Python Package abstcal: An Open-Source Tool for Calculating Abstinence From Timeline Followback Data.

INTRODUCTION: In smoking cessation clinical trials, timeline followback (TLFB) interviews are widely used to track daily cigarette consumption. However, there are no standard tools for calculating abstinence based on TLFB data. Individual research groups have to develop their own calculation tools, which is not only time- and resource-consuming but might also lead to variability in the data processing and calculation procedures. AIMS AND METHODS: To address these issues, we developed a novel open-source Python package named abstcal to calculate abstinence using TLFB data. This package provides data verification, duplicate and outlier detection, missing-data imputation, integration of biochemical verification data, and calculation of a variety of definitions of abstinence, including continuous, point-prevalence, and prolonged abstinence. RESULTS: We verified the accuracy of the calculator using data derived from a clinical smoking cessation study. To improve the package's accessibility, we have made it available as a free web app. CONCLUSIONS: The abstcal package is a reliable abstinence calculator with open-source access, providing a shared validated online tool to the addiction research field. We expect that this open-source abstinence calculation tool will improve the rigor and reproducibility of smoking and addiction research by standardizing TLFB-based abstinence calculation. IMPLICATIONS: Abstinence calculation is an essential task in any smoking intervention study. However, there have not been standard open-source tools available to the researchers. This commentary describes a Python-based package called abstcal that can calculate abstinence from TLFB data, a common methodology to collect smoking consumption data in research settings. The package supports the calculation of point-prevalence, prolonged, and continuous abstinence. Importantly, the package has a web app interface that allows researchers to use the tool without any coding experience. This tool will facilitate smoking research by providing a standardized and easy-to-use abstinence calculation tool.

You Don't Need an App-Conducting Mobile Smoking Research Using a Qualtrics-Based Approach.

With the increasing availability of smartphones, many tobacco researchers are exploring smartphone-delivered mobile smoking interventions as a disseminable means of treatment. Most effort has been focused on the development of smartphone applications (apps) to conduct mobile smoking research to implement and validate these interventions. However, developing project-specific smartphone apps that work across multiple mobile platforms (e.g., iOS and Android) can be costly and time-consuming. Here, using a hypothetical study, we present an alternate approach to demonstrate how mobile smoking cessation and outcome evaluation can be conducted without the need of a dedicated app. Our approach uses the Qualtrics platform, a popular online survey host that is used under license by many academic institutions. This platform allows researchers to conduct device-agnostic screening, consenting, and administration of questionnaires through Qualtrics's native survey engine. Researchers can also collect ecological momentary assessment data using text messaging prompts with the incorporation of Amazon Web Services' Pinpoint. Besides these assessment capabilities, Qualtrics has the potential for delivering personalized behavioral interventions through the use of JavaScript code. By customizing the question's web elements in Qualtrics (e.g., using texts, images, videos, and buttons), researchers can integrate interactive web-based interventions and complicated behavioral and cognitive tasks into the survey. In conclusion, this Qualtrics-based methodology represents a novel and cost-effective approach for conducting mobile smoking cessation and assessment research.

Prospective analysis of factors related to migraine attacks: the PAMINA study.

Migraine is related to numerous factors such as hormones, stress or nutrition, but information about their actual importance is limited. Therefore, we analysed prospectively a wide spectrum of factors related to headache in migraineurs. We examined 327 migraineurs recruited via newspapers who kept a comprehensive diary for 3 months. Statistical analysis comprising 28 325 patient days and 116 dichotomous variables was based on the interval between two successive headache attacks. We calculated univariate Cox regression analyses and included covariables with a P-value of <0.05 in two stepwise multivariate Cox regression analyses, the first accounting for a correlation of the event times within a subject, the second stratified by the number of headache-free intervals. We performed similar analyses for the occurrence of migraine attacks and for the persistence of headache and migraine. Menstruation had the most prominent effect, increasing the hazard of occurrence or persistence of headache and migraine by up to 96%. All other factors changed the hazard by <35%. The two days before menstruation and muscle tension in the neck, psychic tension, tiredness, noise and odours on days before headache onset increased the hazard of headache or migraine, whereas days off, a divorced marriage, relaxation after stress, and consumption of beer decreased the hazard. In addition, three meteorological factors increased and two others decreased the hazard. In conclusion, menstruation is most important in increasing the risk of occurrence and persistence of headache and migraine. Other factors increase the risk less markedly or decrease the risk.

