julilili42/papers huggingface dataset:
Improving ancient DNA genome assembly
2017-04-05

Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer. We used this two-layer assembly to generate assemblies for two different ancient samples and compared the results to current de novo assembly approaches. We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.
Quantifying the added value of high resolution climatemodels: A systematic comparison of WRF simulations for complex Himalayan terrain
2017-04-05

Abstract. Mesoscale dynamical refinements of global climate models or atmospheric reanalysis have shown their potential to resolve the intricate atmospheric processes, their land surface interactions, and subsequently, realistic distribution of climatic fields in complex terrains. Given that such potential is yet to be explored within the central Himalayan region of Nepal, we investigate the skill of the Weather Research and Forecasting (WRF) model with different spatial resolutions in reproducing the spatial, seasonal and diurnal characteristics of the near-surface air temperature and precipitation, as well as, the spatial shifts in the diurnal monsoonal precipitation peak over the Khumbu (Everest), Rolwaling and adjacent southern areas. Therefore, the ERA-Interim (0.75°) reanalysis has been dynamically refined to 25, 5 and 1 km (D1, D2 and D3) for one complete hydrological year (Oct 2014–Sep 2015), using the one-way nested WRF model run with mild-nudging and parameterized convection for the outer but explicitly resolved convection for the inner domains. Our results suggest that D3 realistically reproduces the monsoonal precipitation, as compared to its underestimation by D1 but overestimation by D2. All three resolutions however overestimate precipitation from the westerly disturbances, owing to simulating anomalously higher intensity of few intermittent events. Temperatures are though generally well reproduced by all resolutions, winter and pre-monsoon seasons feature a high cold bias for high elevations while lower show a simultaneous warm bias. Contrary to higher resolutions, D1 fails to realistically reproduce the regional-scale nocturnal monsoonal peak precipitation observed at the Himalayan foothills and its diurnal shift towards high elevations, whereas D2 resolves these characteristics but exhibits a limited skill in reproducing such peak at the river valley scale due to the limited representation of the narrow valleys at 5 km resolution. Nonetheless, featuring a substantial skill over D1 and D2, D3 simulates almost realistic shapes of the seasonal and diurnal precipitation and the peak timings even at valley scales. These findings clearly suggest an added value of the convective scale resolutions in realistically resolving the topo-climates over the central Himalaya, which in turn allow simulating their interactions with the synoptic scale weather systems prevailing over High Asia.
Noise spectroscopy with a quantum gas
2017-04-05

We report on the spectral analysis and the local measurement of intensity\\ncorrelations of microwave fields using ultra cold quantum gases. The\\nfluctuations of the electromagnetic field induce spin flips in a magnetically\\ntrapped quantum gas and generate a multi-mode atomlaser. The output of the\\natomlaser is measured with high temporal resolution on the single atom level,\\nfrom which the spectrum and intensity correlations of the generating microwave\\nfield are reconstructed. We give a theoretical description of the atomlaser\\noutput and its correlations in response to resonant microwave fields and verify\\nthe model with measurements on an atom chip. The measurement technique is\\napplicable for the local analysis of classical and quantum noise of\\nelectromagnetic fields, for example on chips, in the vicinity of quantum\\nelectronic circuits.\\n
Peer Review #1 of "Improving ancient DNA genome assembly (v0.1)"
2017-04-05

Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference.In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used.However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated.In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer.We used this two-layer assembly to generate assemblies for two different ancient samples and compared the results to current de novo assembly approaches.We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.
Peer Review #1 of "Improving ancient DNA genome assembly (v0.2)"
2017-04-05

Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference.In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used.However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated.In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer.We used this two-layer assembly to generate assemblies for two different ancient samples and compared the results to current de novo assembly approaches.We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.
Testing black hole candidates with electromagnetic radiation
2017-04-06

Astrophysical black hole candidates are thought to be the Kerr black holes of\\ngeneral relativity, but there is not yet direct observational evidence that the\\nspacetime geometry around these objects is described by the Kerr solution. The\\nstudy of the properties of the electromagnetic radiation emitted by gas or\\nstars orbiting these objects can potentially test the Kerr black hole\\nhypothesis. In this paper, I review the state of the art of this research\\nfield, describing the possible approaches to test the Kerr metric with current\\nand future observational facilities and discussing current constraints.\\n
Nonrandom domain organization of the Arabidopsis genome at the nuclear periphery
2017-04-06

