bluuebunny/crossref_metadata_2025_split huggingface dataset:
Innovation and cumulative culture through tweaks and leaps in online programming contests
Authors: Miu Elena , Gulley Ned , Laland Kevin N. , Rendell Luke 
Published: June 2018

AbstractThe ability to build progressively on the achievements of earlier generations is central to human uniqueness, but experimental investigations of this cumulative cultural evolution lack real-world complexity. Here, we studied the dynamics of cumulative culture using a large-scale data set from online collaborative programming competitions run over 14 years. We show that, within each contest population, performance increases over time through frequent ‘tweaks’ of the current best entry and rare innovative ‘leaps’ (successful tweak:leap ratio = 16:1), the latter associated with substantially greater variance in performance. Cumulative cultural evolution reduces technological diversity over time, as populations focus on refining high-performance solutions. While individual entries borrow from few sources, iterative copying allows populations to integrate ideas from many sources, demonstrating a new form of collective intelligence. Our results imply that maximising technological progress requires accepting high levels of failure.
A modular transcriptional signature identifies phenotypic heterogeneity of human tuberculosis infection
Authors: Singhania Akul , Verma Raman , Graham Christine M. , Lee Jo , Tran Trang , Richardson Matthew , Lecine Patrick , Leissner Philippe , Berry Matthew P. R. , Wilkinson Robert J. , Kaiser Karine , Rodrigue Marc , Woltmann Gerrit , Haldar Pranabashis , O’Garra Anne 
Published: June 2018

AbstractWhole blood transcriptional signatures distinguishing active tuberculosis patients from asymptomatic latently infected individuals exist. Consensus has not been achieved regarding the optimal reduced gene sets as diagnostic biomarkers that also achieve discrimination from other diseases. Here we show a blood transcriptional signature of active tuberculosis using RNA-Seq, confirming microarray results, that discriminates active tuberculosis from latently infected and healthy individuals, validating this signature in an independent cohort. Using an advanced modular approach, we utilise the information from the entire transcriptome, which includes overabundance of type I interferon-inducible genes and underabundance of IFNG and TBX21, to develop a signature that discriminates active tuberculosis patients from latently infected individuals or those with acute viral and bacterial infections. We suggest that methods targeting gene selection across multiple discriminant modules can improve the development of diagnostic biomarkers with improved performance. Finally, utilising the modular approach, we demonstrate dynamic heterogeneity in a longitudinal study of recent tuberculosis contacts.
A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes
Authors: Papachristou Evangelia K. , Kishore Kamal , Holding Andrew N. , Harvey Kate , Roumeliotis Theodoros I. , Chilamakuri Chandra Sekhar Reddy , Omarjee Soleilmane , Chia Kee Ming , Swarbrick Alex , Lim Elgene , Markowetz Florian , Eldridge Matthew , Siersbaek Rasmus , D’Santos Clive S. , Carroll Jason S. 
Published: June 2018

AbstractUnderstanding the dynamics of endogenous protein–protein interactions in complex networks is pivotal in deciphering disease mechanisms. To enable the in-depth analysis of protein interactions in chromatin-associated protein complexes, we have previously developed a method termed RIME (Rapid Immunoprecipitation Mass spectrometry of Endogenous proteins). Here, we present a quantitative multiplexed method (qPLEX-RIME), which integrates RIME with isobaric labelling and tribrid mass spectrometry for the study of protein interactome dynamics in a quantitative fashion with increased sensitivity. Using the qPLEX-RIME method, we delineate the temporal changes of the Estrogen Receptor alpha (ERα) interactome in breast cancer cells treated with 4-hydroxytamoxifen. Furthermore, we identify endogenous ERα-associated proteins in human Patient-Derived Xenograft tumours and in primary human breast cancer clinical tissue. Our results demonstrate that the combination of RIME with isobaric labelling offers a powerful tool for the in-depth and quantitative characterisation of protein interactome dynamics, which is applicable to clinical samples.
Network biology discovers pathogen contact points in host protein-protein interactomes
Authors: Ahmed Hadia , Howton T. C. , Sun Yali , Weinberger Natascha , Belkhadir Youssef , Mukhtar M. Shahid 
Published: June 2018

