Miracle-dz/UniFAR-FTUs huggingface dataset:
Targeted resequencing reveals geographical patterns of differentiation for loci implicated in parallel evolution

Parallel divergence and speciation provide evidence for the role of divergent selection in generating biological diversity. Recent studies indicate that parallel phenotypic divergence may not have the same genetic basis in different geographical locations – ‘outlier loci’ (loci potentially affected by divergent selection) are often not shared among parallel instances of phenotypic divergence. However, limited sharing may be due, in part, to technical issues if false‐positive outliers occur. Here, we test this idea in the marine snail Littorina saxatilis, which has evolved two partly isolated ecotypes (adapted to crab predation vs. wave action) in multiple locations independently. We argue that if the low extent of sharing observed in earlier studies in this system is due to sampling effects, we expect outliers not to show elevated FST when sequenced in new samples from the original locations and also not to follow predictable geographical patterns of elevated FST. Following a hierarchical sampling design (within vs. between country), we applied capture sequencing, targeting outliers from earlier studies and control loci. We found that outliers again showed elevated levels of FST in their original location, suggesting they were not generated by sampling effects. Outliers were also likely to show increased FST in geographically close locations, which may be explained by higher levels of gene flow or shared ancestral genetic variation compared with more distant locations. However, in contrast to earlier findings, we also found some outlier types to show elevated FST in geographically distant locations. We discuss possible explanations for this unexpected result.
late life depression : a combined cortical thickness and structural covariance analysis

Late-life depression (LLD) has been associated with both generalized and focal neuroanatomical changes including grey matter atrophy and white mat ter bnormalities. However, previous literature has not been consistent and, in particular, its imp act on the topology organisation of brain networks remains to be established. In this multi-modal study, we first examined cortic al thickness, and applied graph theory to investigate structural cova riance networks in LLD. 33 subjects with LLD and 25 controls underwent T1-weighted, fluid attenu ated inversion recovery (FLAIR) and clinical assessments. Freesurfer was used to perform vertexwis comparisons of cortical thickness, while the Graph Analysis Toolbox (GAT) was implemented to construct and analyze the structural covariance networks. LLD showed a trend of lower th ickness in the left insular region (p<0.001 uncorrected). In addition, the structural network o f LLD was characterised by greater segregation, particularly showing higher transitivity (i.e. meas ure of clustering) and modularity (i.e. tendency fo r a network to be organised into sub-networks). It wa s also less robust against random failure and targeted attacks. Despite relative cortical preserv ation, the topology of the LLD network showed significant changes particularly in segregation. Th ese findings demonstrate the potential for graph theoretical approaches to complement conventional s tructural imaging analyses and provide novel insights into the heterogeneous aetiology and patho genesis of LLD. M AN US CR IP T AC CE PT ED ACCEPTED MANUSCRIPT Mak et al 3
Coordination and Cheap Talk in a Battle of the Sexes

We consider a Battle of the Sexes game with incomplete information and allow cheap talk regarding players' private information before the game is played. We prove that the unique fully revealing symmetric cheap talk equilibrium has a desirable coordination property. Such coordination can also be obtained as a partially revealing cheap talk equilibrium. These outcomes can also be achieved using corresponding incentive compatible mechanisms, however, for different ranges of the prior probability.
Affect Expression and Self-Regulation Capacities of Infants Exposed in utero to Psychotropics

