified to be included in the model based on statistical evidence of differences between haplotypes. RESULTS: The final model includes seven polymorphisms and fits the phenotype, 30-min after D2-nicotine oral administration, with R=0.719. The predictive power of the model is robust: parameter estimates calculated in men (n=89) predict the phenotype in women (n=100) with R=0.758 and vice versa with R=0.617; estimates calculated in current smokers (n=102) predict the phenotype in former-smokers (n=86) with R=0.690 and vice versa with R=0.703. Comparisons of haplotypes also demonstrate that CYP2A6*12 is a loss-of-function allele indistinguishable from CYP2A6*4 and CYP2A6*2 and that the CYP2A6*1B 5'-untranslated region conversion has negligible impact on metabolism. After controlling for CYP2A6 genotype, modest associations were found between increased metabolism and both female sex (P=4.8×10) and current smoking (P=0.02). CONCLUSION: Among European-Americans, seven polymorphisms in the CYP2A6 gene explain the majority of variability in the metabolism of nicotine to cotinine after oral administration. Parameters determined from this in-vivo experiment can be used to predict nicotine metabolism based on CYP2A6 genotype.

Arizona's Insanity Defense, Clark, and the 2007 Legislature.

In the post-Hinckley era, four states (Montana, Idaho, Utah, and Kansas) abolished their traditional insanity statutes in 1979 in favor of what are in certain circumstances mens rea insanity statutes. These changes were controversial and attracted early attention of legal scholars and courts in the individual states and at the U.S. Supreme Court. A 2006 Supreme Court decision in Clark v. Arizona had distinct but related concerns that helped crystallize the Court's attention on both mens rea and traditional insanity defense statutes. This decision led to a dramatic precedent that may have settled these matters for generations to come. This article will discuss the changes in the Arizona statutory and case law and the interplay between these changes and the important decisions of the U.S. Supreme Court during the same time span. The result of the changes has led to a situation in Arizona where, for the most serious criminal defendants with mental illness, there is no current mechanism to acquit a defendant on the basis of insanity by a mens rea statute or otherwise.

The Ninth Circuit Court of Appeals and Jail-Based Competency Evaluation and Restoration.

The U.S. Ninth Circuit is the largest of the federal appeals courts, encompassing the states of Alaska, Washington, and Oregon to the north, Hawaii, Guam, and the Northern Mariana Islands to the west, California and Arizona to the west and southwest, along with the three intermountain states of Idaho, Montana, and Nevada. The landmass within the Ninth Circuit represents great diversity of geography, climate, population density, and cultural and political traditions. This article considers two landmark Ninth Circuit decisions, one from Oregon and the other from Washington, two states that share geography, culture, and political orientation. Informed by these decisions, we consider how the Ninth Circuit might view the jail-based competency evaluation and restoration programs in the state of Arizona. We explore: the due process rights of jail detainees who are awaiting an evaluation of trial competency; and the time necessary for admission to, and the adequacy of, Arizona's jail-based competency restoration programs after a finding of incompetency.

Mens Rea, Competency to Stand Trial, and Guilty but Mentally Ill.

The recent U.S. Supreme Court case of Kahler v. Kansas determined that the Kansas mens rea laws were sufficient to stand as the state's only insanity defense statute. In this issue of The Journal, Landess and Holoyda describe the legal reasoning that led to this decision and the persistent concerns about the wisdom of the decision. This commentary is meant to serve as a mirror image to Landess and Holoyda's article, as it focuses on the impact of Kahler on severely mentally ill individuals faced with criminal charges in the four mens rea states: Montana, Idaho, Utah, and Kansas. The authors assert that the absence of a traditional insanity defense disrupts the criminal justice process, adds the pressure of greater numbers of individuals pushed into the competency-to-stand-trial and competency-restoration systems, resurrects the guilty but mentally ill verdict from the condemnation of history, and forces people with serious mental iillness into prisons without any evidence that the prisons are up to the task of adequately caring for them.

Incompetent to Stand Trial, Not Restorable, and Dangerous.

