The ambiguity of nestedness under soft and hard constraints.

Abstract:

:Many real networks feature the property of nestedness, i.e. the neighbours of nodes with a few connections are hierarchically nested within the neighbours of nodes with more connections. Despite the abstract simplicity of this notion, various mathematical definitions of nestedness have been proposed, sometimes giving contrasting results. Moreover, there is an ongoing debate on the statistical significance of nestedness, since random networks where the number of connections (degree) of each node is fixed to its empirical value are typically as nested as real ones. By using only ergodic and unbiased null models, we propose a clarification that exploits the recent finding that random networks where the degrees are enforced as hard constraints (microcanonical ensembles) are thermodynamically different from random networks where the degrees are enforced as soft constraints (canonical ensembles). Indeed, alternative definitions of nestedness can be negatively correlated in the microcanonical one, while being positively correlated in the canonical one. This result disentangles distinct notions of nestedness captured by different metrics and highlights the importance of making a principled choice between hard and soft constraints in null models of ecological networks.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Bruno M,Saracco F,Garlaschelli D,Tessone CJ,Caldarelli G

doi

10.1038/s41598-020-76300-1

subject

Has Abstract

pub_date

2020-11-16 00:00:00

pages

19903

issue

1

issn

2045-2322

pii

10.1038/s41598-020-76300-1

journal_volume

10

pub_type

杂志文章
  • Myocardial Injury After Ischemia/Reperfusion Is Attenuated By Pharmacological Galectin-3 Inhibition.

    abstract::Although optimal therapy for myocardial infarction includes reperfusion to restore blood flow to the ischemic region, ischemia/reperfusion (IR) also initiates an inflammatory response likely contributing to adverse left ventricular (LV) extracellular matrix (ECM) remodeling. Galectin-3 (Gal-3), a β-galactoside-binding...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-46119-6

    authors: Ibarrola J,Matilla L,Martínez-Martínez E,Gueret A,Fernández-Celis A,Henry JP,Nicol L,Jaisser F,Mulder P,Ouvrard-Pascaud A,López-Andrés N

    更新日期:2019-07-03 00:00:00

  • Strongly Confined Spoof Surface Plasmon Polaritons Waveguiding Enabled by Planar Staggered Plasmonic Waveguides.

    abstract::We demonstrate a novel route to achieving highly efficient and strongly confined spoof surface plasmon polaritons (SPPs) waveguides at subwavelength scale enabled by planar staggered plasmonic waveguides (PSPWs). The structure of these new waveguides consists of an ultrathin metallic strip with periodic subwavelength ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep38528

    authors: Ye L,Xiao Y,Liu Y,Zhang L,Cai G,Liu QH

    更新日期:2016-12-05 00:00:00

  • Origami-based self-folding of co-cultured NIH/3T3 and HepG2 cells into 3D microstructures.

    abstract::This paper describes an origami-inspired self-folding method to form three-dimensional (3D) microstructures of co-cultured cells. After a confluent monolayer of fibroblasts (NIH/3T3 cells) with loaded hepatocytes (HepG2 cells) was cultured onto two-dimensional (2D) microplates, degradation of the alginate sacrificial ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-22598-x

    authors: He Q,Okajima T,Onoe H,Subagyo A,Sueoka K,Kuribayashi-Shigetomi K

    更新日期:2018-03-14 00:00:00

  • Modulation of activation and inactivation by Ca2+ and 2-APB in the pore of an archetypal TRPM channel from Nematostella vectensis.

    abstract::The archetypal TRPM2-like channel of the sea anemone Nematostella vectensis is gated by ADPR like its human orthologue but additionally exhibits properties of other vertebrate TRPM channels. Thus it can help towards an understanding of gating and regulation of the whole subfamily. To elucidate further the role of Ca2+...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-07652-4

    authors: Kühn FJP,Mathis W,Cornelia K,Hoffmann DC,Lückhoff A

    更新日期:2017-08-03 00:00:00

  • Hydrogen Bond Variations of Influenza A Viruses During Adaptation in Human.