AbstractIn all organisms, major biological processes are controlled by complex protein–protein interactions networks (interactomes), yet their structural complexity presents major analytical challenges. Here, we integrate a compendium of over 4300 phenotypes with Arabidopsis interactome (AI-1MAIN). We show that nodes with high connectivity and betweenness are enriched and depleted in conditional and essential phenotypes, respectively. Such nodes are located in the innermost layers of AI-1MAIN and are preferential targets of pathogen effectors. We extend these network-centric analyses to Cell Surface Interactome (CSILRR) and predict its 35 most influential nodes. To determine their biological relevance, we show that these proteins physically interact with pathogen effectors and modulate plant immunity. Overall, our findings contrast with centrality-lethality rule, discover fast information spreading nodes, and highlight the structural properties of pathogen targets in two different interactomes. Finally, this theoretical framework could possibly be applicable to other inter-species interactomes to reveal pathogen contact points.
Helicase promotes replication re-initiation from an RNA transcript
Authors: Sun Bo , Singh Anupam , Sultana Shemaila , Inman James T. , Patel Smita S. , Wang Michelle D. 
Published: June 2018

AbstractTo ensure accurate DNA replication, a replisome must effectively overcome numerous obstacles on its DNA substrate. After encountering an obstacle, a progressing replisome often aborts DNA synthesis but continues to unwind. However, little is known about how DNA synthesis is resumed downstream of an obstacle. Here, we examine the consequences of a non-replicating replisome collision with a co-directional RNA polymerase (RNAP). Using single-molecule and ensemble methods, we find that T7 helicase interacts strongly with a non-replicating T7 DNA polymerase (DNAP) at a replication fork. As the helicase advances, the associated DNAP also moves forward. The presence of the DNAP increases both helicase’s processivity and unwinding rate. We show that such a DNAP, together with its helicase, is indeed able to actively disrupt a stalled transcription elongation complex, and then initiates replication using the RNA transcript as a primer. These observations exhibit T7 helicase’s novel role in replication re-initiation.
NEK7 regulates dendrite morphogenesis in neurons via Eg5-dependent microtubule stabilization
Authors: Freixo Francisco , Martinez Delgado Paula , Manso Yasmina , Sánchez-Huertas Carlos , Lacasa Cristina , Soriano Eduardo , Roig Joan , Lüders Jens 
Published: June 2018

AbstractOrganization of microtubules into ordered arrays is best understood in mitotic systems, but remains poorly characterized in postmitotic cells such as neurons. By analyzing the cycling cell microtubule cytoskeleton proteome through expression profiling and targeted RNAi screening for candidates with roles in neurons, we have identified the mitotic kinase NEK7. We show that NEK7 regulates dendrite morphogenesis in vitro and in vivo. NEK7 kinase activity is required for dendrite growth and branching, as well as spine formation and morphology. NEK7 regulates these processes in part through phosphorylation of the kinesin Eg5/KIF11, promoting its accumulation on microtubules in distal dendrites. Here, Eg5 limits retrograde microtubule polymerization, which is inhibitory to dendrite growth and branching. Eg5 exerts this effect through microtubule stabilization, independent of its motor activity. This work establishes NEK7 as a general regulator of the microtubule cytoskeleton, controlling essential processes in both mitotic cells and postmitotic neurons.
A new interhemispheric teleconnection increases predictability of winter precipitation in southwestern US
Authors: Mamalakis Antonios , Yu Jin-Yi , Randerson James T. , AghaKouchak Amir , Foufoula-Georgiou Efi 
Published: June 2018

AbstractReliable prediction of seasonal precipitation in the southwestern US (SWUS) remains a challenge with significant implications for the economy, water security and ecosystem management of the region. Winter precipitation in the SWUS has been linked to several climate modes, including the El Niño-Southern Oscillation (ENSO), with limited predictive ability. Here we report evidence that late-summer sea surface temperature and geopotential height anomalies close to New Zealand exhibit higher correlation with SWUS winter precipitation than ENSO, enhancing the potential for earlier and more accurate prediction. The teleconnection depends on a western Pacific ocean-atmosphere pathway, whereby sea surface temperature anomalies propagate from the southern to the northern hemisphere during boreal summer. Analysis also shows an amplification of this new teleconnection over the past four decades. Our work highlights the need to understand the dynamic nature of the coupled ocean-atmosphere system in a changing climate for improving future predictions of regional precipitation.
Inferring collective dynamical states from widely unobserved systems
Authors: Wilting Jens , Priesemann Viola 
Published: June 2018

