julilili42/papers huggingface dataset:
Bayesian model averaging to explore the worth of data for soil‐plant model selection and prediction
2015-03-29

Abstract A Bayesian model averaging (BMA) framework is presented to evaluate the worth of different observation types and experimental design options for (1) more confidence in model selection and (2) for increased predictive reliability. These two modeling tasks are handled separately because model selection aims at identifying the most appropriate model with respect to a given calibration data set, while predictive reliability aims at reducing uncertainty in model predictions through constraining the plausible range of both models and model parameters. For that purpose, we pursue an optimal design of measurement framework that is based on BMA and that considers uncertainty in parameters, measurements, and model structures. We apply this framework to select between four crop models (the vegetation components of CERES, SUCROS, GECROS, and SPASS), which are coupled to identical routines for simulating soil carbon and nitrogen turnover, soil heat and nitrogen transport, and soil water movement. An ensemble of parameter realizations was generated for each model using Monte‐Carlo simulation. We assess each model's plausibility by determining its posterior weight, which signifies the probability to have generated a given experimental data set. Several BMA analyses were conducted for different data packages with measurements of soil moisture, evapotranspiration ( ET a ), and leaf area index (LAI). The posterior weights resulting from the different BMA runs were compared to the weight distribution of a reference run with all data types to investigate the utility of different data packages and monitoring design options in identifying the most appropriate model in the ensemble. We found that different (combinations of) data types support different models and none of the four crop models outperforms all others under all data scenarios. The best model discrimination was observed for those data where the competing models disagree the most. The data worth for reducing prediction uncertainty depends on the prediction to be made. LAI data have the highest utility for predicting ET a , while soil moisture data are better for predicting soil water drainage. Our study illustrates, that BMA provides an objective framework for data worth analysis with respect to both model discrimination and model calibration for a wide range of applications.
Loss of CX3CR1 increases accumulation of inflammatory monocytes and promotes gliomagenesis
2015-03-30

The most abundant populations of non-neoplastic cells in the glioblastoma (GBM) microenvironment are resident microglia, macrophages and infiltrating monocytes from the blood circulation. The mechanisms by which monocytes infiltrate into GBM, their fate following infiltration, and their role in GBM growth are not known. Here we tested the hypothesis that loss of the fractalkine receptor CX3CR1 in microglia and monocytes would affect gliomagenesis. Deletion of Cx3cr1 from the microenvironment resulted in increased tumor incidence and shorter survival times in glioma-bearing mice. Loss of Cx3cr1 did not affect accumulation of microglia/macrophages in peri-tumoral areas, but instead indirectly promoted the trafficking of CD11b+CD45hiCX3CR1lowLy-6ChiLy-6G-F4/80-/low circulating inflammatory monocytes into the CNS, resulting in their increased accumulation in the perivascular area. Cx3cr1-deficient microglia/macrophages and monocytes demonstrated upregulation of IL1β expression that was inversely proportional to Cx3cr1 gene dosage. The Proneural subgroup of the TCGA GBM patient dataset with high IL1β expression showed shorter survival compared to patients with low IL1β. IL1β promoted tumor growth and increased the cancer stem cell phenotype in murine and human Proneural glioma stem cells (GSCs). IL1β activated the p38 MAPK signaling pathway and expression of monocyte chemoattractant protein (MCP-1/CCL2) by tumor cells. Loss of Cx3cr1 in microglia in a monocyte-free environment had no impact on tumor growth and did not alter microglial migration. These data suggest that enhancing signaling to CX3CR1 or inhibiting IL1β signaling in intra-tumoral macrophages can be considered as potential strategies to decrease the tumor-promoting effects of monocytes in Proneural GBM.
Sequence Variation within the KIV-2 Copy Number Polymorphism of the Human LPA Gene in African, Asian, and European Populations
2015-03-30

