bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of intergeneric sexual hybridization between transgenic Brassica oleracea and Sinapis alba
Authors: Li Jun , Zhang Chunlei , Guan Chunyun , Luo Lixia , Ren Li , Wei Wenhui , Lu Guangyuan , Fang Xiaoping 
Published: November 2017

AbstractSinapis alba possesses a number of desirable traits that can be employed to broaden genetic variability in Brassica oleracea or B. napus. Using transgenic B. oleracea (CC, 2n = 18) as paternal plants and non-transgenic S. alba (SS, 2n = 24) as maternal plants, 11 hybrid plants were successfully obtained by using a combination of ovary culture and embryo rescue, while 2 seedlings of the reciprocal cross were generated but lost during the propagation. The hybridity of these plants was confirmed by flower color and other agronomic characteristics, chromosome counting, and pollen viability. Most of the intergeneric F1 plants showed only one set each of S and C chromosome (SC, 2n = 21) and were male sterile, while a few plants were semi-fertile and had one set of S chromosomes but two sets of C chromosomes (CCS, 2n = 30). PCR, genomic Southern blotting and qRT-PCR for bar gene revealed that among the F1 hybrid plants only 9.1% was bar positive and could be forwarded to F2 and F3 generation. The majority of F3 plants obtained sufficient resistance to Alternaria brassicae. Thus, the generation of disease (A. brassicae) and herbicide (Bastar) resistant intergeneric hybrids was of importance for breeding program. The existence of bar gene in these intermediate materials will facilitate the identification of hybridity and transfer of S.alba traits into target genetic background.
Pre-residency publication and its association with paediatric residency match outcome—a&nbsp;retrospective analysis of a&nbsp;national database
Authors: Gupta Ronish , Norris Mark L. , Barrowman Nicholas , Writer Hilary 
Published: November 2017

Introduction Scholarly activity is considered valuable in the resident selection process by candidates and program directors alike, despite existing literature suggesting applicants with scholarly work do not perform better in the match. These studies, however, are limited in that they have only measured whether candidates have successfully matched or not. To try and reconcile the existing disconnect in the value of pre-residency scholarly activity, we sought to deepen the understanding by investigating whether pre-residency publication is associated with a higher rank-order list match achievement.
Methods Anonymized data were collected from the Canadian Residency Matching Service for individuals matched to paediatric programs from 2007–2012. The primary analysis was to identify whether documentation of ≥1 pre-residency publication was associated with achieving a first-choice match. Secondary analyses included evaluating for an association between multiple pre-residency publications, academic presentations or a graduate degree and match outcome.
Results Of a total of 843 matched individuals, 406 (48.2%) listed ≥1 pre-residency publication and 494 (58.6%) matched to their first-choice program. The possession of ≥1 pre-residency publications was not associated with matching to a candidate’s first-choice program (odds ratio = 0.94 [95% confidence interval = 0.71–1.24], p = 0.66). Similarly, listing ≥2 publications, ≥3 publications, a graduate degree, or an academic presentation was not associated with achieving a first-choice match.
Conclusions The results provide increased support for the notion that in aggregate, candidate scholarly activity does not influence match outcome.
Bonhoeffer's Lutheran assertions: Cataphasis as teaching responsibility to the ‘other’
Authors: Sanchez Michelle C. 
Published: November 2017

AbstractStructural similarities have been noted between Dietrich Bonhoeffer's account of ethical responsibility and more recent accounts advocated by philosophers who emphasise responsibility to alterity. Yet, there remains one stubborn difference between Bonhoeffer and these philosophers: his unequivocal embrace of strongly cataphatic speech. This raises the following question: it is possible for contemporary Christian ethicists and theologians to enlist Bonhoeffer in the aim of reconceiving an ethic of responsibility to the ‘other’ when Bonhoeffer himself relies on such concrete, exclusive language? This article will argue that attention to Martin Luther's defence of theological assertions provides a lens through which the performative force of Bonhoeffer's cataphatic language can be better understood as a particular and traditional use of language that teaches an ethical posture of epistemic humility.
Essence and fullness: Evaluating the creator–creature distinction in Jonathan Edwards
Authors: Salladin James 
Published: November 2017

AbstractSoteriological participation in God, variously termed theosis, divinisation or deification commands widespread interest across the spectrum of Christian theology. A key difficulty is how to maintain the creator–creature distinction, while bridging it to gain intimacy. Jonathan Edwards provides a Reformed perspective on this conversation, by way of his distinction between the incommunicable divine essence and the communicable divine fullness. This article clarifies this distinction by evaluating its coherence and exploring whether it divorces God's immanent and economic life. It argues that distinguishing two forms of participation – methexis verses koinonia – clarifies coherence and shows that it does not divide God's being from act.
Sergii Bulgakov's ‘Sofiologiia smerti’
Authors: Smith T. Allan 
Published: November 2017