AbstractWhen assessing spatially extended complex systems, one can rarely sample the states of all components. We show that this spatial subsampling typically leads to severe underestimation of the risk of instability in systems with propagating events. We derive a subsampling-invariant estimator, and demonstrate that it correctly infers the infectiousness of various diseases under subsampling, making it particularly useful in countries with unreliable case reports. In neuroscience, recordings are strongly limited by subsampling. Here, the subsampling-invariant estimator allows to revisit two prominent hypotheses about the brain’s collective spiking dynamics: asynchronous-irregular or critical. We identify consistently for rat, cat, and monkey a state that combines features of both and allows input to reverberate in the network for hundreds of milliseconds. Overall, owing to its ready applicability, the novel estimator paves the way to novel insight for the study of spatially extended dynamical systems.
Ocean acidification conditions increase resilience of marine diatoms
Authors: Valenzuela Jacob J. , López García de Lomana Adrián , Lee Allison , Armbrust E. V. , Orellana Mónica V. , Baliga Nitin S. 
Published: June 2018

AbstractThe fate of diatoms in future acidified oceans could have dramatic implications on marine ecosystems, because they account for ~40% of marine primary production. Here, we quantify resilience of Thalassiosira pseudonana in mid-20th century (300 ppm CO2) and future (1000 ppm CO2) conditions that cause ocean acidification, using a stress test that probes its ability to recover from incrementally higher amount of low-dose ultraviolet A (UVA) and B (UVB) radiation and re-initiate growth in day–night cycles, limited by nitrogen. While all cultures eventually collapse, those growing at 300 ppm CO2 succumb sooner. The underlying mechanism for collapse appears to be a system failure resulting from “loss of relational resilience,” that is, inability to adopt physiological states matched to N-availability and phase of the diurnal cycle. Importantly, under elevated CO2 conditions diatoms sustain relational resilience over a longer timeframe, demonstrating increased resilience to future acidified ocean conditions. This stress test framework can be extended to evaluate and predict how various climate change associated stressors may impact microbial community resilience.
Crossover from lattice to plasmonic polarons of a spin-polarised electron gas in ferromagnetic EuO
Authors: Riley J. M. , Caruso F. , Verdi C. , Duffy L. B. , Watson M. D. , Bawden L. , Volckaert K. , van der Laan G. , Hesjedal T. , Hoesch M. , Giustino F. , King P. D. C. 
Published: June 2018

AbstractStrong many-body interactions in solids yield a host of fascinating and potentially useful physical properties. Here, from angle-resolved photoemission experiments and ab initio many-body calculations, we demonstrate how a strong coupling of conduction electrons with collective plasmon excitations of their own Fermi sea leads to the formation of plasmonic polarons in the doped ferromagnetic semiconductor EuO. We observe how these exhibit a significant tunability with charge carrier doping, leading to a polaronic liquid that is qualitatively distinct from its more conventional lattice-dominated analogue. Our study thus suggests powerful opportunities for tailoring quantum many-body interactions in solids via dilute charge carrier doping.
Tuneable near white-emissive two-dimensional covalent organic frameworks
Authors: Li Xing , Gao Qiang , Wang Juefan , Chen Yifeng , Chen Zhi-Hui , Xu Hai-Sen , Tang Wei , Leng Kai , Ning Guo-Hong , Wu Jishan , Xu Qing-Hua , Quek Su Ying , Lu Yixin , Loh Kian Ping 
Published: June 2018