Amazingly little sequence variation is reported for the kringle IV 2 copy number variation (KIV 2 CNV) in the human LPA gene. Apart from whole genome sequencing projects, this region has only been analyzed in some detail in samples of European populations. We have performed a systematic resequencing study of the exonic and flanking intron regions within the KIV 2 CNV in 90 alleles from Asian, European, and four different African populations. Alleles have been separated according to their CNV length by pulsed field gel electrophoresis prior to unbiased specific PCR amplification of the target regions. These amplicons covered all KIV 2 copies of an individual allele simultaneously. In addition, cloned amplicons from genomic DNA of an African individual were sequenced. Our data suggest that sequence variation in this genomic region may be higher than previously appreciated. Detection probability of variants appeared to depend on the KIV 2 copy number of the analyzed DNA and on the proportion of copies carrying the variant. Asians had a high frequency of so-called KIV 2 type B and type C (together 70% of alleles), which differ by three or two synonymous substitutions respectively from the reference type A. This is most likely explained by the strong bottleneck suggested to have occurred when modern humans migrated to East Asia. A higher frequency of variable sites was detected in the Africans. In particular, two previously unreported splice site variants were found. One was associated with non-detectable Lp(a). The other was observed at high population frequencies (10% to 40%). Like the KIV 2 type B and C variants, this latter variant was also found in a high proportion of KIV 2 repeats in the affected alleles and in alleles differing in copy numbers. Our findings may have implications for the interpretation of SNP analyses in other repetitive loci of the human genome.
NuSTAR J095551+6940.8: a highly magnetized neutron star with super-Eddington mass accretion
2015-03-30

The identification of the Ultraluminous X-ray source (ULX) X-2 in M82 as an\\naccreting pulsar has shed new light on the nature of a subset of ULXs, while\\nrising new questions on the nature of the super-Eddington accretion. Here, by\\nnumerically solving the torque equation of the accreting pulsar within the\\nframework of the magnetically threaded-disk scenario, we show that three\\nclasses of solutions, corresponding to different values of the magnetic field,\\nare mathematically allowed. We argue that the highest magnetic field one,\\ncorresponding to B G, is favoured based on physical\\nconsiderations and the observed properties of the source. In particular, that\\nis the only solution which can account for the observed variations in \\n(over four time intervals) without requiring major changes in , which\\nwould be at odds with the approximately constant X-ray emission of the source\\nduring the same time. For this solution, we find that the source can only\\naccomodate a moderate amount of beaming, 0.5 . Last, we show\\nthat the upper limit on the luminosity, L erg s \\nfrom archival observations, is consistent with a highly-magnetized neutron star\\nbeing in the propeller phase at that time.\\n
Processing of Dynamic Affective Information in Adults With ADHD
2015-03-30

Objective: ADHD has been repeatedly linked to problems in social functioning. Although some theories assume that the emotion recognition deficits are explained by general attentional deficits, mounting evidence suggests that they may actually constitute a distinct impairment. However, it remains unclear whether the deficient processing affects specific emotional categories or may generalize to all basic emotions. The present study aims to investigate these questions by assessing the sensitivity to all six basic emotions in adults with ADHD. Method: The participants judged the emotion onset in animated morph clips displaying facial expressions that slowly changed from neutral to emotional. Results: ADHD participants exhibited an impaired recognition of sad and fearful facial expressions. Conclusion: The present findings indicate that ADHD is possibly associated with a specific deficit in the recognition of facial emotions signaling negative social feedback.
Haemodynamic and electrophysiological markers of pragmatic language comprehension in schizophrenia
2015-03-30

Our results indicate group differences in cortical electrophysiological and haemodynamic activation that represent rather general impairments in the processing of complex language. Simultaneous EEG/NIRS applications are useful to depict these neural markers and to investigate their relationship. Future studies are needed to clarify the nature of respective anomalies and their potential as putative neural markers in schizophrenia research.
FTIR Study of the Impact of PC[60]BM on the Photodegradation of the Low Band Gap Polymer PCPDTBT under O-2 Environment
2015-03-30

