julilili42/papers huggingface dataset:
Image-based methods for phenotyping growth dynamics and fitness components inArabidopsis thaliana
2017-10-25

Abstract Background The model species Arabidopsis thaliana has extensive resources to investigate intraspecific trait variability and the genetic bases of ecologically relevant traits. However, the cost of equipment and software required for high-throughput phenotyping is often a bottleneck for large-scale studies, such as mutant screening or quantitative genetics analyses. Simple tools are needed for the measurement of fitness-related traits, like relative growth rate and fruit production, without investment in expensive infrastructures. Here, we describe methods that enable the estimation of biomass accumulation and fruit number from the analysis of rosette and inflorescence images taken with a regular camera. Results We developed two models to predict plant dry mass and fruit number from the parameters extracted with the analysis of rosette and inflorescence images. Predictive models were trained by sacrificing growing individuals for dry mass estimation, and manually measuring a fraction of individuals for fruit number at maturity. Using a cross-validation approach, we showed that quantitative parameters extracted from image analysis predicts more 90% of both plant dry mass and fruit number. When used on 451 natural accessions, the method allowed modelling growth dynamics, including relative growth rate, throughout the life cycle of various ecotypes. Estimated growth-related traits had high heritability (0.65 &lt; H 2 &lt; 0.93), as well as estimated fruit number ( H 2 = 0.68). In addition, we validated the method for estimating fruit number with rev5 , a mutant with increased flower abortion. Conclusions The method we propose here is based on the automated computerization of plant images with ImageJ, and subsequent statistical modelling in R. It allows plant biologists to measure growth dynamics and fruit number in hundreds of individuals with simple computing steps that can be repeated and adjusted to a wide range of laboratory conditions. It is thus a flexible toolkit for the measurement of fitness-related traits in large plant populations.
Neutron star mass and radius measurements from atmospheric model fits to X-ray burst cooling tail spectra
2017-10-26

Observations of thermonuclear X-ray bursts from accreting neutron stars (NSs)\\nin low-mass X-ray binary systems can be used to constrain NS masses and radii.\\nMost previous work of this type has set these constraints using Planck function\\nfits as a proxy: both the models and the data are fit with diluted blackbody\\nfunctions to yield normalizations and temperatures which are then compared\\nagainst each other. Here, for the first time, we fit atmosphere models of X-ray\\nbursting NSs directly to the observed spectra. We present a hierarchical\\nBayesian fitting framework that uses state-of-the-art X-ray bursting NS\\natmosphere models with realistic opacities and relativistic exact Compton\\nscattering kernels as a model for the surface emission. We test our approach\\nagainst synthetic data, and find that for data that are well-described by our\\nmodel we can obtain robust radius, mass, distance, and composition\\nmeasurements. We then apply our technique to Rossi X-ray Timing Explorer\\nobservations of five hard-state X-ray bursts from 4U 1702-429. Our joint fit to\\nall five bursts shows that the theoretical atmosphere models describe the data\\nwell but there are still some unmodeled features in the spectrum corresponding\\nto a relative error of 1-5% of the energy flux. After marginalizing over this\\nintrinsic scatter, we find that at 68% credibility the circumferential radius\\nof the NS in 4U 1702-429 is R = 12.4+-0.4 km, the gravitational mass is\\nM=1.9+-0.3 Msun, the distance is 5.1 &lt; D/kpc &lt; 6.2, and the hydrogen mass\\nfraction is X &lt; 0.09.\\n
Interactions between metabolic, reward and cognitive processes in appetite control: Implications for novel weight management therapies
2017-10-26

Traditional models of appetite control have emphasised the role of parallel homeostatic and hedonic systems, but more recently the distinction between independent homeostatic and hedonic systems has been abandoned in favour of a framework that emphasises the cross talk between the neurochemical substrates of the two systems. In addition, evidence has emerged more recently, that higher level cognitive functions such as learning, memory and attention play an important role in everyday appetite control and that homeostatic signals also play a role in cognition. Here, we review this evidence and present a comprehensive model of the control of appetite that integrates cognitive, homeostatic and reward mechanisms. We discuss the implications of this model for understanding the factors that may contribute to disordered patterns of eating and suggest opportunities for developing more effective treatment approaches for eating disorders and weight management.
Janus-Faced Neutrophil Extracellular Traps in Periodontitis
2017-10-26

