Collection Kit Research Articles

Protocol for a national probability survey using home specimen collection methods to assess prevalence and incidence of SARS-CoV-2 infection and antibody response

PurposeThe U.S. response to the SARS-CoV-2 epidemic has been hampered by early and ongoing delays in testing for infection; without data on where infections were occurring and the magnitude of the epidemic, early public health responses were not data-driven. Understanding the prevalence of SARS-CoV-2 infections and immune response is critical to developing and implementing effective public health responses. Most serological surveys have been limited to localities that opted to conduct them and/or were based on convenience samples. Moreover, results of antibody testing might be subject to high false positive rates in the setting of low prevalence of immune response and imperfect test specificity. MethodsWe will conduct a national serosurvey for SARS-CoV-2 PCR positivity and immune experience. A probability sample of U.S. addresses will be mailed invitations and kits for the self-collection of anterior nares swab and finger prick dried blood spot specimens. Within each sampled household, one adult 18 years or older will be randomly selected and asked to complete a questionnaire and to collect and return biological specimens to a central laboratory. Nasal swab specimens will be tested for SARS-CoV-2 RNA by RNA PCR; dried blood spot specimens will be tested for antibodies to SARS-CoV-2 (i.e., immune experience) by enzyme-linked immunoassays. Positive screening tests for antibodies will be confirmed by a second antibody test with different antigenic basis to improve predictive value of positive (PPV) antibody test results. All persons returning specimens in the baseline phase will be enrolled into a follow-up cohort and mailed additional specimen collection kits 3 months after baseline. A subset of 10% of selected households will be invited to participate in full household testing, with tests offered for all household members aged ≥3 years. The main study outcomes will be period prevalence of infection with SARS-CoV-2 and immune experience, and incidence of SARS-CoV-2 infection and antibody responses. ResultsPower calculations indicate that a national sample of 4000 households will facilitate estimation of national SARS-CoV-2 infection and antibody prevalence with acceptably narrow 95% confidence intervals across several possible scenarios of prevalence levels. Oversampling in up to seven populous states will allow for prevalence estimation among subpopulations. Our 2-stage algorithm for antibody testing produces acceptable PPV at prevalence levels ≥1.0%. Including oversamples in states, we expect to receive data from as many as 9156 participants in 7495 U.S. households. ConclusionsIn addition to providing robust estimates of prevalence of SARS-CoV-2 infection and immune experience, we anticipate this study will establish a replicable methodology for home-based SARS-CoV-2 testing surveys, address concerns about selection bias, and improve positive predictive value of serology results. Prevalence estimates of SARS-CoV-2 infection and immune experience produced by this study will greatly improve our understanding of the spectrum of COVID-19 disease, its current penetration in various demographic, geographic, and occupational groups, and inform the range of symptoms associated with infection. These data will inform resource needs for control of the ongoing epidemic and facilitate data-driven decisions for epidemic mitigation strategies.

Exploring alternative swabs for use in SARS-CoV-2 detection from the oropharynx and anterior nares

The COVID-19 pandemic has led to a worldwide shortage of nasopharyngeal swabs and universal transport media. This study evaluated a combined oropharynx/nares (OP/Na) sample collection using two readily-available non-flocked swabs, transported in phosphate-buffered saline, and demonstrates equivalent performance in SARS-CoV-2 detection compared to a previously-validated OP/Na collection kit.

SARS-CoV-2 detection in setting of viral swabs scarcity: Are MRSA swabs and viral swabs equivalent?