The nuclear space is not a homogeneous biochemical environment. Many studies have demonstrated that the transcriptional activity of a gene is linked to its positioning within the nuclear space. Following the discovery of lamin-associated domains (LADs), which are transcriptionally repressed chromatin regions, the nonrandom positioning of chromatin at the nuclear periphery and its biological relevance have been studied extensively in animals. However, it remains unknown whether comparable chromatin organizations exist in plants. Here, using a strategy using restriction enzyme–mediated chromatin immunoprecipitation, we present genome-wide identification of nonrandom domain organization of chromatin at the peripheral zone of Arabidopsis thaliana nuclei. We show that in various tissues, 10%–20% of the regions on the chromosome arms are anchored at the nuclear periphery, and these regions largely overlap between different tissues. Unlike LADs in animals, the identified domains in plants are not gene-poor or A/T-rich. These domains are enriched with silenced protein-coding genes, transposable element genes, and heterochromatic marks, which collectively define a repressed environment. In addition, these domains strongly correlate with our genome-wide chromatin interaction data set (Hi-C) by largely explaining the patterns of chromatin compartments, revealed on Hi-C maps. Moreover, our results reveal a spatial compartment of different DNA methylation pathways that regulate silencing of transposable elements, where the CHH methylation of transposable elements located at the nuclear periphery and in the interior are preferentially mediated by CMT2 and DRM methyltransferases, respectively. Taken together, the results demonstrate functional partitioning of the Arabidopsis genome in the nuclear space.
A common capacity limitation for response and item selection in working memory.
2017-04-06

Successful completion of any cognitive task requires selecting a particular action and the object the action is applied to. Oberauer (2009) suggested a working memory (WM) model comprising a declarative and a procedural part with analogous structures. One important assumption of this model is that both parts work independently of each other, and previous work has indeed reported evidence for the independent selection of memory lists and tasks, for example. The present study focused on the selection of single items in declarative and single responses in procedural WM. To this end, WM updating tasks were implemented as Task 2 in a Psychological Refractory Period setup in 3 experiments. The prediction based on the locus of slack logic is that item switch costs are present with a long but not with a short stimulus onset asynchrony. Contrary to this prediction, item switch costs were neither absent nor at least smaller at the short stimulus onset asynchrony. These results help to further constrain the WM model and thus to refine its computational implementation. (PsycINFO Database Record
Laparoscopic Supracervical Hysterectomy and Laparoscopic Total Hysterectomy in Patients with Very Large Uteri: a Retrospective Single-Center Experience at a Major University Hospital
2017-04-06

<b>Objective</b> The main objectives of our study were to demonstrate that laparoscopic supracervical hysterectomy (LSH) or total laparoscopic hysterectomy (TLH) can be performed safely even in patients with a uterine weight ≥ 500 g, to analyze the rate of conversions to laparotomy due to uterine size and to estimate the incidence and type of intraoperative and long-term postoperative complications. <b>Study Design</b> Retrospective open, single-center, comparative interventional study of LSH and TLH. <b>Results</b> The present study comprised a total of 138 patients that underwent laparoscopic hysterectomy with a uterine weight ≥ 500 g; 109 patients (79.0 %) underwent LSH and 29 patients (21.0 %) underwent TLH. Median uterine weight across the entire cohort was 602 g, with the largest uterus weighing 1860 g. A total of 24 cases (17.4 %) among the 138 hysterectomies were converted to a laparotomy due to lack of adequate intraabdominal space and size of the uterus. Mean uterine weight of the patients in the LSH group that underwent conversion was 883 g (SD 380 g, n = 13) and 757 g (SD 371 g, n = 11) in the TLH group. The rate of conversion to laparotomy due to the uterine weight was significantly lower in the LSH group (11.9 %) compared to the TLH group (37.9 %) (p = 0.002). Intraoperative complications requiring laparotomy for other reasons but uterine size occurred in 6 patients of the study cohort (6/138; 4.3 %). Long-term postoperative complications occurred in 2 patients (2/138, 1.4 %), both patients from LSH group had to be re-operated on due to adhesions. <b>Conclusions</b> Our study adds further insight in the limited data set of laparoscopic hysterectomy for increased uterine weight and shows that LSH and TLH are safe and feasible even in patients with very large uteri (≥ 500 g).
Fear processing deficit in violent offenders: Intact attentional guidance but impaired explicit categorization.
2017-04-06