Periodontitis is characterized by PMN infiltration and formation of neutrophil extracellular traps (NETs). However, their functional role for periodontal health remains complex and partially understood. The main function of NETs appears to be evacuation of dental plaque pathogen-associated molecular patterns. The inability to produce NETs is concomitant with aggressive periodontitis. But in cases with exaggerated NET production, NETs are unable to maintain periodontal health and bystander damages occur. This pathology can be also demonstrated in animal models using lipopolysaccharide as PMN activator. The progress of periodontitis appears to be a consequence of the formation of gingival pockets obstructing the evacuation of both pathogen-associated and damage-associated molecular patterns, which are responsible for the self-perpetuation of inflammation. Thus, besides the pathogenic effects of the periodontal bacteria, the dysregulation of PMN activation appears to play a main role in the periodontal pathology. Consequently, modulation of PMN activation might be a useful approach to periodontal therapy.
Do public sector industrial relations challenge the Swedish model?
2017-10-26

This article discusses recent developments in public sector labour relations in Sweden from a historical, gender and power relations perspective. The main question is whether these trends challenge the established Swedish industrial relations system. Our point of departure - yet chronologically also the point of arrival - is the Swedish Municipal Workers' Union, Kommunal's, exit from the coordinated wage setting model within the Swedish Trade Union Confederation (Landsorganisationen, LO) in 2015/2016. The immediate reason was that Kommunal, representing one-third of the LO members, including many low-paid women, turned down the LO's proposal on a general wage increase for low-wage groups. Instead, Kommunal urged to upgrade wages for a specific member group, the auxiliary nurses. This broke an almost uninterrupted 20-year-long period of labour market cooperation and coordination that was introduced in 1997 through the so-called Industry Agreement (Industriavtalet). This agreement was launched in the wake of the deep financial crisis in the early 1990s, and the neoliberal move towards a complete decentralization of pay negotiations. How should this move by Kommunal be interpreted? Why, and when, has the centralized system become a straitjacket for Kommunal, when for decades it seemingly was a precondition for both private and public union strength?
Germany: an intertwined two-part system of unilateralism and collective bargaining
2017-10-26

Public sector industrial relations in Germany consist of two parts. On the one hand, wages and working conditions for civil servants are unilaterally determined by law, and on the other, there is a completely developed industrial relations system for non-civil servants (employees) working in the sector. Remarkably, although they have no right to take industrial action, civil servants are not in a worse situation than employees. In view of a simple concept of industrial relations where employers and workers are in complementary labour market roles, this seems difficult to explain. Indeed, public sector industrial relations are more complex. The article suggests that bargaining in the public sector is less an economic procedure than a dispute over the political, societal and statutory recognition of public services and an adequate participation of employees. Being aware of this special character of public sector industrial relations, the United Services Trade Union (Ver.di) tries to back strikes by organising societal support, whereas the German Federation of Civil Servants (DBB) operates more by lobbying in the political sphere and by recourse to the constitution. In spite of a general decline in collective bargaining and trade union density, and long years of austerity, both types of industrial relations are relatively stable.
Testing the effects of topography, geometry and kinematics on modeled thermochronometer cooling ages in the eastern Bhutan Himalaya
2017-10-26

