bluuebunny/crossref_metadata_2025_split huggingface dataset:
A nucleotide resolution map of Top2-linked DNA breaks in the yeast and human genome
Authors: Gittens William H. , Johnson Dominic J. , Allison Rachal M. , Cooper Tim J. , Thomas Holly , Neale Matthew J. 
Published: October 2019

AbstractDNA topoisomerases are required to resolve DNA topological stress. Despite this essential role, abortive topoisomerase activity generates aberrant protein-linked DNA breaks, jeopardising genome stability. Here, to understand the genomic distribution and mechanisms underpinning topoisomerase-induced DNA breaks, we map Top2 DNA cleavage with strand-specific nucleotide resolution across the S. cerevisiae and human genomes—and use the meiotic Spo11 protein to validate the broad applicability of this method to explore the role of diverse topoisomerase family members. Our data characterises Mre11-dependent repair in yeast and defines two strikingly different fractions of Top2 activity in humans: tightly localised CTCF-proximal, and broadly distributed transcription-proximal, the latter correlated with gene length and expression. Moreover, single nucleotide accuracy reveals the influence primary DNA sequence has upon Top2 cleavage—distinguishing sites likely to form canonical DNA double-strand breaks (DSBs) from those predisposed to form strand-biased DNA single-strand breaks (SSBs) induced by etoposide (VP16) in vivo.
Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program
Authors: Wyler Emanuel , Franke Vedran , Menegatti Jennifer , Kocks Christine , Boltengagen Anastasiya , Praktiknjo Samantha , Walch-Rückheim Barbara , Bosse Jens , Rajewsky Nikolaus , Grässer Friedrich , Akalin Altuna , Landthaler Markus 
Published: October 2019

AbstractHerpesvirus infection initiates a range of perturbations in the host cell, which remain poorly understood at the level of individual cells. Here, we quantify the transcriptome of single human primary fibroblasts during the first hours of lytic infection with HSV-1. By applying a generalizable analysis scheme, we define a precise temporal order of early viral gene expression and propose a set-wise emergence of viral genes. We identify host cell genes and pathways relevant for infection by combining three different computational approaches: gene and pathway overdispersion analysis, prediction of cell-state transition probabilities, as well as future cell states. One transcriptional program, which correlates with increased resistance to infection, implicates the transcription factor NRF2. Consequently, Bardoxolone methyl and Sulforaphane, two known NRF2 agonists, impair virus production, suggesting that NRF2 activation restricts viral infection. Our study provides insights into early stages of HSV-1 infection and serves as a general blueprint for the investigation of heterogeneous cell states in virus infection.
Tau deposition is associated with functional isolation of the hippocampus in aging
Authors: Harrison Theresa M. , Maass Anne , Adams Jenna N. , Du Richard , Baker Suzanne L. , Jagust William J. 
Published: October 2019

AbstractThe tau protein aggregates in aging and Alzheimer disease and may lead to memory loss through disruption of medial temporal lobe (MTL)-dependent memory systems. Here, we investigated tau-mediated mechanisms of hippocampal dysfunction that underlie the expression of episodic memory decline using fMRI measures of hippocampal local coherence (regional homogeneity; ReHo), distant functional connectivity and tau-PET. We show that age and tau pathology are related to higher hippocampal ReHo. Functional disconnection between the hippocampus and other components of the MTL memory system, particularly an anterior-temporal network specialized for object memory, is also associated with higher hippocampal ReHo and greater tau burden in anterior-temporal regions. These associations are not observed in the posteromedial network, specialized for context/spatial information. Higher hippocampal ReHo predicts worse memory performance. These findings suggest that tau pathology plays a role in disconnecting the hippocampus from specific MTL memory systems leading to increased local coherence and memory decline.
MT1-MMP directs force-producing proteolytic contacts that drive tumor cell invasion
Authors: Ferrari Robin , Martin Gaëlle , Tagit Oya , Guichard Alan , Cambi Alessandra , Voituriez Raphaël , Vassilopoulos Stéphane , Chavrier Philippe 
Published: October 2019

