Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlated evolution of flower size and seed number in flowering plants (monocotyledons)

Background and Aims Kin selection theory predicts that a parent may minimize deleterious effects of competition among seeds developing within ovaries by increasing the genetic relatedness of seeds within an ovary. Alternatively, the number of developing seeds could be reduced to one or a few. It has also been suggested that single or few seeded fruits may be correlated with small flowers, and multi-ovulate ovaries or many seeded fruits may be associated with large flowers with specialized pollination mechanisms. We examined the correlation between flower size and seed number in 69 families of monocotyledons to assess if correlations are significant and independent of phylogeny. Methods We first examined the effect of phylogenetic history on the evolution of these two traits, flower size and seed number, and then mapped correlations between them on the latest phylogenetic tree of monocotyledons. Results The results provide phylogenetically robust evidence of strong correlated evolution between flower size and seed number and show that correlated evolution of traits is not constrained by phylogenetic history of taxa. Moreover, the two character combinations, small flowers and a single or few seeds per fruit, and large flowers and many seeded fruits, have persisted in monocotyledons longer than other trait combinations. Conclusions The analyses support the suggestion that most angiosperms may fall into two categories, one with large flowers and many seeded fruits and the other with small flowers and single or few seeded fruits, and kin selection within ovaries may explain the observed patterns.
Clinical Characteristics, Life Adversities and Personality Traits in Monozygotic Twins With, at Risk of and Without Affective Disorders

Background: Affective disorders have a long-term impact on psychiatric health and are caused by multiple interacting factors including familial risk, childhood adversity, life events and personality traits. Methods: In this study, monozygotic twins (MZ) at familial risk (indexed by affective disorder in their co-twin; high-risk group), affected MZ twins (indexed by a diagnosis with affective disorder) and MZ twins with no family history of affective disorder (low-risk group) were identified through cross-linking of nation-wide Danish registers. In total, 204 MZ twins were included and psychopathology, personality traits and life adversity were evaluated by semi-structured interviews and questionnaires. Results: Affected MZ twins presented with more subclinical affective symptoms and were functionally impaired as evidenced by higher unemployment rates and reduced functional status. The affected and the high-risk groups reported more childhood adversity and had experienced more stressful life events than the low-risk group. A direct comparison within the discordant twin pairs showed that the high-risk twins presented fewer affective symptoms, better functional status, more extraversion and lower neuroticism scores than their affected co-twins although they had equal levels of life adversity as their affected co-twins. Conclusion: These findings add to the evidence indicating that patients experience higher neuroticism, persistent subclinical symptoms and reduced socio-occupational function after affective episodes. Additionally, neuroticism and extraversion seem capable of moderating the sensitivity to exposure from the environment.
Global agreement on alternative testing.

Mobile genetic elements have significantly contributed to the shaping of mammalian genomes. The RTAnalyzer software tracks sequences of retrotransposed origin by scoring the signature results from an L1-mediated insertion within a genome. More specifically, a sequence of interest is searched for in genomic databases using BLAST. Each hit, along with additional 50 and 30 sequences of pre-defined lengths, is saved. RTAnalyzer searches for specific L1 retrotransposition signatures (i.e. target site duplication, endonuclease cleavage site and poly(A)), and then calculates an overall retrotransposition score. This score represents the likelihood of a given sequence originating from a retrotransposition event involving the L1 machinery. RTAnalyzer may be used under GNU public license, and is available at http://www. riboclub.org/rtanalyzer.
To what extent is the elevated risk of psychological distress in people with diabetes accounted for by physical disability? Findings from a large population-based study