This study explored the affect expression and self-regulation capacities of 8-month-old infants exposed in utero to psychotropic medications. This was a continuation of our previous study conducted on the same cohort when the infants were 3 months old. Psychotropics implicated included selective serotonin reuptake inhibitors (SSRIs), and a benzodiazepine derivative anxiolytic (clonazepam). The three comparison groups were: control (n = 23; infants not exposed to psychotropics in utero), SSRI-alone (n = 22; infants exposed to SSRIs only and having mothers who had a primary diagnosis of depressive disorder without having comorbid anxiety disorder), and SSRI+ group (n = 15; infants gestationally exposed to SSRIs and clonazepam and having mothers that had both clinical depression and anxiety disorder). Using the Parent–Child Early Relational Assessment Scale, infants were assessed in a dyadic context during free play and a structured task. There were significant differences in psychotropic exposed and non-exposed dyads regarding infant negative affect management. There were significant associations between the SSRI+ group of mothers and infant negative affect. This group of mothers also showed significant associations with infants’ averting and avoiding behaviors in both play situations. The SSRI-alone group was similar to the control group and showed variable associations with infant’s positive, negative, and sober moods unlike the SSRI+ group. There were no differences in infants’ capacity for self-regulation in psychotropic exposed and non-exposed groups. Increased awareness of these vulnerable subgroups (SSRI-alone and SSRI+) is needed, in order to safeguard these dyads through better support systems and improved management.
Considerations for screening tool selection and role of predictive and concurrent validity

Purpose of reviewNutrition screening tool selection can be difficult. This review critically examines the relevance of validity, specifically concurrent (agreement between tools) and predictive validity (prediction of outcomes), which have been the focus of several recent studies. An operational framework for screening tool selection is provided to contextualise the findings. Recent findingsStudies of predictive and concurrent validity involving screening tools comprising a variable number of nutritional and non-nutritional items (some nonmodifiable) have yielded inconsistent results. The use of one tool as a gold standard to judge the relative merits of other tools can be misleading because there is no agreed gold standard and different tools were designed for diagnostic, prognostic or other purposes. The use of observed outcomes (without nutritional intervention) as the gold standard may not adequately reflect the value of tools designed to assess nutritional status and need for nutritional intervention. SummaryOver-reliance on concurrent and predictive validity can be confusing and even counter-productive if used inappropriately. A proposed framework for screening tool selection indicates many factors should be considered so that there is purpose and harmony between the screening tool and the screening programme.
CHARACTERIZATION of HIGH STRAIN RATE BEHAVIOR of TAC/CNTs/SIC CMCs PREPARED by SPARK PLASMA SINTERING

Silicon carbide (SiC) ceramics are one of the best candidates for high temperature structural applications. However, due to the inherent drawbacks of hardness, porosity, and brittleness for ceramic materials and the specific application environment involving exposure to oxidation fuels, or aero heating, reinforcements of carbon nanotubes (CNTs) and tantalum carbide (TaC) are considered to improve the overall material properties; of particular interest are the fracture toughness, energy absorption ability, and oxidation resistance. Conventional fabrication of CNTs reinforced ceramic matrix composites (CMCs) involves hot pressing techniques, which are characterized by high pressure and a long processing time, but can destroy CNTs. The current research utilizes a rapid consolidation technique of spark plasma sintering (SPS) which densifies the ceramics at a relatively lower temperature and a much shorter holding time with improved bonding quality and finer microstructure. A two-stage SPS of TaC and/or CNTs reinforced SiC CMCs was developed to investigate the sintering parameters, such as pressure, heating rate, and temperature on the densification behavior and mechanical properties. The oxidation mechanism of CNTs/SiC ceramics, as well as the TaC additives effect on the thermal oxidation resistance of the TaC/CNTs/SiC systems were examined up to 1500 oC. The influences of sample thickness, impact energy (loading rates), temperature and moisture on the compressive dynamic response of TaC and/or CNTs reinforced SiC CMCs were conducted by a penetration split Hopkinson pressure bar (P-SHPB). The fracture mechanics of TaC/CNTs/SiC CMCs were studied both quasi-statically and dynamically by Vickers indentation and a three point bending test on the modified SHPB with a pulse shaper. The possible toughening mechanisms provided by the CNTs reinforcement were directly observed. Wave propagation in SHPB was validated numerically and the prediction of damage evolution was carried out through user-defined material subroutine VUMAT in ABAQUS/explicit. The above investigations provide new perspectives which could impact a wide range of understandings and applications for the TaC/CNTs/SiC CMCs.
Stereotypes Associated With Age-related Conditions and Assistive Device Use in Canadian Media.

