Hydraulics and geology related to beach restoration in Lee County, Florida

The erosion problem on Captiva Island is discussed. It is due to a deficit in the sand budget of the littoral drift system; a system with losses due to attrition of the particles and mass losses into the lagoons, to offshore, and to lateral transport. The effect that reopening Blind Pass would have, and the placement of sediment retaining structures in the surf zone at the northern and southern limits of the Captiva beach system, wave examined. A geological approach was used to study the origin and dynamic changes that have occurred. Through hydraulic modeling, changes that will occur by reopening and stabilizing Blind Pass are predicted. It is concluded that if the island is to be stabilized, beach nourishment with proper amounts and particle size is a necessity and that jetties adequate to restrict lateral and offshore losses are essential. It is shown that the reopening of Blind Pass would have minimal effects on the passes to the north and south, and would improve the environmental conditions in the sound with no adverse effects on the beach system

Group evaluations as self-group distancing:Ingroup typicality moderates evaluative intergroup bias in stigmatized groups

Outgroup favoritism among members of stigmatized groups can be seen as a form of self-group distancing. We examined how intergroup evaluations in stigmatized groups vary as a function of ingroup typicality. In Studies 1 and 2, Black participants (N = 125,915;N = 766) more strongly preferred light-skinned or White relative to dark-skinned or Black individuals the lighter their own skin tone. In Study 3, overweight participants (N = 147,540) more strongly preferred normal-weight relative to overweight individuals the lower their own body weight. In Study 4, participants with disabilities (N = 35,058) more strongly preferred non-disabled relative to disabled individuals the less visible they judged their own disability. Relationships between ingroup typicality and intergroup evaluations were at least partially mediated by ingroup identification (Studies 2 and 3). A meta-analysis across studies yielded an average effect size ofr= .12. Furthermore, higher ingroup typicality was related to both ingroup and outgroup evaluations. We discuss ingroup typicality as an individual constraint to self-group distancing among stigmatized group members and its relation to intergroup evaluations

Profiling allele-specific gene expression in brains from individuals with autism spectrum disorder reveals preferential minor allele usage.

One fundamental but understudied mechanism of gene regulation in disease is allele-specific expression (ASE), the preferential expression of one allele. We leveraged RNA-sequencing data from human brain to assess ASE in autism spectrum disorder (ASD). When ASE is observed in ASD, the allele with lower population frequency (minor allele) is preferentially more highly expressed than the major allele, opposite to the canonical pattern. Importantly, genes showing ASE in ASD are enriched in those downregulated in ASD postmortem brains and in genes harboring de novo mutations in ASD. Two regions, 14q32 and 15q11, containing all known orphan C/D box small nucleolar RNAs (snoRNAs), are particularly enriched in shifts to higher minor allele expression. We demonstrate that this allele shifting enhances snoRNA-targeted splicing changes in ASD-related target genes in idiopathic ASD and 15q11-q13 duplication syndrome. Together, these results implicate allelic imbalance and dysregulation of orphan C/D box snoRNAs in ASD pathogenesis

All-particle cosmic ray energy spectrum measured with 26 IceTop stations

We report on a measurement of the cosmic ray energy spectrum with the IceTop air shower array, the surface component of the IceCube Neutrino Observatory at the South Pole. The data used in this analysis were taken between June and October, 2007, with 26 surface stations operational at that time, corresponding to about one third of the final array. The fiducial area used in this analysis was 0.122 km^2. The analysis investigated the energy spectrum from 1 to 100 PeV measured for three different zenith angle ranges between 0{\deg} and 46{\deg}. Because of the isotropy of cosmic rays in this energy range the spectra from all zenith angle intervals have to agree. The cosmic-ray energy spectrum was determined under different assumptions on the primary mass composition. Good agreement of spectra in the three zenith angle ranges was found for the assumption of pure proton and a simple two-component model. For zenith angles {\theta} < 30{\deg}, where the mass dependence is smallest, the knee in the cosmic ray energy spectrum was observed between 3.5 and 4.32 PeV, depending on composition assumption. Spectral indices above the knee range from -3.08 to -3.11 depending on primary mass composition assumption. Moreover, an indication of a flattening of the spectrum above 22 PeV were observed.Comment: 38 pages, 17 figure

Genetic determinants of co-accessible chromatin regions in activated T cells across humans.

