BAC-HAPPY mapping (BAP mapping): a new and efficient protocol for physical mapping

Physical and linkage mapping underpin efforts to sequence and characterize the genomes of eukaryotic organisms by providing a skeleton framework for whole genome assembly. Hitherto, linkage and physical “contig” maps were generated independently prior to merging. Here, we develop a new and easy method, BAC HAPPY MAPPING (BAP mapping), that utilizes BAC library pools as a HAPPY mapping panel together with an Mbp-sized DNA panel to integrate the linkage and physical mapping efforts into one pipeline. Using Arabidopsis thaliana as an exemplar, a set of 40 Sequence Tagged Site (STS) markers spanning ~10% of chromosome 4 were simultaneously assembled onto a BAP map compiled using both a series of BAC pools each comprising 0.7x genome coverage and dilute (0.7x genome) samples of sheared genomic DNA. The resultant BAP map overcomes the need for polymorphic loci to separate genetic loci by recombination and allows physical mapping in segments of suppressed recombination that are difficult to analyze using traditional mapping techniques. Even virtual “BAC-HAPPY-mapping” to convert BAC landing data into BAC linkage contigs is possible.Giang T. H. Vu, Paul H. Dear, Peter D. S. Caligari and Mike J. Wilkinso

A supportive text message intervention for individuals living with endometriosis (EndoSMS) : randomized controlled pilot and feasibility trial

Introduction: As a high symptom burden chronic condition, endometriosis is associated with diminished quality of life (QoL) and psychological distress. The EndoSMS text message intervention was developed to inform and support individuals living with endometriosis. The primary aim of this study is to assess the acceptability, feasibility and preliminary efficacy of EndoSMS, to improve endometriosis-specific QoL and reduce psychological distress in a randomised controlled trial, compared with care as usual. We will additionally assess the impact of EndoSMS on self-efficacy for managing endometriosis. Methodology: A two-arm parallel pilot randomised controlled trial with waitlist control was conducted. Baseline assessments included QoL, psychological distress, self-efficacy, demographic and medical variables. Following baseline survey completion, participants were randomised to either the Intervention (EndoSMS: 3-months of text messaging) or Control condition. At 3-month follow-up, all participants completed an online survey reassessing outcomes, and Intervention participants provided quantitative and qualitative user feedback on EndoSMS. Results: Data collection commenced on 18 November 2021 and was completed on 30 March 2022. Descriptive statistics will be used to analyse feasibility and acceptability of the intervention. Preliminary efficacy analyses will be conducted using linear mixed models for QoL, psychological distress and self-efficacy outcomes. Subgroup analyses will also be conducted for typically underserved populations (e.g., rural/regional). Conclusion: This pilot will provide acceptability, feasibility and preliminary efficacy evidence for the impact of a supportive text messaging program for endometriosis. It will contribute to understanding how to optimally support individuals in living with and managing their endometriosis. Trial Registration: Australian New Zealand Clinical Trials Registry

Co-design and development of EndoSMS, a supportive text message intervention for individuals living with endometriosis : mixed methods study

Background: Endometriosis, which affects 1 in 10 people assigned female at birth, is a chronic systemic inflammatory disease with a high symptom burden and adverse socioemotional impacts. There is a need for an accessible, cost-effective, and low-burden intervention to support individuals in managing their endometriosis condition. Objective: This study aimed to co-design and evaluate the acceptability, readability, and quality of a bank of supportive SMS text messages (EndoSMS) for individuals with endometriosis. Methods: In phase 1 of this mixed method design, 17 consumer representatives (individuals with endometriosis) participated across three 3-hour web-based (Zoom, Zoom Video Communications, Inc) focus groups. The transcripts were encoded and analyzed thematically. In phase 2, consumer representatives (n=14) and health care professionals (n=9) quantitatively rated the acceptability, readability, and appropriateness of the developed text messages in a web-based survey. All the participants initially completed a background survey assessing sociodemographic and medical factors. Results: Consumer representatives demonstrated diverse sociodemographic characteristics (Mage=33.29), varying in location (metropolitan vs rural or regional), employment, and relationship and educational statuses. Participants reached a consensus regarding the delivery of 4 SMS text messages per week, delivered randomly throughout the week and in one direction (ie, no reply), with customization for the time of day and use of personal names. Seven main areas of unmet need for which participants required assistance were identified, which subsequently became the topic areas for the developed SMS text messages: emotional health, social support, looking after and caring for your body, patient empowerment, interpersonal issues, general endometriosis information, and physical health. Through a web-based survey, 371 co-designed SMS text messages were highly rated by consumers and health care professionals as clear, useful, and appropriate for individuals with endometriosis. Readability indices (Flesch-Kincaid scale) indicated that the SMS text messages were accessible to individuals with a minimum of 7th grade high school education. Conclusions: On the basis of the needs and preferences of a diverse consumer representative group, we co-designed EndoSMS, a supportive SMS text message program for individuals with endometriosis. The initial evaluation of the SMS text messages by consumer representatives and health professionals suggested the high acceptability and suitability of the developed SMS text messages. Future studies should further evaluate the acceptability and effectiveness of EndoSMS in a broader population of individuals with endometriosis

