The K-mer File Format: a standardized and compact disk representation of sets of k-mers.

SUMMARY: Bioinformatics applications increasingly rely on ad hoc disk storage of k-mer sets, e.g. for de Bruijn graphs or alignment indexes. Here, we introduce the K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, realizing space savings of 3-5× compared to other formats, and bringing interoperability across tools. AVAILABILITY AND IMPLEMENTATION: Format specification, C++/Rust API, tools: https://github.com/Kmer-File-Format/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Upcycling Compact Discs for Flexible and Stretchable Bioelectronic Applications.

Electronic waste is a global issue brought about by the short lifespan of electronics. Viable methods to relieve the inundated disposal system by repurposing the enormous amount of electronic waste remain elusive. Inspired by the need for sustainable solutions, this study resulted in a multifaceted approach to upcycling compact discs. The once-ubiquitous plates can be transformed into stretchable and flexible biosensors. Our experiments and advanced prototypes show that effective, innovative biosensors can be developed at a low-cost. An affordable craft-based mechanical cutter allows pre-determined patterns to be scored on the recycled metal, an essential first step for producing stretchable, wearable electronics. The active metal harvested from the compact discs was inert, cytocompatible, and capable of vital biopotential measurements. Additional studies examined the material's resistive emittance, temperature sensing, real-time metabolite monitoring performance, and moisture-triggered transience. This sustainable approach for upcycling electronic waste provides an advantageous research-based waste stream that does not require cutting-edge microfabrication facilities, expensive materials, and high-caliber engineering skills.

Electrochemical detection of chloride ions using Ag-based electrodes obtained from compact disc.

In this work electrochemical sensors fabricated from compact disc material (waste or new) are used to quantify chloride ions in different types of samples. All three electrodes, working, counter, and pseudo-reference electrodes, were fabricated from the compact disc and directly used. Different parameters were studied in order to demonstrate the possibility of using this waste material for efficient and low-cost electrochemical sensors. Chloride sensing performance was evaluated using linear scan voltammetry as the detection technique. A sensitivity of 0.174 mA mM-1 cm-2 with a limit of detection of 20 µM and excellent selectivity against many interferents was observed. Selectivity and reproducibility tests were also carried out, showing excellent results. Sensors were also validated with real samples (drinking and sea water, milk, sweat and physiological solutions) with results comparable to conventional techniques. Our results show the applicability and suitability of these low-cost sensors, for detection of those analytes for which, silver, has high sensitivity and selectivity.

Development of a program to prevent sexual violence among teens in Japan: education using DVD video teaching materials and web-based learning.

BACKGROUND: This study aimed to develop an education system using DVD video-based teaching materials or web-based learning to reduce sexual violence among teens in Japan. METHODS: During the first stage, June 2018 to March 2019, an education program using DVD video teaching materials was carried out at three high schools and four universities with research consent from the director of the facility. From 1337 high school students and first- and second-year university students, subjects in their teen years were targeted for analysis. A survey was conducted at baseline and after the DVD video teaching. During the second stage, November 2019 to March 2020, web-based learning using improved video teaching materials was developed and carried out. From the adolescents who participated in the web-based learning, subjects in their teen years were targeted for analysis. A survey was conducted at baseline and after the web-based learning. RESULTS: In the first stage, 876 students consented to and participated in the education using DVD video teaching materials and baseline and after surveys (collection rate 65.5%). Among these, the number of respondents in their teens both baseline and after education was 705 persons (valid response rate 80.4%). In the second stage, the number of respondents in their teens both baseline and after education was 250 respondents in their teens who received web-based learning using the improved video teaching materials (valid response rate 87.1%). The improvement effect of the two programs was observed in attitudes that lead to physical violence, attitudes that lead to mental violence, attitudes that promote healthy conflict resolution, and dangerous attitudes that lead to sexual violence from persons in the community or through the Internet. The web-based learning program achieved an improvement of preventive attitudes toward sexual violence. CONCLUSIONS: The education program using DVD video teaching materials or web-based learning may help prevent sexual violence among teens in Japan.

Methylene blue contaminated water sanitization with alginate/compact discs waste-derived activated carbon composite beads: Adsorption studies.

The adsorption behavior of different adsorbents has been studied by various research works. But few studies have compared linear and non-linear isotherm and kinetic models alongside phenomenological coefficients. Here, the effect of activated carbon black (ACB) on the methylene blue adsorption behavior of alginate was examined. A low-cost and green adsorbent was fabricated to can easily be detached from water. For this aim waste compact discs were recycled for the preparation of ACB. Loading of 15 wt% ACB related to pure alginate increased removal yield of alginate significantly. Isotherms and kinetic models in linear and non-linear forms were studied and the results were examined by comparing R2 along with different error function values to find the best fitting. The results were well matched with non-linear pseudo-second-order and linear Langmuir. Intraparticle diffusion model and phenomenological coefficients represented control of adsorption by film diffusion and its limiting by pore diffusion.