The global pandemic of Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV2) has resulted in unprecedented challenges for healthcare systems. One barrier to widespread testing has been a paucity of traditional respiratory viral swab collection kits relative to the demand. Whether other sample collection kits, such as widely available MRSA nasal swabs can be used to detect SARS-CoV-2 is unknown. We compared simultaneous nasal MRSA swabs (COPAN ESwabs ® 480C flocked nasal swab in 1mL of liquid Amies medium) and virals wabs (BD H192(07) flexible mini-tip flocked nasopharyngeal swabs in 3mL Universal Transport Medium) for SARS-CoV-2 PCR testing using Simplexa COVID-19 Direct assay on patients over a 4-day period. When the results were discordant, the viral swab sample was run again on the Cepheid Xpert Xpress ® SARS-CoV-2 assay. Of the 81 included samples, there were 19 positives and 62 negatives in viral media and 18 positives and 63 negative in the MRSA swabs. Amongst all included samples, there was concordance between the COPAN ESwabs ® 480C and the viral swabs in 78 (96.3%). We found a high rate of concordance in test results between COPAN ESwabs ® 480C in Amies solution and BD H192(07) nasopharyngeal swabs in in 3 mL of Universal Viral Transport medium viral media. Clinicians and laboratories should feel better informed and assured using COPAN ESwabs ® 480C to help in the diagnosis of COVID-19.

TSLP and IL-7R Variants Are Associated with Persistent Atopic Dermatitis

TSLP and IL-7R Variants Are Associated with Persistent Atopic Dermatitis

Covid-19 preparedness and response: experiences of the Nigerian Institute for Medical Research

The global community is facing a health crisis caused by coronavirus disease 2019 (COVID-19). The coronavirus pandemic is severely disrupting the global economy. Countries are battling to slow the spread of the virus by testing, employing contact tracing, restricting travel, quarantining citizens, and encouraging use of face mask, hand hygiene and social distancing measures. The lockdown imposed in many countries including Nigeria has resulted in increased cost and shortages of reagents and supplies worldwide. Due to the highly contagious nature of the disease, rapid rate of spread, and lack of an effective therapy, it became necessary for nations of the world to mount an efficient response mechanism to curb the spread of the pandemic. The Nigerian Institute of Medical Research (NIMR) has responded actively to the current pandemic with some innovations with respect to sample collection systems, molecular diagnostics, kit development and validation. Due to the highly infectious nature of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) the causative agent of COVID-19, the institute also invested in the production of infection control tools. The extent of response by the institute would not have been possible but for collaboration and partnership with well-meaning organizations and stakeholders. National, State and public cooperation are very essential for effective response to any pandemic. The response of NIMR to the pandemic is herein discussed. Lessons learned and recommendations made are also shared to help institutions interested in combating this and future pandemics of similar nature.

Abstract A057: Biospecimen donation among breast cancer survivors: Opportunities for research among nondonors

Abstract Purpose: Participation in genomic research may further advance effective therapies, yet samples are often not sociodemographically diverse. Information is lacking about strategies to improve biospecimen donation. This pilot study focused on identifying strategies to enhance biospecimen donation among nondonors. Methods: Women diagnosed with hormone receptor-positive (HR+) breast cancer who initiated hormonal therapy were recruited from three integrated health systems. Our sample was limited to women >21 years of age and diagnosed within the past 12 months. The analytical sample (N=144) consisted of women who consented but did not return a saliva sample within one year of baseline; 67% were White, 27% were Black, and 2% represented other races. A brief informational intervention was developed via published literature and preliminary data. Respondents received intervention materials, which included a personalized information letter, a colorful low-literacy instruction sheet, a postage-paid envelope, and collection kits. Descriptive and bivariate statistics were employed to describe and compare factors associated with biospecimen donation. Results: Overall, 29 surveys (20%) were returned, and 17% returned saliva kits. No significant differences were noted by demographic or clinical factors between those who provided biospecimen (vs. not). Women with higher levels of functional well-being and lower ratings of religiosity/spirituality were more likely to return specimens (p <0.005) after receiving the enhanced materials. The most frequently cited factors related to returned specimens were found among participants with higher levels of knowledge and concern about provision of saliva and the usability of biospecimen samples in biomedical research. Conclusion: A brief print intervention inclusive of personalized messages may enhance receipt of biospecimens among diverse survivors. The inclusion of messages with a focus on spirituality and functional wellness may increase biospecimen provision among nondonors; however, further work is needed to support this claim. Citation Format: Arnethea Sutton, Vanessa Sheppard, Megan C. Edmonds, Yvonne Cummings, Justin Thomas, Jessica Chavis. Biospecimen donation among breast cancer survivors: Opportunities for research among nondonors [abstract]. In: Proceedings of the Eleventh AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2018 Nov 2-5; New Orleans, LA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(6 Suppl):Abstract nr A057.

