bluuebunny/crossref_metadata_2025_split huggingface dataset:
MYC functions as a switch for natural killer cell-mediated immune surveillance of lymphoid malignancies
Authors: Swaminathan Srividya , Hansen Aida S. , Heftdal Line D. , Dhanasekaran Renumathy , Deutzmann Anja , Fernandez Wadie D. M. , Liefwalker Daniel F. , Horton Crista , Mosley Adriane , Liebersbach Mariola , Maecker Holden T. , Felsher Dean W. 
Published: June 2020

AbstractThe MYC oncogene drives T- and B- lymphoid malignancies, including Burkitt’s lymphoma (BL) and Acute Lymphoblastic Leukemia (ALL). Here, we demonstrate a systemic reduction in natural killer (NK) cell numbers in SRα-tTA/Tet-O-MYCON mice bearing MYC-driven T-lymphomas. Residual mNK cells in spleens of MYCON T-lymphoma-bearing mice exhibit perturbations in the terminal NK effector differentiation pathway. Lymphoma-intrinsic MYC arrests NK maturation by transcriptionally repressing STAT1/2 and secretion of Type I Interferons (IFNs). Treating T-lymphoma-bearing mice with Type I IFN improves survival by rescuing NK cell maturation. Adoptive transfer of mature NK cells is sufficient to delay both T-lymphoma growth and recurrence post MYC inactivation. In MYC-driven BL patients, low expression of both STAT1 and STAT2 correlates significantly with the absence of activated NK cells and predicts unfavorable clinical outcomes. Our studies thus provide a rationale for developing NK cell-based therapies to effectively treat MYC-driven lymphomas in the future.
Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers
Authors: Hozé Nathanaël , Salje Henrik , Rousset Dominique , Fritzell Camille , Vanhomwegen Jessica , Bailly Sarah , Najm Matthieu , Enfissi Antoine , Manuguerra Jean-Claude , Flamand Claude , Cauchemez Simon 
Published: June 2020

AbstractCharacterizing the circulation of Mayaro virus (MAYV), an emerging arbovirus threat, is essential for risk assessment but challenging due to cross-reactivity with other alphaviruses such as chikungunya virus (CHIKV). Here, we develop an analytical framework to jointly assess MAYV epidemiology and the extent of cross-reactivity with CHIKV from serological data collected throughout French Guiana (N = 2697). We find strong evidence of an important sylvatic cycle for MAYV with most infections occurring near the natural reservoir in rural areas and in individuals more likely to go to the forest (i.e., adult males) and with seroprevalences of up to 18% in some areas. These findings highlight the need to strengthen MAYV surveillance in the region and showcase how modeling can improve interpretation of cross-reacting assays.
Mode of action of teixobactins in cellular membranes
Authors: Shukla Rhythm , Medeiros-Silva João , Parmar Anish , Vermeulen Bram J. A. , Das Sanjit , Paioni Alessandra Lucini , Jekhmane Shehrazade , Lorent Joseph , Bonvin Alexandre M. J. J. , Baldus Marc , Lelli Moreno , Veldhuizen Edwin J. A. , Breukink Eefjan , Singh Ishwar , Weingarth Markus 
Published: June 2020

AbstractThe natural antibiotic teixobactin kills pathogenic bacteria without detectable resistance. The difficult synthesis and unfavourable solubility of teixobactin require modifications, yet insufficient knowledge on its binding mode impedes the hunt for superior analogues. Thus far, teixobactins are assumed to kill bacteria by binding to cognate cell wall precursors (Lipid II and III). Here we present the binding mode of teixobactins in cellular membranes using solid-state NMR, microscopy, and affinity assays. We solve the structure of the complex formed by an improved teixobactin-analogue and Lipid II and reveal how teixobactins recognize a broad spectrum of targets. Unexpectedly, we find that teixobactins only weakly bind to Lipid II in cellular membranes, implying the direct interaction with cell wall precursors is not the sole killing mechanism. Our data suggest an additional mechanism affords the excellent activity of teixobactins, which can block the cell wall biosynthesis by capturing precursors in massive clusters on membranes.
Modular gateway-ness connectivity and structural core organization in maritime network science
Authors: Xu Mengqiao , Pan Qian , Muscoloni Alessandro , Xia Haoxiang , Cannistraci Carlo Vittorio 
Published: June 2020

