A semi-automated workflow for producing time-aligned intermediate tonal representations

Tone can be one of the most daunting aspects of a language to document, particularly at the beginning of a project. Even if tonal categories can be determined in elicitation contexts, tone in running speech and narratives, the core focus of documentary linguistics, is notoriously difficult even for seasoned tonal specialists. When tone marking is included, they are the researcher’s analytical conclusions (e.g. H, L) rather than a representation of the speech melody itself. To address these issues and facilitate the inclusion of objective replicable tonal annotations in language documentation, we have developed a semi-automated computational workflow to take raw phonetic data (fundamental frequency, or f0) and turn it into a more easily interpretable intermediate representation: a system of levels, already used as a descriptive lingua franca in reference grammars either numerically or using dashes (e.g. HL = 51 = ). The analyst can set the number of levels to reflect the desired level of detail. For instance, if the researcher suspects a two-tone system, she may set the number of levels at 4 or 5 to reflect processes such as declination, downdrift or upstep. For more complex tone systems, more levels might be employed. The workflow begins in Praat by creating a TextGrid annotation delimiting the tonal spans to be analyzed; for the most part, these will be vowels or syllable rimes so as to analyze only tone bearing units. A Praat script extracts f0 from multiple points in each span. Next, a Python script converts these f0 values to semitones based on the speaker’s mean f0, excluding outliers. The speaker’s pitch range, excluding these outliers, is then divided into the desired number of levels, and each point designated by the researcher within a syllable (e.g. 20% and 80%) is assigned a number corresponding to that level. The output of the Python script is a text file with time stamps for each annotation, which can be imported into Elan, thus tying together searchable tonal information with the broader text transcription. In this talk, we describe the workflow and demonstrate some analytical uses for the tool, including comparison of elicitation and free speech, interspeaker variation, and first-look analysis of unanalyzed tonal data

Factors associated with changing alcohol consumption during the first UK lockdown

BACKGROUND: In response to COVID-19 there have been lockdowns and restrictions to hospitality services. Drinking behaviours often change in response to traumatic events and changes in the drinking environment, and this is influenced by a range of factors. This study explores self-reported changes in alcohol consumption in the third month of the UK lockdown, associations with socio-demographics factors and with COVID-19-related concerns, and mental health and wellbeing. METHODS: The COVID-19 Psychological Wellbeing Study was a longitudinal, online, three-wave survey of 1958 UK adults. Data were collected during the first UK lockdown; wave 1 launched 23 March 2020, wave 2 was 1 month after and wave 3 2 months after completion of wave 1A hierarchical multinomial regression model was estimated to investigate factors associated with changes in perceived alcohol consumption in the third month of the lockdown. RESULTS: The majority of participants reported changes in drinking (62%) with over one-third indicating increased consumption. Student status and worries about the financial implications of COVID-19 were associated with lower odds of decreased alcohol consumption. Those with above average income and those with children in the household had lower odds of increased alcohol consumption, while younger adults had higher odds of increased alcohol consumption. CONCLUSIONS: This study adds to the growing body of research showing changes in alcohol consumption behaviours during the COVID-19 lockdown restrictions, and identifies risk and protective factors which can aid in targeting intervention at those most in need of support

Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer.

We sequenced 11 germline exomes from five families with familial pancreatic cancer (FPC). One proband had a germline nonsense variant in ATM with somatic loss of the variant allele. Another proband had a nonsense variant in PALB2 with somatic loss of the variant allele. Both variants were absent in a relative with FPC. These findings question the causal mechanisms of ATM and PALB2 in these families and highlight challenges in identifying the causes of familial cancer syndromes using exome sequencing

Homelessness predicts attrition but not alcohol abstinence in outpatients experiencing co-occurring alcohol dependence and serious mental illness.

BACKGROUND: Adults experiencing homelessness and serious mental illnesses (SMI) are at an increased risk of poor mental health and treatment outcomes compared with stably housed adults with SMI. The additional issue of alcohol misuse further complicates the difficulties of those living with homelessness and SMI. In this secondary data analysis, the authors investigated the impact of homelessness on attrition and alcohol use in a contingency management (CM) intervention that rewarded alcohol abstinence in outpatients with SMI. METHODS: The associations between housing status and attrition and alcohol abstinence during treatment, as assessed by ethyl glucuronide (EtG) urine tests, were evaluated in 79 adults diagnosed with alcohol dependence and SMI. RESULTS: Thirty-nine percent (n = 31) of participants reported being homeless at baseline. Individuals who were homeless were more likely to drop out of CM (n = 10, 62.5%) than those who were housed (n = 4, 16.7%), χ CONCLUSIONS: Individuals experiencing homelessness and co-occurring alcohol dependence and SMI receiving CM had higher rates of attrition, relative to those who were housed. Homelessness was not associated with differences in biologically assessed alcohol abstinence

Prevalence and Correlates of Cannabis Use in Outpatients with Serious Mental Illness Receiving Treatment for Alcohol Use Disorders.