AbstractThis article examines S. Bulgakov's treatise ‘Sofiologiia smerti’ (‘Sophiology of Death’), which has been relatively neglected by scholars. Death is a topic that recurs with some frequency throughout Bulgakov's writings; that it merited its own study indicates the importance that he attached to the topic. The article provides a biographical, cultural and intellectual context for the treatise, as well some comments on its literary features. Bulgakov's use of sophiology and kenotic theology to explore the process of dying and the fact of death itself come under review. His reflections on human death and dying lead Bulgakov to explore how the Son of God experienced death and the involvement of the Trinity itself in that experience. Christ becomes fully human when he dies, and his death is the pattern for all human death.
Cell death and cell lysis are separable events during pyroptosis
Authors: DiPeso Lucian , Ji Daisy X , Vance Russell E , Price Jordan V 
Published: November 2017

AbstractAlthough much insight has been gained into the mechanisms by which activation of the inflammasome can trigger pyroptosis in mammalian cells, the precise kinetics of the end stages of pyroptosis have not been well characterized. Using time-lapse fluorescent imaging to analyze the kinetics of pyroptosis in individual murine macrophages, we observed distinct stages of cell death and cell lysis. Our data demonstrate that cell membrane permeability resulting from gasdermin D pore formation is coincident with the cessation of cell movement, loss of mitochondrial activity, and cell swelling, events that can be uncoupled from cell lysis. We propose a model of pyroptosis in which cell death can occur independently of cell lysis. The uncoupling of cell death from cell lysis may allow for better control of cytosolic contents upon activation of the inflammasome.
Zinc-finger proteins in health and disease
Authors: Cassandri Matteo , Smirnov Artem , Novelli Flavia , Pitolli Consuelo , Agostini Massimiliano , Malewicz Michal , Melino Gerry , Raschellà Giuseppe 
Published: November 2017

AbstractZinc-finger proteins (ZNFs) are one of the most abundant groups of proteins and have a wide range of molecular functions. Given the wide variety of zinc-finger domains, ZNFs are able to interact with DNA, RNA, PAR (poly-ADP-ribose) and other proteins. Thus, ZNFs are involved in the regulation of several cellular processes. In fact, ZNFs are implicated in transcriptional regulation, ubiquitin-mediated protein degradation, signal transduction, actin targeting, DNA repair, cell migration, and numerous other processes. The aim of this review is to provide a comprehensive summary of the current state of knowledge of this class of proteins. Firstly, we describe the actual classification of ZNFs, their structure and functions. Secondly, we focus on the biological role of ZNFs in the development of organisms under normal physiological and pathological conditions.
Transcriptional signature of human pro-inflammatory TH17 cells identifies reduced IL10 gene expression in multiple sclerosis
Authors: Hu Dan , Notarbartolo Samuele , Croonenborghs Tom , Patel Bonny , Cialic Ron , Yang Tun-Hsiang , Aschenbrenner Dominik , Andersson Karin M. , Gattorno Marco , Pham Minh , Kivisakk Pia , Pierre Isabelle V. , Lee Youjin , Kiani Karun , Bokarewa Maria , Tjon Emily , Pochet Nathalie , Sallusto Federica , Kuchroo Vijay K. , Weiner Howard L. 
Published: November 2017

AbstractWe have previously reported the molecular signature of murine pathogenic TH17 cells that induce experimental autoimmune encephalomyelitis (EAE) in animals. Here we show that human peripheral blood IFN-γ+IL-17+(TH1/17) and IFN-γ−IL-17+(TH17) CD4+T cells display distinct transcriptional profiles in high-throughput transcription analyses. Compared to TH17 cells, TH1/17 cells have gene signatures with marked similarity to mouse pathogenic TH17 cells. Assessing 15 representative signature genes in patients with multiple sclerosis, we find that TH1/17 cells have elevated expression ofCXCR3and reduced expression ofIFNG,CCL3,CLL4,GZMB, andIL10compared to healthy controls. Moreover, higher expression ofIL10in TH17 cells is found in clinically stable vs. active patients. Our results define the molecular signature of human pro-inflammatory TH17 cells, which can be used to both identify pathogenic TH17 cells and to measure the effect of treatment on TH17 cells in human autoimmune diseases.
Photonic simulation of entanglement growth and engineering after a spin chain quench
Authors: Pitsios Ioannis , Banchi Leonardo , Rab Adil S. , Bentivegna Marco , Caprara Debora , Crespi Andrea , Spagnolo Nicolò , Bose Sougato , Mataloni Paolo , Osellame Roberto , Sciarrino Fabio 
Published: November 2017