Identification of various exon combinations of the ews/fli1 translocation: an optimized RT-PCR method for paraffin embedded tissue -- a report by the CWS-study group.

BACKGROUND: Chromosomal translocations t(11;22) (q24;q12) are characteristic of about 80-90 % of Ewing's sarcoma family of tumors [bone and soft tissue Ewing's sarcoma and peripheral neuroectodermal tumors (PNET)]. They generate ews/fli1 rearrangements showing great diversity in breakpoint exon combination. In about 5 % of Ewing's tumors, ews is fused to the erg gene at 21q22. The various chimeric proteins encoded may function as aberrant oncogenic transcription factors. These specific translocations can be used for exact molecular diagnosis in these poorly differentiated small round-cell tumors. Moreover, the prognostic relevance of different translocational variants has been previously suggested. Furthermore, the sensitive molecular detection of minimal metastatic and residual disease and its clinical significance can be evaluated. To address these questions more definitively in the large number of patients registered in multicenter studies, it is often necessary to access archival paraffin-embedded tumor tissue if no fresh or frozen tumor material is available for analysis by RT (reverse transcription)-PCR. Specific problems arise from formalin-fixed and paraffin-embedded tissue due to the degradation of RNA and insufficient extraction efficiency. Therefore, primer distance and product size are limited for successful PCR amplification. This conflicts with the requirement for identification of various possible exon combinations by PCR simultaneously using one single primer pair with larger distance. PATIENTS: We examined paraffin embedded soft part tumor tissue samples from 47 Ewing's tumor patients. Patients were treated according to either CWS (Cooperative Weichteilsarkomstudie, CWS-91 or CWS-96) or Euro-E.W.I.N.G. 99 therapy protocols. METHOD: We established a novel RT-PCR method, using 3 different exon specific sets of PCR primer pairs, selected according to the coding ews and fli1 nucleotide sequences (NCBI database), suitable for RT-PCR identification of variant ews/fli1 fusion transcripts in RNA isolated from formalin-fixed, paraffin-embedded tissue. For use in combination with ews -primer, an erg specific primer was selected to alternatively test for ews/erg fusion transcripts. As positive control for the integrity of isolated mRNA, we used the ubiquitously expressed gapdh transcript for RT-PCR amplification in each sample. RESULTS: In 31 cases (= 66 %) of 47 paraffin samples of Ewing's tumors analysed, gapdh control indicated adequate quality of RNA. In 16 cases no gapdh control fragment was amplifiable, nevertheless in 2 of these 16 samples distinct ews fusion products could be detected. In 23 cases we identified ews fusion transcripts. Thereof in 65 % ews exon 7 being fused to fli1 exon 6 (fusion type I), in 22 % to fli1 exon 5 (fusion type II). In 4 % each ews exon 10 being juxtaposed to fli1 either exon 6 or exon 5, respectively. An ews/erg fusion was detected in 4 % ( ews exon 7 fused to erg exon 6). In 10 samples, a gapdh fragment was amplified, but no ews/fli1 or - erg fusion transcript could be identified. The reference pathological review (I. L., Kiel, Germany) disproved the primary histopathology in 5 cases. CONCLUSIONS: Using our different sets of exon specific primer pairs, it was possible to detect 4 different breakpoints of ews/fli1 fusion transcripts and the ews/erg fusion by RT-PCR in RNA isolates from formalin-fixed, paraffin-embedded Ewing's tumor tissue. This method can be a very useful alternative in clinical situations (to ensure diagnosis and perform minimal metastatic and residual disease investigations) and in order to assess prognostic significance of translocation subtypes when no fresh tumor tissue is available.