The photodegradation of the low band gap polymer poly[2,6-(4,4-bis(2-ethylhexyl)-4H-cyclopenta[2,1-b;3,4-b′]dithiophene)-alt-4,7(2,1,3-benzothiadiazole)] (PCPDTBT) during irradiation under white li...
Evaluation of Treatment Integrity: The Treatment Specificity Index
2015-03-30

Objective To differentiate between treatments in a randomized controlled trial (RCT), therapies need to display not only high purity but also high specificity. The aim of this study was to demonstrate the benefits of calculating a treatment specificity index for the evaluation of treatment differentiation. Method Based on an RCT of relapse prevention in depression, comparing a cognitive with a psychoeducational treatment, the specificity and the purity index were calculated. Results As indicated by the specificity index, both conditions differed in their levels of implemented specific and common interventions. A significant relationship was found between symptom change before a therapy session and treatment specificity. Conclusions The specificity index is an appropriate method for enhancing the internal validity of RCTs in evaluating treatment integrity.
The Punctum Fixum-Punctum Mobile Model: A Neuromuscular Principle for Efficient Movement Generation?
2015-03-30

According to the "punctum fixum-punctum mobile model" that was introduced in prior studies, for generation of the most effective intentional acceleration of a body part the intersegmental neuromuscular onset succession has to spread successively from the rotation axis (punctum fixum) toward the body part that shall be accelerated (punctum mobile). The aim of the present study was to investigate whether this principle is, indeed, fundamental for any kind of efficient rotational accelerations in general, independent of the kind of movements, type of rotational axis, the current body position, or movement direction. Neuromuscular onset succession was captured by surface electromyography of relevant muscles of the anterior and posterior muscle chain in 16 high-level gymnasts during intentional accelerating movement phases while performing 18 different gymnastics elements (in various body positions to forward and backward, performed on high bar, parallel bars, rings and trampoline), as well as during non-sport specific pivot movements around the longitudinal axis. The succession patterns to generate the acceleration phases during these movements were described and statistically evaluated based on the onset time difference between the muscles of the corresponding muscle chain. In all the analyzed movement phases, the results clearly support the hypothesized succession pattern from punctum fixum to punctum mobile. This principle was further underlined by the finding that the succession patterns do change their direction running through the body when the rotational axis (punctum fixum) has been changed (e.g., high bar or rings [hands] vs. floor or trampoline [feet]). The findings improve our understanding of intersegmental neuromuscular coordination patterns to generate intentional movements most efficiently. This could help to develop more specific methods to facilitate such patterns in particular contexts, thus allowing for shorter motor learning procedures of context-specific key movement sequences in different disciplines of sports, as well as during non-sport specific movements.
Improved Estimation and Interpretation of Correlations in Neural Circuits
2015-03-31

Ambitious projects aim to record the activity of ever larger and denser neuronal populations in vivo. Correlations in neural activity measured in such recordings can reveal important aspects of neural circuit organization. However, estimating and interpreting large correlation matrices is statistically challenging. Estimation can be improved by regularization, i.e. by imposing a structure on the estimate. The amount of improvement depends on how closely the assumed structure represents dependencies in the data. Therefore, the selection of the most efficient correlation matrix estimator for a given neural circuit must be determined empirically. Importantly, the identity and structure of the most efficient estimator informs about the types of dominant dependencies governing the system. We sought statistically efficient estimators of neural correlation matrices in recordings from large, dense groups of cortical neurons. Using fast 3D random-access laser scanning microscopy of calcium signals, we recorded the activity of nearly every neuron in volumes 200 μm wide and 100 μm deep (150-350 cells) in mouse visual cortex. We hypothesized that in these densely sampled recordings, the correlation matrix should be best modeled as the combination of a sparse graph of pairwise partial correlations representing local interactions and a low-rank component representing common fluctuations and external inputs. Indeed, in cross-validation tests, the covariance matrix estimator with this structure consistently outperformed other regularized estimators. The sparse component of the estimate defined a graph of interactions. These interactions reflected the physical distances and orientation tuning properties of cells: The density of positive 'excitatory' interactions decreased rapidly with geometric distances and with differences in orientation preference whereas negative 'inhibitory' interactions were less selective. Because of its superior performance, this 'sparse+latent' estimator likely provides a more physiologically relevant representation of the functional connectivity in densely sampled recordings than the sample correlation matrix.
Phosphoproteome of the cyanobacterium Synechocystis sp. PCC 6803 and its dynamics during nitrogen starvation
2015-03-31