AbstractThe time evolution of quantum many-body systems is one of the most important processes for benchmarking quantum simulators. The most curious feature of such dynamics is the growth of quantum entanglement to an amount proportional to the system size (volume law) even when interactions are local. This phenomenon has great ramifications for fundamental aspects, while its optimisation clearly has an impact on technology (e.g., for on-chip quantum networking). Here we use an integrated photonic chip with a circuit-based approach to simulate the dynamics of a spin chain and maximise the entanglement generation. The resulting entanglement is certified by constructing a second chip, which measures the entanglement between multiple distant pairs of simulated spins, as well as the block entanglement entropy. This is the first photonic simulation and optimisation of the extensive growth of entanglement in a spin chain, and opens up the use of photonic circuits for optimising quantum devices.
Author Correction: Reactive astrocytes function as phagocytes after brain ischemia via ABCA1-mediated pathway
Authors: Morizawa Yosuke M. , Hirayama Yuri , Ohno Nobuhiko , Shibata Shinsuke , Shigetomi Eiji , Sui Yang , Nabekura Junichi , Sato Koichi , Okajima Fumikazu , Takebayashi Hirohide , Okano Hideyuki , Koizumi Schuichi 
Published: November 2017

AbstractThe original version of this Article contained an error in the spelling of the author Nobuhiko Ohno, which was incorrectly given as Noubuhiko Ohno. This has now been corrected in both the PDF and HTML versions of the Article.
Loss of HIF-1α in natural killer cells inhibits tumour growth by stimulating non-productive angiogenesis
Authors: Krzywinska Ewelina , Kantari-Mimoun Chahrazade , Kerdiles Yann , Sobecki Michal , Isagawa Takayuki , Gotthardt Dagmar , Castells Magali , Haubold Johannes , Millien Corinne , Viel Thomas , Tavitian Bertrand , Takeda Norihiko , Fandrey Joachim , Vivier Eric , Sexl Veronika , Stockmann Christian 
Published: November 2017

AbstractProductive angiogenesis, a prerequisite for tumour growth, depends on the balanced release of angiogenic and angiostatic factors by different cell types within hypoxic tumours. Natural killer (NK) cells kill cancer cells and infiltrate hypoxic tumour areas. Cellular adaptation to low oxygen is mediated by Hypoxia-inducible factors (HIFs). We found that deletion of HIF-1α in NK cells inhibited tumour growth despite impaired tumour cell killing. Tumours developing in these conditions were characterised by a high-density network of immature vessels, severe haemorrhage, increased hypoxia, and facilitated metastasis due to non-productive angiogenesis. Loss of HIF-1α in NK cells increased the bioavailability of the major angiogenic cytokine vascular endothelial growth factor (VEGF) by decreasing the infiltration of NK cells that express angiostatic soluble VEGFR-1. In summary, this identifies the hypoxic response in NK cells as an inhibitor of VEGF-driven angiogenesis, yet, this promotes tumour growth by allowing the formation of functionally improved vessels.
Fast-forwarding of Hamiltonians and exponentially precise measurements
Authors: Atia Yosi , Aharonov Dorit 
Published: November 2017

AbstractThe time-energy uncertainty relation (TEUR) $$\Delta {\it{t}}\Delta {\it{E}}\,{\bf{ \ge }}\,{\textstyle{{\bf{1}} \over {\bf{2}}}}$$
Δ
t
Δ
E

≥

1

2

holds if the Hamiltonian is completely unknown, but can be violated otherwise; here we initiate a rigorous study describing when and to what extent such violations can occur. To this end, we propose a computational version of the TEUR (cTEUR), in which Δt is replaced by the computational complexity of simulating the measurement. cTEUR violations are proved to occur if and only if the Hamiltonian can be fast forwarded (FF), namely, simulated for time t with complexity significantly smaller than t. Shor’s algorithm provides an example of exponential cTEUR violations; we show that so do commuting local Hamiltonians and quadratic fermion Hamiltonians. A general FF method is ruled out, but finding further examples, as well as experimental demonstrations, are left for future work. We discuss possible connections to sensing and quantum gravity. This work initiates a rigorous theory of efficiency versus accuracy in energy measurements using computational complexity language.
Wiskott-Aldrich syndrome protein regulates autophagy and inflammasome activity in innate immune cells
Authors: Lee Pamela P. , Lobato-Márquez Damián , Pramanik Nayani , Sirianni Andrea , Daza-Cajigal Vanessa , Rivers Elizabeth , Cavazza Alessia , Bouma Gerben , Moulding Dale , Hultenby Kjell , Westerberg Lisa S. , Hollinshead Michael , Lau Yu-Lung , Burns Siobhan O. , Mostowy Serge , Bajaj-Elliott Mona , Thrasher Adrian J. 
Published: November 2017

