bluuebunny/crossref_metadata_2025_split huggingface dataset:
Game theoretical inference of human behavior in social networks
Authors: Pagan Nicolò , Dörfler Florian 
Published: December 2019

AbstractSocial networks emerge as a result of actors’ linking decisions. We propose a game-theoretical model of socio-strategic network formation on directed weighted graphs, in which every actors’ benefit is a parametric trade-off between centrality measure, brokerage opportunities, clustering coefficient, and sociological network patterns. We use two different stability definitions to infer individual behavior of homogeneous, rational agents from network structure, and to quantify the impact of cooperation. Our theoretical analysis confirms results known for specific network motifs studied previously in isolation, yet enables us to precisely quantify the trade-offs in the space of user preferences. To deal with complex networks of heterogeneous and irrational actors, we construct a statistical behavior estimation method using Nash equilibrium conditions. We provide evidence that our results are consistent with empirical, historical, and sociological observations on real-world data-sets. Furthermore, our method offers sociological and strategic interpretations of random networks models, such as preferential attachment and small-world networks.
The coincidence of ecological opportunity with hybridization explains rapid adaptive radiation in Lake Mweru cichlid fishes
Authors: Meier Joana I. , Stelkens Rike B. , Joyce Domino A. , Mwaiko Salome , Phiri Numel , Schliewen Ulrich K. , Selz Oliver M. , Wagner Catherine E. , Katongo Cyprian , Seehausen Ole 
Published: December 2019

AbstractThe process of adaptive radiation was classically hypothesized to require isolation of a lineage from its source (no gene flow) and from related species (no competition). Alternatively, hybridization between species may generate genetic variation that facilitates adaptive radiation. Here we study haplochromine cichlid assemblages in two African Great Lakes to test these hypotheses. Greater biotic isolation (fewer lineages) predicts fewer constraints by competition and hence more ecological opportunity in Lake Bangweulu, whereas opportunity for hybridization predicts increased genetic potential in Lake Mweru. In Lake Bangweulu, we find no evidence for hybridization but also no adaptive radiation. We show that the Bangweulu lineages also colonized Lake Mweru, where they hybridized with Congolese lineages and then underwent multiple adaptive radiations that are strikingly complementary in ecology and morphology. Our data suggest that the presence of several related lineages does not necessarily prevent adaptive radiation, although it constrains the trajectories of morphological diversification. It might instead facilitate adaptive radiation when hybridization generates genetic variation, without which radiation may start much later, progress more slowly or never occur.
An independent poor-prognosis subtype of breast cancer defined by a distinct tumor immune microenvironment
Authors: Tekpli Xavier , Lien Tonje , Røssevold Andreas Hagen , Nebdal Daniel , Borgen Elin , Ohnstad Hege Oma , Kyte Jon Amund , Vallon-Christersson Johan , Fongaard Marie , Due Eldri Undlien , Svartdal Lisa Gregusson , Sveli My Anh Tu , Garred Øystein ,   OSBREAC, Børresen-Dale Anne-Lise , Schlichting Ellen , Sauer Torill , Geisler Jürgen , Hofvind Solveig , Bathen Tone F. , Engebråten Olav , Geitvik Gry Aarum , Langerød Anita , Kåresen Rolf , Mælandsmo Gunhild Mari , Lingjærde Ole Christian , Skjerven Helle Kristine , Park Daehoon , Fritzman Britt , Frigessi Arnoldo , Sahlberg Kristine Kleivi , Sørlie Therese , Russnes Hege G. , Naume Bjørn , Kristensen Vessela N. 
Published: December 2019

AbstractHow mixtures of immune cells associate with cancer cell phenotype and affect pathogenesis is still unclear. In 15 breast cancer gene expression datasets, we invariably identify three clusters of patients with gradual levels of immune infiltration. The intermediate immune infiltration cluster (Cluster B) is associated with a worse prognosis independently of known clinicopathological features. Furthermore, immune clusters are associated with response to neoadjuvant chemotherapy. In silico dissection of the immune contexture of the clusters identified Cluster A as immune cold, Cluster C as immune hot while Cluster B has a pro-tumorigenic immune infiltration. Through phenotypical analysis, we find epithelial mesenchymal transition and proliferation associated with the immune clusters and mutually exclusive in breast cancers. Here, we describe immune clusters which improve the prognostic accuracy of immune contexture in breast cancer. Our discovery of a novel independent prognostic factor in breast cancer highlights a correlation between tumor phenotype and immune contexture.
Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI
Authors: Goubran Maged , Leuze Christoph , Hsueh Brian , Aswendt Markus , Ye Li , Tian Qiyuan , Cheng Michelle Y. , Crow Ailey , Steinberg Gary K. , McNab Jennifer A. , Deisseroth Karl , Zeineh Michael 
Published: December 2019