Comparing the effect of group- based training along with text messaging and compact disc- based training on men's knowledge and attitude about participation in perinatal care: a cluster randomized control trial.

BACKGROUND: Men's participation in perinatal care is one of the key factors in promoting maternal and neonatal health. The effects of various methods of training on men's knowledge and attitude about participation in perinatal care can be different. So, this study aimed to compare the effect of two methods of training on men's knowledge and attitude about participation in perinatal care. METHODS: This cluster randomized control trial was conducted in three midwifery clinics in Tabriz, Iran between May and August 2018. Each clinic was randomly assigned to intervention (group- based training along with text messaging and CD- based training) and control groups. Seventy-five men were enrolled in three groups and evaluated for their knowledge and attitude about participation in perinatal care. Before and 3 months after the intervention, a researcher-made questionnaire was completed by the participants. Data were analyzed using descriptive and inferential statistics (paired t-test, one-way ANOVA, ANCOVA, chi-square, Kruskal-Wallis and Fisher exact tests). RESULTS: The mean (SD) score of men, s knowledge and attitude about participation in perinatal care had a significant increase in group- based training along with text messaging after the intervention compared to the score of before the intervention (p < 0.001, p = 0.005, respectively), but the mean (SD) score of men, s knowledge and attitude had not a significant increase in CD- based training and control group after the intervention compared to the score of before the intervention. The mean (SD) score of men,s knowledge and attitude about participation in perinatal care in group- based training along with text messaging were significantly higher than in CD- based training (p < 0.001, p = 0.039, respectively) and control group (p = 0.001, p = 0.021, respectively) after the intervention, respectively. However, the mean (SD) score of men, s knowledge and attitude in CD- based training were not significantly different from the control group after the intervention. CONCLUSION: Group- based training along with text messaging was more effective in improving the knowledge and attitude of men about participation in perinatal care compared to CD- based training. So, its implication in educational programs for the men is recommended. TRIAL REGISTRATION: IRCT, IRCT20160224026756N4 . Registered 27 May 2018.

A novel smartphone-based CD-spectrometer for high sensitive and cost-effective colorimetric detection of ascorbic acid.

As a powerful tool for medical diagnosis and bioanalysis, conventional optical spectrometers are generally expensive, bulky and always require an accompanying data processing device. In this work, we developed a novel smartphone-based CD-spectrometer (SCDS) for high sensitive and ultra-portable colorimetric analysis, with the advantage of cost-effective and simplicity. The distance between the light source and slit, the structure of SCDS and the parameters of camera in the smartphone were all optimized to ensure the best analytical performance. Besides, the SCDS employed HSV color model and utilized the overall intensity calculated by summing V-value of adjacent position for the absorbance measurement. In this way the errors caused by the low resolution of CD-grating can effectively be eliminated to promote the sensitivity of the SCDS. The performance of the SCDS was first validated for colorimetric detection of BSA with a detection limit of 0.0073 mg/mL, which is superior compared to that of the microtiter plate reader (MTPR). Moreover, by combining with 3,3',5,5'-tetramethylbenzidine-manganese dioxide (TMB-MnO2) nanosheets reaction, a high sensitive and specific system for ascorbic acid detection was established. The SCDS gives a detection range from 0.6250 µM to 40 µM with a detection limit of 0.4946 µM for AA detection. Compared to other studies, the SCDS features wide detection range and very low detection limit with low cost instrument. Therefore, the SCDS will be an ideal and promising colorimetric system for point-of-care (POC) application in food security, disease diagnosis and environmental monitoring.

Testing and Calibration of CDs as Radon Detectors at Highly Variable Radon Concentrations and Temperatures.

The application of the compact disk (CD) method for radon measurements at mines, caves and other workplaces needs testing under highly variable exposure conditions. We present the results from a blind comparison of CDs exposed in the Laboratory of Natural Radiation (Saelices el Chico, Spain). During the exposure the temperature varied from 6.5 to 24.9 °C (average 12.6 °C) and the 222Rn activity concentrations varied from <10 Bq m-3 to 147 kBq m-3. Good correspondence was observed between the integrated 222Rn activity concentration determined by the reference instruments in the laboratory (122,500 ± 6100 kBq h m-3) and that assessed by analysis of the CDs at a depth 80 µm beneath the front surface (118,000 ± 12,000 kBq h m-3) and at a depth of 120 µm (106,000 ± 12,000 kBq h m-3). The theoretical modeling of the CD response under variable temperature and radon concentration suggested that the small bias is probably due to the time variation of the calibration factor because of the time variations of the temperature.