AbstractAround 80% of global trade by volume is transported by sea, and thus the maritime transportation system is fundamental to the world economy. To better exploit new international shipping routes, we need to understand the current ones and their complex systems association with international trade. We investigate the structure of the global liner shipping network (GLSN), finding it is an economic small-world network with a trade-off between high transportation efficiency and low wiring cost. To enhance understanding of this trade-off, we examine the modular segregation of the GLSN; we study provincial-, connector-hub ports and propose the definition of gateway-hub ports, using three respective structural measures. The gateway-hub structural-core organization seems a salient property of the GLSN, which proves importantly associated to network integration and function in realizing the cargo transportation of international trade. This finding offers new insights into the GLSN’s structural organization complexity and its relevance to international trade.
Transcriptomics and proteomics reveal a cooperation between interferon and T-helper 17 cells in neuromyelitis optica
Authors: Agasing Agnieshka M. , Wu Qi , Khatri Bhuwan , Borisow Nadja , Ruprecht Klemens , Brandt Alexander Ulrich , Gawde Saurabh , Kumar Gaurav , Quinn James L. , Ko Rose M. , Mao-Draayer Yang , Lessard Christopher J. , Paul Friedemann , Axtell Robert C. 
Published: June 2020

AbstractType I interferon (IFN-I) and T helper 17 (TH17) drive pathology in neuromyelitis optica spectrum disorder (NMOSD) and in TH17-induced experimental autoimmune encephalomyelitis (TH17-EAE). This is paradoxical because the prevalent theory is that IFN-I inhibits TH17 function. Here we report that a cascade involving IFN-I, IL-6 and B cells promotes TH17-mediated neuro-autoimmunity. In NMOSD, elevated IFN-I signatures, IL-6 and IL-17 are associated with severe disability. Furthermore, IL-6 and IL-17 levels are lower in patients on anti-CD20 therapy. In mice, IFN-I elevates IL-6 and exacerbates TH17-EAE. Strikingly, IL-6 blockade attenuates disease only in mice treated with IFN-I. By contrast, B-cell-deficiency attenuates TH17-EAE in the presence or absence of IFN-I treatment. Finally, IFN-I stimulates B cells to produce IL-6 to drive pathogenic TH17 differentiation in vitro. Our data thus provide an explanation for the paradox surrounding IFN-I and TH17 in neuro-autoimmunity, and may have utility in predicting therapeutic response in NMOSD.
Mutational bias and the protein code shape the evolution of splicing enhancers
Authors: Rong Stephen , Buerer Luke , Rhine Christy L. , Wang Jing , Cygan Kamil J. , Fairbrother William G. 
Published: June 2020

AbstractExonic splicing enhancers (ESEs) are enriched in exons relative to introns and bind splicing activators. This study considers a fundamental question of co-evolution: How did ESE motifs become enriched in exons prior to the evolution of ESE recognition? We hypothesize that the high exon to intron motif ratios necessary for ESE function were created by mutational bias coupled with purifying selection on the protein code. These two forces retain certain coding motifs in exons while passively depleting them from introns. Through the use of simulations, genomic analyses, and high throughput splicing assays, we confirm the key predictions of this hypothesis, including an overlap between protein and splicing information in ESEs. We discuss the implications of mutational bias as an evolutionary driver in other cis-regulatory systems.
Fast sulfate formation from oxidation of SO2 by NO2 and HONO observed in Beijing haze
Authors: Wang Junfeng , Li Jingyi , Ye Jianhuai , Zhao Jian , Wu Yangzhou , Hu Jianlin , Liu Dantong , Nie Dongyang , Shen Fuzhen , Huang Xiangpeng , Huang Dan Dan , Ji Dongsheng , Sun Xu , Xu Weiqi , Guo Jianping , Song Shaojie , Qin Yiming , Liu Pengfei , Turner Jay R. , Lee Hyun Chul , Hwang Sungwoo , Liao Hong , Martin Scot T. , Zhang Qi , Chen Mindong , Sun Yele , Ge Xinlei , Jacob Daniel J. 
Published: June 2020