Abstract. The temporal and kinematic evolution of fold-thrust belts is a critical component for evaluating the viability of proposed plate tectonic, geodynamic and even climatic processes in regions of convergence. Thermochronometer data have the potential to provide temporal constraints, but interpretations of these data are sensitive to both exhumational and deformational processes. In this study, reconstructions of a balanced geologic cross section in the Himalayan fold-thrust belt of eastern Bhutan are used in a flexural and thermal-kinematic model to understand the sensitivity of predicted cooling ages to changes in fault kinematics, geometry and topography. We sequentially deform the cross section with ~ 10 km deformation steps and apply flexural loading and erosional unloading at each step to develop a high-resolution evolution of deformation, erosion, and burial over time. Comparison of model-predicted cooling ages to published thermochronometer data reveals that cooling ages are most sensitive to (1) location and magnitude of fault ramps, (2) variable shortening rates between 68-6.4 mm/yr, and (3) timing and magnitude of out-of-sequence faulting. The predicted ages are less sensitive to (4) radiogenic heat production, and (5) estimates of topographic evolution. We propose a revised cross section geometry that separates one large ramp previously proposed for the modern decollement into two smaller ramps. The revised cross section results in an improved fit to observed ages, particularly young AFT ages (2–6 Ma) located north of the Main Central Thrust.
Physical Plasma Elicits Immunogenic Cancer Cell Death and Mitochondrial Singlet Oxygen
2017-10-27

Plasma oncotherapy receives increasing attention due to considerable success in preclinical research. Different plasma sources were shown to induce cancer cell death in vitro and in vivo. Plasmas for medicine expel reactive species of many kinds. These have been implicated in the induction of immunogenic cancer cell death that increases the visibility of killed cells to the immune system. Cell membrane-bound calreticulin (CRT) serves as key damage-associated molecular pattern molecule to elicit antitumor immune responses. To investigate CRT translocation upon challenge with medical plasma, CT26 colon cancer cells were treated in vitro using the atmospheric pressure argon plasma jet kINPen. Cells underwent apoptosis, which was accompanied by exposure of CRT. Interestingly, CRT was upregulated on viable as well as dead cells, and remained upregulated up to 72 h post-treatment. Cell death was preceded by loss of membrane potential in mitochondria. These endosymbionts are capable of generating singlet oxygen, a molecule that has been suggested to drive radical chains in plasma cancer cell death. Using fluorescent probes, we identified a role of endogenous (mitochondrial-derived) over exogenous (plasma-derived) singlet oxygen in plasma-treated cancer cells.
Orientation-Dependent Work-Function Modification Using Substituted Pyrene-Based Acceptors
2017-10-27

The adsorption of molecular acceptors is a viable method for tuning the work function of metal electrodes. This, in turn, enables adjusting charge injection barriers between the electrode and organic semiconductors. Here, we demonstrate the potential of pyrene-tetraone (PyT) and its derivatives dibromopyrene-tetraone (Br-PyT) and dinitropyrene-tetraone (NO<sub>2</sub>-PyT) for modifying the electronic properties of Au(111) and Ag(111) surfaces. The systems are investigated by complementary theoretical and experimental approaches, including photoelectron spectroscopy, the X-ray standing wave technique, and density functional theory simulations. For some of the investigated interfaces the trends expected for Fermi-level pinning are observed, i.e., an increase of the metal work function along with increasing molecular electron affinity and the same work function for Au and Ag with monolayer acceptor coverage. Substantial deviations are, however, found for Br-PyT/Ag(111) and NO<sub>2</sub>-PyT/Ag(111), where in the latter case an adsorption-induced work function increase of as much as 1.6 eV is observed. This behavior is explained as arising from a face-on to edge-on reorientation of molecules in the monolayer. Our calculations show that for an edge-on orientation much larger work-function changes can be expected despite the prevalence of Fermi-level pinning. This is primarily ascribed to a change of the electron affinity of the adsorbate layer that results from a change of the molecular orientation. This work provides a comprehensive understanding of how changing the molecular electron affinity as well as the adsorbate structure impacts the electronic properties of electrodes.
Implementation of a 5-Minute Magnetic Resonance Imaging Screening Protocol for Prostate Cancer in Men With Elevated Prostate-Specific Antigen Before Biopsy
2017-10-27

