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Multivariate binary probability distribution in the Grassmann formalism.

Authors:
Takashi Arai

Phys Rev E 2021 Jun;103(6-1):062104

Faculty of Science, Yamagata University, Yamagata 990-8560, Japan.

We propose a probability distribution for multivariate binary random variables. The probability distribution is expressed as principal minors of the parameter matrix, which is a matrix analogous to the inverse covariance matrix in the multivariate Gaussian distribution. In our model, the partition function, central moments, and the marginal and conditional distributions are expressed analytically. Read More

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Phase Separation and Protein Partitioning in Compartmentalized Cell-Free Expression Reactions.

Biomacromolecules 2021 Jul 14. Epub 2021 Jul 14.

Department of Physics, Kyushu University, Motooka 744, Fukuoka 819-0395, Japan.

Liquid-liquid phase separation (LLPS) is important to control a wide range of reactions from gene expression to protein degradation in a cell-sized space. To bring a better understanding of the compatibility of such phase-separated structures with protein synthesis, we study emergent LLPS in a cell-free transcription-translation (TXTL) reaction. When the TXTL reaction composed of many proteins is concentrated, the uniformly mixed state becomes unstable, and membrane-less phases form spontaneously. Read More

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Dynamic expression of brain functional systems disclosed by fine-scale analysis of edge time series.

Netw Neurosci 2021 27;5(2):405-433. Epub 2021 Apr 27.

Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN, USA.

Functional connectivity (FC) describes the statistical dependence between neuronal populations or brain regions in resting-state fMRI studies and is commonly estimated as the Pearson correlation of time courses. Clustering or community detection reveals densely coupled sets of regions constituting resting-state networks or functional systems. These systems manifest most clearly when FC is sampled over longer epochs but appear to fluctuate on shorter timescales. Read More

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The Role of Elements Partition and Austenite Grain Size in the Ferrite-Bainite Banding Formation during Hot Rolling.

Materials (Basel) 2021 May 1;14(9). Epub 2021 May 1.

Institute of Engineering Technology, University of Science and Technology Beijing, Beijing 100083, China.

The partitioning and diffusion of solute elements in hot rolling and the effect of the partitioning and diffusion on the ferrite-bainite banding formation after hot rolling in the 20CrMnTi steel were experimentally examined by EPMA (electron probe microanalysis) technology and simulated by DICTRTA and MATLAB software. The austenite grain size related to the hot rolling process and the effect of austenite grain size on the ferrite-bainite banding formation were studied. The results show that experimental steel without banding has the most uniform hardness distribution, which is taken from the edge of the cast slab and 1/4 diameter position of the cast slab, heating at 1100 °C for 2 h and above 1200 °C for 2-4 h during the hot rolling, respectively. Read More

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Ecosystem engineering in the arboreal realm: heterogeneity of wood-boring beetle cavities and their use by cavity-nesting ants.

Oecologia 2021 Jun 10;196(2):427-439. Epub 2021 May 10.

Department of Biology and the Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO, 63121, USA.

Wood-boring beetle larvae act as ecosystem engineers by creating stem cavities that are used secondarily as nests by many arboreal ant species. Understanding the heterogeneity and distribution of available cavities and their use by ants is therefore key to understanding arboreal ant community assembly and diversity. Our goals were to quantify the abundance and diversity of beetle-produced cavity resources in a tropical canopy, reveal how ants use these resources, and determine which characteristics of the cavity resource contribute to ant use. Read More

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HU-AB simulacrum: Fusion of HU-B and HU-A into HU-B-A, a functional analog of the Escherichia coli HU-AB heterodimer.

Biochem Biophys Res Commun 2021 Jun 5;560:27-31. Epub 2021 May 5.

Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Knowledge City, Sector-81, SAS Nagar, Punjab, 140306, India. Electronic address:

In enteric bacteria such as Escherichia coli, there are two homologs of the DNA-binding nucleoid associated protein (NAP) known as HU. The two homologs are known as HU-A and HU-B, and exist either in the form of homodimers (HU-AA, or HU-BB) or as heterodimers (HU-AB), with different propensities to form higher-order oligomers. The three different dimeric forms dominate different stages of bacterial growth, with the HU-AB heterodimer dominating cultures in the stationary phase. Read More

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Local spin and open quantum systems: clarifying misconceptions, unifying approaches.