AbstractSevere events of wintertime particulate air pollution in Beijing (winter haze) are associated with high relative humidity (RH) and fast production of particulate sulfate from the oxidation of sulfur dioxide (SO2) emitted by coal combustion. There has been considerable debate regarding the mechanism for SO2 oxidation. Here we show evidence from field observations of a haze event that rapid oxidation of SO2 by nitrogen dioxide (NO2) and nitrous acid (HONO) takes place, the latter producing nitrous oxide (N2O). Sulfate shifts to larger particle sizes during the event, indicative of fog/cloud processing. Fog and cloud readily form under winter haze conditions, leading to high liquid water contents with high pH (>5.5) from elevated ammonia. Such conditions enable fast aqueous-phase oxidation of SO2 by NO2, producing HONO which can in turn oxidize SO2 to yield N2O.This mechanism could provide an explanation for sulfate formation under some winter haze conditions.
Single-atom Pt in intermetallics as an ultrastable and selective catalyst for propane dehydrogenation
Authors: Nakaya Yuki , Hirayama Jun , Yamazoe Seiji , Shimizu Ken-ichi , Furukawa Shinya 
Published: June 2020

AbstractPropylene production via propane dehydrogenation (PDH) requires high reaction temperatures to obtain sufficient propylene yields, which results to prominent catalyst deactivation due to coke formation. Developing highly stable catalysts for PDH without deactivation even at high temperatures is of great interest and benefit for industry. Here, we report that single-atom Pt included in thermally stable intermetallic PtGa works as an ultrastable and selective catalyst for PDH at high temperatures. Intermetallic PtGa displays three-hold-Pt ensembles and single Pt atoms isolated by catalytically inert Ga at the surface, the former of which can be selectively blocked and disabled by Pb deposition. The PtGa-Pb/SiO2 catalyst exhibits 30% conversion with 99.6% propylene selectivity at 600 °C for 96 h without lowering the performance. The single-atom Pt well catalyzes the first and second C–H activation, while effectively inhibits the third one, which minimizes the side reactions to coke and drastically improves the selectivity and stability.
Rab35-regulated lipid turnover by myotubularins represses mTORC1 activity and controls myelin growth
Authors: Sawade Linda , Grandi Federica , Mignanelli Marianna , Patiño-López Genaro , Klinkert Kerstin , Langa-Vives Francina , Di Guardo Roberta , Echard Arnaud , Bolino Alessandra , Haucke Volker 
Published: June 2020

AbstractInherited peripheral neuropathies (IPNs) represent a broad group of disorders including Charcot-Marie-Tooth (CMT) neuropathies characterized by defects primarily arising in myelin, axons, or both. The molecular mechanisms by which mutations in nearly 100 identified IPN/CMT genes lead to neuropathies are poorly understood. Here we show that the Ras-related GTPase Rab35 controls myelin growth via complex formation with the myotubularin-related phosphatidylinositol (PI) 3-phosphatases MTMR13 and MTMR2, encoded by genes responsible for CMT-types 4B2 and B1 in humans, and found that it downregulates lipid-mediated mTORC1 activation, a pathway known to crucially regulate myelin biogenesis. Targeted disruption of Rab35 leads to hyperactivation of mTORC1 signaling caused by elevated levels of PI 3-phosphates and to focal hypermyelination in vivo. Pharmacological inhibition of phosphatidylinositol 3,5-bisphosphate synthesis or mTORC1 signaling ameliorates this phenotype. These findings reveal a crucial role for Rab35-regulated lipid turnover by myotubularins to repress mTORC1 activity and to control myelin growth.
Probing the pinning strength of magnetic vortex cores with sub-nanometer resolution
Authors: Holl Christian , Knol Marvin , Pratzer Marco , Chico Jonathan , Fernandes Imara Lima , Lounis Samir , Morgenstern Markus 
Published: June 2020

AbstractUnderstanding interactions of magnetic textures with defects is crucial for applications such as racetrack memories or microwave generators. Such interactions appear on the few nanometer scale, where imaging has not yet been achieved with controlled external forces. Here, we establish a method determining such interactions via spin-polarized scanning tunneling microscopy in three-dimensional magnetic fields. We track a magnetic vortex core, pushed by the forces of the in-plane fields, and discover that the core (~ 104 Fe-atoms) gets successively pinned close to single atomic-scale defects. Reproducing the core path along several defects via parameter fit, we deduce the pinning potential as a mexican hat with short-range repulsive and long-range attractive part. The approach to deduce defect induced pinning potentials on the sub-nanometer scale is transferable to other non-collinear spin textures, eventually enabling an atomic scale design of defect configurations for guiding and reliable read-out in race-track type devices.
DNA origami-based single-molecule force spectroscopy elucidates RNA Polymerase III pre-initiation complex stability
Authors: Kramm Kevin , Schröder Tim , Gouge Jerome , Vera Andrés Manuel , Gupta Kapil , Heiss Florian B. , Liedl Tim , Engel Christoph , Berger Imre , Vannini Alessandro , Tinnefeld Philip , Grohmann Dina 
Published: June 2020