Interplay of Coriolis effect with rheology results in unique blood dynamics on a compact disc.

We investigate the influence of rotational forces on blood dynamics in a microfluidic device. The special confluence of Coriolis force and blood rheology is brought forth by analyzing the flow at different hematocrit (volume fraction of red blood cells) levels and rotational speeds. We further study the effects of channel layout and alignment with regard to the axis of rotation to understand this intricate interplay. We provide a sound basis for efficient designing of a lab on a compact disc (lab on CD) platform by harnessing the effects of Coriolis force at relatively much lower rotational speeds, in sharp contrast with the reported findings where Coriolis effects have been considered to be effective only for exceptionally high rotational speeds. Our results show that over certain intermediate regimes of rotational speeds, the flow profiles for different hematocrit levels are noticeably different. This, in turn, could be harnessed as a possible diagnostic signature of the hematocrit (or equivalently, packed cell volume) level, without necessitating the deployment of chemical consumables, in an energy efficient paradigm.

Evaluation of the acceptability and clinical utility of an Arabic-language mindfulness CD in an Australian community setting.

The cultural, linguistic, and religious diversity of Australia's population presents challenges for mental health service delivery. Arabic-speaking communities in Australia underutilise mental health services despite high levels of trauma and psychological distress. Clinicians who work with this population lack linguistically and culturally appropriate clinical resources. The aim of this study was to explore the acceptability and clinical utility of a Mindfulness Skills CD translated into formal Arabic. The 70 participants were Arabic-speaking adults, mostly Lebanese-born Muslim women, who enrolled in a 5-week mindfulness program using the CD and agreed to follow-up at 12 weeks. Both recruitment and data collection were undertaken by a female project officer who is a widely respected member of the Arabic community in south-east Sydney. Compliance with the program protocol was high and all but 4 participants continued to use the CD beyond the 5 weeks. Overall, participants reported that mindfulness techniques fitted well with their way of life and were compatible with their cultural and religious practices. Most found mindfulness complementary to their regular reflective prayer. Using the Mindfulness Skills CD was associated with statistically significant reductions in psychological distress as measured by the Kessler Scale (K10) and the Depression, Anxiety, and Stress Scale (DASS21) postprogram (K10; DASS21 Depression and Stress subscales) and at follow-up (all measures). The evaluation showed that the Arabic Mindfulness Skills CD is an effective and culturally appropriate mental health resource for this population group. This low-cost, easily distributed resource is suitable for use in individual self-management and as an adjunct to primary and specialist mental health care.

Identifying radon priority areas and dwellings with radon exceedances in Bulgaria using stored CD/DVDs.

The implementation of the 2013/59/EURATOM directive in the part related to radon exposure imposes challenges for radon measurement methodology and radon survey design. Among them is the need to have estimates (preferably direct) of the annual average radon concentrations, which can be directly compared to the recommended reference levels. On this basis, the surveys should make possible the identification of dwellings with indoor radon above the reference levels and "radon priority areas" where significant proportion of the dwellings falls in this category. The performance of the CD/DVD method for radon measurements as a tool to address these issues is presented. A recent large scale field study based on the CD/DVD method that was carried out in the suburb area of Sofia, Bulgaria is described. Part of the studied area was affected in the past by the uranium mining and milling industry. In total 462 disks (CDs and DVDs) taken from 335 private dwellings from 10 districts in the region were analyzed. The results revealed the large heterogeneity in radon distribution in the area, with the percentage of dwellings with a 222Rn level above 300 Bq m-3 ranking from about 7% to 74%. The district of Yana, for which this percent was 74, was identified as the area of highest radon priority in the region. The paper also discusses how prompt identification of dwellings with radon above the reference level by CD/DVDs can be incorporated within an integrated approach to the radon problem. Within this approach the radon hazard is identified shortly after the stakeholder's decision to test, which allows fast solution of the problem without waiting the long (and usually demotivating) one-year period needed for direct results by the commonly used prospective methods.

Hacking CD/DVD/Blu-ray for Biosensing.

