Miracle-dz/UniFAR-FTUs huggingface dataset:
Brain transcriptome of the violet-eared waxbill Uraeginthus granatina and recent evolution in the songbird genome

Songbirds are important models for the study of social behaviour and communication. To complement the recent genome sequencing of the domesticated zebra finch, we sequenced the brain transcriptome of a closely related songbird species, the violet-eared waxbill (Uraeginthus granatina). Both the zebra finch and violet-eared waxbill are members of the family Estrildidae, but differ markedly in their social behaviour. Using Roche 454 RNA sequencing, we generated an assembly and annotation of 11 084 waxbill orthologues of 17 475 zebra finch genes (64%), with an average transcript length of 1555 bp. We also identified 5985 single nucleotide polymorphisms (SNPs) of potential utility for future population genomic studies. Comparing the two species, we found evidence for rapid protein evolution (ω) and low polymorphism of the avian Z sex chromosome, consistent with prior studies of more divergent avian species. An intriguing outlier was putative chromosome 4A, which showed a high density of SNPs and low evolutionary rate relative to other chromosomes. Genome-wide ω was identical in zebra finch and violet-eared waxbill lineages, suggesting a similar demographic history with efficient purifying natural selection. Further comparisons of these and other estrildid finches may provide insights into the evolutionary neurogenomics of social behaviour.
Arrays and pointers considered harmful

Formal methods of software development are becoming important topics in software engineering as evidenced by the fact that three important publications IEEE Transactions on Software Engineering, IEEE Software and IEEE Computer were recently devoted to this topic. This paper looks at the effect that current problems with formal methods might have on language design. The paper describes what a formal method of software development is, provides an example of a mathematical specification and then, by examining the problems involved in formal data refinement, puts forward the proposition that we should now regard the array and the pointer in the same way that we regarded the goto statement during the seventies.
Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana

Significance Anticipating the effect of climate change on plants requires understanding its evolutionary consequence on traits and genes in complex realistic environments. How seasonal variation has an impact on the dynamics of adaptation in natural populations remains unclear. We simulated adaptation to different climate change scenarios, grounding our analysis in experimental data and explicitly exploring seasonal variation. Seasonal variation dramatically affected the dynamics of adaptation: Marked seasonality led to genetic differentiation within the population to different seasonal periods, whereas low seasonality led to a single population with fast-evolving fitness. Our results suggest the prevalence of phenotypic plasticity across environmental conditions in determining how climate change will shift selection on traits and loci. In this unpredictable context, maintaining broad genomic diversity is critical. Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico “resurrection experiments” showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.
Analysis of BRCA1 and BRCA2 mutations in Brazilian breast cancer patients with positive family history.

CONTEXT AND OBJECTIVE BRCA1 and BRCA2 are the two principal hereditary breast cancer susceptibility genes, and the prevalence of their mutations among Brazilian women is unknown. The objective was to detect BRCA1 and BRCA2 mutations in Brazilian patients with breast cancer, so as to establish genetic profiles. DESIGN AND SETTING Cross-sectional study, in Centro de Atenção Integral à Saúde da Mulher, Universidade Estadual de Campinas, Brazil, and Institute of Pathology and Molecular Immunology, University of Porto, Portugal. METHODS Thirty-one breast cancer patients with positive family history (criteria from the Breast Cancer Linkage Consortium) were studied, and genomic DNA was extracted from peripheral blood. Single-strand conformation polymorphism was used for the analysis of exons 2, 3, 5, and 20 of BRCA1. Cases showing PCR products with abnormal bands were sequenced. Exon 11 of BRCA1 and exons 10 and 11 of BRCA2 were directly sequenced in both directions. RESULTS Four mutations were detected: one in BRCA1 and three in BRCA2. The BRCA1 mutation is a frameshift located at codon 1756 of exon 20: 5382 ins C. Two BRCA2 mutations were nonsense mutations located at exon 11: S2219X and the other was an unclassified variant located at exon 11: C1 290Y. CONCLUSION The BRCA1 or BRCA2 mutation prevalence found among women with breast cancer and such family history was 13% (4/31). Larger studies are needed to establish the significance of BRCA mutations among Brazilian women and the prevalence of specific mutations.
A perception‐driven autonomous urban vehicle