Phys Chem Chem Phys 2021 Apr 30;23(14):8375-8392. Epub 2021 Mar 30.

Departamento de Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain.

The theory of open quantum systems (OQSs) is applied to partition the squared spin operator into fragment (local spin) and interfragment (spin-coupling) contributions in a molecular system. An atomic or fragment subsystem is described by a quantum mechanical mixed density operator composed of sectors, characterized by different integer number of electrons that appear with specific probabilities. The OQS fragment spin operators coincide with those defined by Clark and Davidson in their paper on local spins (J. Read More

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The Bacteriostatic Activity of 2-Phenylethanol Derivatives Correlates with Membrane Binding Affinity.

Membranes (Basel) 2021 Mar 31;11(4). Epub 2021 Mar 31.

Department of Chemistry, Biochemistry, Johannes Gutenberg University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128 Mainz, Germany.

The hydrophobic tails of aliphatic primary alcohols do insert into the hydrophobic core of a lipid bilayer. Thereby, they disrupt hydrophobic interactions between the lipid molecules, resulting in a decreased lipid order, i.e. Read More

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A new hypothetical model for pancreatic development based on change in the cell division orientation.

Gene 2021 Jun 26;785:145607. Epub 2021 Mar 26.

Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science & Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., Isfahan, Iran. Electronic address:

Although lifelong renewal and additional compensatory growth in response to demand are undeniable facts, so far, no specific stem cells have been found for pancreatic cells. According to the consensus model, the development of pancreas results from the hierarchical differentiation of pluripotent stem cells towards the appearance of the first endocrine and exocrine cells at approximately 7.5 to 8th gestation week (GW) of human embryo. Read More

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Controllable stroke-based sketch synthesis from a self-organized latent space.

Neural Netw 2021 May 28;137:138-150. Epub 2021 Jan 28.

Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China. Electronic address:

Learning to synthesize free-hand sketches controllably according to specified categories and sketching styles is a challenging task, due to the lack of training data with category labels and style labels. One choice to control the synthesis is by self-organizing a latent coding space to preserve the similarity of structural patterns of the observed data. A practical way is introducing a Gaussian mixture prior over the latent codes, where each Gaussian component represents a specific categorical or stylistic pattern. Read More

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Seasonality of primary productivity affects coastal species more than its magnitude.

Sci Total Environ 2021 Feb 16;757:143740. Epub 2020 Nov 16.

Department of Zoology and Entomology, Rhodes University, Grahamstown 6140, South Africa.

While the importance of extreme conditions is recognised, patterns in species' abundances are often interpreted through average environmental conditions within their distributional range. For marine species with pelagic larvae, temperature and phytoplankton concentration are key variables. Along the south coast of South Africa, conspicuous spatial patterns in recruitment rates and the abundances of different mussel species exist, with focal areas characterized by large populations. Read More

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February 2021

Equilibrium properties of two-species reactive lattice gases on random catalytic chains.

Phys Rev E 2020 Sep;102(3-1):032121

Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600), 4 Place Jussieu, 75252 Paris Cedex 05, France.

We focus here on the thermodynamic properties of adsorbates formed by two-species A+B→⊘ reactions on a one-dimensional infinite lattice with heterogeneous "catalytic" properties. In our model hard-core A and B particles undergo continuous exchanges with their reservoirs and react when dissimilar species appear at neighboring lattice sites in presence of a "catalyst." The latter is modeled by supposing either that randomly chosen bonds in the lattice promote reactions (Model I) or that reactions are activated by randomly chosen lattice sites (Model II). Read More

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September 2020

Detrital food web contributes to aquatic ecosystem productivity and rapid salmon growth in a managed floodplain.

PLoS One 2020 18;15(9):e0216019. Epub 2020 Sep 18.

California Trout-San Francisco, San Francisco, CA, United States of America.