Abstract3D histology, slice-based connectivity atlases, and diffusion MRI are common techniques to map brain wiring. While there are many modality-specific tools to process these data, there is a lack of integration across modalities. We develop an automated resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling the analysis of histological features across multiple fiber tracts and networks, and their correlation within-vivobiomarkers. We apply our pipeline in a murine stroke model, demonstrating not only strong correspondence between MRI abnormalities and CLARITY-tissue staining, but also uncovering acute cellular effects in areas connected to the ischemic core. We provide improved maps of connectivity by quantifying projection terminals from CLARITY viral injections, and integrate diffusion MRI with CLARITY viral tracing to compare connectivity maps across scales. Finally, we demonstrate tract-level histological changes of stroke through this multimodal integration. This resource can propel investigations of network alterations underlying neurological disorders.
Using somatic variant richness to mine signals from rare variants in the cancer genome
Authors: Chakraborty Saptarshi , Arora Arshi , Begg Colin B. , Shen Ronglai 
Published: December 2019

AbstractTo date, the vast preponderance of somatic variants observed in the cancer genome have been rare variants, and it is common in practice to encounter in a new tumor variants that have not been observed previously. Here we focus on probability estimation for encountering such hitherto unseen variants. We draw upon statistical methodology that has been developed in other fields of study, notably in species estimation in ecology, and word frequency estimation in computational linguistics. Analysis of whole-exome and targeted panel sequencing data sets reveal substantial variability in variant “richness” between genes that could be harnessed for clinically relevant problems. We quantify the variant-tissue association and show a strong gene-specific, lineage-dependent pattern of encountering new variants. This variability is largely determined by the proportion of observed variants that are rare. Our findings suggest that variants that occur at very low frequencies can harbor important signals that are clinically consequential.
Single-spin qubits in isotopically enriched silicon at low magnetic field
Authors: Zhao R. , Tanttu T. , Tan K. Y. , Hensen B. , Chan K. W. , Hwang J. C. C. , Leon R. C. C. , Yang C. H. , Gilbert W. , Hudson F. E. , Itoh K. M. , Kiselev A. A. , Ladd T. D. , Morello A. , Laucht A. , Dzurak A. S. 
Published: December 2019

AbstractSingle-electron spin qubits employ magnetic fields on the order of 1 Tesla or above to enable quantum state readout via spin-dependent-tunnelling. This requires demanding microwave engineering for coherent spin resonance control, which limits the prospects for large scale multi-qubit systems. Alternatively, singlet-triplet readout enables high-fidelity spin-state measurements in much lower magnetic fields, without the need for reservoirs. Here, we demonstrate low-field operation of metal-oxide-silicon quantum dot qubits by combining coherent single-spin control with high-fidelity, single-shot, Pauli-spin-blockade-based ST readout. We discover that the qubits decohere faster at low magnetic fields with $${T}_{2}^{\,\text{Rabi}\,}=18.6$$T2Rabi=18.6 μs and $${T}_{2}^{* }=1.4$$T2*=1.4 μs at 150 mT. Their coherence is limited by spin flips of residual 29Si nuclei in the isotopically enriched 28Si host material, which occur more frequently at lower fields. Our finding indicates that new trade-offs will be required to ensure the frequency stabilization of spin qubits, and highlights the importance of isotopic enrichment of device substrates for the realization of a scalable silicon-based quantum processor.
Molecular engineering of organic semiconductors enables noble metal-comparable SERS enhancement and sensitivity
Authors: Demirel Gokhan , Gieseking Rebecca L. M. , Ozdemir Resul , Kahmann Simon , Loi Maria A. , Schatz George C. , Facchetti Antonio , Usta Hakan 
Published: December 2019

