The uniqueome: a mappability resource for short-tag sequencing

Summary: Quantification applications of short-tag sequencing data (such as CNVseq and RNAseq) depend on knowing the uniqueness of specific genomic regions at a given threshold of error. Here, we present the ‘uniqueome’, a genomic resource for understanding the uniquely mappable proportion of genomic sequences. Pre-computed data are available for human, mouse, fly and worm genomes in both color-space and nucletotide-space, and we demonstrate the utility of this resource as applied to the quantification of RNAseq data

K-Band Spectroscopy of (Pre-)Cataclysmic Variables: Are Some Donor Stars Really Carbon Poor?

We present a new sample of $K$-band spectral observations for CVs: non-magnetic and magnetic as well as present day and pre CVs. The purpose of this diverse sample is to address the recent claim that the secondary stars in dwarf novae are carbon deficient, having become so through a far more evolved evolution than the current paradigm predicts. Our new observations, along with previous literature results, span a wide range of orbital period and CV type. In general, dwarf novae in which the secondary star is seen show weak to no CO absorption while polar and pre-CV donor stars appear to have normal CO absorption for their spectral type. However, this is not universal. The presence of normal looking CO absorption in the dwarf nova SS Aur and the hibernating CV QS Vir and a complete lack of CO absorption in the long period polar V1309 Ori cloud the issue. A summary of the literature pointing to non-solar abundances including enhanced NV/CIV ratios is presented. It appears that some CVs have non-solar abundance material accreting onto the white dwarf suggesting an evolved secondary star while for others CO emission in the accretion disk may play a role. However, the exact mechanism or combination of factors causing the CO absorption anomaly in CVs is not yet clear.Comment: Accepted in A

Assessing the Potential Effects of Fungicides on Nontarget Gut Fungi (Trichomycetes) and Their Associated Larval Black Fly Hosts

Fungicides are moderately hydrophobic and have been detected in water and sediment, particularly in agricultural watersheds, but typically are not included in routine water quality monitoring efforts. This is despite their widespread use and frequent application to combat fungal pathogens. Although the efficacy of these compounds on fungal pathogens is well documented, little is known about their effects on nontarget fungi. This pilot study, a field survey in southwestern Idaho from April to December 2010 on four streams with varying pesticide inputs (two agricultural and two reference sites), was conducted to assess nontarget impact of fungicides on gut fungi, or trichomycetes. Tissues of larval black flies (Diptera: Simuliidae), hosts of gut fungi, were analyzed for pesticide accumulation. Fungicides were detected in hosts from streams within agricultural watersheds but were not detected in hosts from reference streams. Gut fungi from agricultural sites exhibited decreased percent infestation, density and sporulation within the gut, and black fly tissues had elevated pesticide concentrations. Differences observed between the sites demonstrate a potential effect on this symbiotic system. Future research is needed to parse out the details of the complex biotic and abiotic relationships; however, these preliminary results indicate that impacts to nontarget organisms could have far-reaching consequences within aquatic ecosystems

The Metabochip, a Custom Genotyping Array for Genetic Studies of Metabolic, Cardiovascular, and Anthropometric Traits

PMCID: PMC3410907This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Urban-Rural Disparities in Chronic Obstructive Pulmonary Disease Management and Access in Uganda.

Introduction: Almost 90% of chronic obstructive pulmonary disease (COPD) deaths occur in low- and middle-income countries (LMICs), where there are large rural populations and access to health care for COPD is poor. The purpose of this study was to compare urban-rural provider experiences regarding systemic facilitators and barriers to COPD management and treatment access. Methods: We conducted a qualitative study using direct observations and in-depth semi-structured interviews with 16 and 10 health care providers in urban Kampala and rural Nakaseke, Uganda, respectively. We analyzed interviews by performing inductive coding using generated topical codes. Results: In both urban and rural districts, exposure to evidence-based practices for COPD diagnosis and treatment was limited. The biomedical definition of COPD is not well distinguished in rural communities and was commonly confused with asthma and other respiratory diseases. Urban and rural participants alike described low availability of medications, limited access to diagnostic tools, poor awareness of the disease, and lack of financial means for medical care as common barriers to seeking and receiving care for COPD. While there was greater access to COPD treatment in urban areas, rural populations faced more pronounced barriers in access to diagnostic equipment, following standard treatment guidelines, and training medical personnel in non-communicable disease (NCD) management and treatment. Conclusion: Our results suggest that health system challenges for the treatment of COPD may disproportionately affect rural areas in Uganda. Implementation of diagnostic and treatment guidelines and training health professionals in COPD, with a special emphasis on rural communities, will assist in addressing these barriers

Response inhibition and serotonin in autism:a functional MRI study using acute tryptophan depletion

