julilili42/papers huggingface dataset:
The SysteMHC Atlas project
2017-07-21

Mass spectrometry (MS)-based immunopeptidomics investigates the repertoire of peptides presented at the cell surface by major histocompatibility complex (MHC) molecules. The broad clinical relevance of MHC-associated peptides, e.g. in precision medicine, provides a strong rationale for the large-scale generation of immunopeptidomic datasets and recent developments in MS-based peptide analysis technologies now support the generation of the required data. Importantly, the availability of diverse immunopeptidomic datasets has resulted in an increasing need to standardize, store and exchange this type of data to enable better collaborations among researchers, to advance the field more efficiently and to establish quality measures required for the meaningful comparison of datasets. Here we present the SysteMHC Atlas (https://systemhcatlas.org), a public database that aims at collecting, organizing, sharing, visualizing and exploring immunopeptidomic data generated by MS. The Atlas includes raw mass spectrometer output files collected from several laboratories around the globe, a catalog of context-specific datasets of MHC class I and class II peptides, standardized MHC allele-specific peptide spectral libraries consisting of consensus spectra calculated from repeat measurements of the same peptide sequence, and links to other proteomics and immunology databases. The SysteMHC Atlas project was created and will be further expanded using a uniform and open computational pipeline that controls the quality of peptide identifications and peptide annotations. Thus, the SysteMHC Atlas disseminates quality controlled immunopeptidomic information to the public domain and serves as a community resource toward the generation of a high-quality comprehensive map of the human immunopeptidome and the support of consistent measurement of immunopeptidomic sample cohorts.
Growth and morbidity of extremely preterm infants after early full enteral nutrition
2017-07-21

Objectives To evaluate feasibility and consequences of accelerated feeding advancement on short-term outcomes in extremely low gestational age neonates (ELGANs) who stayed in our institution for &gt;28 days. Methods Retrospective single-centre cohort analysis covering the years 2011–2013. Data are presented as median (IQR). Results Infants '(n=77) birth weight was 745 (640 to 960) g and gestational age at birth 26.7 (25.1 to 27.4) weeks. Full enteral feeds were attained by postnatal day 7 (5 to 11). Weight gain from birth to discharge was 14.3 (13.3 to 16.1) g/kg/day, change in SD score for weight −0.03 (−0.55 to 0.46) and 0.09 (−0.78 and 0.82) for head circumference. Rates of necrotising enterocolitis and spontaneous intestinal perforation in all ELGANs admitted during the study period were 3.1% and 9.4%, respectively. Conclusions This cohort of ELGANs showed good weight gain and head growth after early full enteral nutrition. The impact of this feeding practice on neonatal morbidity and long-term outcome remains to be tested in adequately powered randomised trials.
Construction and updating of event models in auditory event processing
2017-07-21

Humans segment the continuous stream of sensory information into distinct events at points of change. Between two events, humans perceive an event boundary. Present theories propose changes in the sensory information to trigger updating processes of the present event model. Increased encoding effort finally leads to a memory benefit at event boundaries. Evidence from reading time studies (increased reading times with increasing amount of change) suggest that updating of event models is incremental. We present results from five experiments that studied event processing (including memory formation processes and reading times) using an audio drama as well as a transcript thereof as stimulus material. Experiments 1a and 1b replicated the event boundary advantage effect for memory. In contrast to recent evidence from studies using visual stimulus material, Experiments 2a and 2b found no support for incremental updating with normally sighted and blind participants for recognition memory. In Experiment 3, we replicated Experiment 2a using a written transcript of the audio drama as stimulus material allowing us to disentangle encoding and retrieval processes. Our results indicate incremental updating processes at encoding (as measured with reading times). At the same time, we again found recognition performance to be unaffected by the amount of change. We discuss these findings in the light of current event cognition theories.
Dimethyl fumarate modulates neutrophil extracellular trap formation in a glutathione‐ and superoxide‐dependent manner
2017-07-22

We report DMF as a potent, stimulus-specific, GSH- and ROS-dependent modulator of NET formation. Our results support the notion that modulation of NET formation contributes to the beneficial effects of FAEs in a variety of inflammatory conditions.
Androgen-mediated sex bias impairs efficiency of leukotriene biosynthesis inhibitors in males
2017-07-23