Similar to many large river valleys globally, the Sacramento River Valley has been extensively drained and leveed, hydrologically divorcing river channels from most floodplains. Today, the former floodplain is extensively managed for agriculture. Lack of access to inundated floodplains is recognized as a significant contributing factor in the decline of native Chinook Salmon (Oncorhynchus tshawytscha). Read More

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October 2020

Liver regeneration after performing associating liver partition and portal vein occlusion for staged hepatectomy (ALPPS) is histologically similar to that occurring after liver transplantation using a small-for-size graft.

Surg Today 2021 Mar 9;51(3):374-383. Epub 2020 Aug 9.

Department of General and Gastroenterological Surgery, Showa University Fujigaoka Hospital, 1-30 Fujigaoka, Aoba-ku, Yokohama, 227-8501, Japan.

Purpose: Associating liver partition and portal vein ligation for staged hepatectomy (ALPPS) can achieve marked future liver remnant (FLR) hypertrophy but this procedure is associated with a risk of mortality due to liver failure because of an insufficient FLR functional increase, a situation comparable to small-for-size syndrome (SFSS) after living-donor liver transplantation (LDLT).

Methods: The clinical data, morphologic volume changes, and histopathologic and immunohistochemical findings in hepatocytes and bile ductules were compared between ALPPS (n = 10) and LDLT with a risk for SFSS (n = 12).

Results: Although the patient characteristics and short-term outcome differed between the groups, the mean hypertrophy ratios with respect to liver volume for the FLR after performing the first-stage ALPPS procedures resembled those in small-for-size grafts after similar time intervals: 1. Read More

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Triacylglycerols sequester monotopic membrane proteins to lipid droplets.

Nat Commun 2020 08 7;11(1):3944. Epub 2020 Aug 7.

Laboratoire de Physique de l'École Normale Supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005, Paris, France.

Triacylglycerols (TG) are synthesized at the endoplasmic reticulum (ER) bilayer and packaged into organelles called lipid droplets (LDs). LDs are covered by a single phospholipid monolayer contiguous with the ER bilayer. This connection is used by several monotopic integral membrane proteins, with hydrophobic membrane association domains (HDs), to diffuse between the organelles. Read More

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Myelin-Associated MAL and PLP Are Unusual among Multipass Transmembrane Proteins in Preferring Ordered Membrane Domains.

J Phys Chem B 2020 07 4;124(28):5930-5939. Epub 2020 Jun 4.

Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States.

Eukaryotic membranes can be partitioned into lipid-driven membrane microdomains called lipid rafts, which function to sort lipids and proteins in the plane of the membrane. As protein selectivity underlies all functions of lipid rafts, there has been significant interest in understanding the structural and molecular determinants of raft affinity. Such determinants have been described for lipids and single-spanning transmembrane proteins; however, how multipass transmembrane proteins (TMPs) partition between ordered and disordered phases has not been widely explored. Read More

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Sorting Signed Permutations by Intergenic Reversals.

IEEE/ACM Trans Comput Biol Bioinform 2020 May 7;PP. Epub 2020 May 7.

Genome rearrangements are mutations affecting large portions of a genome, and a reversal is one of the most studied genome rearrangements in the literature through the Sorting by Reversals (SbR) problem. SbR is solvable in polynomial time on signed permutations (i.e. Read More

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RNA-Seq transcriptome profiling in three liver regeneration models in rats: comparative analysis of partial hepatectomy, ALLPS, and PVL.

Sci Rep 2020 03 23;10(1):5213. Epub 2020 Mar 23.

Department of Surgery and Organ Transplantation Center, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.

The liver is a unique organ that has a phenomenal capacity to regenerate after injury. Different surgical procedures, including partial hepatectomy (PH), intraoperative portal vein ligation (PVL), and associated liver partition and portal vein ligation for staged hepatectomy (ALPPS) show clinically distinct recovery patterns and regeneration. The observable clinical differences likely mirror some underlying variations in the patterns of gene activation and regeneration pathways. Read More

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Long-Term Follow-Up after Prostatectomy for Prostate Cancer and the Need for Active Monitoring.