AbstractMost two-dimensional (2D) covalent organic frameworks (COFs) are non-fluorescent in the solid state even when they are constructed from emissive building blocks. The fluorescence quenching is usually attributed to non-irradiative rotation-related or π–π stacking-caused thermal energy dissipation process. Currently there is a lack of guiding principle on how to design fluorescent, solid-state material made of COF. Herein, we demonstrate that the eclipsed stacking structure of 2D COFs can be used to turn on, and tune, the solid-state photoluminescence from non-emissive building blocks by the restriction of intramolecular bond rotation via intralayer and interlayer hydrogen bonds among highly organized layers in the eclipse-stacked COFs. Our COFs serve as a platform whereby the size of the conjugated linkers and side-chain functionalities can be varied, rendering the emission colour-tuneable from blue to yellow and even white. This work provides a guide to design new solid-state emitters using COFs.
The TRPV4 channel links calcium influx to DDX3X activity and viral infectivity
Authors: Doñate-Macián P. , Jungfleisch J. , Pérez-Vilaró G. , Rubio-Moscardo F. , Perálvarez-Marín A. , Diez J. , Valverde M. A. 
Published: June 2018

AbstractIon channels are well placed to transduce environmental cues into signals used by cells to generate a wide range of responses, but little is known about their role in the regulation of RNA metabolism. Here we show that the TRPV4 cation channel binds the DEAD-box RNA helicase DDX3X and regulates its function. TRPV4-mediated Ca2+ influx releases DDX3X from the channel and drives DDX3X nuclear translocation, a process that involves calmodulin (CaM) and the CaM-dependent kinase II. Genetic depletion or pharmacological inhibition of TRPV4 diminishes DDX3X-dependent functions, including nuclear viral export and translation. Furthermore, TRPV4 mediates Ca2+ influx and nuclear accumulation of DDX3X in cells exposed to the Zika virus or the purified viral envelope protein. Consequently, targeting of TRPV4 reduces infectivity of dengue, hepatitis C and Zika viruses. Together, our results highlight the role of TRPV4 in the regulation of DDX3X-dependent control of RNA metabolism and viral infectivity.
Lipid vesicles chaperone an encapsulated RNA aptamer
Authors: Saha Ranajay , Verbanic Samuel , Chen Irene A. 
Published: June 2018

AbstractThe organization of molecules into cells is believed to have been critical for the emergence of living systems. Early protocells likely consisted of RNA functioning inside vesicles made of simple lipids. However, little is known about how encapsulation would affect the activity and folding of RNA. Here we find that confinement of the malachite green RNA aptamer inside fatty acid vesicles increases binding affinity and locally stabilizes the bound conformation of the RNA. The vesicle effectively ‘chaperones’ the aptamer, consistent with an excluded volume mechanism due to confinement. Protocellular organization thereby leads to a direct benefit for the RNA. Coupled with previously described mechanisms by which encapsulated RNA aids membrane growth, this effect illustrates how the membrane and RNA might cooperate for mutual benefit. Encapsulation could thus increase RNA fitness and the likelihood that functional sequences would emerge during the origin of life.
Controlled synthesis of highly-branched plasmonic gold nanoparticles through peptoid engineering
Authors: Yan Feng , Liu Lili , Walsh Tiffany R. , Gong Yu , El-Khoury Patrick Z. , Zhang Yanyan , Zhu Zihua , De Yoreo James J. , Engelhard Mark H. , Zhang Xin , Chen Chun-Long 
Published: June 2018

AbstractIn nature, specific biomolecules interacting with mineral precursors are responsible for the precise production of nanostructured inorganic materials that exhibit complex morphologies and superior performance. Despite advances in developing biomimetic approaches, the design rules for creating sequence-defined molecules that lead to the synthesis of inorganic nanomaterials with predictable complex morphologies are unknown. Herein we report the design of sequence-defined peptoids for controlled synthesis of highly branched plasmonic gold particles. By engineering peptoid sequences and investigating the resulting particle formation mechanisms, we develop a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped nanoparticles. Through a combination of hyperspectral UV-Vis extinction microscopy and three-photon photoemission electron microscopy, we demonstrate that the individual coral-shaped gold nanoparticles exhibit a plasmonic enhancement as high as 105-fold. This research significantly advances our ultimate vision of predictive bio-inspired materials synthesis using sequence-defined synthetic molecules that mimic proteins and peptides.
Thermo-responsive gels that absorb moisture and ooze water
Authors: Matsumoto Kazuya , Sakikawa Nobuki , Miyata Takashi 
Published: June 2018