Objectives People with diabetes experience an elevated risk of psychological distress compared with people without diabetes. It is unclear how much of this elevated risk is attributable to the greater levels of physical disability in people with diabetes, and how this risk varies according to sociodemographic and health-behavioural characteristics. This study quantified levels of psychological distress in people with and without diabetes, considering these factors. Design Cross-sectional analysis of questionnaire data. Setting Men and women aged ≥45 years, in the 45 and Up Study, from New South Wales, Australia. Participants 236 441 people who completed the baseline postal questionnaire (distributed from 1 January 2006–31 December 2008), with valid data for diabetes status and psychological distress. Primary outcome measures High psychological distress (Kessler-10 >22). Modified Poisson regression with robust error variance was used to estimate prevalence ratios (PRs), comparing prevalence of high psychological distress among those with and without diabetes and across physical functional limitation (PFL) levels, adjusting for potential confounders. Results Overall, 8.4% (19 803/236 441) of participants reported diabetes. 11.8% (2339) of individuals with diabetes and 7.2% (15 664) without diabetes had high psychological distress: age-adjusted and sex-adjusted PR=1.89 (95% CI 1.81 to 1.97), becoming 1.58 (1.52 to 1.65) and 1.22 (1.17 to 1.27) following additional adjustment for sociodemographic factors, health behaviours and additionally for PFL, respectively. Compared with individuals with neither diabetes nor PFL, the adjusted PRs for high psychological distress were: 1.37 (1.17 to 1.60) with diabetes but no PFL, 7.33 (7.00 to 7.67) without diabetes but with severe PFL and 8.89 (8.36 to 9.46) with both diabetes and severe PFL. Conclusions People with diabetes have a 60% greater risk of high psychological distress than people without diabetes; a substantial proportion of this elevation is attributable to higher levels of disability with diabetes, especially factoring in measurement error. Psychological distress is strongly related to physical impairment.
On Compositionality of Dinatural Transformations

Natural transformations are ubiquitous in mathematics, logic and computer science. For operations of mixed variance, such as currying and evaluation in the lambda-calculus, Eilenberg and Kelly’s notion of extranatural transformation, and often the even more general dinatural transformation, is required. Unfortunately dinaturals are not closed under composition except in special circumstances. This paper presents a new suﬃcient condition for composability. We propose a generalised notion of dinatural transformation in many variables, and extend the Eilenberg-Kelly account of composition for extranaturals to these transformations. Our main result is that a composition of dinatural transformations which creates no cyclic connections between arguments yields a dinatural transformation. We also extend the classical notion of horizontal composition to our generalized dinaturals and demonstrate that it is associative and has identities.
The Pediatric Critical Care Transfusion and Anemia Expertise Initiative Consensus Conference Methodology

Objectives: This article describes the methodology used for Pediatric Critical Care Transfusion and Anemia Expertise Initiative Consensus Conference. Design: Consensus conference of international experts in pediatric critical care and transfusion medicine, following standards set by the Institute of Medicine, using the Research and Development/UCLA Appropriateness Method, modeled after the Pediatric Acute Lung Injury Consensus Conference. Topics related to RBC transfusion in children with or at risk for critical illness were divided into nine subgroups with a systematic review of the literature. Methods: The panel of 38 content and four methodology experts met three times over the course of 2 years and collaborated to develop evidence-based and, when evidence was lacking, expert-based clinical recommendations as well as research priorities for RBC transfusions in critically ill children or those at risk for critical illness. Electronic searches were conducted using PubMed, Embase, and Cochrane Library databases from 1980 to May 2017. Agreement was obtained using the Research and Development/UCLA Appropriateness Method. We used a standardized data extraction form to construct evidence tables and graded the evidence using the Grading of Recommendations Assessment, Development, and Evaluation system. Main Results: The consensus conference resulted in 102 recommendation statements, of which 57 were clinical (20 evidence based and 37 based on expert consensus) and 45 detailed recommendations for future research. Dissemination was done via decision tree, a primary publication listing all statements, and separate publications for each subtopic that include supporting arguments for each recommendation. Conclusions: A consensus conference of experts from around the world developed recommendations for RBC transfusions in critically ill children or children at risk for critical illness, the identification of current research gaps, and future research priorities.
Multi-Source Syntactic Neural Machine Translation