4429 Powering precision medicine research with the efficient construction of large diverse cohorts

OBJECTIVES/GOALS: There is an imperative need to initiate translational genetic studies of hidradenitis suppurativa (HS). Such work requires large cohorts and no HS registries exist. Precision medicine initiatives provide new resources and methods for efficiently constructing cohorts, but empirically informed best practice guidelines are needed. METHODS/STUDY POPULATION: Traditional methods for building cohorts rely on clinical encounters to identify patients and collect phenotype data. Precision medicine initiatives aim to decrease the time and cost of data collection by using alternative sources, including electronic health records (EHR) and remote collection of patient-reported data. The public’s use of the Internet to obtain and exchange health-related information coupled with the success of direct-to-consumer genetic companies suggests that it is feasible to remotely ascertain research participants for genetic studies. Importantly, Internet cohorts provide an opportunity to include research participants who are disconnected from healthcare, and thus remain hidden from research that relies on EHR or clinical services. RESULTS/ANTICIPATED RESULTS: First, to conduct studies in EHR we are developing an analytic pipeline for the automated extraction of an accurate HS diagnosis using natural language processing of clinical notes. In our preliminary work we are also using ICD codes to build cohorts in two EHR systems with and without linked genetic data. Second, we have developed Internet advertising campaigns for symptom-based recruitment. Informed consent and patient-reported data is collected on-line through a series of short surveys. Patients who complete the surveys and express interest in participating in genetic studies are sent saliva collection kits and return mailing material. Finally, we have established an HS biobank that has DNA from 300 participants identified through clinical services. Enrollment is on going. DISCUSSION/SIGNIFICANCE OF IMPACT: Our goal is to assemble an HS cohort that is large enough to power genetic discoveries. Our work is generating empirical evidence for precision medicine guidelines and will improve our knowledge about HS. The methods we are developing can be applied to efficiently create new cohorts for genetic studies of other diseases across different clinical areas.

0039 The Clinical Utility of Dim Light Melatonin Onset in Treatment of Delayed Sleep-Wake Phase Disorder: Preliminary Findings

Abstract Introduction Delayed sleep-wake phase disorder (DSWPD) is common, debilitating, and challenging to treat. In an ongoing randomized trial, we are comparing exogenous melatonin treatment outcomes in DSWPD participants for whom dim light melatonin onset (DLMO) is measured objectively vs. estimated. Methods Thus far, 13 participants (27±6 years old, 67% female) have completed a randomized, controlled, double-blind 4-week trial of 0.5 mg of exogenous melatonin timed to either 3 h before measured DLMO (M-DLMO, n = 6) or 3 h before DLMO estimated at 2 h before average sleep onset time based on at least 7 days of wrist actigraphy and sleep diary (E-DLMO, n = 7). All participants met International Classification of Sleep Disorders-3 diagnostic criteria for DSWPD and were otherwise healthy. Participants completed 4 weekly treatment sessions with a blinded psychologist; time of melatonin administration and bed-rise schedule were advanced up to 1 h/week. A validated home saliva collection kit measured DLMO in all participants. Between-group t-tests and Hedges’ g effect sizes (ES) were calculated at post-treatment for the following outcomes: DLMO; Pittsburgh Sleep Quality Index (PSQI) global score; Morningness-Eveningness Questionnaire (MEQ); and the actigraphy parameters sleep efficiency (SE) and clock time of sleep onset and offset. A paired-sample t-test compared the measured vs. estimated DLMO at baseline. Results The M-DLMO group had a 65±88 mins DLMO advance vs. 27±30 mins in the E-DLMO group (ES=0.51 p=.381). PSQI scores were similar between groups (M-DLMO=6.67±2.06, E-DLMO=7.1± 1.57, ES=-0.24, p=.646), as were MEQ scores (M-DLMO=43±4.98, E-DLMO=48±12.72, ES=-0.47, p=.387). Sleep onset time (M-DLMO=0:32±1:02, E-DLMO=0:31±1:38, ES=0.01, p=.98) and offset time (M-DLMO=8:05±1:03, E-DLMO=8:08±2:14, ES=-0.02, p=.968) were similar between the groups, although sleep was more efficient in M-DLMO vs. E-DLMO (84%±3% vs. 76%±10%, ES=0.94, p=.096). On average, baseline measured DLMO occurred 123±83 mins earlier than estimated DLMO (p=.001). Conclusion We are continuing to enroll participants in this trial. Preliminary results suggest some potential benefit of measuring the DLMO, but results will need to be clarified in a larger sample. Support American Sleep Medicine Foundation Strategic Research Award