This paper describes the architecture and implementation of an autonomous passenger vehicle designed to navigate using locally perceived information in preference to potentially inaccurate or incomplete map data. The vehicle architecture was designed to handle the original DARPA Urban Challenge requirements of perceiving and navigating a road network with segments defined by sparse waypoints. The vehicle implementation includes many heterogeneous sensors with significant communications and computation bandwidth to capture and process high‐resolution, high‐rate sensor data. The output of the comprehensive environmental sensing subsystem is fed into a kinodynamic motion planning algorithm to generate all vehicle motion. The requirements of driving in lanes, three‐point turns, parking, and maneuvering through obstacle fields are all generated with a unified planner. A key aspect of the planner is its use of closed‐loop simulation in a rapidly exploring randomized trees algorithm, which can randomly explore the space while efficiently generating smooth trajectories in a dynamic and uncertain environment. The overall system was realized through the creation of a powerful new suite of software tools for message passing, logging, and visualization. These innovations provide a strong platform for future research in autonomous driving in global positioning system–denied and highly dynamic environments with poor a priori information. © 2008 Wiley Periodicals, Inc.
Why are gainers more risk seeking

The phenomenon that prior gains may increase people’s willingness to accept risky gambles is named as the house money effect (Thaler and Johnson, 1990). Many studies have shown that the “house money effect” is a robust phenomenon but few scholars explain the mechanism of it well. We suppose the reason for the house money effect is that the ante (starting amount) is from the prior gambling profits, and its potential loss has relatively low psychological value. To test this hypothesis, we designed a series of studies using two-stage gambles. A total of 915 university students participated. In Study 1, in addition to a standard condition (which replicated the basic effect), we test how people respond to “prospect theory, with memory” frame, a “concreteness” frame and “quasi-hedonic” editing. None of these types of frames result in a significant house money effect. In Study 2, we certify the reference point shift to 100 Yuan in the second-stage gamble, thus the house money effect can be regarded as the absence of loss aversion; Study 3, consisting of 3 sub-experiments, indicated that gambling profits and normal income will open different mental accounts which are spent quite differently. The pain of losing 100 Yuan allowance is more serious than that of losing 100 Yuan gambling wins. People will typically reject the gamble of 50/50 chance to gain or lose 100 Yuan if the ante is from the “normal income account”, but accept if the ante is from the “windfall account”. The results of the series of experiments prove the accuracy of our hypothesis mostly.
Hypotension , Hypoxia , and Head Injury

Results: One hundred seven patients met the enrollment criteria (median Glasgow Coma Score, 7). Overall mortality was 43%. Twenty-six patients (24%) had hypotension while in the emergency department, with an average of 1.5 episodes per patient (mean duration, 9.1 minutes). Of these 26 patients with hypotension, 17 (65%) died (P=.01). When the number of hypotensive episodes increased from 1 to 2 or more, the odds ratio for death increased from 2.1 to 8.1. Forty-one patients (38%) had hypoxia, with an average of 2.1 episodes per patient (mean duration, 8.7 minutes). Of these 41 patients with hypoxia, 18 (44%) died (P=.68).
Improved Endothelium-Dependent Vasodilation After Blockade of Endothelin Receptors in Patients With Essential Hypertension

Background—Hypertensive patients have both impaired endothelium-dependent vasodilation and increased activity of the endothelin (ET-1) system, which participate in their increased vascular tone and may predispose them to atherosclerosis. This study investigated the contribution of increased ET-1 activity to the impaired endothelium-dependent vasodilator function of hypertensive patients. Methods and Results—Forearm blood flow (FBF) responses to intraarterial infusion of acetylcholine (ACh; 7.5, 15, and 30 &mgr;g/min) and sodium nitroprusside (SNP; 0.8,1.6, and 3.2 &mgr;g/min) were assessed by strain-gauge plethysmography before and after nonselective blockade of ETA and ETB receptors by combined infusion of BQ-123 (ETA blocker; 100 nmol/min) and BQ-788 (ETB blocker; 50 nmol/min). During saline administration, the vasodilator response to ACh was significantly blunted in hypertensive patients compared with controls (P <0.001), whereas the vasodilator effect of SNP was not different between groups (P =0.74). Blockade of ET-1 receptors resulted in a significant increase in FBF from baseline in hypertensive patients (P <0.008) but not in controls (P =0.15). In hypertensive patients, a combined ETA/B blockade resulted in a significant potentiation of the vasodilator response to ACh compared with saline (P =0.01), whereas the response to SNP was unchanged (P =0.44). In contrast, the response to ACh was not significantly modified by ET-1 receptor antagonism in healthy subjects (P =0.14 compared with saline). Conclusions—These findings indicate that blockade of ET-1 receptors improves endothelium-dependent vasodilator function in hypertensive patients, thereby suggesting that an increased ET-1 activity may play a role in the pathophysiology of this abnormality.
Characterization and Comparison of the Structural Features, Immune-Modulatory and Anti-Avian Influenza Virus Activities Conferred by Three Algal Sulfated Polysaccharides

