MapOptics: A light-weight, cross-platform visualisation tool for optical mapping alignment

Availability and implementation: MapOptics is implemented in Java 1.8 and released under an MIT licence. MapOptics can be downloaded from https://github.com/FadyMohareb/mapoptics and run on any standard desktop computer equipped with a Java Virtual Machine (JVM). Supplementary data are available at Bioinformatics online.Bionano optical mapping is a technology that can assist in the final stages of genome assembly by lengthening and ordering scaffolds in a draft assembly by aligning the assembly to a genomic map. However, currently, tools for visualisation are limited to use on a Windows operating system or are developed initially for visualising large-scale structural variation. MapOptics is a lightweight cross-platform tool that enables the user to visualise and interact with the alignment of Bionano optical mapping data and can be used for in depth exploration of hybrid scaffolding alignments. It provides a fast, simple alternative to the large optical mapping analysis programs currently available for this area of research

Revisiting competition in a classic model system using formal links between theory and data

Formal links between theory and data are a critical goal for ecology. However, while our current understanding of competition provides the foundation for solving many derived ecological problems, this understanding is fractured because competition theory and data are rarely unified. Conclusions from seminal studies in space-limited benthic marine systems, in particular, have been very influential for our general understanding of competition, but rely on traditional empirical methods with limited inferential power and compatibility with theory. Here we explicitly link mathematical theory with experimental field data to provide a more sophisticated understanding of competition in this classic model system. In contrast to predictions from conceptual models, our estimates of competition coefficients show that a dominant space competitor can be equally affected by interspecific competition with a poor competitor (traditionally defined) as it is by intraspecific competition. More generally, the often-invoked competitive hierarchies and intransitivities in this system might be usefully revisited using more sophisticated empirical and analytical approaches

Factors Related to Mental Health Stigma Among Church-Affiliated African Americans

Title from PDF of title page viewed July 6, 2022Thesis advisor: Jannette Berkley-PattonIncludes bibliographical references (pages 66-86)VitaThesis (M.A.)--Department of Psychology. University of Missouri--Kansas City, 2022African Americans make up 13% of the U.S. population, yet represent nearly 20% of persons diagnosed with a mental illness. Studies suggest African Americans experience higher levels of mental health related stigma (MHS) than whites. In addition, African Americans have the highest rate of church attendance compared to all other racial/ethnic groups, and they are more likely to seek counsel from religious leaders. Although there is a growing body of research on MHS with African Americans, few studies have explored MHS predictors among church-affiliated African Americans – a population that may be important to examine given studies have shown that African American churches have great influence on health behaviors and beliefs among their members. This study used the Health Stigma and Discrimination Framework’s key constructs (e.g., domains, facilitators, stigma marking, manifestations) to guide examination of predictors (e.g., mental health fear, awareness, and social support, cultural and social norms, access to mental health services, demographics, mental health conditions, and mental health-related stigma beliefs) of MHS among an African American church-affiliated population. Baseline survey data from the religiously-tailored Healthy Actions to Impact Mind and Soul (Healthy AIMS) pilot intervention study, which focused on mental health screening and linkage to care services and took place in four African American churches (N=200 participants) in Kansas City, MO, was used to determine potential predictors of mental health stigma for examination. Most participants were female (79.5%), church members (78.5%) and an average age of 53 (SD = 17). Participants endorsed moderate to high levels of MHS (M = 39.03; SD = 6.8; range 11-55). Results indicated that social support (support from others and beliefs), collaborative and self-directive religious coping, and engaging in religious activities (e.g., thinking of God, meditating, praying) were significantly related to MHS. Linear regression analysis indicated that self-directive religious coping was a positive predictor of MHS. African Americans may engage in self-directive religious coping due to negative beliefs about the connection between having a mental illness and religiosity/spirituality. Future interventions may consider addressing MHS through providing tailored education and offering screening in a trusted setting, such as African American churches.Introduction -- Method -- Results -- Discussion -- Appendi

Using Mobile Devices to Facilitate Student Questioning in a Large Undergraduate Science Class