    abstract::Many host specific mutations have been detected in influenza A viruses (IAVs). However, their effects on hydrogen bond (H-bond) variations have rarely been investigated. In this study, 60 host specific sites were identified in the internal proteins of avian and human IAVs, 27 of which contained mutations with effects ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14533-3

    authors: Luo J,Deng L,Ding X,Quan L,Wu A,Jiang T

    更新日期:2017-10-30 00:00:00

  • Accuracy of Two Point-of-Care Tests for Rapid Diagnosis of Bovine Tuberculosis at Animal Level using Non-Invasive Specimens.

    abstract::Bovine tuberculosis (BTB) testing in cattle requires a significant investment of time, equipment, and labor. Novel, rapid, cheaper and accurate methods are needed. The Alere Determine TB lipoarabinomannan antigen (LAM-test) is a World Health Organization-endorsed point-of-care urine test designed to detect active TB d...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-62314-2

    authors: Kelley HV,Waibel SM,Sidiki S,Tomatis-Souverbielle C,Scordo JM,Hunt WG,Barr N,Smith R,Silwani SN,Averill JJ,Baer S,Hengesbach J,Yildiz VO,Pan X,Gebreyes WA,Balada-Llasat JM,Wang SH,Torrelles JB

    更新日期:2020-03-25 00:00:00

  • Ecosystem experiment reveals benefits of natural and simulated beaver dams to a threatened population of steelhead (Oncorhynchus mykiss).

    abstract::Beaver have been referred to as ecosystem engineers because of the large impacts their dam building activities have on the landscape; however, the benefits they may provide to fluvial fish species has been debated. We conducted a watershed-scale experiment to test how increasing beaver dam and colony persistence in a ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep28581

    authors: Bouwes N,Weber N,Jordan CE,Saunders WC,Tattam IA,Volk C,Wheaton JM,Pollock MM

    更新日期:2016-07-04 00:00:00

  • Niche differentiation of bacterial communities at a millimeter scale in Shark Bay microbial mats.

    abstract::Modern microbial mats can provide key insights into early Earth ecosystems, and Shark Bay, Australia, holds one of the best examples of these systems. Identifying the spatial distribution of microorganisms with mat depth facilitates a greater understanding of specific niches and potentially novel microbial interaction...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep15607

    authors: Wong HL,Smith DL,Visscher PT,Burns BP

    更新日期:2015-10-26 00:00:00

  • Wild chimpanzees show group differences in selection of agricultural crops.

    abstract::The ability of wild animals to respond flexibly to anthropogenic environmental changes, including agriculture, is critical to survival in human-impacted habitats. Understanding use of human foods by wildlife can shed light on the acquisition of novel feeding habits and how animals respond to human-driven land-use chan...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep05956

    authors: McLennan MR,Hockings KJ

    更新日期:2014-08-05 00:00:00

  • Prediction of high anti-angiogenic activity peptides in silico using a generalized linear model and feature selection.

    abstract::Screening and in silico modeling are critical activities for the reduction of experimental costs. They also speed up research notably and strengthen the theoretical framework, thus allowing researchers to numerically quantify the importance of a particular subset of information. For example, in fields such as cancer a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-33911-z

    authors: Blanco JL,Porto-Pazos AB,Pazos A,Fernandez-Lozano C

    更新日期:2018-10-24 00:00:00

  • The horizontal gene transfer of Agrobacterium T-DNAs into the series Batatas (Genus Ipomoea) genome is not confined to hexaploid sweetpotato.