BARCODE 1: A pilot study investigating the use of genetic profiling to identify men in the general population with the highest risk of prostate cancer to invite for targeted screening.

1505 Background: Genetic profiling could be used to target population screening for prostate cancer (PrCa). Approximately 170 single nucleotide polymorphisms (SNPs) have been identified that associate with PrCa development. Although these confer a low to moderate risk of PrCa, the risk is cumulative with increasing number of risk alleles. BARCODE1 is the first study to prospectively investigate the use of a genetic profile in PrCa screening in the UK general population. Methods: A custom Eurek Genomics (EG) SNP assay was developed. Healthy males aged 55-69 were invited to participate via their General Practitioners (GPs). Saliva samples were collected via mailed collection kits. After DNA extraction, genotyping was conducted using the EG assay and a polygenic risk score (PRS) was calculated for each participant. The PRS was calculated using the sum of the weighted alleles for 130 risk loci. Men in the top 10% of the genetic risk profile were invited for prostate MRI and biopsy at the Royal Marsden Hospital (RMH) in London. Results: Invitation letters were sent to 1434 men; overall uptake was 26% (range 13%-47%). 87% of responders were eligible for study entry. DNA was extracted from 303 samples and genotyped. Data were available for 285 men following QC. Mean PRS was 10.33 with a standard deviation of 0.64; twenty-five participants with a PRS above the 90th centile were identified for screening with MRI and prostate biopsy. Of these men (after exclusions due to medical comorbidity/invitations declined) 9 out of 20 had an abnormal MRI (45%) and 18 men underwent biopsy with 7 diagnoses of PrCa (38.8%). All cancers were low-risk with a mean PSA of 1.8 and were managed with Active Surveillance (AS). There were two adverse events following biopsy, both simple lower urinary tract infections managed with oral antibiotics. Average duration of follow-up is 4.5 months (range 1-11). Conclusions: Successful completion of recruitment has shown this community study to be feasible, with an average uptake of 26%. Approximately 70 GP sites have been identified to allow a transition to the full BARCODE-1 study which will recruit 5000 men. The use of genetic profiles to guide PrCa screening is attractive; it requires a one-off test utilising germline DNA which can be assessed for risk loci which are constant, unlike PSA which fluctuates. The results of the BARCODE1 study will be important in defining the role of genetic profiling in targeted PrCa population screening.

Hybrid cord blood banks may be advantageous for scientific as well as economic reasons