We introduce a novel multi-source technique for incorporating source syntax into neural machine translation using linearized parses. This is achieved by employing separate encoders for the sequential and parsed versions of the same source sentence; the resulting representations are then combined using a hierarchical attention mechanism. The proposed model improves over both seq2seq and parsed baselines by over 1 BLEU on the WMT17 English-German task. Further analysis shows that our multi-source syntactic model is able to translate successfully without any parsed input, unlike standard parsed methods. In addition, performance does not deteriorate as much on long sentences as for the baselines.
Protein acetylation in skeletal muscle mitochondria is involved in impaired fatty acid oxidation and exercise intolerance in heart failure

Exercise intolerance is a common clinical feature and is linked to poor prognosis in patients with heart failure (HF). Skeletal muscle dysfunction, including impaired energy metabolism in the skeletal muscle, is suspected to play a central role in this intolerance, but the underlying mechanisms remain elusive. Lysine acetylation, a recently identified post‐translational modification, has emerged as a major contributor to the derangement of mitochondrial metabolism. We thus investigated whether mitochondrial protein acetylation is associated with impaired skeletal muscle metabolism and lowered exercise capacity in both basic and clinical settings of HF.
Partnerships to protect.

Background: Antisense oligonucleotides (AOs) can interfere with exon recognition and intron removal during pre-mRNA processing, and induce excision of a targeted exon from the mature gene transcript. AOs have been used in vitro and in vivo to redirect dystrophin pre-mRNA processing in human and animal cells. Targeted exon skipping of selected exons in the dystrophin gene transcript can remove nonsense or frame-shifting mutations that would otherwise have lead to Duchenne Muscular Dystrophy, the most common childhood form of muscle wasting. Results: Although many dystrophin exons can be excised using a single AO, several exons require two motifs to be masked for efficient or specific exon skipping. Some AOs were inactive when applied individually, yet pronounced exon excision was induced in transfected cells when the AOs were used in select combinations, clearly indicating synergistic rather than cumulative effects on splicing. The necessity for AO cocktails to induce efficient exon removal was observed with 2 different chemistries, 2'-O-methyl modified bases on a phosphorothioate backbone and phosphorodiamidate morpholino oligomers. Similarly, other trends in exon skipping, as a consequence of 2'-O-methyl AO action, such as removal of additional flanking exons or variations in exon skipping efficiency with overlapping AOs, were also seen when the corresponding sequences were prepared as phosphorodiamidate morpholino oligomers. Conclusion: The combination of 2 AOs, directed at appropriate motifs in target exons was found to induce very efficient targeted exon skipping during processing of the dystrophin pre-mRNA. This combinatorial effect is clearly synergistic and is not influenced by the chemistry of the AOs used to induce exon excision. A hierarchy in exon skipping efficiency, observed with overlapping AOs composed of 2'-O-methyl modified bases, was also observed when these same sequences were evaluated as phosphorodiamidate morpholino oligomers, indicating design parameters established with one chemistry may be applied to the other. Published: 2 July 2007 BMC Molecular Biology 2007, 8:57 doi:10.1186/1471-2199-8-57 Received: 13 February 2007 Accepted: 2 July 2007 This article is available from: http://www.biomedcentral. com/1471-2199/8/57 © 2007 Adams et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Large-Scale Cover Song Detection in Digital Music Libraries Using Metadata, Lyrics and Audio Features

Cover song detection is a very relevant task in Music Information Retrieval (MIR) studies and has been mainly addressed using audio-based systems. Despite its potential impact in industrial contexts, low performances and lack of scalability have prevented such systems from being adopted in practice for large applications. In this work, we investigate whether textual music information (such as metadata and lyrics) can be used along with audio for large-scale cover identification problem in a wide digital music library. We benchmark this problem using standard text and state of the art audio similarity measures. Our studies shows that these methods can significantly increase the accuracy and scalability of cover detection systems on Million Song Dataset (MSD) and Second Hand Song (SHS) datasets. By only leveraging standard tf-idf based text similarity measures on song titles and lyrics, we achieved 35.5% of absolute increase in mean average precision compared to the current scalable audio content-based state of the art methods on MSD. These experimental results suggests that new methodologies can be encouraged among researchers to leverage and identify more sophisticated NLP-based techniques to improve current cover song identification systems in digital music libraries with metadata.
Observation and interpretation of negative remanent magnetization and inverted hysteresis loops in a thin film of La0.7Sr0.3MnO3