The optical pickup unit (OPU) within a CD/DVD/Blu-ray drive integrates 780, 650, and 405 nm wavelength lasers, diffraction-limited optics, a high-bandwidth optoelectronic transducer up to 400 MHz, and a nanoresolution x-, z-axis, and tilt actuator in a compact size. In addition, the OPU is a remarkable piece of engineering and could enable different scientific applications such as sub-angstrom displacement sensing, micro- and nanoimaging, and nanolithography. Although off-the-shelf OPUs can be easily obtained, manufacturers protect their datasheets under nondisclosure agreements to impede their availability to the public. Thus, OPUs are black boxes that few people can use for research, and only experienced researchers can access all their functions. This review details the OPU mechanism and components. In addition, we explain how to utilize three commercially available triple-wavelength OPUs from scratch and optimize sensing quality. Then, we discuss scientific research using OPUs, from standard optical drive-based turnkey-biomarker array reading and OPU direct bioapplications (cytometry, optical tweezing, bioimaging) to modified OPU-based biosensing (DNA chip fluorescence scanning, biomolecular diagnostics). We conclude by presenting future trends on optical storage devices and potential applications. Hacking low-cost and high-performance OPUs may spread micro- and nanoscale biosensing research from research laboratories to citizen scientists around the globe.

A Breast Cancer Education Program for D/deaf Women.

Barriers to obtaining breast cancer prevention knowledge and breast cancer screening have been noted among D/deaf women. A randomized controlled trial (RCT) is described that tested a culturally and linguistically tailored breast cancer education program conducted among a racially/ethnically diverse sample of 209 D/deaf women age 40 years or older. The study focused on D/deaf women with no more than a secondary education, a population at relatively high risk for incomplete breast health knowledge and services. This population's inadequate breast cancer knowledge and screening practices and the value of the education program were confirmed. Knowledge increased from -baseline to 12-month follow-up in the intervention group, and in some instances the control group; increased intention to get a mammogram was observed in the intervention group. Possible reasons for the few significant intervention/control group differences at 12 months were examined. Materials from the RCT are available online.

RADON-222 IN SOIL-GAS MEASUREMENTS BY COMPACT DISCS. COMPARISON TO DIFFUSION CHAMBER MEASUREMENTS.

This work presents the results from simultaneous measurements of 222Rn in soil-gas by compact discs (CDs) and diffusion chambers. The measurements were performed in three terrains with high, medium and low 222Rn-in-soil-gas concentrations. Good correlations between the CD measurements and the reference diffusion chamber measurements are observed. The results indicate that it is important to apply temperature correction in the CD measurements, in order to account for the actual temperature during the exposure of the CDs in the soil.

Rapid Enzyme-linked Immunosorbent Assays for Diagnosis of Diabetes in a Compact Disc-shaped Microfluidic Device.

We have developed a compact disc (CD)-shaped microfluidic device for multiple, rapid enzyme-linked immunosorbent assays (ELISA). The device has a versatile design that can be adapted for the detection of various proteins by selecting the push-in-type reaction parts and appropriate reagents for each target. In this paper, we report the rapid quantification of insulin, adiponectin, and leptin, which can be used for the early diagnosis of diabetes, in human serum in only 16 min with our device.

The EAST-Dem study: a pilot cluster randomized controlled trial.

ABSTRACTWe recruited eight general practice (GP) practices for a pilot cluster randomized controlled trial (RCT) of a digital versatile disc/leaflet encouraging South Asian people to seek timely help for memory problems. Primary outcomes were feasibility (proportion of patients expressing interest, consenting) and acceptability. Seventy-eight of one hundred and two (76%) potential participants consented; 76/78 (97%) were followed-up. Thirty-seven of forty-one (90%) receiving the intervention rated this acceptable. Only 17/41 (41%) accessed it; they appeared then to be more likely to seek timely help. The intervention was acceptable and feasible but a full-scale RCT would be very expensive. It may be proportionate to make this intervention available without a full-scale RCT.

Compromise of Radiology Studies From Nonstandardized Viewing Platforms.

There is no standardization of proprietary radiology viewing software platform functions allowing recorded digital radiographic imaging studies on compact discs (CDs) to be viewed in a standardized manner at subsequent institutions. Primary concerns include the following: (1) a large number of image viewing software platforms with a wide variety of features making familiarity with use difficult, (2) an inordinate amount of time required to load imaging data, (3) imaging data may not upload or be viewed with the care center's picture archiving and communication system, (4) navigation through imaging studies is inconsistent and tedious, and (5) image viewing requires additional software downloads. Additionally, images generated from "outside CDs" are frequently of low quality and resolution, eliminating the ability to render a reliable diagnosis. The authors sought to determine the frequency and extent of these functional problems by analyzing a sample of 50 consecutive radiology CDs containing imaging studies referred to a university orthopedic oncology practice. Eighteen different viewing software platforms were encountered. Only 24 (48%) of the CDs met all optimal system criteria. Mean time required to load the studies was 3.4 seconds using the picture archiving and communication system and 37.9 seconds using the proprietary viewing software (P<.001). Fifteen (30%) of the CDs did not upload to the institution's picture archiving and communication system, and 18 (36%) required additional downloads and/or license agreements. Four CDs did not contain Digital Imaging and Communications in Medicine images. Physicians using radiology studies on CDs encounter numerous difficulties in evaluating patients' imaging data because of the plethora of viewing software platforms. These difficulties add time and cost and compromise patient care. [Orthopedics. 2018; 41(1):e136-e141.].

