Spectral identification and quantification of salts in the Atacama Desert

This work was part-funded by a Research Incentive Grant from The Carnegie Trust (REF: 70335) and a Royal Society of Edinburgh Research Fellowship to C. Cousins. J, Harris acknowledges funding from STFC (consolidated grant ST/N000528/1).Salt minerals are an important natural resource. The ability to quickly and remotely identify and quantify salt deposits and salt contaminated soils and sands is therefore a priority goal for the various industries and agencies that utilise salts. The advent of global hyperspectral imagery from instruments such as Hyperion on NASA’s Earth-Observing 1 satellite has opened up a new source of data that can potentially be used for just this task. This study aims to assess the ability of Visible and Near Infrared (VNIR) spectroscopy to identify and quantify salt minerals through the use of spectral mixture analysis. The surface and near-surface soils of the Atacama Desert in Chile contain a variety of well-studied salts, which together with low cloud coverage, and high aridity, makes this region an ideal testbed for this technique. Two forms of spectral data ranging 0.35 – 2.5 μm were collected: laboratory spectra acquired using an ASD FieldSpec Pro instrument on samples from four locations in the Atacama desert known to have surface concentrations of sulfates, nitrates, chlorides and perchlorates; and images from the EO-1 satellite’s Hyperion instrument taken over the same four locations. Mineral identifications and abundances were confirmed using quantitative XRD of the physical samples. Spectral endmembers were extracted from within the laboratory and Hyperion spectral datasets and together with additional spectral library endmembers fed into a linear mixture model. The resulting identification and abundances from both dataset types were verified against the sample XRD values. Issues of spectral scale, SNR and how different mineral spectra interact are considered, and the utility of VNIR spectroscopy and Hyperion in particular for mapping specific salt concentrations in desert environments is established. Overall, SMA was successful at estimating abundances of sulfate minerals, particularly calcium sulfate, from both hyperspectral image and laboratory sample spectra, while abundance estimation of other salt phase spectral end-members was achieved with a higher degree of error.Publisher PD

School Leadership Interventions Under the Every Student Succeeds Act: Evidence Review - Updated and Expanded

This RAND analysis offers guidance to states and districts on how they can choose to use the Every Student Succeeds Act to help achieve their school improvement goals by supporting principals and other school leaders

Spontaneous self-affirmation is associated with psychological well-being: evidence from a US national adult survey sample

Emerging evidence suggests that individuals spontaneously self-affirm, by reflecting on values and strengths, in response to daily threats. We examined the prevalence and demographic and well-being correlates of spontaneous self-affirmation in the general population. Participants (n = 3185) completed the cross-sectional, nationally representative 2013 Health Information National Trends Survey (HINTS 4, Cycle 3), and answered questions about spontaneous self-affirmation, demographic factors, well-being, and affect. The majority of the population reported spontaneously self-affirming. Black and Hispanic respondents reported engaging in more spontaneous self-affirmation. Engaging in spontaneous self-affirmation was related to greater happiness, hopefulness, optimism, subjective health, and personal health efficacy, and less anger and sadness

Five-Year Clinical Outcomes of a Randomized Trial of Anterior Cruciate Ligament Treatment Strategies: An Evidence-Based Practice Paper

REFERENCE/CITATION: Frobell RB, Roos HP, Roos EM, Roemer FW, Ranstam J, Lohmander LS. Treatment for acute anterior cruciate ligament tear: five year outcome of randomised trial. BMJ. 2013;346:F232. CLINICAL QUESTION: Does early anterior cruciate ligament (ACL) reconstruction with rehabilitation lead to better patient-reported outcomes and a lower incidence of osteoarthritis at 5 years postinjury compared with delayed ACL reconstruction with rehabilitation? STUDY SELECTION: This randomized controlled trial with extended follow-up at 5 years postrandomization was conducted in 2 Swedish orthopaedic departments. DATA EXTRACTION: The authors studied a total of 121 moderately active adults (age = 18–35 years) with an acute ACL rupture in a knee with no other history of trauma. Excluded were patients with a collateral ligament rupture, full-thickness cartilage defect, or extensive meniscal fixation. One patient assigned to the early ACL-reconstruction group did not attend the 5-year follow-up visit. Patients were randomly assigned to (1) an early ACL reconstruction plus structured rehabilitation group (n = 62, surgery within 10 weeks of injury) or (2) optional-delayed ACL reconstruction plus structured rehabilitation group (n = 59). The primary outcome measure was change in the average of 4 out of 5 subscales of the Knee Injury and Osteoarthritis Outcome Score (KOOS). The authors also assessed crude KOOS (combined 4 subscales), KOOS subscale scores, general physical and mental health (Short-Form 36), activity level (Tegner Activity Scale), mechanical knee stability (Lachman and pivot shift tests), meniscal surgery status, and presence of knee osteoarthritis on radiographs. MAIN RESULTS: Among patients randomized to the optional-delayed ACL-reconstruction group, 30 (51%) opted for an ACL reconstruction. The treatment groups had comparable 5-year patient-reported outcomes and changes in patient-reported outcomes (eg, knee pain, knee symptoms, activities of daily living, sport and recreational levels, knee-related quality of life, general physical health, and general mental health). Patients in the optional-delayed ACL-reconstruction group had greater mechanical knee instability than patients who received early ACL reconstruction; however, this was primarily among the patients opting for conservative management alone. In the overall sample, 61 knees (51%) required meniscal surgery over 5 years, regardless of treatment group. At 5 years, radiographs were available for 113 patients (93%). Overall, 29 patients (26%) had knee osteoarthritis at 5 years. Specifically, 13 patients (12%) developed tibiofemoral radiographic osteoarthritis (9 patients [16%] in the early ACL-reconstruction group, 4 [7%] in the optional-delayed ACL-reconstruction group) and 22 (19%) developed patellofemoral osteoarthritis (14 patients [24%] in the early ACL-reconstruction group, 8 [15%] in the optional-delayed ACL-reconstruction group). Patients with patellar tendon grafts (n = 40) had a greater incidence of ipsilateral patellofemoral osteoarthritis than patients with hamstrings tendon grafts (n = 51), but the 2 groups had similar incidences of ipsilateral tibiofemoral osteoarthritis. Six knees (5%) had both tibiofemoral and patellofemoral osteoarthritis. CONCLUSIONS: Early ACL reconstruction plus rehabilitation did not provide better results at 5 years compared with optional-delayed ACL reconstruction plus rehabilitation. Furthermore, the authors found no radiographic differences among patients with early ACL reconstruction, delayed ACL reconstruction, or no ACL reconstruction (rehabilitation alone)

