ILC2s chew the fat.

In this issue of JEM, Rana et al. (https://doi.org/10.1084/jem.20190689) report that adipose tissue multipotent stromal cells (MSCs) provide multifaceted support for adipose tissue-resident ILC2s through contact-mediated proliferation and IL-33-mediated stress-induced activation

Two and three electrons in a quantum dot: 1/|J| - expansion

We consider systems of two and three electrons in a two-dimensional parabolic quantum dot. A magnetic field is applied perpendicularly to the electron plane of motion. We show that the energy levels corresponding to states with high angular momentum, J, and a low number of vibrational quanta may be systematically computed as power series in 1/|J|. These states are relevant in the high-B limit.Comment: LaTeX, 15 pages,6 postscript figure

Internal transitions of negatively charged magnetoexcitons in quantum dots

We report calculations of oscillator strengths for the far infrared absorption of light by the excitonic complexes Xn- (the excess charge, n, ranging from one to four) confined in quantum dots. The magnetic field is varied in an interval which corresponds to ``filling factors'' between 2 and 3/5. Electron-hole interaction effects are seen in the deviations of the peak positions from the Kohn lines, and in the spreading of the oscillator strengths over a few final states. Transition densities are used as an additional tool to characterize the absorption peaks.Comment: Presented as a poster in the Third Stig Lundqvist Conference on Advancing Frontiers of Condensed Matter Physics: Fundamental Interactions and Excitations in Confined Systems, Trieste, August 11 - 1

Portability vs. Precedent: IMUs vs. 3D Motion Capture for Collecting Kinematic Data in Dancers

The emergence of portable kinematic data collection systems (Inertial Measurement Units - IMUs) have become a potential alternative to 3D video motion capture systems for real-world application. However, there remains little research on the application of IMU technology for the evaluation of dancers’ biomechanical movement. PURPOSE: To assess the validity of the Noraxon IMU system compared with the Cortex 3D video motion capture system for kinematic data collection during a sauté. METHODS: 10 healthy, advanced female dancers were equipped with both a Noraxon IMU (200Hz) system and reflective markers used with a 12-camera Motion Analysis system (Cortex, 250 Hz) for simultaneous data collection. Participants completed an independent After a 10-minute warmup, each participant performed one trial of 10 stationary sautés while barefoot, with feet in second position and arms in fifth position in time with music at 95 bpm. The middle 5 jumps of each participant’s trial were processed and analyzed with Visual3D and MATLAB for the Cortex data, and through Noraxon’s reporting system for the Noraxon data. All results were compared through SPSS with repeated-measures ANOVAs. RESULTS: A main effect of measurement system was found for peak joint angles in the sagittal ((6,4)=0.009, p \u3c 0.001), frontal ((9,1)=0.12, p \u3c 0.001), and transverse ((9,1)=0.009, p \u3c 0.001) planes. Pairwise comparisons revealed significant differences in peak hip flexion, hip extension, knee flexion, knee extension, ankle plantar flexion, ankle dorsiflexion, hip adduction, knee adduction, ankle inversion, hip internal rotation, hip external rotation, knee internal rotation, knee external rotation, and ankle internal rotation. No significant main effect was found between measurement systems for sagittal, frontal, and transverse plane joint excursions ((9,1)=0.12, p=0.253). CONCLUSION: Significant differences in most peak joint angles indicate that Noraxon IMUs do not have strong validity for capturing absolute joint angles compared to 3D video motion capture. However, joint excursion measurements were similar, indicating that Noraxon IMUs may be valid for measuring the total amount of motion during a particular movement. Additional analysis is warranted for further understanding of this technology

Evidence for internal field in graphite: A conduction electron spin resonance study

We report conduction electron spin resonance measurements performed on highly oriented pyrolitic graphite samples between 10 K and 300 K using S (f = 4 GHz), X (f = 9.4 GHz), and Q (f = 34.4 GHz) microwave bands for the external dc-magnetic field applied parallel (H || c) and perpendicular (H perp c) to the sample hexagonal c-axis. The results obtained in the H || c geometry are interpreted in terms of the presence of an effective internal ferromagnetic-like field Heff-int(T,H) that increases as the temperature decreases and the applied dc-magnetic field increases. We associate the occurrence of the Heff-int(T,H) with the field-induced metal-insulator transition in graphite and discuss its origin in the light of relevant theoretical models.Comment: 10 pages (tex), 5 figures (ps

Functional, genetic and bioinformatic characterization of a calcium/calmodulin kinase gene in Sporothrix schenckii