Over 90% of genetic variants associated with complex human traits map to non-coding regions, but little is understood about how they modulate gene regulation in health and disease. One possible mechanism is that genetic variants affect the activity of one or more cis-regulatory elements leading to gene expression variation in specific cell types. To identify such cases, we analyzed ATAC-seq and RNA-seq profiles from stimulated primary CD4+ T cells in up to 105 healthy donors. We found that regions of accessible chromatin (ATAC-peaks) are co-accessible at kilobase and megabase resolution, consistent with the three-dimensional chromatin organization measured by in situ Hi-C in T cells. Fifteen percent of genetic variants located within ATAC-peaks affected the accessibility of the corresponding peak (local-ATAC-QTLs). Local-ATAC-QTLs have the largest effects on co-accessible peaks, are associated with gene expression and are enriched for autoimmune disease variants. Our results provide insights into how natural genetic variants modulate cis-regulatory elements, in isolation or in concert, to influence gene expression

High-resolution genetic mapping with pooled sequencing

Background: Modern genetics has been transformed by high-throughput sequencing. New experimental designs in model organisms involve analyzing many individuals, pooled and sequenced in groups for increased efficiency. However, the uncertainty from pooling and the challenge of noisy sequencing data demand advanced computational methods. Results: We present MULTIPOOL, a computational method for genetic mapping in model organism crosses that are analyzed by pooled genotyping. Unlike other methods for the analysis of pooled sequence data, we simultaneously consider information from all linked chromosomal markers when estimating the location of a causal variant. Our use of informative sequencing reads is formulated as a discrete dynamic Bayesian network, which we extend with a continuous approximation that allows for rapid inference without a dependence on the pool size. MULTIPOOL generalizes to include biological replicates and case-only or case-control designs for binary and quantitative traits. Conclusions: Our increased information sharing and principled inclusion of relevant error sources improve resolution and accuracy when compared to existing methods, localizing associations to single genes in several cases. MULTIPOOL is freely available at http://cgs.csail.mit.edu/multipool/ webcite.National Science Foundation (U.S.) (Graduate Research Fellowship Grant 0645960

Evaluation of saliency tracking as an alternative for health monitoring in PMSM-drives under nonstationary conditions

This paper evaluates the capability of saliency tracking to assess the health condition of permanent magnet synchronous motor (PMSM) drives operating under nonstationary conditions. The evaluated scheme is based on saliency tracking methods, which are associated to the accurate sensorless control of AC drives without zero speed limitations. In this work two representative saliency tracking architectures are evaluated: High Frequency (HF) injection, and PWM transient excitation. Although a monitoring approach based on HF injection was previously reported, a comparative study to evaluate the most representative saliency tracking schemes to assess health condition in drives was still missing. The aim of this work is to fill out this gap by evaluating and comparing two saliency-based monitoring schemes (one based on HF-injection and the other based on PWM transient excitation) to evaluate their performance in the presence of inter-turn winding faults. Simulation and experimental results are presented which confirm that both schemes offer excellent detection capabilities and that are suitable for drives operating under nonstationary conditions including standstill operation. Significant differences are also found for instance, PWM transient excitation offers improved accuracy since the approach is not affected by the inverter nonlinearities and is suitable for full-speed range applications. The main drawback here is complexity and the hardware requirements. Schemes based on HF-injection proved to be very simple and provide comparable results; however a good performance is only guaranteed for the zero-to-medium speed range applications which limit their applicability

Patient expression of emotions and neurologist responses in first multiple sclerosis consultations