Comparison of gut-directed hypnotherapy and unspecific hypnotherapy as self-help format in children and adolescents with functional abdominal pain or irritable bowel syndrome: a randomized pilot study.

OBJECTIVE: Psychosocial treatments for chronic abdominal pain in childhood or adolescence are effective, but time consuming and hardly available. In the present study, gut-directed hypnotherapy (GDHT) and unspecific hypnotherapy (UHT) were compared to evaluate the feasibility and efficacy of a hypnotherapeutic self-help intervention. PARTICIPANTS AND METHODS: Children/adolescents between 6 and 17 years of age with chronic abdominal pain were randomized to GDHT or UHT. The treatment period was 12 weeks each. Measurements were performed before and after treatment. The primary outcome was a pain diary. Analysis was carried out as per protocol. RESULTS: Of 45 participants included, 13 were lost to follow-up. Thirty-two participants (14 GHDT, 18 UHT) were analyzed. Dropouts had higher pain severity. Completers in both conditions showed good adherence and a similar decrease in days with pain and pain duration. Pain intensity decreased only in the UHT condition. Eleven participants (two GDHT, nine UHT) achieved clinical remission (>80% improvement) and 13 participants (seven GDHT, six UHT) improved significantly (30-80%). CONCLUSION: Results suggest a high efficacy of standardized home-based hypnotherapy for children/adolescents with abdominal pain. Children/adolescents with high pain severity are at risk of dropping out. The UHT condition showed slight evidence of superiority, but conditions were equivalent on most outcomes. Taken together, self-help approaches based on hypnotherapy could close a treatment gap and prevent chronification.

Effectiveness of training patients using DVD in the accurate use of inhalers for the treatment of bronchial asthma.

BACKGROUND: Inhalants are the standard treatment for patients with bronchial asthma. Inaccurate inhaler use leads to inadequate therapeutic effects and unnecessary dosage increases. However, it is a challenge for practitioners to master the various devices available and train patients on the accurate use of inhalers. Thus, establishing a system to instruct patients on how to accurately use inhalers is essential. We prepared a DVD and accompanying user manual explaining the operation of each inhaler device used in Japan. This pilot study aimed to examine the efficacy of these materials. METHODS: The subjects were 33 outpatients with bronchial asthma who received treatment in our facility for asthma and had already received conventional inhalant training. The oral medication and inhalants used by the patients were not changed. The patients were randomly assigned to a DVD viewing group or non-viewing group; various parameters were comparatively examined after 4 weeks. RESULTS: Significant improvements in Asthma Control Test scores, inhalation technique, forced vital capacity, forced expiratory volume in 1 s, impulse oscillometry resonant frequency, and induced sputum eosinophil count were observed in the DVD viewing group at 4 weeks post training. CONCLUSIONS: Pulmonary function and inflammatory parameters improved significantly in the DVD viewing group. These findings suggest that unnecessary step-up of asthma treatment can be avoided, leading to treatment cost reduction. Training patients with asthma in accurate inhaler use improves quality of life and therefore has great clinical significance. Hence, this method should be used more extensively in Japan and worldwide.

Use of a CD laser pickup head to fabricate microelectrodes in polymethylmethacrylate substrates for biosensing applications.

In this work, we report a simple fabrication method for microelectrodes on a polymethylmethacrylate substrate, using a low-cost laser platform based on a CD-DVD unit for direct rapid-prototyping. We used this laser microfabrication technique to etch any desired design on polymethylmethacrylate substrates to produce microchannels with controlled geometry, with a highly repeatable micron-scale resolution. Those shallow microchannels were then filled with a conductive paste of material of our choice that was converted into microelectrodes of desired shapes and geometries after drying. To validate our process, different geometries, sizes and materials were used as electrodes, and then tested for amperometry and impedance measurements. Development of these microelectrodes is motivated by their potential application in sensors and biosensors, such as glucose and cell counting, as demonstrated in this paper.