AbstractUnraveling the mechanisms that govern the formation and function of invadopodia is essential towards the prevention of cancer spread. Here, we characterize the ultrastructural organization, dynamics and mechanical properties of collagenotytic invadopodia forming at the interface between breast cancer cells and a physiologic fibrillary type I collagen matrix. Our study highlights an uncovered role for MT1-MMP in directing invadopodia assembly independent of its proteolytic activity. Electron microscopy analysis reveals a polymerized Arp2/3 actin network at the concave side of the curved invadopodia in association with the collagen fibers. Actin polymerization is shown to produce pushing forces that repel the confining matrix fibers, and requires MT1-MMP matrix-degradative activity to widen the matrix pores and generate the invasive pathway. A theoretical model is proposed whereby pushing forces result from actin assembly and frictional forces in the actin meshwork due to the curved geometry of the matrix fibers that counterbalance resisting forces by the collagen fibers.
Thermophysical properties of liquid Zr52.5Cu17.9Ni14.6Al10Ti5—prospects for bulk metallic glass manufacturing in space
Authors: Mohr M. , Wunderlich R. K. , Hofmann D. C. , Fecht H.-J. 
Published: October 2019

AbstractBulk metallic glasses are of critical interest for a wide range of applications, including their use in spacecraft gearboxes and mechanisms due to their excellent low-temperature, unlubricated wear resistance. Also of interest, is the potential for in-space manufacturing of metal alloys and the use of microgravity to determine fundamental thermophysical properties to inform ground-based modeling and experimentation. In this work, a Zr-based bulk metallic glass was processed in the electromagnetic levitator ISS-EML to determine undercooling, electrical resistivity, specific heat capacity, surface tension, and viscosity. A 6.5 mm sphere was vitrified during the processing, resulting in the first bulk metallic glass manufactured on board the international space station (ISS).
The effect of irradiation on the atomic structure and chemical durability of calcite and dolomite
Authors: Hsiao Yi-Hsuan , Wang Bu , La Plante Erika Callagon , Pignatelli Isabella , Krishnan N. M. Anoop , Le Pape Yann , Neithalath Narayanan , Bauchy Mathieu , Sant Gaurav 
Published: October 2019

AbstractWhen exposed to irradiation—e.g., in nuclear power plant environments—minerals may experience alterations in their atomic structure which, in turn, result in changes in their physical and chemical properties. Herein, we mimic via Ar+ implantation the effects of neutron irradiation on calcite (CaCO3) and dolomite (CaMg(CO3)2) – two carbonate minerals that often find use as aggregates in concrete: a material that is extensively used in the construction of critical structural and safety components in nuclear power plants. By a pioneering combination of nanoscale quantifications of mineral dissolution rates (i.e., a proxy for chemical durability) in alkaline solutions, vibrational (infrared and Raman) spectroscopy, and molecular simulations, we find that irradiation minimally affects the atomic structure and properties of these carbonate minerals. This insensitivity to radiation arises from the predominantly ionic nature of the interatomic bonds in these minerals which can relax and recover their initial configuration, thus ensuring minimal damage and permanent alterations to these minerals following radiation exposure. The outcomes have significant implications on the selection, use, and specification of mineral aggregates for use in nuclear concrete construction.
Accelerated low water corrosion: the microbial sulfur cycle in microcosm
Authors: Smith Martin , Bardiau Marjorie , Brennan Richard , Burgess Heidi , Caplin Jonathan , Ray Santanu , Urios Thomas 
Published: October 2019