Purpose The aims of this study were to establish a 5-minute magnetic resonance (MR) screening protocol for prostate cancer in men before biopsy and to evaluate effects on Prostate Imaging Reporting and Data System (PI-RADS) V2 scoring in comparison to a conventional, fully diagnostic multiparametric MR imaging (mpMRI) approach. Materials and Methods Fifty-two patients with elevated prostate-specific antigen levels and without prior biopsy were prospectively included in this institutional review board–approved study. In all patients, an mpMRI protocol according to the PI-RADS recommendations was acquired on a 3 T MRI system. In addition, an accelerated diffusion-weighted imaging sequence was acquired using simultaneous multislice technique (DW-EPI SMS ). Two readers independently evaluated the images for the presence/absence of prostate cancer according to the PI-RADS criteria and for additional findings. In a first reading session, only the screening protocol consisting of axial T2-weighted and DW-EPI SMS images was made available. In a subsequent reading session, the mpMRI protocol was assessed blinded to the results of the first reading, serving as reference standard. Results Both readers successfully established a final diagnosis according to the PI-RADS criteria in the screening and mpMRI protocol. Mean lesion size was 1.2 cm in the screening and 1.4 cm in the mpMRI protocol ( P = 0.4) with 35% (18/52) of PI-RADS IV/V lesions. Diagnostic performance of the screening protocol was excellent with a sensitivity and specificity of 100% for both readers with no significant differences in comparison to the mpMRI standard ( P = 1.0). In 3 patients, suspicious lymph nodes were reported as additional finding, which were equally detectable in the screening and mpMRI protocol. Conclusions A 5-minute MR screening protocol for prostate cancer in men with elevated prostate-specific antigen levels before biopsy is applicable for clinical routine with similar diagnostic performance as the full diagnostic mpMRI approach.
A modular toolbox for Golden‐Gate‐based plasmid assembly streamlines the generation of Ralstonia solanacearum species complex knockout strains and multi‐cassette complementation constructs
2017-10-27

Summary Members of the Ralstonia solanacearum species complex ( Rssc ) cause bacterial wilt, a devastating plant disease that affects numerous economically important crops. Like other bacterial pests, Rssc injects a cocktail of effector proteins via the bacterial type III secretion system into host cells that collectively promote disease. Given their functional relevance in disease, the identification of Rssc effectors and the investigation of their in planta function are likely to provide clues on how to generate pest‐resistant crop plants. Accordingly, molecular analysis of effector function is a focus of Rssc research. The elucidation of effector function requires corresponding gene knockout strains or strains that express the desired effector variants. The cloning of DNA constructs that facilitate the generation of such strains has hindered the investigation of Rssc effectors. To overcome these limitations, we have designed, generated and functionally validated a toolkit consisting of DNA modules that can be assembled via Golden‐Gate (GG) cloning into either desired gene knockout constructs or multi‐cassette expression constructs. The Ralstonia ‐GG‐kit is compatible with a previously established toolkit that facilitates the generation of DNA constructs for in planta expression. Accordingly, cloned modules, encoding effectors of interest, can be transferred to vectors for expression in Rssc strains and plant cells. As many effector genes have been cloned in the past as GATEWAY entry vectors, we have also established a conversion vector that allows the implementation of GATEWAY entry vectors into the Ralstonia ‐GG‐kit. In summary, the Ralstonia ‐GG‐kit provides a valuable tool for the genetic investigation of genes encoding effectors and other Rssc genes.
Inversion of the decay of the cyclotron line energy in Hercules X-1
2017-10-27

\\n Recent observations of Her X-1 with NuSTAR and INTEGRAL in 2016 have provided evidence that the 20-year decay of the cyclotron line energy found between 1996 and 2015 has ended and that an inversion with a new increase, possibly similar to the one observed around 1990–1993, has started. We consider this a strong motivation for further observations and for enhanced efforts to significantly improve our theoretical understanding of the accretion process in binary X-ray pulsars. We speculate about the physics behind the long-term decay and its inversion, a possible cyclic behavior, and correlations with other variable observables. \\n
Imaging response assessment of immunotherapy in patients with renal cell and urothelial carcinoma
2017-10-27

While monitoring response to immunotherapy still relies on RECIST criteria, immune-related response criteria have been established to better address the imaging changes occurring under immunotherapy. Further studies with long-term follow-up are needed to properly identify and predict response after treatment beyond progression. Because of the expanding clinical use of immune checkpoint inhibitors, radiologists, urologist, and oncologists should be familiar with common imaging findings under this respective therapy.
On the star-forming ability of Molecular Clouds
2017-10-27