<p>Abstract</p> <p>Background</p> <p><it>Sporothrix schenckii </it>is a pathogenic, dimorphic fungus, the etiological agent of sporotrichosis, a subcutaneous lymphatic mycosis. Dimorphism in <it>S. schenckii </it>responds to second messengers such as cAMP and calcium, suggesting the possible involvement of a calcium/calmodulin kinase in its regulation. In this study we describe a novel calcium/calmodulin-dependent protein kinase gene in <it>S. schenckii, sscmk1</it>, and the effects of inhibitors of calmodulin and calcium/calmodulin kinases on the yeast to mycelium transition and the yeast cell cycle.</p> <p>Results</p> <p>Using the PCR homology approach a new member of the calcium/calmodulin kinase family, SSCMK1, was identified in this fungus. The cDNA sequence of <it>sscmk1 </it>revealed an open reading frame of 1,221 nucleotides encoding a 407 amino acid protein with a predicted molecular weight of 45.6 kDa. The genomic sequence of <it>sscmk1 </it>revealed the same ORF interrupted by five introns. Bioinformatic analyses of SSCMK1 showed that this protein had the distinctive features that characterize a calcium/calmodulin protein kinase: a serine/threonine protein kinase domain and a calmodulin-binding domain. When compared to homologues from seven species of filamentous fungi, SSCMK1 showed substantial similarities, except for a large and highly variable region that encompasses positions 330 – 380 of the multiple sequence alignment. Inhibition studies using calmodulin inhibitor W-7, and calcium/calmodulin kinase inhibitors, KN-62 and lavendustin C, were found to inhibit budding by cells induced to re-enter the yeast cell cycle and to favor the yeast to mycelium transition.</p> <p>Conclusion</p> <p>This study constitutes the first evidence of the presence of a calcium/calmodulin kinase-encoding gene in <it>S. schenckii </it>and its possible involvement as an effector of dimorphism in this fungus. These results suggest that a calcium/calmodulin dependent signaling pathway could be involved in the regulation of dimorphism in this fungus. The results suggest that the calcium/calmodulin kinases of yeasts are evolutionarily distinct from those in filamentous fungi.</p

Information management in DNA replication modeled by directional, stochastic chains with memory

[EN] Stochastic chains represent a key variety of phenomena in many branches of science within the context of information theory and thermodynamics. They are typically approached by a sequence of independent events or by a memoryless Markov process. Stochastic chains are of special significance to molecular biology, where genes are conveyed by linear polymers made up of molecular subunits and transferred from DNA to proteins by specialized molecular motors in the presence of errors. Here, we demonstrate that when memory is introduced, the statistics of the chain depends on the mechanism by which objects or symbols are assembled, even in the slow dynamics limit wherein friction can be neglected. To analyze these systems, we introduce a sequence-dependent partition function, investigate its properties, and compare it to the standard normalization defined by the statistical physics of ensembles. We then apply this theory to characterize the enzyme-mediated information transfer involved in DNA replication under the real, non-equilibrium conditions, reproducing measured error rates and explaining the typical 100-fold increase in fidelity that is experimentally found when proofreading and edition take place. Our model further predicts that approximately 1 kT has to be consumed to elevate fidelity in one order of magnitude. We anticipate that our results are necessary to interpret configurational order and information management in many molecular systems within biophysics, materials science, communication, and engineering. Published by AIP Publishing.It is a pleasure to thank J. M. R. Parrondo and D. G. Aleja for fruitful discussion. This work was supported the Spanish Ministry of Economy and Competitiveness (Grant Nos. MAT2013-49455-EXP and MAT2015-71806-R).Arias-Gonzalez, JR. (2016). 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Tissue signals imprint ILC2 identity with anticipatory function.

Group 2 innate lymphoid cells (ILC2s) are distributed systemically and produce type 2 cytokines in response to a variety of stimuli, including the epithelial cytokines interleukin (IL)-25, IL-33, and thymic stromal lymphopoietin (TSLP). Transcriptional profiling of ILC2s from different tissues, however, grouped ILC2s according to their tissue of origin, even in the setting of combined IL-25-, IL-33-receptor-, and TSLP-receptor-deficiency. Single-cell profiling confirmed a tissue-organizing transcriptome and identified ILC2 subsets expressing distinct activating receptors, including the major subset of skin ILC2s, which were activated preferentially by IL-18. Tissue ILC2 subsets were unaltered in number and expression in germ-free mice, suggesting that endogenous, tissue-derived signals drive the maturation of ILC2 subsets by controlling expression of distinct patterns of activating receptors, thus anticipating tissue-specific perturbations occurring later in life

ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS based metabolomics

We present ProbMetab, an R package which promotes substantial improvement in automatic probabilistic LC-MS based metabolome annotation. The inference engine core is based on a Bayesian model implemented to: (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and; (ii) allow sensitive selection of biologically meaningful biochemical reactions databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand alone versions. ProbMetab was implemented in a modular fashion to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp.usp.br/methods/probmetab/.Comment: Manuscript to be submitted very soon. 7 pages, 3 color figures. There is a companion material, the two case studies, which are going to be posted here together with the main text in next updated versio

A Preliminary Investigation into Search and Matching for Tumour Discrimination in WHO Breast Taxonomy Using Deep Networks

Breast cancer is one of the most common cancers affecting women worldwide. They include a group of malignant neoplasms with a variety of biological, clinical, and histopathological characteristics. There are more than 35 different histological forms of breast lesions that can be classified and diagnosed histologically according to cell morphology, growth, and architecture patterns. Recently, deep learning, in the field of artificial intelligence, has drawn a lot of attention for the computerized representation of medical images. Searchable digital atlases can provide pathologists with patch matching tools allowing them to search among evidently diagnosed and treated archival cases, a technology that may be regarded as computational second opinion. In this study, we indexed and analyzed the WHO breast taxonomy (Classification of Tumours 5th Ed.) spanning 35 tumour types. We visualized all tumour types using deep features extracted from a state-of-the-art deep learning model, pre-trained on millions of diagnostic histopathology images from the TCGA repository. Furthermore, we test the concept of a digital "atlas" as a reference for search and matching with rare test cases. The patch similarity search within the WHO breast taxonomy data reached over 88% accuracy when validating through "majority vote" and more than 91% accuracy when validating using top-n tumour types. These results show for the first time that complex relationships among common and rare breast lesions can be investigated using an indexed digital archive