Considering the impact of situation-specific motivations and constraints in the design of naturally ventilated and hybrid buildings

A simple logical model of the interaction between a building and its occupants is presented based on the principle that if free to do so, people will adjust their posture, clothing or available building controls (windows, blinds, doors, fans, and thermostats) with the aim of achieving or restoring comfort and reducing discomfort. These adjustments are related to building design in two ways: first the freedom to adjust depends on the availability and ease-of-use of control options; second the use of controls affects building comfort and energy performance. Hence it is essential that these interactions are considered in the design process. The model captures occupant use of controls in response to thermal stimuli (too warm, too cold etc.) and non-thermal stimuli (e.g. desire for fresh air). The situation-specific motivations and constraints on control use are represented through trigger temperatures at which control actions occur, motivations are included as negative constraints and incorporated into a single constraint value describing the specifics of each situation. The values of constraints are quantified for a range of existing buildings in Europe and Pakistan. The integration of the model within a design flow is proposed and the impact of different levels of constraints demonstrated. It is proposed that to minimise energy use and maximise comfort in naturally ventilated and hybrid buildings the designer should take the following steps: 1. Provide unconstrained low energy adaptive control options where possible, 2. Avoid problems with indoor air quality which provide motivations for excessive ventilation rates, 3. Incorporate situation-specific adaptive behaviour of occupants in design simulations, 4. Analyse the robustness of designs against variations in patterns of use and climate, and 5. Incorporate appropriate comfort standards into the operational building controls (e.g. BEMS)

Mitochondrial Genomes Reveal an Explosive Radiation of Extinct and Extant Bears near the Miocene-Pliocene Boundary

Background: Despite being one of the most studied families within the Carnivora, the phylogenetic relationships among the members of the bear family (Ursidae) have long remained unclear. Widely divergent topologies have been suggested based on various data sets and methods. Results: We present a fully resolved phylogeny for ursids based on ten complete mitochondrial genome sequences from all eight living and two recently extinct bear species, the European cave bear (Ursus spelaeus) and the American giant short-faced bear (Arctodus simus). The mitogenomic data yield a well-resolved topology for ursids, with the sloth bear at the basal position within the genus Ursus. The sun bear is the sister taxon to both the American and Asian black bears, and this clade is the sister clade of cave bear, brown bear and polar bear confirming a recent study on bear mitochondrial genomes. Conclusion: Sequences from extinct bears represent the third and fourth Pleistocene species for which complete mitochondrial genomes have been sequenced. Moreover, the cave bear specimen demonstrates that mitogenomic studies can be applied to Pleistocene fossils that have not been preserved in permafrost, and therefore have a broad application within ancient DNA research. Molecular dating of the mtDNA divergence times suggests a rapid radiation of bears in both the Old and New Worlds around 5 million years ago, at the Miocene-Pliocene boundary. This coincides with major global changes, such as the Messinian crisis and the first opening of the Bering Strait, and suggests a global influence of such events on species radiations

Indoor environmental quality and occupant satisfaction in green-certified buildings

Green building certification systems aim at improving the design and operation of buildings. However, few detailed studies have investigated whether green rating leads to higher occupant satisfaction with indoor environmental quality (IEQ). This research builds on previous work to address this. Based on the analysis of a subset of the Center for the Built Environment Occupant Indoor Environmental Quality survey database featuring 11,243 responses from 93 LEED-rated office buildings, we explored the relationships between the points earned in the IEQ category and the satisfaction expressed by occupants with the qualities of their indoor environment. We found that the achievement of a specific IEQ credit did not substantively increase satisfaction with the corresponding IEQ factor, while the rating level, and the product and version under which certification had been awarded, did not affect workplace satisfaction. There could be several reasons for this lack of relationships, some of which are outside the control of designers and beyond the scope of rating systems based primarily on design intent. We conclude with a discussion of the challenges and priorities that building professionals, researchers, and green building certification systems need to consider for moving us towards more comfortable, higher performing, and healthier green-rated buildings

Genetic Variants of Ehrlichia phagocytophila1, Rhode Island and Connecticut

Primers were used to amplify a 561-bp region of the 16S rRNA gene of Ehrlichia phagocytophila from Ixodes scapularis ticks and small mammals collected in Rhode Island and Connecticut. DNA sequences for all 50 E. phagocytophila-positive samples collected from 1996 through 1998 in southwestern Connecticut were identical to the sequence reported for E. phagocytophila DNA from confirmed human cases. In contrast, the sequences from 92 of 123 E. phagocytophila-positive Rhode Island samples collected from 1996 through 1999 included several variants differing by 1-2 nucleotides from that in the agent infecting humans. While 11.9% of 67 E. phagocytophila-positive ticks collected during 1997 in Rhode Island harbored ehrlichiae with sequences identical to that of the human agent, 79.1% had a variant sequence not previously described. The low incidence of human ehrlichiosis in Rhode Island may in part result from interference by these variant ehrlichiae with maintenance and transmission of the true agent of human disease