The star-forming ability of a molecular cloud depends on the fraction of gas\\nit can cycle into the dense-phase. Consequently, one of the crucial questions\\nin reconciling star-formation in clouds is to understand the factors that\\ncontrol this process. While it is widely accepted that the variation in ambient\\nconditions can alter significantly the ability of a cloud to spawn stars, the\\nobserved variation in the star-formation rate in nearby clouds that experience\\nsimilar ambient conditions, presents an interesting question. In this work we\\nattempted to reconcile this variation within the paradigm of colliding flows.\\nTo this end we develop self-gravitating, hydrodynamic realisations of identical\\nflows, but allowed to collide off-centre. Typical observational diagnostics\\nsuch as the gas-velocity dispersion, the fraction of dense-gas, the column\\ndensity distribution ({\\\\small N-PDF}), the distribution of gas mass as a\\nfunction of -band extinction and the strength of compressional/solenoidal\\nmodes in the post-collision cloud were deduced for different choices of the\\nimpact parameter of collision. We find that a strongly sheared cloud is\\nterribly inefficient in cycling gas into the dense phase and that such a cloud\\ncan possibly reconcile the sluggish nature of star-formation reported for some\\nclouds. Within the paradigm of cloud-formation via colliding flows this is\\npossible in case of flows colliding with a relatively large impact parameter.\\nWe conclude that compressional modes - though probably essential - are\\ninsufficient to ensure a relatively higher star-formation efficiency in a\\ncloud.\\n
Physics opportunities for vector-boson scattering at a future 100 TeV hadron collider
2017-10-27

Vector-boson scattering (VBS) processes provide particularly promising means\\nfor probing the mechanism of electroweak symmetry breaking and to search for\\nnew physics in the weak sector. In the environment of a future proton-proton\\ncollider operating at a center-of-mass energy of 100 TeV, unprecedented\\nopportunities arise for the investigation of this important class of reactions.\\nWe highlight the prominent features of VBS processes in this energy regime and\\ndiscuss how the VBS signal can be isolated in the presence of a priori large\\nQCD backgrounds. We find excellent opportunities for the analysis of VBS\\nreactions in a kinematic range that is inaccessible to present colliders.\\n
A Longitudinal Approach to Biological Psychiatric Research: The PsyCourse Study
2017-10-27

In current diagnostic systems, schizophrenia and bipolar disorder are still conceptualized as distinct categorical entities. Recently, both clinical and genetic evidence have challenged this Kraepelinian dichotomy. There are only few longitudinal studies addressing the potential overlaps between these conditions. Here, we present design and first results of the PsyCourse study, an ongoing transdiagnostic study of the affective-to-psychotic continuum that combines longitudinal deep phenotyping and dimensional assessment of psychopathology with an extensive collection of biomaterial. Within the DSM-IV framework, we compare two broad diagnostic groups: one consisting of predominantly affective and one of predominantly psychotic disorders. Depressive, manic, and psychotic symptoms as well as global functioning over time were analyzed. Furthermore, we explore the effects of polygenic risk scores for schizophrenia on diagnostic group membership and address their effects on non-participation in follow-up visits. While phenotypic results show differences in both current psychotic and manic symptoms, depressive symptoms did not vary between both groups. Polygenic risk scores for schizophrenia significantly explained part of the variability of the diagnostic group. Furthermore, there was a trend that a higher polygenic loading for schizophrenia was associated with attrition. Because of its unique properties, the PsyCourse study presents a prime resource for the interrogation of complex genotype-phenotype relationships.
PCI Strategies in Patients with Acute Myocardial Infarction and Cardiogenic Shock
2017-10-30

Among patients who had multivessel coronary artery disease and acute myocardial infarction with cardiogenic shock, the 30-day risk of a composite of death or severe renal failure leading to renal-replacement therapy was lower among those who initially underwent PCI of the culprit lesion only than among those who underwent immediate multivessel PCI. (Funded by the European Union 7th Framework Program and others; CULPRIT-SHOCK ClinicalTrials.gov number, NCT01927549 .).