Three marine macroalgae, i.e., Grateloupia filicina, Ulva pertusa and Sargassum qingdaoense, were selected as the deputies of Rhodophyta, Chlorophyta and Ochrophyta for comparative analysis of the molecular structures and biological activities of sulfated polysaccharides (SP). The ratio of water-soluble polysaccharides, the monosaccharide composition and the sulfated contents of three extracted SPs were determined, and their structures were characterized by Fourier transformation infrared spectroscopy. In addition, biological activity analysis showed that all three SPs had immune-modulatory activity both in vitro and in vivo, and SPs from S. qingdaoense had the best effect. Further bioassays showed that three SPs could not only enhance the immunity level stimulated by inactivated avian influenza virus (AIV) in vivo but also significantly inhibited the activity of activated AIV (H9N2 subtype) in vitro. G. filicina SP exhibited the strongest anti-AIV activity. These results revealed the variations in structural features and bioactivities among three SPs and indicated the potential adjuvants for immune-enhancement and anti-AIV.
Dissecting Anomalies

The anomalous returns associated with net stock issues, accruals, and momentum are pervasive; they show up in all size groups (micro, small, and big) in cross-section regressions, and they are also strong in sorts, at least in the extremes. The asset growth and profitability anomalies are less robust. There is an asset growth anomaly in average returns on microcaps and small stocks, but it is absent for big stocks. Among profitable firms, higher profitability tends to be associated with abnormally high returns, but there is little evidence that unprofitable firms have unusually low returns.
Primary Sclerosing Cholangitis Associated with Elevated ImmunoglobulinG4: Clinical Characteristics and Response to Therapy

Steroid responsive biliary strictures in patients fulfilling criteria for primary sclerosing cholangitis (PSC) have been reported. The clinical course and response to therapy in patients with PSC with elevated immunoglobulin G4 (IgG4) levels has not been investigated previously. Patients with PSC were screened for IgG4-related biliary disease during 2006 to 2008 and data were collected prospectively. A total of 33 out of 285 (12%) patients with PSC (18 males) had elevated IgG4 (>140mg/dL) with a median age of 46 years (interquartile range 29-60); 24 could be evaluated. All patients had both intrahepatic and extrahepatic biliary strictures. Pancreatic disorders were found in 4 (17%), and 11 of 24 (46%) presented with jaundice; 8 of 24 (33%) received biliary stenting for a median time of 4 months (0-6). Liver cirrhosis was diagnosed in 12 of the 24 (50%). Overall, 18 patients were treated with corticosteroids and 6 patients managed conservatively. Nine of 10 patients with elevated bilirubin had improvement. Alkaline phosphatase decreased significantly at 2 months and at last follow-up. IgG4 levels at baseline were 242 (216-357) mg/dL and decreased to 109 (80-236) at 2 months (P < 0.05) and 174 (115-269) at last follow-up (P < 0.05). A total of 39% had adverse effects of steroids, mostly hyperglycemia. Relapses occurred in 7 of the 14 (50%), but biliary stents could be removed in all. Elevated IgG4 levels were observed in 12% of typical patients with PSC. Prevalence of cirrhosis was high, suggesting a severe liver disease course. Most patients had a good biochemical response to steroids, but adverse effects were common. Future work should be directed at finding therapy that is more effective, better tolerated, and of more lasting benefit.
Sample-Level CNN Architectures for Music Auto-Tagging Using Raw Waveforms

Recent work has shown that the end-to-end approach using convolutional neural network (CNN) is effective in various types of machine learning tasks. For audio signals, the approach takes raw waveforms as input using an 1-D convolution layer. In this paper, we improve the 1-D CNN architecture for music auto-tagging by adopting building blocks from state-of-the-art image classification models, ResNets and SENets, and adding multi-level feature aggregation to it. We compare different combinations of the modules in building CNN architectures. The results show that they achieve significant improvements over previous state-of-the-art models on the MagnaTagATune dataset and comparable results on Million Song Dataset. Furthermore, we analyze and visualize our model to show how the 1-D CNN operates.
Quantification of topological changes in retinal vascular architecture in essential and malignant hypertension