Background & Aim BACKGROUND AND AIM: Public cord blood banks have thresholds for accepting cord blood unit (CBU) collections for processing based on economic models developed using surrogate markers of suitability, i.e. volume and total nucleated cell count (TNCC). Only after processing has it been possible to look at CD34+ cell numbers and colony forming units (CFU). Since as few as 0.52 × 105 CD34+ cells can be expanded in vitro and used successfully for transplant, it is important to understand what is in the smaller collections that public bank guidelines currently prevent from being processed. Hybrid public/private cord blood banks permit economic support from the private bank to help support the public bank. They also offer an opportunity to evaluate products outside public banking thresholds because all collections are processed. AIM To present data from the first 72 private cord blood unit (CBU) collections processed for the Cord Blood Bank of Arkansas, showing the relationship between collection volume, TNCC and CD34+ cell numbers. Methods, Results & Conclusion METHODS: The CBBA is a hybrid bank, providing cord blood banking for public, private and research use. Parents are informed of the different options for banking available, document their informed consent, and then receive a collection kit to bring to the delivering obstetrician. Cord blood is collected with the placenta in utero using Pall model # 791-08 collection kits. Collections are processed within 72 h of collection at a central site with plasma and red cells removed. Pre-processing TNCC are performed with a Beckman Coulter Ac.T Diff2 cell counter and TNCC determined as follows: actual cord blood weight x WBC 103/100=TNCC. Flow cytometry is performed using the ISHAGE technique with a Beckman Coulter CytoFLOW. RESULTS Mean maternal age for CBU was 34y (range 26-45). Of 72 CBU donated (37 male, 35 female), delivery route was spontaneous vaginal for 50 (69.45%) and caesarian section for 22 (30.55%). Mean birth weight was 3341.5 g (median 3355; range 2296-4337). Mean gestational age was 38.92 weeks (median 39; range 36-41.14). CONCLUSION Data on hematopoietic potential of low volume/low TNCC products are currently available only from a hybrid or private bank. Here we show that CBU below threshold TNCC and volume for public banks can have a significant number of CD34+ cells available for expansion and use in transplant.

Detection of SARS-CoV-2 RNA and Antibodies in Diverse Samples: Protocol to Validate the Sufficiency of Provider-Observed, Home-Collected Blood, Saliva, and Oropharyngeal Samples.

BackgroundThe response in the United States to the coronavirus disease (COVID-19) pandemic has been hampered by a lack of aggressive testing for the infection. Testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cornerstone of an effective public health response. However, efforts to test have been hampered by limited reagents, limitations in the availability of swabs used for the collection of nasopharyngeal swab (NPS) specimens, limitations in personal protective equipment (PPE) for health care providers collecting the NPS specimens, and limitations in viral transport media for transporting the specimens. Therefore, more flexible options for screening for SARS-CoV-2 RNA and serologic responses are critical to inform clinical and public health responses.ObjectiveWe aim to document the ability of patients to self-collect sufficient specimens for SARS-CoV-2 viral detection and serology.MethodsPatient self-collection of samples will be done with observation by a health care provider during a telemedicine session. Participants will be mailed a specimen collection kit, engage in a telehealth session with a provider through a HIPPA (Health Insurance Portability and Accountability Act of 1996)-compliant video meeting, and collect specimens while being observed by the provider. Providers will record whether they are confident in the suitability of the specimen for laboratory testing that would inform clinical decision making. We will objectively assess the sufficiency of biological material in the mailed-in specimens.ResultsThe protocol was approved by the Emory University Institutional Review Board (IRB) on March 30, 2020 (Protocol number 371). To date, we have enrolled 159 participants.ConclusionsDefining a conceptual framework for assessing the sufficiency of patient-collected samples for the detection of SARS-CoV-2 RNA and serologic responses to infection is critical for facilitating public health responses and providing PPE-sparing options to increase testing. Validation of alternative methods of specimen collection should include objective measures of the sufficiency of specimens for testing. A strong evidence base for diversifying testing modalities will improve tools to guide public health responses to the COVID-19 pandemic.

Abstract B13: Development of a low-cost method for collecting fecal samples in clinical trials