AbstractNanostructured molecular semiconductor films are promising Surface-Enhanced Raman Spectroscopy (SERS) platforms for both fundamental and technological research. Here, we report that a nanostructured film of the small molecule DFP-4T, consisting of a fully π-conjugated diperfluorophenyl-substituted quaterthiophene structure, demonstrates a very large Raman enhancement factor (>105) and a low limit of detection (10−9 M) for the methylene blue probe molecule. This data is comparable to those reported for the best inorganic semiconductor- and even intrinsic plasmonic metal-based SERS platforms. Photoluminescence spectroscopy and computational analysis suggest that both charge-transfer energy and effective molecular interactions, leading to a small but non-zero oscillator strength in the charge-transfer state between the organic semiconductor film and the analyte molecule, are required to achieve large SERS enhancement factors and high molecular sensitivities in these systems. Our results provide not only a considerable experimental advancement in organic SERS figure-of-merits but also a guidance for the molecular design of more sensitive SERS systems.
Strong spin resonance mode associated with suppression of soft magnetic ordering in hole-doped Ba1-xNaxFe2As2
Authors: Waßer Florian , Park Jitae T. , Aswartham Saicharan , Wurmehl Sabine , Sidis Yvan , Steffens Paul , Schmalzl Karin , Büchner Bernd , Braden Markus 
Published: December 2019

AbstractSpin-resonance modes (SRM) are taken as evidence for magnetically driven pairing in Fe-based superconductors, but their character remains poorly understood. The broadness, the splitting and the spin-space anisotropies of SRMs contrast with the mostly accepted interpretation as spin excitons. We study hole-doped Ba1−xNaxFe2As2 that displays a spin reorientation transition. This reorientation has little impact on the overall appearance of the resonance excitations with a high-energy isotropic and a low-energy anisotropic mode. However, the strength of the anisotropic low-energy mode sharply peaks at the highest doping that still exhibits magnetic ordering resulting in the strongest SRM observed in any Fe-based superconductor so far. This remarkably strong SRM is accompanied by a loss of about half of the magnetic Bragg intensity upon entering the SC phase. Anisotropic SRMs thus can allow the system to compensate for the loss of exchange energy arising from the reduced antiferromagnetic correlations within the SC state.
Layer specificity of inputs from supplementary motor area and dorsal premotor cortex to primary motor cortex in macaque monkeys
Authors: Ninomiya Taihei , Inoue Ken-ichi , Hoshi Eiji , Takada Masahiko 
Published: December 2019

AbstractThe primate frontal lobe processes diverse motor information in parallel through multiple motor-related areas. For example, the supplementary motor area (SMA) is mainly involved in internally-triggered movements, whereas the premotor cortex (PM) is highly responsible for externally-guided movements. The primary motor cortex (M1) deals with both aspects of movements to execute a single motor behavior. To elucidate how the cortical motor system is structured to process a variety of information, the laminar distribution patterns of signals were examined between SMA and M1, or PM and M1 in macaque monkeys by using dual anterograde tract-tracing. Dense terminal labeling was observed in layers 1 and upper 2/3 of M1 after one tracer injection into SMA, another tracer injection into the dorsal division of PM resulted in prominent labeling in the deeper portion of layer 2/3. Weaker labeling was also visible in layer 5 in both cases. On the other hand, inputs from M1 terminated in both the superficial and the deep layers of SMA and PM. The present data indicate that distinct types of motor information are arranged in M1 in a layer-specific fashion to be orchestrated through a microcircuit within M1.
Practical Security Analysis of Reference Pulses for Continuous-Variable Quantum Key Distribution
Authors: Zhao Wei , Shi Ronghua , Huang Duan 
Published: December 2019