AbstractDysregulation of autophagy and inflammasome activity contributes to the development of auto-inflammatory diseases. Emerging evidence highlights the importance of the actin cytoskeleton in modulating inflammatory responses. Here we show that deficiency of Wiskott–Aldrich syndrome protein (WASp), which signals to the actin cytoskeleton, modulates autophagy and inflammasome function. In a model of sterile inflammation utilizing TLR4 ligation followed by ATP or nigericin treatment, inflammasome activation is enhanced in monocytes from WAS patients and in WAS-knockout mouse dendritic cells. In ex vivo models of enteropathogenic Escherichia coli and Shigella flexneri infection, WASp deficiency causes defective bacterial clearance, excessive inflammasome activation and host cell death that are associated with dysregulated septin cage-like formation, impaired autophagic p62/LC3 recruitment and defective formation of canonical autophagosomes. Taken together, we propose that dysregulation of autophagy and inflammasome activities contribute to the autoinflammatory manifestations of WAS, thereby identifying potential targets for therapeutic intervention.
Nucleosome acidic patch-targeting binuclear ruthenium compounds induce aberrant chromatin condensation
Authors: Davey Gabriela E. , Adhireksan Zenita , Ma Zhujun , Riedel Tina , Sharma Deepti , Padavattan Sivaraman , Rhodes Daniela , Ludwig Alexander , Sandin Sara , Murray Benjamin S. , Dyson Paul J. , Davey Curt A. 
Published: November 2017

AbstractThe ‘acidic patch’ is a highly electronegative cleft on the histone H2A–H2B dimer in the nucleosome. It is a fundamental motif for protein binding and chromatin dynamics, but the cellular impact of targeting this potentially therapeutic site with exogenous molecules remains unclear. Here, we characterize a family of binuclear ruthenium compounds that selectively target the nucleosome acidic patch, generating intra-nucleosomal H2A-H2B cross-links as well as inter-nucleosomal cross-links. In contrast to cisplatin or the progenitor RAPTA-C anticancer drugs, the binuclear agents neither arrest specific cell cycle phases nor elicit DNA damage response, but rather induce an irreversible, anomalous state of condensed chromatin that ultimately results in apoptosis. In vitro, the compounds induce misfolding of chromatin fibre and block the binding of the regulator of chromatin condensation 1 (RCC1) acidic patch-binding protein. This family of chromatin-modifying molecules has potential for applications in drug development and as tools for chromatin research.
TLR7 mediated viral recognition results in focal type I interferon secretion by dendritic cells
Authors: Saitoh Shin-Ichiroh , Abe Fumiko , Kanno Atsuo , Tanimura Natsuko , Mori Saitoh Yoshiko , Fukui Ryutaro , Shibata Takuma , Sato Katsuaki , Ichinohe Takeshi , Hayashi Mayumi , Kubota Kazuishi , Kozuka-Hata Hiroko , Oyama Masaaki , Kikko Yorifumi , Katada Toshiaki , Kontani Kenji , Miyake Kensuke 
Published: November 2017

AbstractPlasmacytoid dendritic cells (pDC) sense viral RNA through toll-like receptor 7 (TLR7), form self-adhesive pDC–pDC clusters, and produce type I interferons. This cell adhesion enhances type I interferon production, but little is known about the underlying mechanisms. Here we show that MyD88-dependent TLR7 signaling activates CD11a/CD18 integrin to induce microtubule elongation. TLR7+ lysosomes then become linked with these microtubules through the GTPase Arl8b and its effector SKIP/Plekhm2, resulting in perinuclear to peripheral relocalization of TLR7. The type I interferon signaling molecules TRAF3, IKKα, and mTORC1 are constitutively associated in pDCs. TLR7 localizes to mTORC1 and induces association of TRAF3 with the upstream molecule TRAF6. Finally, type I interferons are secreted in the vicinity of cell–cell contacts between clustered pDCs. These results suggest that TLR7 needs to move to the cell periphery to induce robust type I interferon responses in pDCs.
Capturing an initial intermediate during the P450nor enzymatic reaction using time-resolved XFEL crystallography and caged-substrate
Authors: Tosha Takehiko , Nomura Takashi , Nishida Takuma , Saeki Naoya , Okubayashi Kouta , Yamagiwa Raika , Sugahara Michihiro , Nakane Takanori , Yamashita Keitaro , Hirata Kunio , Ueno Go , Kimura Tetsunari , Hisano Tamao , Muramoto Kazumasa , Sawai Hitomi , Takeda Hanae , Mizohata Eiichi , Yamashita Ayumi , Kanematsu Yusuke , Takano Yu , Nango Eriko , Tanaka Rie , Nureki Osamu , Shoji Osami , Ikemoto Yuka , Murakami Hironori , Owada Shigeki , Tono Kensuke , Yabashi Makina , Yamamoto Masaki , Ago Hideo , Iwata So , Sugimoto Hiroshi , Shiro Yoshitsugu , Kubo Minoru 
Published: November 2017

