Networking Frameworks: a Method for Analyzing the Complexities of Classroom Cultures Focusing on Justifying

In this paper, we network five frameworks (cognitive demand, lesson cohesion, cognitive engagement, collective argumentation, and student contribution) for an analytic approach that allows us to present a more holistic picture of classrooms which engage students in justifying. We network these frameworks around the edges of the instructional triangle as a means to coordinate them to illustrate the observable relationships among teacher, students(s), and content. We illustrate the potential of integrating these frameworks via analysis of two lessons that, while sharing surface level similarities, are profoundly different when considering the complexities of a classroom focused on justifying. We found that this integrated comparison across all dimensions (rather than focusing on just one or two) was a useful way to compare lessons with respect to a classroom culture that is characterized by students engaging in justifying

An improved ovine reference genome assembly to facilitate in depth functional annotation of the sheep genome

BACKGROUND: The domestic sheep (Ovis aries) is an important agricultural species raised for meat, wool, and milk across the world. A high-quality reference genome for this species enhances the ability to discover genetic mechanisms influencing biological traits. Furthermore, a high-quality reference genome allows for precise functional annotation of gene regulatory elements. The rapid advances in genome assembly algorithms and emergence of sequencing technologies with increasingly long reads provide the opportunity for an improved de novo assembly of the sheep reference genome. FINDINGS: Short-read Illumina (55× coverage), long-read Pacific Biosciences (75× coverage), and Hi-C data from this ewe retrieved from public databases were combined with an additional 50× coverage of Oxford Nanopore data and assembled with canu v1.9. The assembled contigs were scaffolded using Hi-C data with Salsa v2.2, gaps filled with PBsuitev15.8.24, and polished with Nanopolish v0.12.5. After duplicate contig removal with PurgeDups v1.0.1, chromosomes were oriented and polished with 2 rounds of a pipeline that consisted of freebayes v1.3.1 to call variants, Merfin to validate them, and BCFtools to generate the consensus fasta. The ARS-UI_Ramb_v2.0 assembly is 2.63 Gb in length and has improved continuity (contig NG50 of 43.18 Mb), with a 19- and 38-fold decrease in the number of scaffolds compared with Oar_rambouillet_v1.0 and Oar_v4.0. ARS-UI_Ramb_v2.0 has greater per-base accuracy and fewer insertions and deletions identified from mapped RNA sequence than previous assemblies. CONCLUSIONS: The ARS-UI_Ramb_v2.0 assembly is a substantial improvement in contiguity that will optimize the functional annotation of the sheep genome and facilitate improved mapping accuracy of genetic variant and expression data for traits in sheep

Oxidative stress links periodontal inflammation and renal function

Aims: Patients with chronic kidney disease (CKD) are also susceptible to periodontitis. The causal link between periodontitis and CKD may be mediated via systemic inflammation/oxidative stress. Using structural equation modelling (SEM), this cross-sectional study aimed to explore the causal relationship between periodontal inflammation (PI) and renal function. Materials and methods: Baseline data on 770 patients with stage 3–5 (pre-dialysis) CKD from an ongoing cohort study were used. Detailed, bioclinical data on PI and renal function, as well as potential confounders and mediators of the relationship between the two, were collected. SEMs of increasing complexity were created to test the causal assumption that PI affects renal function and vice versa. Results: Structural equation modelling confirmed the assumption that PI and renal function are causally linked, mediated by systemic oxidative stress. The magnitude of this effect was such that a 10% increase in PI resulted in a 3.0% decrease in renal function and a 10% decrease in renal function resulted in a 25% increase in PI. Conclusions: Periodontal inflammation represents an occult source of oxidative stress in patients with CKD. Further clinical studies are needed to confirm whether periodontal therapy, as a non-pharmacological approach to reducing systemic inflammatory/oxidative stress burden, can improve outcomes in CKD

PRNP Haplotype Associated with Classical BSE Incidence in European Holstein Cattle

Background: Classical bovine spongiform encephalopathy (BSE) is an acquired prion disease of cattle. The bovine prion gene (PRNP) contains regions of both high and low linkage disequilibrium (LD) that appear to be conserved across Bos taurus populations. The region of high LD, which spans the promoter and part of intron 2, contains polymorphic loci that have been associated with classical BSE status. However, the complex genetic architecture of PRNP has not been systematically tested for an association with classical BSE. Methodology/Principal Findings: In this study, haplotype tagging single nucleotide polymorphisms (htSNPs) within PRNP were used to test for association between PRNP haplotypes and BSE disease. A combination of Illumina goldengate assay, sequencing and PCR amplification was used to genotype 18 htSNPs and 2 indels in 95 BSE case and 134 control animals. A haplotype within the region of high LD was found to be associated with BSE unaffected animals (p-value = 0.000114). Conclusion/Significance: A PRNP haplotype association with classical BSE incidence has been identified. This result suggests that a genetic determinant in or near PRNP may influence classical BSE incidence in cattle