AbstractThe TATA-binding protein (TBP) and a transcription factor (TF) IIB-like factor are important constituents of all eukaryotic initiation complexes. The reason for the emergence and strict requirement of the additional initiation factor Bdp1 in the RNA polymerase (RNAP) III system, however, remained elusive. A poorly studied aspect in this context is the effect of DNA strain arising from DNA compaction and transcriptional activity on initiation complex formation. We made use of a DNA origami-based force clamp to follow the assembly of human initiation complexes in the RNAP II and RNAP III systems at the single-molecule level under piconewton forces. We demonstrate that TBP-DNA complexes are force-sensitive and TFIIB is sufficient to stabilise TBP on a strained promoter. In contrast, Bdp1 is the pivotal component that ensures stable anchoring of initiation factors, and thus the polymerase itself, in the RNAP III system. Thereby, we offer an explanation for the crucial role of Bdp1 for the high transcriptional output of RNAP III.
Manipulating magnetoelectric energy landscape in multiferroics
Authors: Huang Yen-Lin , Nikonov Dmitri , Addiego Christopher , Chopdekar Rajesh V. , Prasad Bhagwati , Zhang Lei , Chatterjee Jyotirmoy , Liu Heng-Jui , Farhan Alan , Chu Ying-Hao , Yang Mengmeng , Ramesh Maya , Qiu Zi Qiang , Huey Bryan D. , Lin Chia-Ching , Gosavi Tanay , Íñiguez Jorge , Bokor Jeffrey , Pan Xiaoqing , Young Ian , Martin Lane W. , Ramesh Ramamoorthy 
Published: June 2020

AbstractMagnetoelectric coupling at room temperature in multiferroic materials, such as BiFeO3, is one of the leading candidates to develop low-power spintronics and emerging memory technologies. Although extensive research activity has been devoted recently to exploring the physical properties, especially focusing on ferroelectricity and antiferromagnetism in chemically modified BiFeO3, a concrete understanding of the magnetoelectric coupling is yet to be fulfilled. We have discovered that La substitutions at the Bi-site lead to a progressive increase in the degeneracy of the potential energy landscape of the BiFeO3 system exemplified by a rotation of the polar axis away from the 〈111〉pc towards the 〈112〉pc discretion. This is accompanied by corresponding rotation of the antiferromagnetic axis as well, thus maintaining the right-handed vectorial relationship between ferroelectric polarization, antiferromagnetic vector and the Dzyaloshinskii-Moriya vector. As a consequence, La-BiFeO3 films exhibit a magnetoelectric coupling that is distinctly different from the undoped BiFeO3 films.
Differential contributions of the two cerebral hemispheres to temporal and spectral speech feedback control
Authors: Floegel Mareike , Fuchs Susanne , Kell Christian A. 
Published: June 2020

AbstractProper speech production requires auditory speech feedback control. Models of speech production associate this function with the right cerebral hemisphere while the left hemisphere is proposed to host speech motor programs. However, previous studies have investigated only spectral perturbations of the auditory speech feedback. Since auditory perception is known to be lateralized, with right-lateralized analysis of spectral features and left-lateralized processing of temporal features, it is unclear whether the observed right-lateralization of auditory speech feedback processing reflects a preference for speech feedback control or for spectral processing in general. Here we use a behavioral speech adaptation experiment with dichotically presented altered auditory feedback and an analogous fMRI experiment with binaurally presented altered feedback to confirm a right hemisphere preference for spectral feedback control and to reveal a left hemisphere preference for temporal feedback control during speaking. These results indicate that auditory feedback control involves both hemispheres with differential contributions along the spectro-temporal axis.
A synthesis of bacterial and archaeal phenotypic trait data
Authors: Madin Joshua S. , Nielsen Daniel A. , Brbic Maria , Corkrey Ross , Danko David , Edwards Kyle , Engqvist Martin K. M. , Fierer Noah , Geoghegan Jemma L. , Gillings Michael , Kyrpides Nikos C. , Litchman Elena , Mason Christopher E. , Moore Lisa , Nielsen Søren L. , Paulsen Ian T. , Price Nathan D. , Reddy T. B. K. , Richards Matthew A. , Rocha Eduardo P. C. , Schmidt Thomas M. , Shaaban Heba , Shukla Maulik , Supek Fran , Tetu Sasha G. , Vieira-Silva Sara , Wattam Alice R. , Westfall David A. , Westoby Mark 
Published: June 2020