Abstract Although immune checkpoint inhibitors (ICIs) have shown promise in treating various cancers, fewer than half of patients with most tumor types experience a durable response. Thus, there is a need for biomarkers to better predict outcomes. Recent studies suggest that the presence of a handful of microbial species and greater alpha-diversity in the gut may serve as a biomarker for and might facilitate ICI responses. However, the specific bacteria, or bacterial communities, that associate with improved ICI responses vary across study populations, and the factors that contribute to these discrepant findings remain elusive. Thus, a standardized method by which biospecimens may be collected, transported, and stored for gut microbiome studies in the context of ICI therapy is needed. In this study, we evaluated a method for shipping fecal samples using a low-cost (<$3.00) ThinPrep Pap Test® methanol-based preservative kit. Under an IRB-approved protocol, we recruited patients with melanoma, Merkel cell carcinoma, endometrial cancer, and non-small cell lung cancer who had experienced >1 year of durable tumor response after ICI therapy. Patients were provided with stool collection kits and either asked to collect fecal samples at home within 48 hours of their clinic visit and store at 4°C (fresh) or asked to place stool in preservative and ship at ambient temperature to our laboratory (fixed). For fresh samples, a portion of each sample was frozen and another portion placed into preservative as a paired control. DNA was extracted using Zymo Quick-DNA™ Fecal/Soil Microbe kit. For fixed samples, methanol was removed by evaporation prior to DNA extraction. Microbial composition was analyzed with 16S rRNA amplicon sequencing with V1-V2 primers with 150bp paired-end sequencing using an Illumina platform. Among n=10 samples collected in clinic, fixed portions demonstrated decreased alpha-diversity and a uniform shift in beta-diversity compared to the paired frozen portions. In all fixed samples, Faecalibacterium and Roseburia relative abundance decreased with a corresponding increase in Bacteroides. Among a second set of n=11 samples that were placed in preservative by patients and then shipped to our laboratory, we analyzed the effects of shipping by comparing fresh stool samples and shipped fixed samples collected by the same patient within one month. The data revealed similar trends, suggesting that fixation, rather than shipping, drives the overall effect. We are currently verifying the relative abundance of specific bacterial species in both sets of samples using quantitative RT-PCR. Our data show that methanol-based preservation must be optimized prior to clinical utilization for accurate assessment. If optimized, we have identified a low-cost method to collect fecal samples that could be adopted in community practices and low-income areas. Ongoing work from our group includes optimization of processing procedures, ratio of fecal matter to preservative, and storage conditions. Citation Format: Kimberly E. Peloza, Joell J. Gills, Fyza Y. Shaikh, James R. White, Sara Glass, Carisse Lansiquot, Courtney Stevens, William Assan, William H. Sharfman, Dung T. Le, Jarushka Naidoo, Evan J. Lipson, Drew M. Pardoll, Cynthia L. Sears. Development of a low-cost method for collecting fecal samples in clinical trials [abstract]. In: Proceedings of the AACR Special Conference on the Microbiome, Viruses, and Cancer; 2020 Feb 21-24; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2020;80(8 Suppl):Abstract nr B13.

Salivary Leptin and Chemerin; a novel way of gestational diabetes screening

Introduction Oral glucose tolerance testing (OGTT) is the recommended approach for the diagnosis of gestational diabetes mellitus (GDM). Leptin and chemerin are two examples of hormones from adipokine family, which mostly takes part in glucose metabolism and inflammatory processes. We aim to find a possible new and tolerable screening technique for GDM using salivary levels of leptin and chemerin. Material and method Saliva samples of pregnant patients, on their 24–28th weeks of gestation, are collected via saliva collection kit. Leptin and chemerin ELISA tests were run from serum samples being hold at -80 °C following their thawing session. Patients are divided into two groups depending on their GDM status. OGTT results of patients are compared with their ELISA results. Results ELISA study for leptin showed an insignificant difference between patients with GDM and patients without where the values were 0.44 ± 0.33 and 0.34 ± 0.24 respectively (p: 0.155). Chemerin study revealed a significant difference between patients with GDM and without 631.06 ± 344.42, 334.81 ± 244.91 respectively (p < .001). Conclusion Leptin and chemerin can be detected in saliva. Chemerin levels are significantly higher in patients with GDM, thus this knowledge can be used to develop a new screening method for OGTT.