It has been suggested that the restricted, stereotyped and repetitive behaviours typically found in autism are underpinned by deficits of inhibitory control. The biological basis of this is unknown but may include differences in the modulatory role of neurotransmitters, such as serotonin, which are implicated in the condition. However, this has never been tested directly. We therefore assessed the modifying role of serotonin on inhibitory brain function during a Go/No-Go task in 14 adults with autism and normal intelligence and 14 control subjects that did not differ in gender, age and intelligence. We undertook a double-blind, placebo-controlled, crossover trial of acute tryptophan depletion using functional magnetic resonance imaging. Following sham, adults with autism relative to controls had reduced activation in key inhibitory regions of inferior frontal cortex and thalamus, but increased activation of caudate and cerebellum. However, brain activation was modulated in opposite ways by depletion in each group. Within autistic individuals depletion upregulated fronto-thalamic activations and downregulated striato-cerebellar activations toward control sham levels, completely 'normalizing' the fronto-cerebellar dysfunctions. The opposite pattern occurred in controls. Moreover, the severity of autism was related to the degree of differential modulation by depletion within frontal, striatal and thalamic regions. Our findings demonstrate that individuals with autism have abnormal inhibitory networks, and that serotonin has a differential, opposite, effect on them in adults with and without autism. Together these factors may partially explain the severity of autistic behaviours and/or provide a novel (tractable) treatment target

Micrometeoroid Events in LISA Pathfinder

The zodiacal dust complex, a population of dust and small particles that pervades the Solar System, provides important insight into the formation and dynamics of planets, comets, asteroids, and other bodies. Here we present a new set of data obtained using a novel technique: direct measurements of momentum transfer to a spacecraft from individual particle impacts. This technique is made possible by the extreme precision of the instruments flown on the LISA Pathfinder spacecraft, a technology demonstrator for a future space-based gravitational wave observatory that operated near the first Sun-Earth Lagrange point from early 2016 through Summer of 2017. Using a simple model of the impacts and knowledge of the control system, we show that it is possible to detect impacts and measure properties such as the transferred momentum (related to the particle's mass and velocity), direction of travel, and location of impact on the spacecraft. In this paper, we present the results of a systematic search for impacts during 4348 hours of Pathfinder data. We report a total of 54 candidates with momenta ranging from 0.2$\,\mu\textrm{Ns}$ to 230$\,\mu\textrm{Ns}$. We furthermore make a comparison of these candidates with models of micrometeoroid populations in the inner solar system including those resulting from Jupiter-family comets, Oort-cloud comets, Hailey-type comets, and Asteroids. We find that our measured population is consistent with a population dominated by Jupiter-family comets with some evidence for a smaller contribution from Hailey-type comets. This is in agreement with consensus models of the zodiacal dust complex in the momentum range sampled by LISA Pathfinder.Comment: 22 pages, 14 figures, accepted in Ap

Human embryonic stem cells from aneuploid blastocysts identified by pre-implantation genetic screening

Human embryonic stem cells are derived from the inner cell mass of pre-implantation embryos. The cells have unlimited proliferation potential and capacity to differentiate into the cells of the three germ layers. Human embryonic stem cells are used to study human embryogenesis and disease modeling and may in the future serve as cells for cell therapy and drug screening. Human embryonic stem cells are usually isolated from surplus normal frozen embryos and were suggested to be isolated from diseased embryos detected by pre-implantation genetic diagnosis. Here we report the isolation of 12 human embryonic stem cell lines and their thorough characterization. The lines were derived from embryos detected to have aneuploidy by pre-implantation genetic screening. Karyotype analysis of these cell lines showed that they are euploid, having 46 chromosomes. Our interpretation is that the euploid cells originated from mosaic embryos, and in vitro selection favored the euploid cells. The undifferentiated cells exhibited long-term proliferation and expressed markers typical for embryonic stem cells such as OCT4, NANOG, and TRA-1-60. The cells manifested pluripotent differentiation both in vivo and in vitro. To further characterize the different lines, we have analyzed their ethnic origin and the family relatedness among them. The above results led us to conclude that the aneuploid mosaic embryos that are destined to be discarded can serve as source for normal euploid human embryonic stem cell lines. These lines represent various ethnic groups; more lines are needed to represent all populations

Development and validation of an interstitial lung disease exposure questionnaire for sub-Saharan Africa.

Background American Thoracic Society/European Respiratory Society guidelines recommend context-specific exposure assessments to diagnose interstitial lung disease (ILD). In sub-Saharan Africa, ILD diagnoses are rare, and locally validated ILD exposure questionnaires are not used. Methods A physician-administered ILD exposure questionnaire was developed using a four-step mixed-methods modified Delphi approach. First, ILD questionnaires from high-income countries and data from Pneumotox were reviewed, compiled and face-validated. Second, a local pilot group of ILD experts ranked item relevance using a Likert scale and suggested additions. Third, the questionnaire format and pilot rankings were addressed in a focus group discussion that was analysed using grounded theory. Finally, following focus group discussion modifications, the resulting items (with three duplicate item groups for evaluation of internal consistency) were ranked for importance by members of the Pan-African Thoracic Society (PATS). Results Face validation resulted in 82 items in four categories: “Smoking and Drugs”, “Environmental Exposures”, “Occupations” and “Medications”. Pilot group (n=10) ranking revealed 27 outliers and 30 novel suggestions. Focus group (n=12) discussion resulted in 10 item deletions, 14 additions and 22 re-wordings; themes included desire for extensive questionnaires and stigma sensitivity. Final validation involved 58 PATS members (mean±sd age 46±10.6  years, 76% male, from 17 countries) ranking 84 items derived from previous steps and three duplicate question groups. The questionnaire was internally consistent (Cronbach's α >0.80) and ultimately included 73 items. Conclusion This mixed-methods study included experts from 17 countries in sub-Saharan Africa and successfully developed a 73-item ILD exposure questionnaire for sub-Saharan Africa. African pulmonary experts valued region-specific additions and ranked several items from existing ILD questionnaires as unimportant