Cyanobacteria have shaped the earth's biosphere as the first oxygenic photoautotrophs and still play an important role in many ecosystems. The ability to adapt to changing environmental conditions is an essential characteristic in order to ensure survival. To this end, numerous studies have shown that bacteria use protein post-translational modifications such as Ser/Thr/Tyr phosphorylation in cell signaling, adaptation, and regulation. Nevertheless, our knowledge of cyanobacterial phosphoproteomes and their dynamic response to environmental stimuli is relatively limited. In this study, we applied gel-free methods and high accuracy mass spectrometry toward the detection of Ser/Thr/Tyr phosphorylation events in the model cyanobacterium Synechocystis sp. PCC 6803. We could identify over 300 phosphorylation events in cultures grown on nitrate as exclusive nitrogen source. Chemical dimethylation labeling was applied to investigate proteome and phosphoproteome dynamics during nitrogen starvation. Our dataset describes the most comprehensive (phospho)proteome of Synechocystis to date, identifying 2382 proteins and 183 phosphorylation events and quantifying 2111 proteins and 148 phosphorylation events during nitrogen starvation. Global protein phosphorylation levels were increased in response to nitrogen depletion after 24 h. Among the proteins with increased phosphorylation, the PII signaling protein showed the highest fold-change, serving as positive control. Other proteins with increased phosphorylation levels comprised functions in photosynthesis and in carbon and nitrogen metabolism. This study reveals dynamics of Synechocystis phosphoproteome in response to environmental stimuli and suggests an important role of protein Ser/Thr/Tyr phosphorylation in fundamental mechanisms of homeostatic control in cyanobacteria.
Evaluating cerebellar dentatotomy for the treatment of spasticity with or without dystonia
2015-03-31

Spasticity represents a common and very often incapacitating neurologic condition, for which a limited number of treatment options are available. Stereotactic ablation of the dentate cerebellar nuclei (dentatotomy) was widely used in the past with variable results. In the present study, we reviewed 12 consecutive cases operated on at the Midland Centre for Neurosurgery and Neurology at Birmingham University (Smetwick, UK) in the 1980s. The following clinical aspects were analyzed: severity of spasticity, occurrence of abnormal movements (dystonia/athetosis), language fluency, gait, and overall clinical condition. Follow-up ranged from 0.5 to 94 (mean: 31.6) months. Immediate improvement was noted in 10 patients, and five of them had sustained this improvement at the time of the last assessment. A more pronounced improvement was observed for gait, relative to speech and abnormal movements. No significant morbidity related to the procedure was observed. We conclude that dentatotomy is a safe procedure that should still be considered in specific cases. Here, we review the cases reported in the literature, and present a mechanistic hypothesis about how dentatotomy influences motor tonus, in light of the current knowledge about cerebellar physiology. We believe that this issue is critical for the development of alternative surgical approaches targeting the cerebellum, such as chronic electric stimulation.
Topology of Platonic Spherical Manifolds: From Homotopy to Harmonic Analysis
2015-03-31