Asking scientific questions is the first practice of science and engineering listed in the Next Generation Science Standards. However, getting students to ask unsolicited questions in a large class can be difficult. In this qualitative study, undergraduate students sent SMS text messages to the instructor who received them on his mobile phone and via Google Glass. Using observations, coding of texts, and interviews, the researchers investigated the types and level of questions students asked and the perceptions of the instructor and TAs on how the messages were received. From the findings of this study, it is evident that students asked a wide variety of question types and levels. It would appear that important distinctions between voice and text questions are that: (a) a shy or insecure questioner can remain anonymous; (b) questions can be asked in an interactive, but not interruptive manner; (c) there is no time limit to answering questions; and (d) the record of questions on the instructor\u27s phone can be used to guide revision of lecture notes for future semesters

Impact testing to determine the mechanical properties of articular cartilage in isolation and on bone

The original publication is available at www.springerlink.comNon peer reviewedPostprin

Using Intercultural Sensitivity to Predict Culturally Responsive Classroom Management Self-Efficacy among Preservice Teachers

As student diversity increases, it is imperative that Educator Preparation Programs (EPPs) prepare preservice teachers to manage these classrooms. Educators are expected to possess the skillset, experience, and confidence necessary to engage diverse students from varying cultural backgrounds. Thus, intercultural sensitivity is an important affective trait for teachers, however, the connection between intercultural sensitivity and self-efficacy for culturally responsive classroom management has not been well documented in the preservice teacher literature. In this study, one mid-southern university examined the relationship between preservice teachers’ perceptions of their intercultural sensitivity and their self-efficacy for tasks related to culturally responsive classroom management. Findings indicated that preservice teachers are confident in their ability to manage classrooms in a culturally responsive manner and that intercultural sensitivity significantly predicted and explained about a third of variance in culturally responsive classroom management self-efficacy. While EPPs could consider requiring coursework in cultural diversity and classroom management, the results of this study indicated that coursework alone was not enough to improve preservice teachers’ self-efficacy

Cosmological hydrogen recombination: Lyn line feedback and continuum escape

We compute the corrections to the cosmological hydrogen recombination history due to delayed feedback of Lyman-series photons and the escape in the Lyman-continuum. The former process is expected to slightly delay recombination, while the latter should allow the medium to recombine a bit faster. It is shown that the subsequent feedback of released Lyman-n photons on the lower lying Lyman-(n-1) transitions yields a maximal correction of DN_e/N_e 0.22% at z~ 1050. Including only Lyman-\beta feedback onto the Lyman-\alpha transition, accounts for most of the effect. We find corrections to the cosmic microwave background TT and EE power spectra \change{with typical peak to peak amplitude |DC^{TT}_l/C^{TT}_l|~0.15% and |\Delta C^{EE}_l/C^{EE}_l|~0.36% at l<~3000. The escape in the Lyman-continuum and feedback of Lyman-\alpha photons on the photoionization rate of the second shell lead to modifications of the ionization history which are very small (less than |DN_e/N_e|~few x 10^{-6}).Comment: 5+epsilon pages, 7 figures, accepted versio

Free-bound emission from cosmological hydrogen recombination

In this paper we compute the emission coming from the direct recombination of free electrons to a given shell (n>=2) during the epoch of cosmological hydrogen recombination. This contribution leads to a total of one photon per recombined hydrogen atom and therefore a ~30-88% increase of the recombination spectrum within the frequency range 1 GHz<=nu<=100 GHz. In particular the Balmer-continuum emission increases the distortion at nu~ 690 GHz by ~92%. With our 100 shell calculations for the hydrogen atom we find that a total of ~5 photons per hydrogen atom are emitted when including all the bound-bound transitions, the 2s two-photon decay channel and the optically thin free-bound transitions. Since the direct recombination continuum at high n is very broad only a few n-series continuua are distinguishable and most of this additional emission below nu<~30 GHz is completely featureless.Comment: 4 pages, 2 figures, submitted to A&A Letter