Hackflex library preparation enables low-cost metagenomic profiling.

Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/µL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

Hackflex library preparation enables low-cost metagenomic profiling.

Shotgun metagenomic sequencing provides valuable insights into microbial communities, but the high cost of library preparation with standard kits and protocols is a barrier for many. New methods such as Hackflex use diluted commercially available reagents to greatly reduce library preparation costs. However, these methods have not been systematically validated for metagenomic sequencing. Here, we evaluate Hackflex performance by sequencing metagenomic libraries from known mock communities as well as mouse fecal samples prepared by Hackflex, Illumina DNA Prep, and Illumina TruSeq methods. Hackflex successfully recovered all members of the Zymo mock community, performing best for samples with DNA concentrations <1 ng/uL. Furthermore, Hackflex was able to delineate microbiota of individual inbred mice from the same breeding stock at the same mouse facility, and statistical modeling indicated that mouse ID explained a greater fraction of the variance in metagenomic composition than did library preparation method. These results show that Hackflex is suitable for generating inventories of bacterial communities through metagenomic sequencing.

Home-site advantage for host species-specific gut microbiota.

Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here, we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wild-type (WT) and Rag1-knockout (Rag1-/-) house mice revealed widespread fitness advantages for native gut bacteria. Native bacterial lineages significantly outcompeted non-native lineages in both WT and Rag1-/- mice, indicating home-site advantage for native microbiota independent of host adaptive immunity. However, a minority of native Bacteriodetes and Firmicutes favored by selection in WT hosts were not favored or disfavored in Rag1-/- hosts, indicating that Rag1 mediates fitness advantages of these strains. This study demonstrates home-site advantage for native gut bacteria, consistent with local adaptation of gut microbiota to their mammalian species.

Applicants to a Special Education Advocacy Training Program: "Insiders" in the Disability Advocacy World.

Although social groups have "insiders," this construct has not been measured within the disability advocacy community. Examining 405 individuals who applied for an advocacy training program, this study examined the nature of insiderness within the disability advocacy community and ties to individual roles. Participants showed differences in mean ratings across 10 insider items. A principal components analysis revealed two distinct factors: Organizational Involvement and Social Connectedness. Non-school providers scored highest on Organizational Involvement; family members/self-advocates highest on Social Connectedness. Themes from open-ended responses supported the factors and showed differences in motivation and information sources across insiderness levels and roles. Qualitative analysis revealed two additional aspects of insiderness not addressed in the scale. Implications are discussed for future practice and research.

A Tale of Two Adaptations of a Special Education Advocacy Program.

Special education advocacy programs support families to secure services for their children with intellectual and developmental disabilities. Although research demonstrates the efficacy of one such program (the Volunteer Advocacy Project), its effectiveness when replicated by others is unknown. Replication research is critical to ensure that programs can remain effective. The purpose of this study was to explore the adaptation process for two agencies that replicated an advocacy program. Quantitative and qualitative data were collected to examine feasibility, acceptability, and effectiveness. Although it took resources to replicate the advocacy program, agencies reported ongoing implementation would be easier once adaptations were completed. The adapted programs were effective in increasing participants' knowledge, empowerment, advocacy, and insiderness. Implications for research and practice are discussed.

Culture-enriched community profiling improves resolution of the vertebrate gut microbiota.

Vertebrates harbour gut microbial communities containing hundreds of bacterial species, most of which have never been cultivated or isolated in the laboratory. The lack of cultured representatives from vertebrate gut microbiotas limits the description and experimental interrogation of these communities. Here, we show that representatives from >50% of the bacterial genera detected by culture-independent sequencing in the gut microbiotas of fence lizards, house mice, chimpanzees, and humans were recovered in mixed cultures from frozen faecal samples plated on a panel of nine media under a single growth condition. In addition, culturing captured >100 rare bacterial genera overlooked by culture-independent sequencing, more than doubling the total number of bacterial sequence variants detected. Our approach recovered representatives from 23 previously uncultured candidate bacterial genera, 12 of which were not detected by culture-independent sequencing. Results identified strategies for both indiscriminate and selective culturing of the gut microbiota that were reproducible across vertebrate species. Isolation followed by whole-genome sequencing of 161 bacterial colonies from wild chimpanzees enabled the discovery of candidate novel species closely related to the opportunistic pathogens of humans Clostridium difficile and Hungatella hathewayi. This study establishes culturing methods that improve inventories and facilitate isolation of gut microbiota constituents from a wide diversity of vertebrate species.

Flavored waterpipe tobacco preferences, perceptions, and use in pregnant women: A latent factor mapping approach.