Proinflammatory leukotrienes (LTs) are produced by 5-lipoxygenase (5-LO) aided by 5-LO-activating protein (FLAP). LT biosynthesis inhibitors are currently under clinical investigation as treatments for respiratory and cardiovascular diseases. Here, we have revealed a sex bias in the efficiency of clinically relevant LT biosynthesis inhibitors, showing that their effects are superior in females. We found that androgens cause these sex differences by impeding the LT-biosynthetic 5-LO/FLAP complex assembly. Lower doses of the FLAP inhibitor MK886 were required to reduce LTB4 levels in exudates of female versus male mice and rats. Following platelet-activating factor-induced shock, MK886 increased survival exclusively in female mice, and this effect was abolished by testosterone administration. FLAP inhibitors and the novel-type 5-LO inhibitors licofelone and sulindac sulfide exhibited higher potencies in human blood from females, and bioactive 5-LO/FLAP complexes were formed in female, but not male, human and murine leukocytes. Supplementation of female blood or leukocytes with 5α-dihydrotestosterone abolished the observed sex differences. Our data suggest that females may benefit from anti-LT therapy to a greater extent than males, prompting consideration of sex issues in LT modifier development.
Urban Nature: Perception and Acceptance of Alternative Green Space Management and the Change of Awareness after Provision of Environmental Information. A Chance for Biodiversity Protection
2017-07-23

Measurable ecological data, e.g., species diversity, provide inadequate information for achieving the comprehensive protection of biodiversity, because human acceptance attitudes can be important factors in undermining nature protection schemes. We have analysed an ecologically driven urban management system presented to urban habitants. A photograph-based survey answered by 424 participants was used to evaluate their impressions of natural meadows. The positive effect of provided information tables was demonstrated by pre- and post-test designs. Attitudes towards urban nature protection showed a statistical preference for green-area management systems optimising insect protection compared with more regularly mowed meadows and lawns. Thus, the perceptions of people should be considered in processes of biodiversity protection. Our results correlate with personal attitude and education, support the aims of extensive green-space management and should encourage urban planners to integrate biodiversity protection zones into urban planning.
The great trade collapse and the Spanish export miracle: Firm‐level evidence from the crisis
2017-07-23

Abstract We provide novel evidence on the microstructure of international trade during the 2008 financial crisis and subsequent global recession by exploring a rich firm‐level data set from Spain. The focus of our analysis is on changes at the extensive and intensive firm‐level margins of trade, as well as on performance differences (jobs, productivity and firm survival) across firms that differ in their export status. We find no adverse effects of the financial crisis on foreign market entry or exit, but a considerable increase in the export intensity of firms after the financial crisis. Moreover, we find that exporters were more resilient to the crisis than non‐exporters. Finally, while exporters showed a significantly more favourable development of total factor productivity after 2009 than non‐exporters, aggregate productivity declined substantially in a large number of industries in Spanish manufacturing. We also briefly explore two factors that might help explain the surprisingly strong export performance of Spain in the aftermath of the great trade collapse: improved aggregate competitiveness due to internal and external devaluation and a substitutive relationship between domestic and foreign sales at the firm level.
Is Overimitation a Uniquely Human Phenomenon? Insights From Human Children as Compared to Bonobos
2017-07-24

Imitation is a key mechanism of human culture and underlies many of the intricacies of human social life, including rituals and social norms. Compared to other animals, humans appear to be special in their readiness to copy novel actions as well as those that are visibly causally irrelevant. This study directly compared the imitative behavior of human children to that of bonobos, our understudied great ape relatives. During an action‐copying task involving visibly causally irrelevant actions, only 3‐ to 5‐year‐old children ( N = 77) readily copied, whereas no bonobo from a large sample did ( N = 46). These results highlight the distinctive nature of the human cultural capacity and contribute important insights into the development and evolution of human cultural behaviors.
BACE inhibition-dependent repair of Alzheimer’s pathophysiology
2017-07-24

Significance The accumulation of amyloid-β (Aβ) proteins in the brain contributes to Alzheimer ́s disease (AD). Reducing Aβ by inhibiting its production with a β-secretase (BACE) inhibitor represents a novel mechanism for treating AD; however, whether this therapeutic strategy is capable of repairing impaired brain circuits associated with AD is unknown. Here we demonstrate that BACE inhibition is beneficial to all levels of impairment in an AD mouse model: cellular, long-range circuitry, and memory. We provide evidence that the rescue is dependent on the reduction of soluble forms of Aβ surrounding amyloid plaques. These results have mechanistic and therapeutic implications for AD, including Aβ-related memory defects.
Implication of pulmonary hypertension in patients undergoing MitraClip therapy: results from the German transcatheter mitral valve interventions (TRAMI) registry
2017-07-24