Introduction: People with serious mental illness (SMI) use cannabis more than any other illicit drug. Cannabis use is associated with increased psychotic symptoms and is highly comorbid with alcohol use disorders (AUDs). Despite the national trend toward decriminalization, little is known about the prevalence, correlates, and impact of cannabis use on those with SMI receiving treatment for substance use disorders, a group at high risk for the negative effects of cannabis use. Methods: In this secondary data analysis, cannabis use prevalence, correlates, and impact on treatment outcomes were examined in 121 adults with cooccurring SMI and AUDs receiving outpatient addiction treatment in a randomized trial of contingency management (CM) for alcohol. Prevalence and frequency of cannabis use were calculated across the 7-month study period using self-report and urine tests. Cannabis users were compared with nonusers by SMI diagnosis, psychiatric symptoms, medical problems, legal problems, and HIV-risk behavior. The relationship between cannabis use and longest duration of alcohol abstinence in participants randomized to CM (n=40) was assessed. Results: Fifty-seven (47%) of participants submitted at least one cannabis-positive urine sample during the study. Out of the 2834 total samples submitted, 751 (27%) were positive for cannabis. Cannabis users were 2.2 times more likely to submit an alcohol-positive sample, and 2.5 times more likely to submit a cocaine-positive sample at baseline, relative to noncannabis users (p=0.01). Cannabis users were more likely to engage in risky sexual behavior (p=0.01) and to report being homeless (p=0.03) than nonusers. When controlling for pretreatment alcohol use, the relationship between comorbid cannabis use and alcohol abstinence during CM was not significant (p=0.77). Conclusion: Rates of comorbid cannabis use were high in this sample of adults with SMI and AUDs. Cannabis use was correlated with recent alcohol and cocaine use, risky sexual behavior, and homelessness, but not with alcohol abstinence during CM

Pretreatment ethyl glucuronide levels predict response to a contingency management intervention for alcohol use disorders among adults with serious mental illness.

BACKGROUND AND OBJECTIVES: This study investigated if pretreatment ethyl glucuronide (EtG) levels corresponding to light (100 ng/mL), heavy (500 ng/mL), and very heavy (1,000 ng/mL) drinking predicted longest duration of alcohol abstinence (LDA) and proportion of EtG-negative urine tests in outpatients receiving a 12-week EtG-based contingency management (CM) intervention for alcohol dependence. METHODS: Participants were 40 adults diagnosed with alcohol use disorders and serious mental illness who submitted up to 12 urine samples for EtG analysis during a 4-week observation period and were then randomized to 12-weeks of CM for alcohol abstinence and addiction treatment attendance. Alcohol use outcomes during CM as assessed by EtG and self-report were compared across those who did and did not attain a pre-treatment average EtG level of 500 ng/mL-a level that equates to frequent heavy drinking. RESULTS: Only the 500 ng/mL cutoff was associated with significant differences in LDA and proportion of EtG-negative samples during CM. Those with a pre-treatment EtG \u3c 500 ng/mL attained a LDA 2.3 (alcohol) to 2.9 (drugs) weeks longer than pre-treatment heavy drinkers. DISCUSSION AND CONCLUSIONS: The EtG biomarker can be used to determine who will respond to a CM intervention for alcohol use disorders and could inform future trials that are designed to be tailored to individual patients. SCIENTIFIC SIGNIFICANCE: Results suggest pre-treatment EtG cutoffs equivalent to heavy and very heavy drinking predict outcomes in CM. (Am J Addict 2017;26:673-675)

Interaction between pre-treatment drug use and heterogeneity of psychiatric diagnosis predicts outcomes in outpatients with co-occurring disorders.

We examined whether the interaction of baseline stimulant use, assessed by urine drug tests, and type of serious mental illness (SMI) diagnosis predicted stimulant use in a trial of contingency management (CM). The interaction between baseline stimulant use and SMI diagnoses was significant in the overall sample (p=0.002) when controlling for the main effects of treatment condition, baseline stimulant use, and SMI diagnosis. Similar results were also found within the CM sample. Individuals with bipolar disorder were more or less likely, depending on their baseline stimulant-drug test results, to use stimulants during treatment compared to those with other SMI diagnoses

A Randomized Controlled Trial of Ethyl Glucuronide-Based Contingency Management for Outpatients With Co-Occurring Alcohol Use Disorders and Serious Mental Illness.

OBJECTIVE: The authors examined whether a contingency management intervention using the ethyl glucuronide (EtG) alcohol biomarker resulted in increased alcohol abstinence in outpatients with co-occurring serious mental illnesses. Secondary objectives were to determine whether contingency management was associated with changes in heavy drinking, treatment attendance, drug use, cigarette smoking, psychiatric symptoms, and HIV-risk behavior. METHOD: Seventy-nine (37% female, 44% nonwhite) outpatients with serious mental illness and alcohol dependence receiving treatment as usual completed a 4-week observation period and were randomly assigned to 12 weeks of contingency management for EtG-negative urine samples and addiction treatment attendance, or reinforcement only for study participation. Contingency management included the variable magnitude of reinforcement prize draw procedure contingent on EtG-negative samples (/mL) three times a week and weekly gift cards for outpatient treatment attendance. Urine EtG, drug test, and self-report outcomes were assessed during the 12-week intervention and 3-month follow-up periods. RESULTS: Contingency management participants were 3.1 times (95% CI=2.2-4.5) more likely to submit an EtG-negative urine test during the 12-week intervention period, attaining nearly 1.5 weeks of additional alcohol abstinence compared with controls. Contingency management participants had significantly lower mean EtG levels, reported less drinking and fewer heavy drinking episodes, and were more likely to submit stimulant-negative urine and smoking-negative breath samples, compared with controls. Differences in self-reported alcohol use were maintained at the 3-month follow-up. CONCLUSIONS: This is the first randomized trial utilizing an accurate and validated biomarker (EtG) to demonstrate the efficacy of contingency management for alcohol dependence in outpatients with serious mental illness