Objective: Impaired recognition of fearful expressions has been documented across a wide range of antisocial populations but it remains unresolved whether this deficit reflects impaired attention to fearful expressions or is restricted to categorization. Here, we used visual search to investigate the relationship between impaired visual attention and emotion recognition in a group of violent offenders and healthy controls. Method: Task 1 measured attentional guidance by physical and affective saliency. Participants indicated the gender of a face identity singleton in an array of neutral distractor faces with a different identity. Singletons were paired with additional physical (color) or affective (happy, angry, fearful expression) task-irrelevant features. Task 2 used similar search displays but required participants to categorize the emotional expression of a happy, angry, or fearful target face in an array of neutral distractors. Results: In Task 1, both groups’ visual search was aided by both physical and affective features, providing no evidence for impaired incidental processing of affective or physical saliency in violent offenders. In Task 2, violent offenders showed impaired explicit categorization performance, particularly for fearful expressions. Visual search performance was not correlated with self reported psychopathy. Conclusion: Impaired processing of affective stimuli in antisociality results from later processing stages related to explicit recognition and categorization. These deficits are not restricted to individuals with elevated psychopathic traits but are linked to antisociality more generally. These findings represent a first step in localizing the fear processing deficit along the processing hierarchy in violent offenders, demonstrating intact attentional guidance but impaired categorization.
Vessels, T cells, and GVHD: time matters
2017-04-06

In this issue of Blood , [Riesner et al][1] describe that neovascularization precedes infiltration of inflammatory cells in graft-versus-host disease (GVHD) and colitis models, revealing a new pathophysiological sequence of disease initiation.[1][2] ![Figure][3] Pathomechanism of GVHD
Skeletal Muscle as an Endocrine Organ: The Role of Myokines in Exercise Adaptations
2017-04-07

Exercise stimulates the release of proteins with autocrine, paracrine, or endocrine functions produced in skeletal muscle, termed myokines. Based on the current state of knowledge, the major physiological function of myokines is to protect the functionality and to enhance the exercise capacity of skeletal muscle. Myokines control adaptive processes in skeletal muscle by acting as paracrine regulators of fuel oxidation, hypertrophy, angiogenesis, inflammatory processes, and regulation of the extracellular matrix. Endocrine functions attributed to myokines are involved in body weight regulation, low-grade inflammation, insulin sensitivity, suppression of tumor growth, and improvement of cognitive function. Muscle-derived regulatory RNAs and metabolites, as well as the design of modified myokines, are promising novel directions for treatment of chronic diseases.
Convergence or Divergence? Educational Discrepancies in Work-Care Arrangements of Mothers with Young Children in Germany
2017-04-07

This study examines how educational differences in work-care patterns among mothers with young children in Germany changed between 1997 and 2013. Since the mid-2000s, Germany has undergone a paradigm shift in parental leave and childcare policies. Our comparative analysis of East and West Germany provides new evidence on whether the long-standing gender regime differences interact with recent developments of social class inequalities in the changing family policy context. The analyses include pooled binary and multinomial logistic regressions based on 17,764 observations of 8604 children below the age of three years from the German Socio-Economic Panel Study (SOEP). The findings point to growing educational divergence in work-care arrangements in East and West Germany: employment and day-care use increased more strongly among families with medium and highly educated mothers compared to those with low education. This has critical implications for the latter’s economic security. The decline in the use of informal childcare options was, however, fairly homogenous.
Modeling language family expansions
2017-04-07

Abstract This paper presents properties of a computer simulation of language migration. It takes as input a simulated phylogeny and a database of today’s populated places. At each time step, a language moves within a geographical quadrilateral defined by the minimal number, ch , of choices of populated places within the quadrilateral. The result is a constrained random walk defined by a combination of the ch parameter and the landscape, which comes into play via the restriction of the walk to populated places. The distribution of move distances is qualitatively similar across values of ch and resembles a Gamma distribution. Through comparisons with densities of real-world language families, the values of ch which yield the closest fits between real and simulated data are found.
Defective Gpsm2/Gαi3 signalling disrupts stereocilia development and growth cone actin dynamics in Chudley-McCullough syndrome
2017-04-07

Abstract Mutations in GPSM2 cause Chudley-McCullough syndrome (CMCS), an autosomal recessive neurological disorder characterized by early-onset sensorineural deafness and brain anomalies. Here, we show that mutation of the mouse orthologue of GPSM2 affects actin-rich stereocilia elongation in auditory and vestibular hair cells, causing deafness and balance defects. The G-protein subunit Gα i3 , a well-documented partner of Gpsm2, participates in the elongation process, and its absence also causes hearing deficits. We show that Gpsm2 defines an ∼200 nm nanodomain at the tips of stereocilia and this localization requires the presence of Gα i3 , myosin 15 and whirlin. Using single-molecule tracking, we report that loss of Gpsm2 leads to decreased outgrowth and a disruption of actin dynamics in neuronal growth cones. Our results elucidate the aetiology of CMCS and highlight a new molecular role for Gpsm2/Gα i3 in the regulation of actin dynamics in epithelial and neuronal tissues.
In-depth analysis of core methanogenic communities from high elevation permafrost-affected wetlands
2017-04-07