Antenatal depression and its potential causal mechanisms among pregnant mothers in Gondar town: application of structural equation model

BackgroundVarious forms of life stressors have been implicated as causes of antenatal depression. However, there is a lack of understanding of which forms of stress lead to antenatal depression and through what mechanisms. Modeling stress processes within a theoretical model framework can enhance an understanding of the mechanisms underlying relationships between stressors and stress outcomes. This study used the stress process model framework to explore the causal mechanisms underlying antenatal depression in Gondar, Ethiopia.MethodsQuestionnaires, using an Online Data collection Kit (ODK) tool were administered face-to-face in 916 pregnant women in their second and third trimesters. Pregnant women were included from six randomly selected urban districts in Gondar, Ethiopia during June and August 2018. The Edinburgh Postnatal Depression Scale (EPDS) was used to screen for antenatal depression. A Structural Equation Model (SEM) was employed to explore the direct, indirect, and total effect of stressors and mediators of antenatal depression.ResultSixty-three participants (6.9%) reported symptoms of depression. Of these, 16 (4.7%) and 47 (8.1%) were in their second and third trimesters, respectively. The SEM demonstrated several direct effects on antenatal depression scores including unplanned pregnancy (standardized β = 0.15), having a history of common mental health disorder (standardized β = 0.18) and fear of giving birth to the current pregnancy (standardized β = 0.29), all of which were associated with a higher depression score. Adequate food access for the last 3 months (standardized β = − 0.11) was associated with decreased depression score. Social support (β = − 0.21), marital agreement (β = − 0.28), and partner support (β = −.18) appeared to partially mediate the link between the identified stressors and the risk of antenatal depression.ConclusionBoth direct and indirect effects contributed to higher antenatal depression score in Ethiopian women. The three psychosocial resources namely marital agreement, social and partner support, mediated reduced antenatal depression scores. Early screening of antenatal depression and enhancing the three psychosocial resources would help to improve maternal resilience.

13C-caffeine breath test identifies single nucleotide polymorphisms associated with caffeine metabolism

We performed a caffeine (N-3-methyl-13C) breath test (CafeBT) to determine whether it can be employed to identify caffeine metabolism-associated single nucleotide polymorphisms. The study included 130 healthy adults (mean age: 21.9 years). Saliva was collected using an Oragene®•DNA saliva collection kit. Breath samples were collected from the subjects. The subjects orally ingested 100 mg 13C-caffeine dissolved in distilled water. Subsequently, breath samples were collected in bags every 10 min for a total of 90 min. An analysis of 13CO2 in the expired breath was performed by infrared spectroscopy, and the sum of Δ13CO2 over 90 min (S90m) was calculated. DNA from saliva samples was genotyped using TaqMan® SNP Genotyping for the following genes: cytochrome P4501A2: rs762551, rs2472297, aryl-hydrocarbon receptor (rs4410790), and adenosine A2A receptor (rs5751876). All subjects had the genotype CC in rs2472297 alleles. No significant difference was observed in S90m among the genotypes of rs762551 and rs5751876; however, a significant difference was found in S90m among the genotypes of rs4410790 (C > T). Our findings suggest that the N-3 demethylation of caffeine is dependent on the rs4410790 allele and that CafeBT may be used to determine rs4410790 genotypes.

Comparison of DNA stabilizers and storage conditions on preserving fecal microbiota profiles

Appropriate storage of fecal samples is a critical step for the unbiased analysis of microbial communities in metagenomic studies. Rapid freezing at -80°C is usually considered to be best practice, but this approach is challenging. DNA stabilizing kits may provide a more convenient method to preserve and store clinical samples. We evaluated the reliability of two collection kits (Stratec stool collection tube with stabilizer, #1038111200 and OMNIgene.GUT OMR-200) on preserving fecal microbiota. Samples were collected from two locations of the fecal specimen, in four healthy volunteers. The samples were sub-aliquoted and stored in a -80°C freezer, in Stratec and OMNIgene.GUT (incubation at ambient temperature for 0, 3, or 7 days). The fecal microbial composition was assessed by 16S rRNA sequencing. We found that alpha diversity was not significantly affected by storage conditions. Samples stored in DNA stabilizers were still representative of the original microbial community after 7 days at ambient temperature. Individual differences were found to have a greater contribution to the differences in microbial community composition than storage conditions or sampling location. Samples subjected to stabilizers displayed microbial community shifts compared with immediately frozen samples. A linear discriminant analysis effect size (LEfSe) analysis showed that the relative abundances of Faecalibacterium were significantly higher in samples stored in Stratec kits. Our study reveals that both Stratec and OMNIgene.GUT kits provide good microbiome preservation for up to 7 days in ambient temperature and would represent good options for fecal sample collection in large scale, population-based studies.