AbstractBy manipulating the reference pulses amplitude, a security vulnerability is caused by self-reference continuous-variable quantum key distribution. In this paper, we formalize an attack strategy for reference pulses, showing that the proposed attack can compromise the practical security of CVQKD protocol. In this scheme, before the beam splitter attack, Eve intercepts the reference pulses emitted by Alice, using Bayesian algorithm to estimate phase shifts. Subsequently, other reference pulses are re-prepared and resubmitted to Bob. In simulations, Bayesian algorithm effectively estimates the phase drifts and has the high robustness to noise. Therefore, the eavesdropper can bias the excess noise due to the intercept-resend attack and the beam splitter attack. And Alice and Bob believe that their excess noise is below the null key threshold and can still share a secret key. Consequently, the proposed attack shows that its practical security can be compromised by transmitting the reference pulses in the continuous-variable quantum key distribution protocol.
Actinomycin D and Telmisartan Combination Targets Lung Cancer Stem Cells Through the Wnt/Beta Catenin Pathway
Authors: Green Ryan , Howell Mark , Khalil Roukiah , Nair Rajesh , Yan Jiyu , Foran Elspeth , Katiri Sandhyabanu , Banerjee Jit , Singh Mandip , Bharadwaj Srinivas , Mohapatra Shyam S. , Mohapatra Subhra 
Published: December 2019

AbstractThe failure of lung cancer treatments has been attributed mostly to the development of drug resistance, however the underlying cellular and molecular mechanisms are poorly understood. Cancer initiating stem cells (CSCs), present in tumors in a small percentage, play critical roles in the development of drug resistance, metastasis, and cancer relapse. Hence, novel treatments targeting both bulk cancer cells and CSCs are under intense investigation. Herein, we report that lung cancer cells grown on a 3D fibrous scaffold form tumoroids that resemble in vivo tumors, expand CSCs, and provide a platform to identify anti-CSC drugs. The screening of an NCI library of FDA-approved drugs using tumoroid cultures led to identification of Actinomycin D (AD) as a top CSC inhibitor. Since CSCs are mostly resident in the tumor’s inner core, AD was combined with an angiotensin receptor antagonist, Telmisartan (TS), which is known to increase drug permeability in tumors and was shown to have anti-CSC activity. Our results showed that AD + TS administered intra-tumorally was significantly more effective than either drug alone in both syngeneic and xenograft mouse models. The results of mechanistic studies revealed that CSC expansion in tumoroids was associated with activation of β catenin signaling and that AD + TS treatment reduced active β catenin levels in tumors. Together, these results establish the utility of the tumoroid culture system to expand CSCs ex vivo for targeted drug screening, to identify promising novel treatments with both anti-CSC and anti-cancer effects, and to individualize treatments for metastatic drug resistant lung cancer patients.
Subendothelial stiffness alters endothelial cell traction force generation while exerting a minimal effect on the transcriptome
Authors: Bastounis Effie E. , Yeh Yi-Ting , Theriot Julie A. 
Published: December 2019

AbstractEndothelial cells respond to changes in subendothelial stiffness by altering their migration and mechanics, but whether those responses are due to transcriptional reprogramming remains largely unknown. We measured traction force generation and also performed gene expression profiling for two endothelial cell types grown in monolayers on soft or stiff matrices: primary human umbilical vein endothelial cells (HUVEC) and immortalized human microvascular endothelial cells (HMEC-1). Both cell types respond to changes in subendothelial stiffness by increasing the traction stresses they exert on stiffer as compared to softer matrices, and exhibit a range of altered protein phosphorylation or protein conformational changes previously implicated in mechanotransduction. However, the transcriptome has only a minimal role in this conserved biomechanical response. Only few genes were differentially expressed in each cell type in a stiffness-dependent manner, and none were shared between them. In contrast, thousands of genes were differentially regulated in HUVEC as compared to HMEC-1. HUVEC (but not HMEC-1) upregulate expression of TGF-β2 on stiffer matrices, and also respond to application of exogenous TGF-β2 by enhancing their endogenous TGF-β2 expression and their cell-matrix traction stresses. Altogether, these findings provide insights into the relationship between subendothelial stiffness, endothelial mechanics and variation of the endothelial cell transcriptome, and reveal that subendothelial stiffness, while critically altering endothelial cells’ mechanical behavior, minimally affects their transcriptome.
Expressivity of the key genes associated with seed and pod development is highly regulated via lncRNAs and miRNAs in Pigeonpea
Authors: Das Antara , Nigam Deepti , Junaid Alim , Tribhuvan Kishor U. , Kumar Kuldeep , Durgesh Kumar , Singh N. K. , Gaikwad Kishor 
Published: December 2019