AbstractThe water content of thermo-responsive hydrogels can be drastically altered by small changes in temperature because their polymer chains change from hydrophilic to hydrophobic above their low critical solution temperature (LCST). In general, such smart hydrogels have been utilized in aqueous solutions or in their wet state, and no attempt has been made to determine the phase-transition behavior of the gels in their dried states. Here we demonstrate an application of the thermo-responsive behavior of an interpenetrating polymer network (IPN) gel comprising thermo-responsive poly(N-isopropylacrylamide) and hydrophilic sodium alginate networks in their dried states. The dried IPN gel absorbs considerable moisture from air at temperatures below its LCST and oozes the absorbed moisture as liquid water above its LCST. These phenomena provide energy exchange systems in which moisture from air can be condensed to liquid water using the controllable hydrophilic/hydrophobic properties of thermo-responsive gels with a small temperature change.
A parthenogenetic quasi-program causes teratoma-like tumors during aging in wild-type C. elegans
Authors: Wang Hongyuan , Zhao Yuan , Ezcurra Marina , Benedetto Alexandre , Gilliat Ann F. , Hellberg Josephine , Ren Ziyu , Galimov Evgeniy R. , Athigapanich Trin , Girstmair Johannes , Telford Maximilian J. , Dolphin Colin T. , Zhang Zhizhou , Gems David 
Published: June 2018

AbstractA long-standing belief is that aging (senescence) is the result of stochastic damage accumulation. Alternatively, senescent pathology may also result from late-life, wild-type gene action (i.e., antagonistic pleiotropy, as argued by Williams) leading to non-adaptive run-on of developmental programs (or quasi-programs) (as suggested more recently by Blagosklonny). In this study, we use existing and new data to show how uterine tumors, a prominent form of senescent pathology in the nematode Caenorhabditis elegans, likely result from quasi-programs. Such tumors develop from unfertilized oocytes which enter the uterus and become hypertrophic and replete with endoreduplicated chromatin masses. Tumor formation begins with ovulation of unfertilized oocytes immediately after exhaustion of sperm stocks. We show that the timing of this transition between program and quasi-program (i.e., the onset of senescence), and the onset of tumor formation, depends upon the timing of sperm depletion. We identify homology between uterine tumors and mammalian ovarian teratomas, which both develop from oocytes that fail to mature after meiosis I. In teratomas, futile activation of developmental programs leads to the formation of differentiated structures within the tumor. We report that older uterine tumors express markers of later embryogenesis, consistent with teratoma-like activation of developmental programs. We also present evidence of coupling of distal gonad atrophy to oocyte hypertrophy. This study shows how the Williams Blagosklonny model can provide a mechanistic explanation of this component of C. elegans aging. It also suggests etiological similarity between teratoma and some forms of senescent pathology, insofar as both are caused by quasi-programs.
The Prognostic Value of Nodal Staging in Triple-Negative Breast Cancer — A Cohort from China
Authors: Yin Liu , Shuang Hao , Sheng Chen , Liang Huang , Sun Xiang-Jie , Yang Wen-Tao , Shao Zhi-Ming 
Published: June 2018

AbstractTo evaluate the clinical outcomes and relationship between tumor size, lymph node status, and prognosis in a large cohort of patients with triple–negative breast cancer (TNBC).849 Patients were categorized by tumor size and nodal status. The Kaplan-Meier method and Cox proportional hazards models were used to determine the association of nodal status and tumor size with survival outcomes. A Sidak adjustment was used for pairwise group comparisons. We conducted six pairwise comparisons between different node status. In univariate and multivariate analyses, it was indicated that N0 patients had similar prognoses as N1 patients (P = 0.072), and the OS of both of these groups was significantly better than that of N2/N3 patients (N0 vs N2, P < 0.001; N0 vs N3, P < 0.001; N1 vs N2, P = 0.014; N1 vs N3, P = 0.005). In summary, we report that in Chinese patients with triple-negative breast cancer, a greater difference in survival was observed between N1 and N2 than between N0 and N1, warranting the possible need of more intensive chemotherapy for N2-3 patients. We also found that tumor size made an impact on survival when lymph nodes were extensively involved, a finding that needs longer follow-up and further validation.