Waterpipe tobacco (WPT) use is increasingly common in young adults including pregnant and reproductive-age women. Sweet flavors contribute to the appeal of WPT and are a promising regulatory target. The present study utilized correspondence analysis of contingency tables, a latent factor mapping technique, to investigate preferences and perceptions of WPT flavors in a sample of racially/ethnically diverse, low-income pregnant women. One hundred pregnant women (mean age = 26 years, 65% racial/ethnic minorities) completed a detailed interview regarding their use, preferences, and perceptions of WPT flavors. Eighty-three percent of participants reported lifetime WPT use; 11% reported prenatal WPT use. Pregnant women reported greatest use of and stronger preferences for sweet (fruit, candy, alcohol) and menthol/mint flavors, and weaker preferences for tobacco flavored WPT. Latent factor mapping revealed clustering of preferred sweet (fruit, candy, alcohol) and menthol/mint flavors versus tobacco flavors, with pungent flavors (coffee, chocolate, spice) clustering between sweet and tobacco flavors. Preferences for sweet and menthol/mint flavors distinguished pregnant women who reported lifetime WPT versus no lifetime WPT use, and prenatal WPT use versus no prenatal WPT use. Harm perceptions did not vary by flavor. Regulations to restrict the availability of WPT flavors may reduce the appeal and use of WPT, especially among pregnant women.

Educating Students with Autism Spectrum Disorders: Is Teacher Certification Area Associated with Academic Outcomes?

Although typically taught by special educators, few studies have examined if certification area is associated with academic outcomes for students with autism spectrum disorders (ASDs). The purpose of this study was to determine whether students with ASD scored better on language arts and mathematics state assessments depending on teacher certification, and whether these associations varied by assessment type. We analyzed 3 years of state administrative data from students with ASD in grades 4-8 receiving special education services. Results showed students taking the regular or alternate assessment had similar academic outcomes regardless of teacher certification. Students who were taught by special education certified teachers and took the modified assessment had lower academic outcomes. Implications for practice, policy, and research are discussed.

Families Requesting Advocates for Children With Disabilities: The Who, What, When, Where, Why, and How of Special Education Advocacy.

Because parents face barriers in advocating for their children within the special education system, some families request help from a special education advocate. In this study, we evaluated the perceptions of caregivers who requested advocacy support to understand why, for whom, when, and where the advocacy services were needed; how the advocate helped; and what the outcomes of the advocacy process were and which variables related to better outcomes. We conducted structured interviews with 36 families who had requested help and connected with an advocate over a 3-year period. Compared to national norms, families were more likely to request an advocate if their child had ASD, was in elementary school, and lived in non-rural areas. Family requests were most often for advocate attendance at IEP meetings; help to resolve disagreements with the school concerning supports and services; and information about school services and parental rights. Most advocate assistance was for a short duration, although a longer duration process, advocate attendance at meetings, and more intensive advocate assistance were all related to better outcomes. Most participants were satisfied with the advocate and with the end-result of the advocacy process. Findings are discussed in terms of implications for future research and practice.

The Impact of Heterogeneity on Single-Cell Sequencing.

The importance of diversity and cellular specialization is clear for many reasons, from population-level diversification, to improved resiliency to unforeseen stresses, to unique functions within metazoan organisms during development and differentiation. However, the level of cellular heterogeneity is just now becoming clear through the integration of genome-wide analyses and more cost effective Next Generation Sequencing (NGS). With easy access to single-cell NGS (scNGS), new opportunities exist to examine different levels of gene expression and somatic mutational heterogeneity, but these assays can generate yottabyte scale data. Here, we model the importance of heterogeneity for large-scale analysis of scNGS data, with a focus on the utilization in oncology and other diseases, providing a guide to aid in sample size and experimental design.

Epigenetic Modifications in Acute Myeloid Leukemia: Prognosis, Treatment, and Heterogeneity.

Leukemia, specifically acute myeloid leukemia (AML), is a common malignancy that can be differentiated into multiple subtypes based on leukemogenic history and etiology. Although genetic aberrations, particularly cytogenetic abnormalities and mutations in known oncogenes, play an integral role in AML development, epigenetic processes have been shown as a significant and sometimes independent dynamic in AML pathophysiology. Here, we summarize how tumors evolve and describe AML through an epigenetic lens, including discussions on recent discoveries that include prognostics from epialleles, changes in RNA function for hematopoietic stem cells and the epitranscriptome, and novel epigenetic treatment options. We further describe the limitations of treatment in the context of the high degree of heterogeneity that characterizes acute myeloid leukemia.

Effects of School-Home Communication With Parent-Implemented Reinforcement on Off-Task Behavior for Students With ASD.