Objective Grading of hypertension severity by fundoscopic appearance is difficult and inaccurate. We investigated whether essential hypertension (EHT) and malignant phase hypertension (MHT) were associated with quantifiable abnormalities of the topology and architecture of the retinal circulation. Methods The topology and architecture of the retinal microvasculature were compared in images from 20 normotensive subjects, 20 patients with EHT and 20 patients with MHT. Digitized retinal photographs were analysed by a novel multiscale image analysis method using a semi-automated program to quantify geometrical and topological properties of arteriolar and venular trees. Results EHT was associated with an increase in the arteriolar length-to-diameter ratio (P < 0.01). There were also alterations in arteriolar topology indicative of rarefaction, including a marked reduction in the number of terminal branches in EHT (P < 0.01). These changes in the arteriolar network were exaggerated in MHT and there was also increased venular tortuosity and venular rarefaction in MHT compared with normotensive subjects. Conclusions Hypertension is associated with marked topological alterations in the retinal vasculature, and quantification of these changes may be a useful novel approach to the assessment of target organ damage in hypertension.
Striatal Dopamine Metabolism in Monoamine Oxidase B‐Deficient Mice : A Brain Dialysis Study

Abstract : We have studied striatal dopamine (DA) metabolism in monoamine oxidase (MAO) B‐deficient mice using brain microdialysis. Baseline DA levels were similar in wild‐type and knock‐out (KO) mice. Administration of a selective MAO A inhibitor, clorgyline (2 mg/kg), increased DA levels and decreased levels of its metabolites in all mice, but a selective MAO B inhibitor, l‐deprenyl (1 mg/kg), had no effect. Administration of 10 and 50 mg/kg l‐DOPA, the precursor of DA, increased the levels of DA similarly in wild‐type and KO mice. The highest dose of l‐DOPA (100 mg/kg) produced a larger increase in DA in KO than wild‐type mice. This difference was abolished by pretreating wild‐type mice with l‐deprenyl. These results suggest that in mice, DA is only metabolized by MAO A under basal conditions and by both MAO A and B at high concentrations. This is in contrast to the rat, where DA is always metabolized by MAO A regardless of concentration.
Antiferromagnetic order of strongly interacting fermions in a trap: real-space dynamical mean-field analysis

We apply dynamical mean-field theory to strongly interacting fermions in an inhomogeneous environment. With the help of this real-space dynamical mean-field theory (R-DMFT) we investigate antiferromagnetic states of repulsively interacting fermions with spin- in a harmonic potential. Within R-DMFT, antiferromagnetic order is found to be stable in spatial regions with total particle density close to one, but persists also in parts of the system where the local density significantly deviates from half filling. In systems with spin imbalance, we find that antiferromagnetism is gradually suppressed and phase separation emerges beyond a critical value of the spin imbalance.
“It Might Actually Work This Time”: Benefits and Barriers to Adapted 12-Step Facilitation Therapy and Mutual-Help Group Attendance From the Perspective of Dually Diagnosed Individuals

AbstractMost U.S. healthcare professionals encourage mutual-help group involvement as an adjunct to treatment or aftercare for individuals with substance use disorders, yet there are multiple challenges in engaging in these community groups. Dually diagnosed individuals (DDIs) may face additional challenges in affiliating with mutual-help groups. Twelve-step facilitation for DDIs (TSF-DD), a manualized treatment to facilitate mutual-help group involvement, was developed to help patients engage in Double Trouble in Recovery (DTR), a mutual-help group tailored to DDIs. Given the promising role that TSF-DD and DTR may have for increasing abstinence while managing psychiatric symptoms, the aim of the current study was to systematically examine reasons for TSF-DD and DTR attendance from the perspective of DDIs using focus group data. Participants were a subset (n = 15) of individuals diagnosed with an alcohol use disorder as well as a major depressive, bipolar, or psychotic disorder who participated in a parent study testing the efficacy of TSF-DD for increasing mutual-help group involvement and reducing alcohol use. Analyses of focus group data revealed that participants construed DTR and TSF-DD as helpful tools in the understanding and management of their disorders. Relative to other mutual-help groups in which participants reported feeling ostracized because of their dual diagnoses, participants reported that it was beneficial to learn about dual disorders in a safe and accepting environment. Participants also expressed aspects that they disliked. Results from this study yield helpful empirical recommendations to healthcare professionals seeking to increase DDIs’ participation in DTR or other mutual-help groups.