Shared Information -- New Insights and Problems in Decomposing Information in Complex Systems

How can the information that a set ${X_{1},...,X_{n}}$ of random variables contains about another random variable $S$ be decomposed? To what extent do different subgroups provide the same, i.e. shared or redundant, information, carry unique information or interact for the emergence of synergistic information? Recently Williams and Beer proposed such a decomposition based on natural properties for shared information. While these properties fix the structure of the decomposition, they do not uniquely specify the values of the different terms. Therefore, we investigate additional properties such as strong symmetry and left monotonicity. We find that strong symmetry is incompatible with the properties proposed by Williams and Beer. Although left monotonicity is a very natural property for an information measure it is not fulfilled by any of the proposed measures. We also study a geometric framework for information decompositions and ask whether it is possible to represent shared information by a family of posterior distributions. Finally, we draw connections to the notions of shared knowledge and common knowledge in game theory. While many people believe that independent variables cannot share information, we show that in game theory independent agents can have shared knowledge, but not common knowledge. We conclude that intuition and heuristic arguments do not suffice when arguing about information.Comment: 20 page

A density-based statistical analysis of graph clustering algorithm performance

This is a pre-copyedited, author-produced version of an article accepted for publication in Journal of Complex Networks following peer review. The version of record: Pierre Miasnikof, Alexander Y Shestopaloff, Anthony J Bonner, Yuri Lawryshyn, Panos M Pardalos, A density-based statistical analysis of graph clustering algorithm performance, Journal of Complex Networks, Volume 8, Issue 3, June 2020, cnaa012, https://doi.org/10.1093/comnet/cnaa012 is available online at: https://doi.org/10.1093/comnet/cnaa012© 2020 The authors. Published by Oxford University Press. All rights reserved. We introduce graph clustering quality measures based on comparisons of global, intra- A nd inter-cluster densities, an accompanying statistical significance test and a step-by-step routine for clustering quality assessment. Our work is centred on the idea that well-clustered graphs will display a mean intra-cluster density that is higher than global density and mean inter-cluster density. We do not rely on any generative model for the null model graph. Our measures are shown to meet the axioms of a good clustering quality function. They have an intuitive graph-theoretic interpretation, a formal statistical interpretation and can be tested for significance. Empirical tests also show they are more responsive to graph structure, less likely to breakdown during numerical implementation and less sensitive to uncertainty in connectivity than the commonly used measures

Isolation and Characterization of Stigmasterol and Bis-(5, 7-diacetyl-catechin-4’-α- rhamnopyranoside) from the Stem bark of Neocarya macrophylla (Sabine) Prance (Chrysobalanaceae)

Neocarya macrophylla belongs to the Chrysobalanaceae family and is extensively used in folk medicine as an antibacterial, antivenin, antiasthmatic, anticancer, analgesic and anti-inflammatory agent. This study was aimed at isolation and characterization of compounds from the stem bark of Neocarya macrophylla.  Pulverized plant material was exhaustively extracted with methanol using maceration method and concentrated invacuo with the aid of rotary evaporator at 40oC to afford a reddish brown crude methanol extract (ME). The methanol extract was successively partitioned into hexane, dichloromethane, ethylacetate, n-butanol and aqueous fractions. Stigmasterol was isolated from the hexane fraction and a catechin glycoside, Bis-(5,7-diacetyl-catechin-4’-α- rhamnopyranoside) was  isolated from the ethylacetate soluble fraction using a combination of silica gel column, gel filtration (sephadex LH-20) and preparative thin layer chromatography. The structures of the compounds were established on the basis of chemical tests, spectroscopic analysis and by comparison with reference spectral data.Keywords: Neocarya macrophylla, phytochemical, stigmasterol, Bis-(5, 7-diacetyl-catechin-4’-α-rhamnopyranoside)