School-home communication is highly valued for parents of students with autism spectrum disorders (ASD) and other developmental disabilities. However, parents report poor communication as a common barrier to developing partnerships with schools. Using a multiple baseline design, we evaluated the effects of a school-home note intervention with parent-implemented reinforcement for decreasing off-task behavior of students with ASD at school. We also evaluated social validity (i.e., feasibility and acceptability) of the intervention and outcomes. Only two of the four participants showed clear behavior change, which precluded the demonstration of functional relations. However, all participating parents and teachers reported the school-home note and parent-implemented contingent reinforcement were highly feasible and acceptable, and indicated positive outcomes relating to improved family-school partnership and communication. Findings of this study, which meets single-case design standards and quality indicators, are discussed in terms of future research and practice.

Report of the European Society of Cardiology Cardiovascular Round Table regulatory workshop update of the evaluation of new agents for the treatment of acute coronary syndrome: Executive summary.

Regulatory authorities interpret the results of randomized controlled trials according to published principles. The European Medicines Agency (EMA) is planning a revision of the 2000 and 2003 guidance documents on clinical investigation of new medicinal products for the treatment of acute coronary syndrome (ACS) to achieve consistency with current knowledge in the field. This manuscript summarizes the key output from a collaborative workshop, organized by the Cardiovascular Round Table and the European Affairs Committee of the European Society of Cardiology, involving clinicians, academic researchers, trialists, European and US regulators, and pharmaceutical industry researchers. Specific questions in four key areas were selected as priorities for changes in regulatory guidance: patient selection, endpoints, methodologic issues and issues related to the research for novel agents. Patients with ST-segment elevation myocardial infarction (STEMI) and non-STEMI (NSTEMI) should be studied separately for therapies aimed at the specific pathophysiology of either condition, particularly for treatment of the acute phase, but can be studied together for other treatments, especially long-term therapy. Unstable angina patients should be excluded from acute phase ACS trials. In general, cardiovascular death and reinfarction are recommended for primary efficacy endpoints; other endpoints may be considered if specifically relevant for the therapy under study. New agents or interventions should be tested against a background of evidence-based therapy with expanded follow-up for safety assessment. In conclusion, new guidance documents for randomized controlled trials in ACS should consider changes regarding patient and endpoint selection and definitions, and trial designs. Specific requirements for the evaluation of novel pharmacological therapies need further clarification.

Correlates of Sustained Volunteering: Advocacy for Students with Disabilities.

Parents of students with disabilities often receive support from special education advocates, who may be trained through a variety of programs. Using a web-based survey, this study examined the post-graduation advocacy activities of 83 graduates of one such volunteer advocacy training program. In the 1-4 years after program graduation, 63.8% (53 of 83) of the graduates advocated for one or more families; these sustained advocates reported stable rates of advocacy over time, and advocates performed activities that were either family-focused or school-focused. For graduates who advocated post-training, amounts of advocacy were positively related to satisfaction with advocating and with higher levels of involvement with other advocates and with the broader disability community. Compared to those not advocating after graduating, sustained advocates reported greater advocacy-role identities, increased involvement in disability groups, and higher likelihood to advocate in the upcoming year. Future research and practice implications are discussed.

Electronic health records to facilitate clinical research.

Electronic health records (EHRs) provide opportunities to enhance patient care, embed performance measures in clinical practice, and facilitate clinical research. Concerns have been raised about the increasing recruitment challenges in trials, burdensome and obtrusive data collection, and uncertain generalizability of the results. Leveraging electronic health records to counterbalance these trends is an area of intense interest. The initial applications of electronic health records, as the primary data source is envisioned for observational studies, embedded pragmatic or post-marketing registry-based randomized studies, or comparative effectiveness studies. Advancing this approach to randomized clinical trials, electronic health records may potentially be used to assess study feasibility, to facilitate patient recruitment, and streamline data collection at baseline and follow-up. Ensuring data security and privacy, overcoming the challenges associated with linking diverse systems and maintaining infrastructure for repeat use of high quality data, are some of the challenges associated with using electronic health records in clinical research. Collaboration between academia, industry, regulatory bodies, policy makers, patients, and electronic health record vendors is critical for the greater use of electronic health records in clinical research. This manuscript identifies the key steps required to advance the role of electronic health records in cardiovascular clinical research.

Identifying the associated factors of mediation and due process in families of students with autism spectrum disorder.

Compared to families of students with other types of disabilities, families of students with autism spectrum disorder (ASD) are significantly more likely to enact their procedural safeguards such as mediation and due process. However, we do not know which school, child, and parent characteristics are associated with the enactment of safeguards. For this study, 507 parents of students with ASD responded to a national web-based survey. Parents who filed for due process or mediation were more likely to advocate for their child, have poor family-school partnerships, and have greater household incomes. Parents were also more likely to utilize their safeguards if their children were older, experiencing more internalizing behaviors, and educated in segregated placements. Implications for research and practice are discussed.