Abstract Aims We sought to evaluate the impact of pulmonary hypertension on outcomes following MitraClip therapy. Methods and results The 643 patients in the TRAnscatheter Mitral valve Interventions ( TRAMI ) registry were divided into three groups according to echocardiographically graded systolic pulmonary artery pressure ( sPAP ) (Group 1: patients with sPAP of ≤36 mmHg ; Group 2: patients with sPAP of 37–50 mmHg ; Group 3: patients with sPAP of &gt;50 mmHg ) and followed for 1 year. Recent cardiac decompensation, aortic valve disease and tricuspid valve insufficiency were observed more frequently in patients with higher sPAP . Furthermore, logEuroSCORE , Society of Thoracic Surgeons score and age were higher with rising sPAP values. No differences were observed in mitral regurgitation ( MR ) severity, co‐morbidities or clinical findings (New York Heart Association class, 6‐min walking distance). Reduction to MR of grade 1 or lower was achieved more often in patients with lower sPAP levels ( P = 0.01). In Groups 2 and 3, sPAP was reduced significantly. Major adverse cardiac or cardiovascular events ( MACCEs ) occurring in hospital (death, myocardial infarction, stroke; &lt;4% in each group), as well as 30‐day rates of MACCEs (6.1% in Group 1, 11.9% in Group 2, 12.4% in Group 3) and rehospitalization (18.9% in Group 1, 24.8% in Group 2, 24.8% in Group 3) did not differ significantly. At 1 year, differences in rates of mortality and MACCEs (20.3% in Group 1, 33.1% in Group 2, 34.7% in Group 3; P &lt; 0.01) were significant. Both Groups 2 [hazard ratio ( HR ) 1.81, P = 0.0122] and 3 ( HR 1.85, P = 0.0092) were independently predictive of death. Rehospitalization rates did not differ during follow‐up. Conclusions Despite higher mortality in patients with elevated sPAP , these data suggest the safety, feasibility and benefit of MitraClip therapy even in advanced stages of disease. An early approach might prevent the progress of pulmonary hypertension and improve outcomes.
Insula‐based networks in professional musicians: Evidence for increased functional connectivity during resting state fMRI
2017-07-24

Abstract Despite considerable research on experience‐dependent neuroplasticity in professional musicians, detailed understanding of an involvement of the insula is only now beginning to emerge. We investigated the effects of musical training on intrinsic insula‐based connectivity in professional classical musicians relative to nonmusicians using resting‐state functional MRI. Following a tripartite scheme of insula subdivisions, coactivation profiles were analyzed for the posterior, ventral anterior, and dorsal anterior insula in both hemispheres. While whole‐brain connectivity across all participants confirmed previously reported patterns, between‐group comparisons revealed increased insular connectivity in musicians relative to nonmusicians. Coactivated regions encompassed constituents of large‐scale networks involved in salience detection (e.g., anterior and middle cingulate cortex), affective processing (e.g., orbitofrontal cortex and temporal pole), and higher order cognition (e.g., dorsolateral prefrontal cortex and the temporoparietal junction), whereas no differences were found for the reversed group contrast. Importantly, these connectivity patterns were stronger in musicians who experienced more years of musical practice, including also sensorimotor regions involved in music performance (M1 hand area, S1, A1, and SMA). We conclude that musical training triggers significant reorganization in insula‐based networks, potentially facilitating high‐level cognitive and affective functions associated with the fast integration of multisensory information in the context of music performance. Hum Brain Mapp 38:4834–4849, 2017 . © 2017 Wiley Periodicals, Inc.
Landed Traders, Trading Agriculturalists? Land in the Economy of the Italian Diaspora in the Greek East
2017-07-24

ABSTRACT This paper revises current understandings of the rôle of land in the economy of the Italian diaspora in the Greek East in the second and first centuries b.c ., arguing that these Italians owned more land than has previously been assumed and that many of these Italian landowners practised a highly commercialized form of agriculture that focused on high-end products. This strategy shaped what empire meant both locally and in Italy and Rome, where the products they marketed fed into the ongoing consumer revolutions of the time. After discussing the evidence for the extent of Italian landholdings and examining their exploitation in three case studies, we conclude by reflecting on the long-term history of such landholdings in the provinces and the implications for our understanding of Roman imperialism more generally.
Darboux transformation in black hole perturbation theory
2017-07-24

The Darboux transformation between ordinary differential equations is a 19th century technique that has seen wide use in quantum theory for producing exactly solvable potentials for the Schr\\"odinger equation with specific spectral properties. In this paper we show that the same transformation appears in black hole theory, relating, for instance, the Zerilli and Regge-Wheeler equations for axial and polar Schwarzschild perturbations. The transformation reveals these two equations to be isospectral, a well known result whose method has been repeatedly reintroduced under different names. We highlight the key role that the so-called algebraically special solutions play in the black hole Darboux theory and show that a similar relation exists between the Chandrasekhar-Detweiler equations for Kerr perturbations. Finally, we discuss the limitations of the method when dealing with long-range potentials and explore the possibilities offered by a generalised Darboux transformation.
Influence of the Fluorination of CoPc on the Interfacial Electronic Structure of the Coordinated Metal Ion
2017-07-24