AbstractTime-resolved serial femtosecond crystallography using an X-ray free electron laser (XFEL) in conjunction with a photosensitive caged-compound offers a crystallographic method to track enzymatic reactions. Here we demonstrate the application of this method using fungal NO reductase, a heme-containing enzyme, at room temperature. Twenty milliseconds after caged-NO photolysis, we identify a NO-bound form of the enzyme, which is an initial intermediate with a slightly bent Fe-N-O coordination geometry at a resolution of 2.1 Å. The NO geometry is compatible with those analyzed by XFEL-based cryo-crystallography and QM/MM calculations, indicating that we obtain an intact Fe3+-NO coordination structure that is free of X-ray radiation damage. The slightly bent NO geometry is appropriate to prevent immediate NO dissociation and thus accept H− from NADH. The combination of using XFEL and a caged-compound is a powerful tool for determining functional enzyme structures during catalytic reactions at the atomic level.
The semiquinone swing in the bifurcating electron transferring flavoprotein/butyryl-CoA dehydrogenase complex from Clostridium difficile
Authors: Demmer Julius K. , Pal Chowdhury Nilanjan , Selmer Thorsten , Ermler Ulrich , Buckel Wolfgang 
Published: November 2017

AbstractThe electron transferring flavoprotein/butyryl-CoA dehydrogenase (EtfAB/Bcd) catalyzes the reduction of one crotonyl-CoA and two ferredoxins by two NADH within a flavin-based electron-bifurcating process. Here we report on the X-ray structure of the Clostridium difficile (EtfAB/Bcd)4 complex in the dehydrogenase-conducting D-state, α-FAD (bound to domain II of EtfA) and δ-FAD (bound to Bcd) being 8 Å apart. Superimposing Acidaminococcus fermentans EtfAB onto C. difficile EtfAB/Bcd reveals a rotation of domain II of nearly 80°. Further rotation by 10° brings EtfAB into the bifurcating B-state, α-FAD and β-FAD (bound to EtfB) being 14 Å apart. This dual binding mode of domain II, substantiated by mutational studies, resembles findings in non-bifurcating EtfAB/acyl-CoA dehydrogenase complexes. In our proposed mechanism, NADH reduces β-FAD, which bifurcates. One electron goes to ferredoxin and one to α-FAD, which swings over to reduce δ-FAD to the semiquinone. Repetition affords a second reduced ferredoxin and δ-FADH−, which reduces crotonyl-CoA.
Methanogenesis in oxygenated soils is a substantial fraction of wetland methane emissions
Authors: Angle Jordan C. , Morin Timothy H. , Solden Lindsey M. , Narrowe Adrienne B. , Smith Garrett J. , Borton Mikayla A. , Rey-Sanchez Camilo , Daly Rebecca A. , Mirfenderesgi Golnazalsdat , Hoyt David W. , Riley William J. , Miller Christopher S. , Bohrer Gil , Wrighton Kelly C. 
Published: November 2017

AbstractThe current paradigm, widely incorporated in soil biogeochemical models, is that microbial methanogenesis can only occur in anoxic habitats. In contrast, here we show clear geochemical and biological evidence for methane production in well-oxygenated soils of a freshwater wetland. A comparison of oxic to anoxic soils reveal up to ten times greater methane production and nine times more methanogenesis activity in oxygenated soils. Metagenomic and metatranscriptomic sequencing recover the first near-complete genomes for a novel methanogen species, and show acetoclastic production from this organism was the dominant methanogenesis pathway in oxygenated soils. This organism, Candidatus Methanothrix paradoxum, is prevalent across methane emitting ecosystems, suggesting a global significance. Moreover, in this wetland, we estimate that up to 80% of methane fluxes could be attributed to methanogenesis in oxygenated soils. Together, our findings challenge a widely held assumption about methanogenesis, with significant ramifications for global methane estimates and Earth system modeling.