Prevalence of chronic traumatic encephalopathy in the Sydney Brain Bank

Chronic traumatic encephalopathy neuropathologic change can only be definitively diagnosed post-mortem. It has been associated with repetitive mild neurotrauma sustained in amateur and professional contact, collision and combat sports, although it has also been documented in people with a single severe traumatic brain injury and in some people with no known history of brain injury. The characteristic neuropathology is an accumulation of perivascular neuronal and astrocytic phosphorylated tau in the depths of the cortical sulci. The tau-immunopositive neurons and astrocytes that are considered pathognomonic for chronic traumatic encephalopathy are morphologically indistinguishable from Alzheimer-related neurofibrillary tangles and ageing-related tau astrogliopathy, respectively, although they are found in different spatial distributions throughout the cortex. The Sydney Brain Bank collection consists of neurodegenerative diseases and neurologically normal controls. We screened 636 of these cases for chronic traumatic encephalopathy neuropathologic change. A subset of 109 cases had a known history of traumatic brain injury. Three cortical regions were screened for the presence of neuronal and astrocytic phosphorylated tau according to the current 2021 National Institute on Neurological Disorders and Stroke/National Institute of Biomedical Imaging and Bioengineering consensus criteria for chronic traumatic encephalopathy. Five cases (0.79%) showed pathological evidence of chronic traumatic encephalopathy and three of these had a history of traumatic brain injury. Three cases had coexisting Alzheimer's and/or Lewy body disease pathology meeting criteria for neurodegenerative disease. Another eight cases almost met criteria for chronic traumatic encephalopathy neuropathological change except for an absence of neuronal tau or a strict perivascular arrangement. Ageing-related tau astrogliopathy was found in all eight cases as a coexisting neuropathology. Traumatic brain injury was associated with increased odds ratio [1.79, confidence interval 1.18-2.72] of having a higher neurofibrillary tangle stage and phosphorylated TAR DNA binding protein 43 (OR 2.48, confidence interval 1.35-4.54). Our study shows a very low rate of chronic traumatic encephalopathy neuropathological change in brains with or without neurodegenerative disease from the Sydney Brain Bank. Our evidence suggests that isolated traumatic brain injury in the general population is unlikely to cause chronic traumatic encephalopathy neuropathologic change but may be associated with increased brain ageing

Hereditary sensory neuropathy type 1-associated deoxysphingolipids cause neurotoxicity, acute calcium handling abnormalities and mitochondrial dysfunction in vitro

Hereditary sensory neuropathy type 1 (HSN-1) is a peripheral neuropathy most frequently caused by mutations in the SPTLC1 or SPTLC2 genes, which code for two subunits of the enzyme serine palmitoyltransferase (SPT). SPT catalyzes the first step of de novo sphingolipid synthesis. Mutations in SPT result in a change in enzyme substrate specificity, which causes the production of atypical deoxysphinganine and deoxymethylsphinganine, rather than the normal enzyme product, sphinganine. Levels of these abnormal compounds are elevated in blood of HSN-1 patients and this is thought to cause the peripheral motor and sensory nerve damage that is characteristic of the disease, by a largely unresolved mechanism. In this study, we show that exogenous application of these deoxysphingoid bases causes dose- and time-dependent neurotoxicity in primary mammalian neurons, as determined by analysis of cell survival and neurite length. Acutely, deoxysphingoid base neurotoxicity manifests in abnormal Ca2+ handling by the endoplasmic reticulum (ER) and mitochondria as well as dysregulation of cell membrane store-operated Ca2+ channels. The changes in intracellular Ca2+ handling are accompanied by an early loss of mitochondrial membrane potential in deoxysphingoid base-treated motor and sensory neurons. Thus, these results suggest that exogenous deoxysphingoid base application causes neuronal mitochondrial dysfunction and Ca2+ handling deficits, which may play a critical role in the pathogenesis of HSN-1

The urologic epithelial stem cell database (UESC) – a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder

Background: Public databases are crucial for analysis of high-dimensional gene and protein expression data. The Urologic Epithelial Stem Cells (UESC) database http://scgap.systemsbiology.net/ is a public database that contains gene and protein information for the major cell types of the prostate, prostate cancer cell lines, and a cancer cell type isolated from a primary tumor. Similarly, such information is available for urinary bladder cell types. Description: Two major data types were archived in the database, protein abundance localization data from immunohistochemistry images, and transcript abundance data principally from DNA microarray analysis. Data results were organized in modules that were made to operate independently but built upon a core functionality. Gene array data and immunostaining images for human and mouse prostate and bladder were made available for interrogation. Data analysis capabilities include: (1) CD (cluster designation) cell surface protein data. For each cluster designation molecule, a data summary allows easy retrieval of images (at multiple magnifications). (2) Microarray data. Single gene or batch search can be initiated with Affymetrix Probeset ID, Gene Name, or Accession Number together with options of coalescing probesets and/or replicates. Conclusion: Databases are invaluable for biomedical research, and their utility depends on data quality and user friendliness. UESC provides for database queries and tools to examine cell typespecific gene expression (normal vs. cancer), whereas most other databases contain only whole tissue expression datasets. The UESC database provides a valuable tool in the analysis of differential gene expression in prostate cancer genes in cancer progression.This work was supported by grant 1U01 DK63630 from NIDDK. Additional funding came from grants CA85859, CA98699 and CA111244 from NCI

The reflectance of human skin in the millimeter-wave band

© 2020 by the authors. Licensee MDPI, Basel, Switzerland. The millimeter-wave band is an ideal part of the electromagnetic radiation to diagnose human skin conditions because this radiation interacts only with tissue down to a depth of a millimetre or less over the band range from 30 GHz to 300 GHz. In this paper, radiometry is used as a non-contact sensor for measuring the human skin reflectance under normal and wet skin conditions. The mean reflectance of the skin of a sample of 50 healthy participants over the (80–100) GHz band was found to be ~0.615 with a standard deviation of ~0.088, and an experimental measurement uncertainty of ±0.005. The thinner skin regions of the back of the hand, the volar forearms and the inner wrist had reflectances 0.068, 0.068 and 0.062 higher than the thicker skin regions of the palm of the hand, the dorsal forearm and the outer wrist skin. Experimental measurements of human skin reflectance in a normal and a wet state on the back of the hand and the palm of the hand regions indicated that the mean differences in the reflectance before and after the application of water were ~0.078 and ~0.152, respectively. These differences were found to be statistically significant as assessed using t-tests (34 paired t-tests and six independent t-tests were performed to assess the significance level of the mean differences in the reflectance of the skin). Radiometric measurements in this paper show the quantitative variations in the skin reflectance between locations, sexes, and individuals. The study reveals that these variations are related to the skin thickness and water content, a capability that has the potential to allow radiometry to be used as a non-contact sensor to detect and monitor skin conditions such as eczema, psoriasis, malignancy, and burn wounds

Correction of both immunodeficiency and hypoparathyroidism by thymus transplantation in complete DiGeorge Syndrome

Combined immune deficiency due to athymia in patients with complete DiGeorge syndrome can be corrected by allogeneic thymus transplantation. Hypoparathyroidism is a frequent concomitant clinical problem in these patients, which persists after thymus transplantation. Cotransplantation of allogeneic thymus and parental parathyroid tissue has been attempted but does not achieve durable correction of the patients' hypoparathyroidism due to parathyroid graft rejection. Surprisingly, we observed correction of hypoparathyroidism in one patient after thymus transplantation. Immunohistochemical analysis and fluorescence in situ hybridization confirmed the presence of allogeneic parathyroid tissue in the patient's thymus transplant biopsy. Despite a lack of HLA‐matching between thymus donor and recipient, the reconstituted immune system displays tolerance toward the thymus donor. Therefore we expect this patient's hypoparathyroidism to be permanently cured. It is recognised that ectopic parathyroid tissue is not infrequently found in the thymus. If such thymuses could be identified, we propose that their use would offer a compelling approach to achieving lasting correction of both immunodeficiency and hypoparathyroidism