HIV and disability : a pilot study exploring the use of the assessment of motor and process skills to measure daily life performance

Introduction: Limitations in performing activities of daily living (ADL) are important indicators of health and overall wellness, yet relatively few studies specifically identify the ADL abilities of people living with HIV/AIDS (PHAs). Given the wide range of abilities and ages of PHAs, there is an urgent need to utilize an assessment of ADL ability that can validly evaluate those who are very able, as well as those who are very disabled, without the presence of ceiling or floor effects, to provide sensitive measures to detect change. Purpose: The purpose of this study was to gather preliminary evidence of the validity of using the Assessment of Motor and Process Skills (AMPS) with PHAs. Methods: By utilizing existing data records of PHAs from the international AMPS database, we explored (a) demographic factors; (b) person response validity by examining person and individual item goodness-of-fit to the AMPS measurement model; and (c) trends in ADL abilities of PHAs. Findings: There were 137 data records in the international AMPS database (0.08% of the database). Goodness-of-fit analyses revealed that >90% of the individuals in the sample fit AMPS measurement model and >99% of the individual item ratings fit the model. More than 80% of the data record had ADL motor abilities that were significantly lower than age expectations, and 67% had ADL process ability measures that were significantly lower than age expectations. Conclusions: The findings indicate that the AMPS is a valid measure of ADL ability for PHAs. Coupled with the lower than expected number of AMPS data records for PHAs and the significant ADL ability challenges that were encountered by this sample, this pilot study may indicate that PHAs encounter barriers to accessing rehabilitation services and/or may not receive referrals until significant ADL challenges are encountered

Virology under the microscope—a call for rational discourse

Viruses have brought humanity many challenges: respiratory infection, cancer, neurological impairment and immunosuppression to name a few. Virology research over the last 60+ years has responded to reduce this disease burden with vaccines and antivirals. Despite this long history, the COVID-19 pandemic has brought unprecedented attention to the field of virology. Some of this attention is focused on concern about the safe conduct of research with human pathogens. A small but vocal group of individuals has seized upon these concerns – conflating legitimate questions about safely conducting virus-related research with uncertainties over the origins of SARS-CoV-2. The result has fueled public confusion and, in many instances, ill-informed condemnation of virology. With this article, we seek to promote a return to rational discourse. We explain the use of gain-of-function approaches in science, discuss the possible origins of SARS-CoV-2 and outline current regulatory structures that provide oversight for virological research in the United States. By offering our expertise, we – a broad group of working virologists – seek to aid policy makers in navigating these controversial issues. Balanced, evidence-based discourse is essential to addressing public concern while maintaining and expanding much-needed research in virology

Predictors and systemic effects of periodontal disease progression

Thesis (Ph.D.)--Boston University PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at [email protected]. Thank you.Periodontal disease is a chronic and inflammatory oral condition, common among adults, with important outcomes such as tooth loss and systemic inflammatory-related events such as coronary heart disease [CHD]. Studies of periodontal disease occurrence permeate the literature; however, longitudinal studies of disease progression are rare. Using data from the Veterans Administration Dental Longitudinal Study and Normative Aging Study we compiled a population of adult men suffering from periodontal disease. Within this population we conducted three prospective cohort studies; two examined the impact of exposures on the progression of disease and one that examined the impact of disease progression on the incidence of CHD events. In the first study, we estimated the effect of smoking on progression of disease. After restricting the population according to age and periodontal disease status at entry, smokers displayed greater progression of periodontal disease over time than nonsmokers (Difference in slopes: 0.14; 95% CI: 0.05, 0.23) after controlling for heavy alcohol use, body mass index [BMI] and diabetic diagnoses. The second study estimated the effect of uric acid on progression of periodontal disease. After implementing marginal structural modeling to address the influence of time-varying covariates and adjusting for heavy alcohol use and smoking, we did not observe any effect of high uric acid levels (Difference in slopes: 0.01; 95% CI: -0.003, 0.02). In the third study, we evaluated the continuous effect of periodontal disease progression on incident CHD events. After restricting the population according to periodontal disease status at entry, incremental increases in periodontal disease were found to be associated with a two-fold increase in risk of CHD events (HR: 1.99; 95% CI: 0.45, 8.83), adjusting for age, SES, BMI, diabetic diagnoses, heavy alcohol use and smoking. This association also appeared to depend on smoking status and heavy alcohol use with smokers and heavy alcohol users observed to have a higher risk of CHD. The results of the current studies provide initial insight into the possible predictors and effects of periodontal disease progression. Most importantly, they highlight the influence of prevalent cohort biases studies of progression and the unique intricacies of studying periodontal health over time