Setting up and utilizing Norwegian twin panels

In the late 1970s, a Norwegian twin panel was set up. It included all like-sexed twin pairs, born in the period 1915 to 1960, where both members were alive and had a known address in Norway at the time. The work was initiated through a grant from the National Institutes of Health in the United States. The aim was to estimate maternal effects to understand the causes of variation in traits and diseases that originate in pregnancy. However, the twin panel was also utilized for estimating genetic and environmental effects on a series of phenotypes, for instance lipoproteins, receptors, coagulation factors, cognitive abilities, educational attainment and left-handedness. A short zygosity questionnaire was sent together with the first invitation letter to the twins. Later questionnaires on general health, lifestyles and pregnancy outcomes were sent out. One important finding was that the fetal genotype had much stronger influence on variation in fetal growth than what had been assumed previously. In the early 1990s, the New Norwegian Twin Panel was created, based on information on plural births in the Medical Birth Registry of Norway (MBRN). The panel included both like-sexed and opposite-sexed pairs born in the years 1967 to 1974. After linking the MBRN to present addresses, using a national identification number, a questionnaire on zygosity, with a few items on health and social background, was sent out. This panel was later expanded to include twins born 1975-1979 and to collect more data on health, well-being and lifestyle factors. The data have been utilized for a series of subprojects, including psychiatric interviews and the collection of DNA samples. Linkage to Norwegian health registries has provided important research opportunities for a variety of phenotypic outcomes

Genome-wide DNA methylation profiling confirms a case of low-level mosaic Kabuki syndrome 1

Kabuki syndrome is a Mendelian disorder of the epigenetic machinery characterized by typical dysmorphic features, intellectual disability, and postnatal growth deficiency. Pathogenic variants in the genes encoding the chromatin modifiers KMT2D and KDM6A are responsible for Kabuki syndrome 1 (KS1) and Kabuki syndrome 2 (KS2), respectively. In addition, 11 cases of KS1 caused by mosaic variants in KMT2D have been reported in the literature. Some of these individuals display milder craniofacial and growth phenotypes, and most do not have congenital heart defects. We report the case of an infant with severe hypoplastic left heart syndrome with mitral atresia and aortic atresia (HLHS MA-AA), pulmonary vein stenosis, and atypical facies with a somatic mosaic de novo nonsense variant in KMT2D (c.8200C\u3eT, p.R2734*) identified on trio exome sequencing of peripheral blood and present in 11.2% of sequencing reads. KS was confirmed with EpiSign, a diagnostic genome-wide DNA methylation platform used to identify epigenetic signatures. This case suggests that use of this newly available clinical test can guide the interpretation of low-level mosaic variants identified through sequencing and suggests a new lower limit of mosaicism in whole blood required for a diagnosis of KS

Quantitative Genetic Mapping and Genome Assembly in the Lesser Wax Moth Achroia grisella

This work is licensed under a Creative Commons Attribution 4.0 International License.Specific characteristics of the male Achroia grisella acoustic mating signal determine a male’s attractiveness toward females. These features are genetically variable in populations, and mapping experiments have been used to identify loci contributing to song variation, and understand the evolutionary forces acting on this important sexual trait. Here we built on this foundation and carried out QTL (Quantitative Trait Locus) mapping using >1,000 recombinant individuals, genotyping this large cohort at thousands of sequence-based markers covering the entire collection of 30 A. grisella chromosomes. This dense marker set, coupled with our development of an annotated, draft genome of A. grisella, allowed us to link >3,000 genome scaffolds, >10,000 predicted genes, and close to 275Mb of genome sequence to chromosomes. Our QTL mapping confirmed a fraction of the QTL identified in a previous study, and additionally revealed novel loci. Collectively, QTL explained only small fractions of the phenotypic variance, suggesting many more causative factors remain below the detection threshold of our study. A surprising, and ultimately challenging feature of our study was the low level of intrachromosomal recombination present in our mapping population. This led to difficulty ordering markers along linkage groups, necessitating a chromosome-by-chromosome mapping approach, rather than true interval mapping, and precluded confident ordering/orienting of scaffolds along each chromosome. Nonetheless, our study increased the genomic resources available for the A. grisella system. Enabled by ever more powerful technologies, future investigators will be able to leverage our data to provide more detailed genetic dissection of male song variation in A. grisella.NSF IOB-0516634NIGMS award P20GM103638NIGMS award P20GM103418NIH R01 GM085260NIH R01 OD01097

Response to comment on "Human-specific gain of function in a developmental enhancer"

Duret and Galtier argue that human-specific sequence divergence and gain of function in the HACNS1 enhancer result from deleterious biased gene conversion (BGC) with no contribution from positive selection. We reinforce our previous conclusion by analyzing hypothesized BGC events genomewide and assessing the effect of recombination rates on human-accelerated conserved noncoding sequence ascertainment. We also provide evidence that AT → GC substitution bias can coexist with positive selection