Interface properties of CoPc and CoPcF16 on Cu-intercalated graphene/Ni(111) were investigated by X-ray photoemission spectroscopy (XPS), ultraviolet photoemission spectroscopy (UPS), and X-ray absorption spectroscopy (XAS). We show that a charge transfer from graphene/Ni(111) to the Co ion of CoPc can be significantly reduced by Cu-intercalation of graphene, resulting in a partial decoupling of graphene from the Ni(111) substrate. This is not the case for CoPcF16 on Cu-intercalated graphene/Ni(111). Possible reasons and charge transfer channels are discussed. The comparison to CoPcF16 on the almost fully decoupled Au-intercalated graphene/Ni(111) suggests that the graphene-substrate coupling in the case of Cu-intercalation remains still significant.
Light and Vision before Ibn al-Haytham: The Perspective of Islamic Theology
2017-07-24

Light is a benefit for mankind; this is why the nations of this world – or their diplomats – decided to celebrate it for an entire year. Light was the first thing to be created by God, as we are told in the Book of Genesis, and we all remember how Haydn in his oratorio Die Schöpfung prepares us for the solemn moment when, after a mysterious pianissimo, the full orchestra and the entire choir rejoice after having reached this word of the text, 'Licht', C major and fortissimo. God was still alone then and Light the first demonstration of His power. The universe did not yet exist; only two days later, according to the Biblical report, the sun and the moon were created. We have to imagine that those who rejoice in the event are angels, not human beings. When, however, in their stead man, 'le maître de la nature' as he was called by Descartes, made an attempt at demonstrating his power in the same way, recently, only 70 years ago, there was not so much to rejoice in. I still remember when, in 1945 after the war had come to an end in Europe, a light 'brighter than a thousand suns' ('heller als tausend Sonnen' to quote the title of Robert Jungk's famous book of 1956) was produced in East Asia, above the town of Hiroshima, light as force de frappe to use the French expression, surpassing in its efficiency everything we had experienced before, with thousands of victims. Afterwards, the crime could only be justified as a test; in contrast to God, man can never be sure of his exploits right away. As a matter of fact, there was a second 'test' shortly afterwards (Nagasaki), and there would have been a third one, on Tokyo, if the Tenno had not been so wise to give in. When man is left alone with his creativity, he is incalculable ('quand il veut faire l'ange il fait la bête', as said Pascal), and only researchers of the forgotten past applied their tests to themselves (Madame Curie, for instance). When we produce too much light, the benefit cannot be taken for granted, and certainly we don't see the stars any more.
Music-space associations are grounded, embodied and situated: examination of cello experts and non-musicians in a standard tone discrimination task
2017-07-25

In recent research, a systematic association of musical pitch with space has been described in the so-called Spatial-Pitch-Association-of-Response Codes-effect (SPARC). Typically, high pitch is associated with upper/right and low pitch with lower/left space. However, a theoretical classification of these associations regarding their experiential sources is difficult. Therefore, we applied a theoretical framework of numerical cognition classifying similar Space-Associated Response Codes (SARC) effects according to their groundedness, embodiedness and situatedness. We tested these attributes with a group of non-musicians and with a group of highly skilled cello players playing high tones with lower hand positions (i.e., reverse SPARC alignment) in a standard SPARC context of a piano and a reversed SPARC context of a cello. The results showed that SPARC is grounded, in general. However, for cello player SPARC is also situated and embodied. We conclude that groundedness, embodiedness and situatedness provide general characteristics of mapping cognitive representations to space.
Assessing body image in anorexia nervosa using biometric self-avatars in virtual reality: Attitudinal components rather than visual body size estimation are distorted
2017-07-26

Background Body image disturbance (BID) is a core symptom of anorexia nervosa (AN), but as yet distinctive features of BID are unknown. The present study aimed at disentangling perceptual and attitudinal components of BID in AN. Methods We investigated n = 24 women with AN and n = 24 controls. Based on a three-dimensional (3D) body scan, we created realistic virtual 3D bodies (avatars) for each participant that were varied through a range of ±20% of the participants’ weights. Avatars were presented in a virtual reality mirror scenario. Using different psychophysical tasks, participants identified and adjusted their actual and their desired body weight. To test for general perceptual biases in estimating body weight, a second experiment investigated perception of weight and shape matched avatars with another identity. Results Women with AN and controls underestimated their weight, with a trend that women with AN underestimated more. The average desired body of controls had normal weight while the average desired weight of women with AN corresponded to extreme AN (DSM-5). Correlation analyses revealed that desired body weight, but not accuracy of weight estimation, was associated with eating disorder symptoms. In the second experiment, both groups estimated accurately while the most attractive body was similar to Experiment 1. Conclusions Our results contradict the widespread assumption that patients with AN overestimate their body weight due to visual distortions. Rather, they illustrate that BID might be driven by distorted attitudes with regard to the desired body. Clinical interventions should aim at helping patients with AN to change their desired weight.