Prostate Cancer 2020 10;2020:7196189. Epub 2020 Mar 10.

Olin Teague VA, Temple, TX 76504, USA.

Background: Only truly long-term follow-up can determine the ultimate outcome in prostate cancer. Most studies have a median follow-up of less than 10 years and then project outcomes out to 15 and 20 years. We sought to follow patients for at least 20 years. Read More

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Differential impact of synthetic antitumor lipid drugs on the membrane organization of phosphatidic acid and diacylglycerol monolayers.

Chem Phys Lipids 2020 07 14;229:104896. Epub 2020 Mar 14.

Department of Biological Sciences, Faculty of Science, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada. Electronic address:

Anti-tumour lipids are synthetic analogues of lysophosphatidylcholine. These drugs are both cytotoxic and cytostatic, and more interestingly, exert these effects preferentially in tumour cells. While the exact mechanism of action isn't fully elucidated, these drugs appear to preferentially partition into rigid lipid domains in cell membranes. Read More

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Swelling, dewetting and breakup in thin polymer films for cultural heritage.

Soft Matter 2020 Feb;16(6):1485-1497

Institut Laue Langevin, Grenoble, France.

The removal of ultrathin amorphous polymer films in contact with nonsolvent/solvent binary mixtures is addressed by means of neutron reflectometry and atomic force microscopy. The high resolution of neutron scattering makes it possible to resolve the distribution profiles of heavy water and benzyl alcohol inside Laropal®A81, often employed as a protective varnish layer for Culture Heritage in restoration of easel paintings. The swelling kinetics and distribution profiles were recorded as a function of time and increasing benzyl alcohol concentration in water. Read More

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February 2020

The bimodal gas exchange strategies of dragonfly nymphs across development.

J Insect Physiol 2020 01 17;120:103982. Epub 2019 Nov 17.

Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada. Electronic address:

Dragonfly nymphs are aquatic and breathe water using a rectal gill. However, it has long been known that the nymphs of many species appear to possess the ability to breathe air, either during their final instar when they leave the water prior to metamorphosis, or during periods of aquatic hypoxia. The aerial gas exchange associated with these activities has not been quantified. Read More

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January 2020

Different factors determined the toxicokinetics of organic chemicals and nanomaterials exposure to zebrafish (Danio Rerio).

Ecotoxicol Environ Saf 2019 Dec 16;186:109810. Epub 2019 Oct 16.

Key Laboratory of Pollution Process and Environmental Criteria of Ministry of Education and Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, Tianjin, 300071, China.

Little is known about how the chemical properties (molecular structure, such as the hydrophobic and hydrophilic end group for organic chemical, and particle size for nanomaterials (NMs)) quantitatively affect the toxicokinetics (TK) in organisms especially in short-term, single-species studies. A novel method based on a first-order one compartment TK model which described the monophasic uptake pattern and two-compartment TK model which adequately described the biphasic metabolism pattern was used to determine the bioconcentration and TK rate constants of organic compounds (n = 17) and nanomaterials (NMs, n = 7) in zebrafish. For both one and two compartment model, the uptake (k and elimination (k) rate constants were fitted using a one- and two-compartment first-order kinetic model, and bioconcentration factors (BCF) and 95% depuration times (t) for all tested chemicals were calculated, respectively. Read More

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December 2019

Mussels partition resources from natural waters under flowing conditions.

Sci Total Environ 2019 Dec 14;696:133870. Epub 2019 Aug 14.

Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada. Electronic address:

The feeding of three co-occurring freshwater mussel species (Ptychobranchus fasciolaris, Quadrula quadrula and Potamilus alatus) of differing conservation status on river water from their collection site was examined under static and ecologically relevant flow conditions using three characteristics of the suspended river seston from a turbid river (Sydenham River, Ontario): (1) Chlorophyll a fluorescence; (2) size of fluorescent particles determined under flow cytometry; and (3) individual algal taxa identified under flow cytometry. Differences in the clearance rate (CR; water volume cleared of material per mussel and time) based on changes in chlorophyll a concentration were observed among species (P. alatus > Q. Read More

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December 2019

α-Glucosidase inhibitory activity and in vivo antihyperglycemic effect of secondary metabolites from the leaf infusion of Ocimum campechianum mill.