AbstractNon-coding RNA’s like miRNA, lncRNA, have gained immense importance as a significant regulatory factor in different physiological and developmental processes in plants. In an effort to understand the molecular role of these regulatory agents, in the present study, 3019 lncRNAs and 227 miRNAs were identified from different seed and pod developmental stages in Pigeonpea, a major grain legume of Southeast Asia and Africa. Target analysis revealed that 3768 mRNAs, including 83 TFs were targeted by lncRNAs; whereas 3060 mRNA, including 154 TFs, were targeted by miRNAs. The targeted transcription factors majorly belong to WRKY, MYB, bHLH, etc. families; whereas the targeted genes were associated with the embryo, seed, and flower development. Total 302 lncRNAs interact with miRNAs and formed endogenous target mimics (eTMs) which leads to sequestering of the miRNAs present in the cell. Expression analysis showed that notably, Cc_lncRNA-2830 expression is up-regulated and sequestrates miR160h in pod leading to higher expression of the miR160h target gene, Auxin responsive factor-18. A similar pattern was observed for SPIKE, Auxin signaling F-box-2, Bidirectional sugar transporter, and Starch synthetase-2 eTMs. All the identified target mRNAs code for transcription factor and genes are involved in the processes like cell division, plant growth and development, starch synthesis, sugar transportation and accumulation of storage proteins which are essential for seed and pod development. On a combinatorial basis, our study provides a lncRNA and miRNA based regulatory insight into the genes governing seed and pod development in Pigeonpea.
Spontaneous categorization of tools based on observation in children and chimpanzees
Authors: Gruber Thibaud , Frick Aurélien , Hirata Satoshi , Adachi Ikuma , Biro Dora 
Published: December 2019

AbstractThe acquisition of the concept of ‘tool’ remains intriguing from both developmental and comparative perspectives. Our current model of tool use development in children is based on humans’ supposedly unique ability to adopt a teleological stance: the understanding of a demonstrator’s goal-based intentions when using a tool. It is however unclear how children and chimpanzees, our closest relatives, combine their knowledge of different objects whose function is to act on other parts of the environment, and assign them to a single category of ‘tools’. Here, we used a function-based approach to address this question. We exposed 7 to 11-year-old children and adult chimpanzees to a Matching-to-Function (MTF) task to explore whether they would sort tools and non-tools separately after demonstration of their function by an experimenter. MTF is a variant of Matching-to-Sample where the sample and the target are from the same category/kind rather than identical. Around 40% of children paired objects according to their function in the MTF task, with only one child younger than 8 years doing so. Moreover, when verbally questioned, these children offered a function-based answer to explain their choices. One of six chimpanzees also successfully paired objects according to function. Children and at least one chimpanzee can thus spontaneously sort tools into functional categories based on observing a demonstrator. The success of a single chimpanzee in our task suggests that teleological reasoning might already have been present in our last common ancestor but also shows that human children more readily conceptualize tools in a spontaneous fashion.
Drivers of bird-window collisions in southern South America: a two-scale assessment applying citizen science
Authors: Rebolo-Ifrán Natalia , di Virgilio Agustina , Lambertucci Sergio A. 
Published: December 2019

AbstractBird-window collisions are one of the main causes of avian mortality worldwide, with estimations reaching up to almost one billion of dead individuals annually due to this cause in Canada and the USA alone. Although this is a growing conservation problem, most of the studies come from North America, evidencing the lack of knowledge and concern in countries with high biodiversity and growing population development. Our objectives were: (1) to estimate the current situation of bird-window collisions in Argentina, a country with around 10% of the world’s avian biodiversity, and, (2) to identify drivers of bird-window collisions at a national and local scale, focusing on a city surrounded by a protected area. We used a citizen science project called “Bird-Window Collisions in Argentina” that consisted of an online survey that collected data on collision metrics and risk factors. We found that more than half of participants reported at least one collision during the last year, suggesting this issue is common and widespread. In addition, our data show that the number of windows and the presence of vegetation reflected in windows are factors that strongly influence the risk of collision at national scale. On the other hand, the environment surrounding buildings affects the rate of bird-window collisions at local scale, being greater in buildings surrounded by tall vegetation than in buildings surrounded by a greater proportion of urbanization (human-made structures). We call for attention on a topic that has been poorly evaluated in South America. We also encourage future scientific studies to evaluate additional risk factors and mitigation strategies accordingly, to provide a better understanding of bird-window collisions particularly in a highly biodiverse region as South America.