The observation of inverted magnetic hysteresis loops and negative magnetic remanence (NRM) in a 7.6 nm thin film of La0.7Sr0. 3MnO3 grown on SrTiO3 substrates is reported. The film was grown employing pulsed laser deposition and characterized by reflection high-energy electron diffraction during growth and using x-ray reflectivity measurements post-growth. Magnetic properties of the film were measured from 5 K to 400 K under both the field-cooled (FC) and zero-field-cooled (ZFC) conditions. The observed results of inverted magnetic hysteresis loops and NRM are interpreted in terms of the co-existence of a magnetically inhomogeneous region consisting of superparamagnetic spin clusters with a blocking temperature TB = 240 K and the ferromagnetic state with an ordering temperature TC = 290 K. Hysteresis loop inversion is observed in the temperature region of TB < T < TC whereas NRM appears in the mixed superparamagnetic and ferromagnetic states for T < TC down to 5 K. These observations of hysteresis loop inversion and NRM are related to the magneto-static interaction between the superparamagnetic and ferromagnetic phases leading to anti-alignment of spin of both magnetic phases with respect to each other.
The opium poppy genome and morphinan production

Poppy genome reveals evolution of opiates The opium poppy has been a source of painkillers since Neolithic times. Attendant risks of addiction threaten many today. Guo et al. now deliver a draft of the opium poppy genome, which encompasses 2.72 gigabases assembled into 11 chromosomes and predicts more than 50,000 protein-coding genes. A particularly complex gene cluster contains many critical enzymes in the metabolic pathway that generates the alkaloid drugs noscapine and morphinan. Science, this issue p. 343 The opium poppy genome reveals gene duplication, rearrangement, and fusion events that led to morphine production. Morphinan-based painkillers are derived from opium poppy (Papaver somniferum L.). We report a draft of the opium poppy genome, with 2.72 gigabases assembled into 11 chromosomes with contig N50 and scaffold N50 of 1.77 and 204 megabases, respectively. Synteny analysis suggests a whole-genome duplication at ~7.8 million years ago and ancient segmental or whole-genome duplication(s) that occurred before the Papaveraceae-Ranunculaceae divergence 110 million years ago. Syntenic blocks representative of phthalideisoquinoline and morphinan components of a benzylisoquinoline alkaloid cluster of 15 genes provide insight into how this cluster evolved. Paralog analysis identified P450 and oxidoreductase genes that combined to form the STORR gene fusion essential for morphinan biosynthesis in opium poppy. Thus, gene duplication, rearrangement, and fusion events have led to evolution of specialized metabolic products in opium poppy.
Gene-by-Environment Interaction of Bcrp−/− and Methionine- and Choline-Deficient Diet–Induced Nonalcoholic Steatohepatitis Alters SN-38 Disposition

Disease progression to nonalcoholic steatohepatitis (NASH) has profound effects on the expression and function of drug-metabolizing enzymes and transporters, which provide a mechanistic basis for variable drug response. Breast cancer resistance protein (BCRP), a biliary efflux transporter, exhibits increased liver mRNA expression in NASH patients and preclinical NASH models, but the impact on function is unknown. It was shown that the transport capacity of multidrug resistance protein 2 (MRP2) is decreased in NASH. SN-38, the active irinotecan metabolite, is reported to be a substrate for Bcrp, whereas SN-38 glucuronide (SN-38G) is a Mrp2 substrate. The purpose of this study was to determine the function of Bcrp in NASH through alterations in the disposition of SN-38 and SN-38G in a Bcrp knockout (Bcrp−/− KO) and methionine- and choline-deficient (MCD) model of NASH. Sprague Dawley [wild-type (WT)] rats and Bcrp−/− rats were fed either a methionine- and choline-sufficient (control) or MCD diet for 8 weeks to induce NASH. SN-38 (10 mg/kg) was administered i.v. , and blood and bile were collected for quantification by liquid chromatography–tandem mass spectrometry. In Bcrp−/− rats on the MCD diet, biliary efflux of SN-38 decreased to 31.9%, and efflux of SN-38G decreased to 38.7% of control, but WT-MCD and KO-Control were unaffected. These data indicate that Bcrp is not solely responsible for SN-38 biliary efflux, but rather implicate a combined role for BCRP and MRP2. Furthermore, the disposition of SN-38 and SN-38G is altered by Bcrp−/− and NASH in a gene-by-environment interaction and may result in variable drug response to irinotecan therapy in polymorphic patients.
Relationship between In Vivo CYP3A4 Activity, CYP3A5 Genotype, and Systemic Tacrolimus Metabolite/Parent Drug Ratio in Renal Transplant Recipients and Healthy Volunteers