This article focuses on the preferred disposition for an individual charged with a serious crime against another person, adjudicated incompetent to stand trial and not restorable to competence, whose original criminal charges are dismissed without prejudice, and who is regarded by the state as dangerous to the general public. Three current models used today in California, Oregon, and Ohio are described. All three rely on modifications of various aspects of civil commitment law. We then propose a fourth model based on a modified version of the 1989 American Bar Association (ABA) Criminal Justice Mental Health Standards, in which individuals who are found incompetent to stand trial and not restorable to competence and are considered dangerous would be committed under the same special procedures governing the management and treatment of insanity acquittees.

Forensic psychiatry and the forensic sciences: in memory of Peter J. Batten, MD.

This commentary is dedicated to the memory of Peter J. Batten, MD. He was a public health physician, a psychiatrist, and a medical examiner who spent his entire career in Salem, the capital of the State of Oregon. Salem was a unique place to work because, early in the history of Oregon, the state elected to build all of its original public institutions in the environs of the city. As the county medical examiner, Dr. Batten reviewed all questionable deaths that occurred within the county and in particular within the public institutions. Many of his findings were subsequently published, and these reports influenced the direction of mental health policy in these same institutions. He also used his position as county medical examiner to examine deaths in road rage incidents and those occurring at railroad crossings in Salem. The commentary also emphasizes the benefits of collaboration within the forensic sciences.

Treatment Refusal in Arizona's Jail-Based Competency to Stand Trial Restoration Programs.

In 2003, Arizona began a jail-based restoration to competency program for detainees in its largest jail system in Phoenix. Today, jail-based competency programs have become the rule statewide to the degree that very few incompetent detainees are now referred to the Arizona State Hospital for restoration services. This article focuses on the topic of treatment refusal and the use of forced medications for detainees who are in these jail-based restoration programs. We describe Arizona's novel statewide jail-based programs, Arizona's statutory and case law approach to treatment refusal, and the restoration to competency programs in one large county jail that has no legal mechanism outside of civil commitment for the determination of whether forced treatment will be permitted. We conclude with a discussion of specific override procedures that might apply directly to incompetent detainees in a jail-based competency restoration program and whether the use of these procedures is prudent in a jail environment.

The Migration of Arizona's Post-Insanity Defense Procedures to a Modified GBMI Model.

Arizona's insanity defense and post-insanity procedures have evolved over the last 30 years into a unique system. Arizona moved from a typical M'Naughten-based insanity defense to an adaptation of the Oregon Psychiatric Security Review Board (PSRB) model and then to its current form, in which the PSRB is cast in a correctional framework. These changes have resulted in a correctional statute, with outcomes that may subject the guilty except insane (GEI) offender to a disposition similar to that of someone found guilty but mentally ill (GBMI). We review the literature on the GBMI defense first developed in Michigan in the 1970s and compare Arizona's current system to the earlier GBMI models. We conclude with a discussion of Arizona's GEI verdict and implications of managing these offenders in a correctional framework, resulting in a modified GBMI statute.

Pharmacokinetics of the Rac/Cdc42 Inhibitor MBQ-167 in Mice by Supercritical Fluid Chromatography-Tandem Mass Spectrometry.

The Rho GTPases Rac and Cdc42 are potential targets against metastatic diseases. We characterized the small molecule MBQ-167 as an effective dual Rac/Cdc42 inhibitor that reduces HER2-type tumor growth and metastasis in mice by ∼90%. This study reports the pharmacokinetics and tissue distribution of MBQ-167 following intraperitoneal and oral single-dose administrations. We first developed and validated a bioanalytical method for the quantitation of MBQ-167 in mouse plasma and tissues by supercritical fluid chromatography coupled with electrospray ionization tandem mass spectrometry. MBQ-167 was rapidly distributed into the kidneys after intraperitoneal dosing, whereas oral administration resulted in higher distribution to lungs. The elimination half-lives were 2.17 and 2.6 h for the intraperitoneal and oral dosing, respectively. The relative bioavailability of MBQ-167 after oral administration was 35%. This investigation presents the first analysis of the pharmacokinetics of MBQ-167 and supports further preclinical evaluation of this drug as a potential anticancer therapeutic.