AbstractA synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients.
Multidimensional imaging of liver injury repair in mice reveals fundamental role of the ductular reaction
Authors: Kamimoto Kenji , Nakano Yasuhiro , Kaneko Kota , Miyajima Atsushi , Itoh Tohru 
Published: June 2020

AbstractUpon severe and/or chronic liver injury, ectopic emergence and expansion of atypical biliary epithelial-like cells in the liver parenchyma, known as the ductular reaction, is typically induced and implicated in organ regeneration. Although this phenomenon has long been postulated to represent activation of facultative liver stem/progenitor cells that give rise to new hepatocytes, recent lineage-tracing analyses have challenged this notion, thereby leaving the pro-regenerative role of the ductular reaction enigmatic. Here, we show that the expanded and remodelled intrahepatic biliary epithelia in the ductular reaction constituted functional and complementary bile-excreting conduit systems in injured parenchyma where hepatocyte bile canalicular networks were lost. The canalicular collapse was an incipient defect commonly associated with hepatocyte injury irrespective of cholestatic statuses, and could sufficiently provoke the ductular reaction when artificially induced. We propose a unifying model for the induction of the ductular reaction, where compensatory biliary epithelial tissue remodeling ensures bile-excreting network homeostasis.
Laser ablation-ICP-TOFMS imaging of germ cell tumors of patients undergoing platinum-based chemotherapy
Authors: Theiner Sarah , Schweikert Andreas , Haberler Christine , Peyrl Andreas , Koellensperger Gunda 
Published: June 2020

Abstract
A low dispersion laser ablation setup in combination with inductively coupled plasma-time-of-flight mass spectrometry (LA-ICP-TOFMS) was applied to clinical samples of patients undergoing platinum-based chemotherapy. The platinum accumulation together with the distribution of elements with biological key functions (Mg, P, S, Ca, Fe, Cu and Zn) was studied in central nervous system germ cell tumor (CNS GCT) tissue, which is an aggressive tumor type located in the brain. Heterogeneous elemental distribution patterns were obtained with a pixel size of 10 μm and were correlated to histological analysis of serial sections using hematoxylin eosin staining. Highest platinum accumulation correlated with areas of necrosis, which exhibited high levels of magnesium, sulphur and calcium. Small traces of gadolinium were found in the tumor sections, which is a result of prior magnetic resonance imaging. Iron accumulated in regions, which were dense in blood vessels, whereas areas with fibrosis scar showed the lowest levels of all detected elements. This LA-ICP-TOFMS study demonstrates that the chemotherapeutic drug cisplatin accumulated in the germ cell tumor located in the brain, which is also reflected by the therapy response of the patients.
Calibrated non‐contact vibrational harmonics measurement based on self‐vibration compensated 2D‐PSD with MEMS accelerometer using FFT analysis
Authors: Das Sampa , Saha Ardhendu , Sujith Kumar Chanda 
Published: June 2020

This study presents a novel fast Fourier transform (FFT)‐based non‐contact vibrational harmonics measurement system using a position sensitive detector (PSD) along with calibration using a piezoelectric accelerometer. Frequency‐domain vibrational analysis is required as the changes in machine dynamics are directly related to its failures and could provide more insight into the vibration signal. In this regard, FFT is used for spectral analysis to detect the harmonics in the vibration signal. The novelty of the applied technique for detecting vibrational harmonics lies in its innate contactless nature where the vibration detection sensor i.e. PSD is placed at a particular distance from the vibrating target. Additionally, the parasitic and external vibrations, which might pose unforeseen errors in the detected vibration data, have been nullified by employing a self‐vibration technique using an ADXL‐345 three‐axis accelerometer. The results obtained through PSD have been calibrated via a standard Brüel & Kjaer (B & K) vibration measurement system which uses a piezoelectric accelerometer (B & K accelerometer). The proposed measurement technique is equipped with NI compact RIO‐9074 that features a real‐time processor and an FPGA. The system was observed to effectively measure the frequency range 5–600 Hz with a maximum relative error of 2% in FFT amplitudes.