PURPOSE OF THE STUDY Newspapers are an important source of information. The discourses within the media can influence public attitudes and support or discourage stereotypical portrayals of older individuals. This study critically examined discourses within a Canadian newspaper in terms of stereotypical depictions of age-related health conditions and assistive technology devices (ATDs). DESIGN AND METHODS Four years (2009-2013) of Globe and Mail articles were searched for terms relevant to the research question. A total of 65 articles were retained, and a critical discourse analysis (CDA) of the texts was conducted. The articles were coded for stereotypes associated with age-related health conditions and ATDs, consequences of the stereotyping, and context (overall setting or background) of the discourse. RESULTS The primary code list included 4 contexts, 13 stereotypes, and 9 consequences of stereotyping. CDA revealed discourses relating to (a) maintaining autonomy in a stereotypical world, (b) ATDs as obstacles in employment, (c) barriers to help seeking for age-related conditions, and (d) people in power setting the stage for discrimination. IMPLICATIONS Our findings indicate that discourses in the Canadian media include stereotypes associated with age-related health conditions. Further, depictions of health conditions and ATDs may exacerbate existing stereotypes about older individuals, limit the options available to them, lead to a reduction in help seeking, and lower ATD use. Education about the realities of age-related health changes and ATDs is needed in order to diminish stereotypes and encourage ATD uptake and use.
Adaptive Bayesian multivariate density estimation with Dirichlet mixtures BY WEINING SHEN

We show that rate-adaptive multivariate density estimation can be performed using Bayesian methods based on Dirichlet mixtures of normal kernels with a prior distribution on the kernel’s covariance matrix parameter. We derive sufficient conditions on the prior specification that guarantee convergence to a true density at a rate that is minimax optimal for the smoothness class to which the true density belongs. No prior knowledge of smoothness is assumed. The sufficient conditions are shown to hold for the Dirichlet location mixture-of-normals prior with a Gaussian base measure and an inverse Wishart prior on the covariance matrix parameter. Locally Hölder smoothness classes and their anisotropic extensions are considered. Our study involves several technical novelties, including sharp approximation of finitely differentiable multivariate densities by normal mixtures and a new sieve on the space of such densities.
The Munich LSTM-RNN Approach to the MediaEval 2014 "Emotion in Music'" Task

In this paper we describe TUM's approach for the MediaEval's \Emotion in Music" task. The goal of this task is to automatically estimate the emotions expressed by music (in terms of Arousal and Valence) in a time-continuous fashion. Our system consists of Long-Short Term Memory Recurrent Neural Networks (LSTM-RNN) for dynamic Arousal and Valence regression. We used two di erent sets of acoustic and psychoacoustic features that have been previously proven as e ective for emotion prediction in music and speech. The best model yielded an average Pearson's correlation coe-cient of 0.354 (Arousal) and 0.198 (Valence), and an average Root Mean Squared Error of 0.102 (Arousal) and 0.079 (Valence).
Marijuana use is associated with risky sexual behaviors in treatment-seeking polysubstance abusers

Abstract Background: Multiple types of substance use are associated with HIV risk behaviors, but relatively little research has examined the association between marijuana use and risky sexual activities in treatment-seeking polysubstance abusing patients. Objectives: This study evaluated the relationship between marijuana use and sexual behaviors in 239 patients with cocaine, opioid or alcohol use disorders who were initiating outpatient substance use treatment. Methods: Participants completed the HIV Risk Behavior Scale and were classified into one of three groups based on their marijuana use histories: never (n = 66), past but not current use (n = 124) or current use (n = 49). Results: Compared to never marijuana users, current and former marijuana users had a greater likelihood of having more than 50 lifetime sexual partners (odds ratio [OR] and 95% confidence interval [CI] = 3.9 [1.0–15.7] and 5.2 [1.6–17.3], respectively). Former marijuana users had increased risk of low frequency condom use with casual partners relative to never users (OR [95% CI] = 2.9 [1.1–7.6]). Moreover, current marijuana users were more likely than never users to have had more than two recent sexual partners (OR [95% CI] = 8.1 [1.94–33.44]). Conclusion: Treatment-seeking polysubstance abusers with current or past marijuana use histories may be at greater risk of HIV infection than their counterparts who do not use marijuana. These data underscore the importance of increasing awareness about the potential association between marijuana use and increased high-risk sexual behavior among polysubstance abusing patients.
Bleb morphology and histology in a rabbit model of glaucoma filtration surgery using Ozurdex® or mitomycin-C