We carry out the harmonic analysis on four Platonic spherical three-manifolds with different topologies. Starting out from the homotopies (Everitt 2004), we convert them into deck operations, acting on the simply connected three-sphere as the cover, and obtain the corresponding variety of deck groups. For each topology, the three-sphere is tiled into copies of a fundamental domain under the corresponding deck group. We employ the point symmetry of each Platonic manifold to construct its fundamental domain as a spherical orbifold. While the three-sphere supports an orthonormal complete basis for harmonic analysis formed by Wigner polynomials, a given spherical orbifold leads to a selection of a specific subbasis. The resulting selection rules find applications in cosmic topology, probed by the cosmic microwave background.
Diethylnitrosamine (DEN)-induced carcinogenic liver injury in mice
2015-04-01

The toxic properties of various nitrosamines in animals and humans are well established. The parenteral or oral administration of the smallest quantities of diethylnitrosamine (DEN) or dimethylnitrosamine (DMN) results in severe liver damage. Most prominent are intense neutrophilic infiltration, extensive centrilobular haemorrhagic necrosis, bile duct proliferation, fibrosis, and bridging necrosis that ends in hepatocarcinogenesis. Due to the robustness of the induced hepatic alterations, the application of DEN in rodents has become an attractive experimental model for studies aimed at understanding the pathogenetic alterations underlying the formation of liver cancer, which represents one of the most common malignancies in humans worldwide. However, several studies have shown that the hepatocarcinogenic effects of nitrosamines might vary with the genetic background of the animals, their sex, their age, and other factors that might impact the outcome of experimentation. We present general guidelines for working with DEN, and a detailed protocol that allows the establishment of highly reproducible liver cancer in mice. The outcome of liver injury after the application of DEN in mice, as estimated by the formation of cirrhosis and cancer, appears to be a suitable animal model for the analysis of some aspects and processes that promote the pathogenesis of hepatocellular carcinoma in humans.
Word problems: a review of linguistic and numerical factors contributing to their difficulty
2015-04-01

Word problems (WPs) belong to the most difficult and complex problem types that pupils encounter during their elementary-level mathematical development. In the classroom setting, they are often viewed as merely arithmetic tasks; however, recent research shows that a number of linguistic verbal components not directly related to arithmetic contribute greatly to their difficulty. In this review, we will distinguish three components of WP difficulty: (i) the linguistic complexity of the problem text itself, (ii) the numerical complexity of the arithmetic problem, and (iii) the relation between the linguistic and numerical complexity of a problem. We will discuss the impact of each of these factors on WP difficulty and motivate the need for a high degree of control in stimuli design for experiments that manipulate WP difficulty for a given age group.
VIH2 Regulates the Synthesis of Inositol Pyrophosphate InsP8 and Jasmonate-Dependent Defenses in Arabidopsis
2015-04-01

Diphosphorylated inositol polyphosphates, also referred to as inositol pyrophosphates, are important signaling molecules that regulate critical cellular activities in many eukaryotic organisms, such as membrane trafficking, telomere maintenance, ribosome biogenesis, and apoptosis. In mammals and fungi, two distinct classes of inositol phosphate kinases mediate biosynthesis of inositol pyrophosphates: Kcs1/IP6K- and Vip1/PPIP5K-like proteins. Here, we report that PPIP5K homologs are widely distributed in plants and that Arabidopsis thaliana VIH1 and VIH2 are functional PPIP5K enzymes. We show a specific induction of inositol pyrophosphate InsP8 by jasmonate and demonstrate that steady state and jasmonate-induced pools of InsP8 in Arabidopsis seedlings depend on VIH2. We identify a role of VIH2 in regulating jasmonate perception and plant defenses against herbivorous insects and necrotrophic fungi. In silico docking experiments and radioligand binding-based reconstitution assays show high-affinity binding of inositol pyrophosphates to the F-box protein COI1-JAZ jasmonate coreceptor complex and suggest that coincidence detection of jasmonate and InsP8 by COI1-JAZ is a critical component in jasmonate-regulated defenses.