J Ethnopharmacol 2019 Oct 15;243:112081. Epub 2019 Jul 15.

Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico. Electronic address:

Ethnopharmacological Relevance: Wild basil (Ocimum campechianum Mill.), an aromatic herb of the Lamiaceae family known as "albahaca de monte" (Spanish) or "x'kakaltun" (Mayan) in Yucatan, is used in Mayan traditional medicine to treat diabetes, as well as to alleviate fever symtoms, stomach pain, conjunctivitis, and various skin affections.

Aim Of The Study: To isolate and identify the bioactive metabolites responsible for the α-glucosidase inhibitory activity previously detected in the leaf infusion O. Read More

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October 2019

Tanycytes and the Control of Thyrotropin-Releasing Hormone Flux Into Portal Capillaries.

Front Endocrinol (Lausanne) 2019 25;10:401. Epub 2019 Jun 25.

Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.

Central and peripheral mechanisms that modulate energy intake, partition and expenditure determine energy homeostasis. Thyroid hormones (TH) regulate energy expenditure through the control of basal metabolic rate and thermogenesis; they also modulate food intake. TH concentrations are regulated by the hypothalamus-pituitary-thyroid (HPT) axis, and by transport and metabolism in blood and target tissues. Read More

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Examining the relationship between metal exposure (Cd and Hg), subcellular accumulation, and physiology of juvenile Crassostrea virginica.

Environ Sci Pollut Res Int 2019 Sep 4;26(25):25958-25968. Epub 2019 Jul 4.

The Graduate Center, City University of New York, 365 Fifth Ave., New York, NY, 10016, USA.

To assess the toxicity and accumulation (total and subcellular partitioning) of cadmium (Cd) and mercury (Hg), juvenile eastern oysters, Crassostrea virginica, were exposed for 4 weeks to a range of concentrations (Control, Low (1×), and High (4×)). Despite the 4-fold increase in metal concentrations, oysters from the High-Cd treatment (2.4 μM Cd) attained a body burden that was only 2. Read More

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September 2019

Heavy Metals in Suspended Particulate Matter of the Zhujiang River, Southwest China: Contents, Sources, and Health Risks.

Int J Environ Res Public Health 2019 05 24;16(10). Epub 2019 May 24.

State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, Guiyang 550081, China.

To investigate the abundance, water/particle interaction behavior, sources, and potential risk of heavy metals in suspended particulate matter (SPM), a total of 22 SPM samples were collected from the Zhujiang River, Southwest China, in July 2014 (wet season). Nine heavy metal(loid)s (V, Cr, Mn, Ni, Cu, Zn, As, Cd and Pb) in SPM were detected. The results show that the selected heavy metal(loid)s in SPM appear in the following order: Mn (982. Read More

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Self-assembly of a dimer system.

Phys Rev E 2019 Apr;99(4-1):042133

Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA.

In the self-assembly process which drives the formation of cellular membranes, micelles, and capsids, a collection of separated subunits spontaneously binds together to form functional and more ordered structures. In this work, we study the statistical physics of self-assembly in a simpler scenario: the formation of dimers from a system of monomers. The properties of the model allow us to frame the microstate counting as a combinatorial problem whose solution leads to an exact partition function. Read More

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Dietary partitioning promotes the coexistence of planktivorous species on coral reefs.

Mol Ecol 2019 05 13;28(10):2694-2710. Epub 2019 May 13.

Coastal Research Center, Marine Science Institute, University of California Santa Barbara, Santa Barbara, California.

Theories involving niche diversification to explain high levels of tropical diversity propose that species are more likely to co-occur if they partition at least one dimension of their ecological niche space. Yet, numerous species appear to have widely overlapping niches based upon broad categorizations of resource use or functional traits. In particular, the extent to which food partitioning contributes to species coexistence in hyperdiverse tropical ecosystems remains unresolved. Read More

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