Purpose To determine the effect of a sustained-release dexamethasone implant (Ozurdex®) on wound healing after glaucoma filtration surgery in a rabbit model. Methods Twelve New Zealand white rabbits were divided into three groups: filtration surgery with intraoperative subconjunctival implantation of Ozurdex® (n=6), filtration surgery with intraoperative topical application of mitomycin-C (MMC; n=6), and filtration surgery with intraoperative topical application of balanced salt solution (BSS; n=12). A standard scale was used to grade bleb vascularity at three and six weeks after the initial operation. Bleb survival was also recorded for comparison between the three groups. Histologic analysis was performed with attention to cellularity and collagen deposition. Results MMC-treated blebs demonstrated decreased numbers of goblet cells compared to all other groups. Blebs treated with Ozurdex® maintained a near normal number of goblet cells with modest collagen deposition. The control eyes treated with only BSS had significant collagen deposition and increased cellularity compared to both the Ozurdex® and MMC groups. Bleb vascularity was not significantly different among groups at the three and six week post-operative evaluations. MMC-treated and Ozurdex®-treated blebs had significantly prolonged bleb survival compared to blebs treated with only BSS. In addition, MMC-treated blebs had significantly longer survival compared to Ozurdex®-treated blebs. Conclusions The results of this study support the utility of extended-release dexamethasone (Ozurdex®) as a wound modulating agent in a rabbit model of filtration surgery. Further animal and human studies are needed to better characterize a possible role for Ozurdex® in filtration surgery.
Joint Design of Network Coding and Channel Decoding for Wireless Networks

Network coding has been receiving much attention recently for its ability to improve network throughput and enhance network robustness. In this paper, we investigate the design of network coding in wireless networks and propose a combined low complexity network coding and channel decoding scheme. We analyze the capacity of the proposed scheme for both the binary symmetric channel (BSC) and AWGN channel and show that it can achieve almost the same channel capacity as traditional network coding with a small degradation in the system bit error rate (BER) performance while achieving almost 50% complexity reduction. It is also shown that the proposed network coding design can be applied in wireless cooperative networks.
Genomic patterns of pleiotropy and the evolution of complexity

Pleiotropy refers to the phenomenon of a single mutation or gene affecting multiple distinct phenotypic traits and has broad implications in many areas of biology. Due to its central importance, pleiotropy has also been extensively modeled, albeit with virtually no empirical basis. Analyzing phenotypes of large numbers of yeast, nematode, and mouse mutants, we here describe the genomic patterns of pleiotropy. We show that the fraction of traits altered appreciably by the deletion of a gene is minute for most genes and the gene–trait relationship is highly modular. The standardized size of the phenotypic effect of a gene on a trait is approximately normally distributed with variable SDs for different genes, which gives rise to the surprising observation of a larger per-trait effect for genes affecting more traits. This scaling property counteracts the pleiotropy-associated reduction in adaptation rate (i.e., the “cost of complexity”) in a nonlinear fashion, resulting in the highest adaptation rate for organisms of intermediate complexity rather than low complexity. Intriguingly, the observed scaling exponent falls in a narrow range that maximizes the optimal complexity. Together, the genome-wide observations of overall low pleiotropy, high modularity, and larger per-trait effects from genes of higher pleiotropy necessitate major revisions of theoretical models of pleiotropy and suggest that pleiotropy has not only allowed but also promoted the evolution of complexity.
The Feedback Robust MPC for LPV Systems With Bounded Rates of Parameter Changes