CYP3A5 genotype is a major determinant of tacrolimus clearance, and has been shown to affect systemic tacrolimus metabolite/parent ratios in healthy volunteers, which may have implications for efficacy and toxicity. In a cohort of 50 renal transplant recipients who underwent quantification of CYP3A4 activity using the oral midazolam drug probe, we confirmed that CYP3A5 genotype is the single most important determinant of tacrolimus metabolite/parent ratio [CYP3A5 expressors displayed 2.7- and 2-fold higher relative exposure to 13-desmethyltacrolimus (DMT) and 31-DMT, respectively; P < 0.001]. There was, however, no relationship between CYP3A4 activity and tacrolimus metabolite/parent ratios. Additional analyses in 16 healthy volunteers showed that dual pharmacological inhibition of CYP3A4 and P-glycoprotein using itraconazole resulted in increased tacrolimus metabolite/parent ratios (+65%, +112%, and 25% for 13-, 15-, and 31-DMT, respectively; P < 0.01). This finding was confirmed in a cohort of nine renal transplant recipients who underwent tacrolimus pharmacokinetic assessments before and during CYP3A4 inhibition (58% increase in overall metabolite/tacrolimus ratio; P = 0.017).
SubMachine: Web‐Based Tools for Exploring Seismic Tomography and Other Models of Earth's Deep Interior

We present SubMachine, a collection of web‐based tools for the interactive visualization, analysis, and quantitative comparison of global‐scale data sets of the Earth's interior. SubMachine focuses on making regional and global‐scale seismic tomography models easily accessible to the wider solid Earth community, in order to facilitate collaborative exploration. We have written software tools to visualize and explore over 30 tomography models—individually, side‐by‐side, or through statistical and averaging tools. SubMachine also serves various nontomographic data sets that are pertinent to the interpretation of mantle structure and complement the tomographies. These include plate reconstruction models, normal mode observations, global crustal structure, shear wave splitting, as well as geoid, marine gravity, vertical gravity gradients, and global topography in adjustable degrees of spherical harmonic resolution. By providing repository infrastructure, SubMachine encourages and supports community contributions via submission of data sets or feedback on the implemented toolkits.
Racism, racial discrimination, and trauma: a systematic review of the social science literature

ABSTRACT Objective: The aim of this paper is to provide a systematic review of studies that examine relationships between racial discrimination and trauma in order to further understand the relationship between racial oppression and psychological functioning. Design: In this review, we describe the characteristics of 28 studies, identified by a comprehensive search strategy, including measurements of racial discrimination and trauma, as well as the nature of the reported associations. Results: Half of studies included in this review were published in the last 6 years. The majority of studies used cross-sectional designs and were conducted in the United States with adults ≥18 years old. African American, White, Latinx, and Asian populations were most frequently included in these studies. Of the 44 associations examined in these studies, 70% of the trauma symptomology outcomes were statistically significantly associated with racial discrimination. Significant positive associations ranged in strength, with the strongest relationships between racial discrimination and trauma occurring in studies examining veteran populations and moderate relationships among these variables in non-veteran, student populations. Conclusions: Our findings reveal that current research on race-based trauma seems to be limited by a lack of measures that capture the stress/intensity associated with race-related events, an inability to account for vicarious/collective/intergenerational experiences of trauma, and failure to control for non-race-based trauma.