    abstract::The discovery of the insertion of IbT-DNA1 and IbT-DNA2 into the cultivated (hexaploid) sweetpotato [Ipomoea batatas (L.) Lam.] genome constitutes a clear example of an ancient event of Horizontal Gene Transfer (HGT). However, it remains unknown whether the acquisition of both IbT-DNAs by the cultivated sweetpotato oc...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-48691-3

    authors: Quispe-Huamanquispe DG,Gheysen G,Yang J,Jarret R,Rossel G,Kreuze JF

    更新日期:2019-08-29 00:00:00

  • Multiplexed Affinity-Based Separation of Proteins and Cells Using Inertial Microfluidics.

    abstract::Isolation of low abundance proteins or rare cells from complex mixtures, such as blood, is required for many diagnostic, therapeutic and research applications. Current affinity-based protein or cell separation methods use binary 'bind-elute' separations and are inefficient when applied to the isolation of multiple low...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep23589

    authors: Sarkar A,Hou HW,Mahan AE,Han J,Alter G

    更新日期:2016-03-30 00:00:00

  • Profiling the neutralizing antibody response in chronically HIV-1 CRF07_BC-infected intravenous drug users naïve to antiretroviral therapy.

    abstract::Characterizing neutralizing antibody (NAb) responses in individuals infected with diverse HIV-1 strains is necessary to reveal the novel targets for regional preventive and therapeutic strategies development. We evaluated the prevalence, breadth, and potency of NAb responses in 98 CRF07_BC-infected individuals using a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46308

    authors: Hu X,Hu Y,Zhao C,Gao H,Greene KM,Ren L,Ma L,Ruan Y,Sarzotti-Kelsoe M,Montefiori DC,Hong K,Shao Y

    更新日期:2017-04-07 00:00:00

  • A new way to synthesize superconducting metal-intercalated C60 and FeSe.

    abstract::Doping with the optimum concentration of carriers (electrons or holes) can modify the physical properties of materials. Therefore, improved ways to achieve carrier doping have been pursued extensively for more than 50 years. Metal-intercalation is one of the most important techniques for electron doping of organic / i...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep18931

    authors: Takahei Y,Tomita K,Itoh Y,Ashida K,Lee JH,Nishimoto N,Kimura T,Kudo K,Nohara M,Kubozono Y,Kambe T

    更新日期:2016-01-06 00:00:00

  • Modifiable lifestyle behaviors, but not a genetic risk score, associate with metabolic syndrome in evening chronotypes.

    abstract::Evening chronotype associates with health complications possibly via lifestyle factors, while the contribution of genetics is unknown. The aim was to study the relative contributions of genetics, lifestyle, and circadian-related physiological characteristics in metabolic risk of evening chronotype. In order to capture...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-18268-z

    authors: Vera B,Dashti HS,Gómez-Abellán P,Hernández-Martínez AM,Esteban A,Scheer FAJL,Saxena R,Garaulet M

    更新日期:2018-01-17 00:00:00

  • Extracellular Cyclic GMP Modulates Membrane Expression of The GluA1 and GluA2 Subunits of AMPA Receptor in Cerebellum: Molecular Mechanisms Involved.

    abstract::There is increasing evidence that extracellular cGMP modulates glutamatergic neurotransmission and some forms of learning. However, the underlying mechanisms remain unknown. We proposed the hypotheses that extracellular cGMP may regulate membrane expression of AMPA receptors. To do this extracellular cGMP should act o...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-18024-3

    authors: Cabrera-Pastor A,Taoro-González L,Cuñat AN,Canet-López D,Balzano T,Felipo V

    更新日期:2017-12-15 00:00:00

  • A direct borohydride fuel cell with a polymer fiber membrane and non-noble metal catalysts.

    abstract::Polymer electrolyte membranes (PEM) and Pt-based catalysts are two crucial components which determine the properties and price of fuel cells. Even though, PEM faces problem of fuel crossover in liquid fuel cells such as direct methanol fuel cell (DMFC) and direct borohydride fuel cell (DBFC), which lowers power output...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00567

    authors: Yang X,Liu Y,Li S,Wei X,Wang L,Chen Y

    更新日期:2012-01-01 00:00:00

  • Disorder versus two transport lifetimes in a strongly correlated electron liquid.