Background: Anxiety and depression are common in people with multiple sclerosis (MS), but data on emotional communication during MS consultations are lacking. We assessed patient expressions of emotion and neurologist responses during first-ever MS consultations using the Verona Coding Definitions of Emotional Sequences (VR-CoDES). Methods: We applied VR-CoDES to recordings/transcripts of 88 outpatient consultations (10 neurologists, four MS Italian centers). Before consultation, patients completed the Hospital Anxiety and Depression Scale (HADS). Multilevel sequential analysis was performed on the number of cues/concerns expressed by patients, and the proportion of reduce space responses by neurologists. Results: Patients expressed 492 cues and 45 concerns (median 4 cues and 1 concern per consultation). The commonest cues were verbal hints of hidden worries (cue type b, 41%) and references to stressful life events (type d, 26%). Variables independently associated with number of cues/concerns were: anxiety (HADS-Anxiety score &gt;8) (incidence risk ratio, IRR 1.08, 95% CI 1.06-1.09; p&lt;0.001); patient age (IRR 0.98, 95% CI 0.98-0.99; p&lt;0.001); neurologist age (IRR 0.94, 95% CI 0.92-0.96; p=0.03); and second opinion consultation (IRR 0.72, 95% CI 0.60-0.86; p=0.007). Neurologists reacted to patient emotions by reducing space (changing subject, taking no notice, giving medical advice) for 58% of cues and 76% of concerns. Anxiety was the only variable significantly associated with 'reduce space' responses (odds ratio 2.17, 95% CI 1.32-3.57; p=0.003). Conclusions: Patient emotional expressions varied widely, but VR-CoDES cues b and d were expressed most often. Patient anxiety was directly associated with emotional expressions; older age of patients and neurologists, and second opinion consultations were inversely associated with patient emotional expression. In over 50% of instances, neurologists responded to these expressions by reducing space, more so in anxious patients. These findings suggest that neurologists need to improve their skills in dealing with patient emotions

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.

Age at menarche is a marker of timing of puberty in females. It varies widely between individuals, is a heritable trait and is associated with risks for obesity, type 2 diabetes, cardiovascular disease, breast cancer and all-cause mortality. Studies of rare human disorders of puberty and animal models point to a complex hypothalamic-pituitary-hormonal regulation, but the mechanisms that determine pubertal timing and underlie its links to disease risk remain unclear. Here, using genome-wide and custom-genotyping arrays in up to 182,416 women of European descent from 57 studies, we found robust evidence (P < 5 × 10(-8)) for 123 signals at 106 genomic loci associated with age at menarche. Many loci were associated with other pubertal traits in both sexes, and there was substantial overlap with genes implicated in body mass index and various diseases, including rare disorders of puberty. Menarche signals were enriched in imprinted regions, with three loci (DLK1-WDR25, MKRN3-MAGEL2 and KCNK9) demonstrating parent-of-origin-specific associations concordant with known parental expression patterns. Pathway analyses implicated nuclear hormone receptors, particularly retinoic acid and γ-aminobutyric acid-B2 receptor signalling, among novel mechanisms that regulate pubertal timing in humans. Our findings suggest a genetic architecture involving at least hundreds of common variants in the coordinated timing of the pubertal transition

Patients' preferences for involvement in treatment decision making in Japan

BACKGROUND: A number of previous studies have suggested that the Japanese have few opportunities to participate in medical decision-making, as a result both of entrenched physician paternalism and national characteristics of dependency and passivity. The hypothesis that Japanese patients would wish to participate in treatment decision-making if adequate information were provided, and the decision to be made was clearly identified, was tested by interview survey. METHODS: The subjects were diabetic patients at a single outpatient clinic in Kyoto. One of three case study vignettes (pneumonia, gangrene or cancer) was randomly assigned to each subject and, employing face-to-face interviews, the subjects were asked what their wishes would be as patients, for treatment information, participation in decision-making and family involvement. RESULTS: 134 patients participated in the study, representing a response rate of 90%. The overall proportions of respondents who preferred active, collaborative, and passive roles were 12%, 71%, and 17%, respectively. Respondents to the cancer vignette were less likely to prefer an active role and were more likely to prefer family involvement in decision-making compared to non-cancer vignette respondents. If a physician's recommendation conflicted with their own wishes, 60% of the respondents for each vignette answered that they would choose to respect the physician's opinion, while few respondents would give the family's preference primary importance. CONCLUSIONS: Our study suggested that a majority of Japanese patients have positive attitudes towards participation in medical decision making if they are fully informed. Physicians will give greater patient satisfaction if they respond to the desire of patients for participation in decision-making