The organic carbon of permafrost affected soils is receiving particular attention with respect to its fate and potential feedback to global warming. The structural and activity changes of methanogenic communities in the degrading permafrost-affected wetlands on the Tibetan Plateau can serve as fundamental elements for modelling feedback interaction of ecosystems to climate change. Hence, we aimed at anticipating if and how the rapid environmental changes occurring especially on the high altitude Tibetan platform will affect methanogenic communities. We identified methanogenic community composition, activity and abundance in wetland soils with different hydrological settings, permafrost extent and soil properties and pinpoint the environmental controls. We show that despite a pronounced natural gradient, the Tibetan high elevation wetland soils host a large methanogenic core microbiome. Hydrogenotrophic methanogens, in particular Methanoregula, and H2-dependent methanogenesis were overall dominant although acetoclastic methanogens in addition to hydrogenotrophs were among the dominating taxa in a minerotrophic fen. Tracing the Methanoregula community of the Tibetan Plateau using public databases revealed its global relevance in natural terrestrial habitats. Unlike the composition, the activity and abundance of methanogens varied strongly in the studied soils with higher values in alpine swamps than in alpine meadows. This study indicates that in the course of current wetland and permafrost degradation and the loss in soil moisture, a decrease in the methane production potential is expected on the high Tibetan Plateau but it will not lead to pronounced changes within the methanogenic community structure.
The influence of biophysical muscle properties on simulating fast human arm movements
2017-04-07

Computational modeling provides a framework to understand human movement control. For this approach, physiologically motivated and experimentally validated models are required to predict the dynamic interplay of the neuronal controller with the musculoskeletal biophysics. Previous studies show, that an adequate model of arm movements should consider muscle fiber contraction dynamics, parallel and serial elasticities, and activation dynamics. Numerous validated macroscopic model representations of these structures and processes exist. In this study, the influence of these structures and processes on maximum movement velocity of goal-directed arm movements was investigated by varying their mathematical model descriptions. It was found that the movement velocity strongly depends on the pre-activation of the muscles (differences up to 91.6%) and the model representing activation dynamics (differences up to 43.3%). Looking at the influence of the active muscle fibers (contractile element), the simulations reveal that velocities systematically differ depending on the width of the force-length relation (differences up to 17.4%). The series elasticity of the tendon influences the arm velocity up to 7.6%. In conclusion, in fast goal-directed arm movements from an equilibrium position, the modeling of the biophysical muscle properties influences the simulation results. To reliably distinguish between mathematical formulations by experimental validation, the initial muscular activity and the activation dynamics have to be modeled validly, as their influence excels. To this end, further experiments systematically varying the initial muscular activity would be needed.
Richness in Functional Connectivity Depends on the Neuronal Integrity within the Posterior Cingulate Cortex
2017-04-07

The brain's connectivity skeleton-a rich club of strongly interconnected members-was initially shown to exist in human structural networks, but recent evidence suggests a functional counterpart. This rich club typically includes key regions (or hubs) from multiple canonical networks, reducing the cost of inter-network communication. The posterior cingulate cortex (PCC), a hub node embedded within the default mode network, is known to facilitate communication between brain networks and is a key member of the "rich club." Here, we assessed how metabolic signatures of neuronal integrity and cortical thickness influence the global extent of a functional rich club as measured using the functional rich club coefficient (fRCC). Rich club estimation was performed on functional connectivity of resting state brain signals acquired at 3T in 48 healthy adult subjects. Magnetic resonance spectroscopy was measured in the same session using a point resolved spectroscopy sequence. We confirmed convergence of functional rich club with a previously established structural rich club. N-acetyl aspartate (NAA) in the PCC is significantly correlated with age (<i>p</i> = 0.001), while the rich club coefficient showed no effect of age <i>(p</i> = 0.106). In addition, we found a significant quadratic relationship between fRCC and NAA concentration in PCC (<i>p</i> = 0.009). Furthermore, cortical thinning in the PCC was correlated with a reduced rich club coefficient after accounting for age and NAA. In conclusion, we found that the fRCC is related to a marker of neuronal integrity in a key region of the cingulate cortex. Furthermore, cortical thinning in the same area was observed, suggesting that both cortical thinning and neuronal integrity in the hub regions influence functional integration of at a whole brain level.