This note addresses the feedback robust model predictive control (FRMPC) for a category of linear parameter varying (LPV) systems with bounded rates of parameter changes. Based on the bounded rates of parameter changes and the detected current system parameters, future model variations can be described by a sequence of polytopic families with the same number of vertices. Then a FRMPC algorithm is developed. Since both the future model variations and the corresponding sequence of feedback control laws are adopted, the FRMPC can achieve high control performance. By transferring main design work to offline design, an efficient FRMPC is also developed. The recursive feasibility and closed-loop stability of the FRMPCs are proved to be guaranteed.
Therapy of Chagas Disease: Implications for Levels of Prevention

This paper reviews the evidence supporting the use of etiological treatment for Chagas disease that has changed the standard of care for patients with Trypanosoma cruzi infection in the last decades. Implications of this evidence on different levels of prevention as well as gaps in current knowledge are also discussed. In this regard, etiological treatment has shown to be beneficial as an intervention for secondary prevention to successfully cure the infection or to delay, reduce, or prevent the progression to disease, and as primary disease prevention by breaking the chain of transmission. Timely diagnosis during initial stages would allow for the prescription of appropriate therapies mainly in the primary health care system thus improving chances for a better quality of life. Based on current evidence, etiological treatment has to be considered as an essential public health strategy useful to reduce disease burden and to eliminate Chagas disease altogether.
Genetic or chemical protease inhibition causes significant changes in the Bacillus subtilis exoproteome

Bacillus subtilis is a prolific producer of enzymes and biopharmaceuticals. However, the susceptibility of heterologous proteins to degradation by (extracellular) proteases is a major limitation for use of B. subtilis as a protein cell factory. An increase in protein production levels has previously been achieved by using either protease‐deficient strains or addition of protease inhibitors to B. subtilis cultures. Notably, the effects of genetic and chemical inhibition of proteases have thus far not been compared in a systematic way. In the present studies, we therefore compared the exoproteomes of cells in which extracellular proteases were genetically or chemically inactivated. The results show substantial differences in the relative abundance of various extracellular proteins. Furthermore, a comparison of the effects of genetic and/or chemical protease inhibition on the stress response triggered by (over) production of secreted proteins showed that chemical protease inhibition provoked a genuine secretion stress response. From a physiological point of view, this suggests that the deletion of protease genes is a better way to prevent product degradation than the use of protease inhibitors. Importantly however, studies with human interleukin‐3 show that chemical protease inhibition can result in improved production of protease‐sensitive secreted proteins even in mutant strains lacking eight extracellular proteases.
A vanishing theorem for log canonical pairs

Using inversion of adjunction, we deduce from Nadel's theorem a vanishing property for ideals sheaves on projective varieties, a special case of which recovers a result due to Bertram--Ein--Lazarsfeld. This enables us to generalize to a large class of projective schemes certain bounds on Castelnuovo--Mumford regularity previously obtained by Bertram--Ein--Lazarsfeld in the smooth case and by Chardin--Ulrich for locally complete intersection varieties with rational singularities. Our results are tested on several examples.
Spurious Local Minima are Common in Two-Layer ReLU Neural Networks

We consider the optimization problem associated with training simple ReLU neural networks of the form $\mathbf{x}\mapsto \sum_{i=1}^{k}\max\{0,\mathbf{w}_i^\top \mathbf{x}\}$ with respect to the squared loss. We provide a computer-assisted proof that even if the input distribution is standard Gaussian, even if the dimension is arbitrarily large, and even if the target values are generated by such a network, with orthonormal parameter vectors, the problem can still have spurious local minima once $6\le k\le 20$. By a concentration of measure argument, this implies that in high input dimensions, \emph{nearly all} target networks of the relevant sizes lead to spurious local minima. Moreover, we conduct experiments which show that the probability of hitting such local minima is quite high, and increasing with the network size. On the positive side, mild over-parameterization appears to drastically reduce such local minima, indicating that an over-parameterization assumption is necessary to get a positive result in this setting.