    abstract::We report on angle-dependent measurements of the sheet resistances and Hall coefficients of electron liquids in SmTiO3/SrTiO3/SmTiO3 quantum well structures, which were grown by molecular beam epitaxy on (001) DyScO3. We compare their transport properties with those of similar structures grown on LSAT [(La0.3Sr0.7)(Al...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10841-w

    authors: Marshall PB,Kim H,Stemmer S

    更新日期:2017-09-04 00:00:00

  • Hearing impairment and associated morphological changes in pituitary adenylate cyclase activating polypeptide (PACAP)-deficient mice.

    abstract::Pituitary adenylate cyclase activating polypeptide (PACAP) is a regulatory and cytoprotective neuropeptide, its deficiency implies accelerated aging in mice. It is present in the auditory system having antiapoptotic effects. Expression of Ca2+-binding proteins and its PAC1 receptor differs in the inner ear of PACAP-de...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-50775-z

    authors: Fulop DB,Humli V,Szepesy J,Ott V,Reglodi D,Gaszner B,Nemeth A,Szirmai A,Tamas L,Hashimoto H,Zelles T,Tamas A

    更新日期:2019-10-10 00:00:00

  • A mouse model of pulmonary Mycobacteroides abscessus infection.

    abstract::There is no preclinical mouse model to investigate pulmonary Mycobacteroides abscessus (formerly Mycobacterium abscessus) infection in an immunocompetent mouse strain, especially in the context of antibiotic testing and regimen development. We developed a mouse model of pulmonary M. abscessus infection using the aeros...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60452-1

    authors: Maggioncalda EC,Story-Roller E,Mylius J,Illei P,Basaraba RJ,Lamichhane G

    更新日期:2020-02-28 00:00:00

  • Correlated clusters of closed reaction centers during induction of intact cells of photosynthetic bacteria.

    abstract::Antenna systems serve to absorb light and to transmit excitation energy to the reaction center (RC) in photosynthetic organisms. As the emitted (bacterio)chlorophyll fluorescence competes with the photochemical utilization of the excitation, the measured fluorescence yield is informed by the migration of the excitatio...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-70966-3

    authors: Maróti P,Kovács IA,Kis M,Smart JL,Iglói F

    更新日期:2020-08-19 00:00:00

  • Whale counting in satellite and aerial images with deep learning.

    abstract::Despite their interest and threat status, the number of whales in world's oceans remains highly uncertain. Whales detection is normally carried out from costly sighting surveys, acoustic surveys or through high-resolution images. Since deep convolutional neural networks (CNNs) are achieving great performance in severa...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-50795-9

    authors: Guirado E,Tabik S,Rivas ML,Alcaraz-Segura D,Herrera F

    更新日期:2019-10-03 00:00:00

  • Comprehensive analysis of The Cancer Genome Atlas reveals a unique gene and non-coding RNA signature of fibrolamellar carcinoma.

    abstract::Fibrolamellar carcinoma (FLC) is a unique liver cancer primarily affecting young adults and characterized by a fusion event between DNAJB1 and PRKACA. By analyzing RNA-sequencing data from The Cancer Genome Atlas (TCGA) for >9,100 tumors across ~30 cancer types, we show that the DNAJB1-PRKACA fusion is specific to FLC...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep44653

    authors: Dinh TA,Vitucci EC,Wauthier E,Graham RP,Pitman WA,Oikawa T,Chen M,Silva GO,Greene KG,Torbenson MS,Reid LM,Sethupathy P

    更新日期:2017-03-17 00:00:00

  • The histamine H3R antagonist DL77 attenuates autistic behaviors in a prenatal valproic acid-induced mouse model of autism.