Efforts to improve diagnosis of bacteraemia by reducing blood culture contamination in an emergency department: strategies and outcome.

To assess the strategies and outcome for reducing blood culture contamination in order to improve the diagnosis of bacteraemia. The interventional study was conducted at a tertiary care hospital in Karachi from January 1, 2013, to December 31, 2016. The blood culture contamination data related to the first year of the study was taken as the baseline pre-intervention data. Strategies were planned as intervention for improvement by consolidating training and education in the form of dedicated lectures, practising on mannequins and developing in-house video, replacing povidone with 2% chlorhexidine preparation spray plus 70% isopropyl alcohol swabs and inducting dedicated phlebotomy team whose only responsibility was blood sample collection and minimising the probability of error. In 2013, there were 8868 samples; 7402 in 2014; 6897 in 2015; and 9756 samples in 2016. The contamination rate in 2013 was 8% which went down to 7.75% in 2014, 4.25% in 2015 and 3.9% in 2016. The decline became statistically significant (p<0.001) after implementing a dedicated phlebotomy team in the emergency department. Apart from teaching and training, the concept of blood culture collection kit with checklist and dedicated blood collection team was found to be vital in reducing blood culture contamination.

SPOCK, an R based package for high-throughput analysis of growth rate, survival, and chronological lifespan in yeast

Plate-reader based methods for high-throughput measurement of growth rate, cellular survival, and chronological lifespan are a compelling addition to the already powerful toolbox of budding yeast Saccharomyces cerevisiae genetics. These methods have overcome many of the limits of traditional yeast biology techniques, but also present a new bottleneck at the point of data-analysis. Herein, we describe SPOCK (Survival Percentage and Outgrowth Collection Kit), an R-based package for the analysis of data created by high-throughput plate reader based methods. This package allows for the determination of chronological lifespan, cellular growth rate, and survival in an efficient, robust, and reproducible fashion.

Sodium and Potassium Intakes and Cardiovascular Risk Profiles in Childhood Cancer Survivors: The SCCSS-Nutrition Study.

Risk of cardiovascular disease (CVD), common in childhood cancer survivors (CCSs), may be affected by diet. We assessed sodium (Na) and potassium (K) intake, estimated from food frequency questionnaires (FFQs) and morning urine spots, and its associations with cardiovascular risk in CCSs. We stratified CCSs into three risk profiles based on (A) personal history (CVD, CVD risk factors, or CVD risk-free), (B) body mass index (obese, overweight, or normal/underweight), and (C) cardiotoxic treatment (anthracyclines and/or chest irradiation, or neither). We obtained an FFQ from 802 and sent a spot urine sample collection kit to 212, of which 111 (52%) returned. We estimated Na intake 2.9 g/day based on spot urine and 2.8 g/day based on FFQ; the estimated K intake was 1.6 g/day (spot urine) and 2.7 g/day (FFQ). CCSs with CVD risk factors had a slightly higher Na intake (3.3 g/day), than CCSs risk free (2.9 g/day) or with CVD (2.7 g/day, p = 0.017), and obese participants had higher Na intake (4.2 g/day) than normal/underweight CCSs (2.7 g/day, p < 0.001). Daily Na intake was above, and daily K intake below, the national recommended levels. Adult survivors of childhood cancer need dietary assistance to reduce Na and increase K intake.

Accurate patient DLMO measurements facilitated by convenient at-home sample collection kits, cell-phone based app and robust salivary immunoassay

Accurate patient DLMO measurements facilitated by convenient at-home sample collection kits, cell-phone based app and robust salivary immunoassay