    abstract::Autistic spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairment in social communication and restricted/repetitive behavior patterns or interests. Antagonists targeting histamine H3 receptor (H3R) are considered potential therapeutic agents for the therapeutic management of different brain...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-31385-7

    authors: Eissa N,Jayaprakash P,Azimullah S,Ojha SK,Al-Houqani M,Jalal FY,Łażewska D,Kieć-Kononowicz K,Sadek B

    更新日期:2018-08-30 00:00:00

  • Hirsutella sinensis mycelium attenuates bleomycin-induced pulmonary inflammation and fibrosis in vivo.

    abstract::Hirsutella sinensis mycelium (HSM), the anamorph of Cordyceps sinensis, is a traditional Chinese medicine that has been shown to possess various pharmacological properties. We previously reported that this fungus suppresses interleukin-1β and IL-18 secretion by inhibiting both canonical and non-canonical inflammasomes...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep15282

    authors: Huang TT,Lai HC,Ko YF,Ojcius DM,Lan YW,Martel J,Young JD,Chong KY

    更新日期:2015-10-26 00:00:00

  • Near-Field Scanning Microwave Microscopy in the Single Photon Regime.

    abstract::The microwave properties of nano-scale structures are important in a wide variety of applications in quantum technology. Here we describe a low-power cryogenic near-field scanning microwave microscope (NSMM) which maintains nano-scale dielectric contrast down to the single microwave photon regime, up to 109 times lowe...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-48780-3

    authors: Geaney S,Cox D,Hönigl-Decrinis T,Shaikhaidarov R,Kubatkin SE,Lindström T,Danilov AV,de Graaf SE

    更新日期:2019-08-29 00:00:00

  • Chemical-Free Technique to Study the Ultrastructure of Primary Cilium.

    abstract::A primary cilium is a hair-like structure with a width of approximately 200 nm. Over the past few decades, the main challenge in the study of the ultrastructure of cilia has been the high sensitivity of cilia to chemical fixation, which is required for many imaging techniques. In this report, we demonstrate a combined...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep15982

    authors: Mohieldin AM,AbouAlaiwi WA,Gao M,Nauli SM

    更新日期:2015-11-02 00:00:00

  • Glutathione S-transferase (GST) of American Cockroach, Periplaneta americana: Classes, Isoforms, and Allergenicity.

    abstract::Insect glutathione S-transferases (GSTs) play important roles in insecticide/drug resistance and stress response. Medically, GSTs of house dust mites (Dermatophagoides pteronyssinus and Blomia tropicalis) and German cockroach (Blattella germanica) are human allergens. In this study, classes, isoforms and B-cell and al...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-18759-z

    authors: Sookrung N,Reamtong O,Poolphol R,Indrawattana N,Seesuay W,Saelim N,Tantilipikorn P,Bunnag C,Chaicumpa W,Tungtrongchitr A

    更新日期:2018-01-11 00:00:00

  • Secondary batteries with multivalent ions for energy storage.

    abstract::The use of electricity generated from clean and renewable sources, such as water, wind, or sunlight, requires efficiently distributed electrical energy storage by high-power and high-energy secondary batteries using abundant, low-cost materials in sustainable processes. American Science Policy Reports state that the n...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep14120

    authors: Xu C,Chen Y,Shi S,Li J,Kang F,Su D

    更新日期:2015-09-14 00:00:00

  • Early loss of subchondral bone following microfracture is counteracted by bone marrow aspirate in a translational model of osteochondral repair.

    abstract::Microfracture of cartilage defects may induce alterations of the subchondral bone in the mid- and long-term, yet very little is known about their onset. Possibly, these changes may be avoided by an enhanced microfracture technique with additional application of bone marrow aspirate. In this study, full-thickness chond...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep45189

    authors: Gao L,Orth P,Müller-Brandt K,Goebel LK,Cucchiarini M,Madry H

    更新日期:2017-03-27 00:00:00