AbstractAccelerated low water corrosion is a form of marine steel corrosion caused by bacterial activity. It has a global spread and is potentially responsible for billions of pounds of damage. We have determined in detail both the chemistry of corrosion products and the associated microbiology at a UK site. The corrosion products form a layered structure with iron sulfides at the steel surface and iron oxides and sulfates in contact with water. The iron sulfides are formed by reaction of steel with hydrogen sulfide formed by sulfate-reducing bacteria and are oxidised through a series of sulfur oxidation states by sulfide-oxidising bacteria, forming acid at all stages and encompassing the whole of the bacterial sulfur cycle. The bacteria involved are endemic in anoxic bed sediment, and the process is a response to the presence of steel as an electron donor, and the generation of anoxic microenvironments within corrosion products.
Global humid tropics forest structural condition and forest structural integrity maps
Authors: Hansen Andrew , Barnett Kevin , Jantz Patrick , Phillips Linda , Goetz Scott J. , Hansen Matt , Venter Oscar , Watson James E. M. , Burns Patrick , Atkinson Scott , Rodríguez-Buritica Susana , Ervin Jamison , Virnig Anne , Supples Christina , De Camargo Rafael 
Published: October 2019

AbstractRemotely sensed maps of global forest extent are widely used for conservation assessment and planning. Yet, there is increasing recognition that these efforts must now include elements of forest quality for biodiversity and ecosystem services. Such data are not yet available globally. Here we introduce two data products, the Forest Structural Condition Index (SCI) and the Forest Structural Integrity Index (FSII), to meet this need for the humid tropics. The SCI integrates canopy height, tree cover, and time since disturbance to distinguish short, open-canopy, or recently deforested stands from tall, closed-canopy, older stands typical of primary forest. The SCI was validated against estimates of foliage height diversity derived from airborne lidar. The FSII overlays a global index of human pressure on SCI to identify structurally complex forests with low human pressure, likely the most valuable for maintaining biodiversity and ecosystem services. These products represent an important step in maturation from conservation focus on forest extent to forest stands that should be considered “best of the last” in international policy settings.
Q Fever Endocarditis in Iran
Authors: Moradnejad Pardis , Esmaeili Saber , Maleki Majid , Sadeghpour Anita , Kamali Monireh , Rohani Mahdi , Ghasemi Ahmad , Bagheri Amiri Fahimeh , Pasha Hamid Reza , Boudagh Shabnam , Bakhshandeh Hooman , Naderi Nasim , Ghadrdoost Behshid , Lotfian Sara , Dehghan Manshadi Seyed Ali , Mostafavi Ehsan 
Published: October 2019

AbstractPatients with the underlying valvular heart disease are at the high risk of developing sub-acute or chronic endocarditis secondary to Coxiella burnetii. Q fever endocarditis is the most common manifestation along with persistent the infection. There is some serologic and molecular evidence of C. burnetii infection in humans and livestock in Iran. As it is possible to observe chronic Q fever in Iran, it seems necessary to study the prevalence of Q fever endocarditis in this country. In the present study, Infective Endocarditis (IE) patients (possible or definite based on Duke Criteria) hospitalized in Rajaie Cardiovascular Medical and Research Center were enrolled from August 2016 to September 2018. Culture-negative endocarditis patients were evaluated by Raoult criteria for diagnosis Q fever endocarditis. The serological results for brucellosis were negative for all subjects. All blood and tissue samples including valve samples were tested for C. burnetii infection using serology and Polymerase Chain Reaction (PCR). In this study, 126 patients who were admitted to the hospital were enrolled; of which 52 subjects were culture-negative IE. Among the participants, 16 patients (30.77%) were diagnosed with Q fever IE and underwent medical treatment. The mean age of patients was 46.6 years ranging from 23 to 69 years and 75% of them were male. Considering the high prevalence of Q fever IE, evaluation of the patients with culture-negative IE for C. burnetii infections was highly recommended.
Retrospective Analysis of 28 Cases of Tuberculosis in Pregnant Women in China
Authors: Li Qiang , Song Yanhua , Chen Hongmei , Xie Li , Gao Mengqiu , Ma Liping , Huang Yinxia 
Published: October 2019

AbstractWhile tuberculosis (TB) in pregnant women is reported globally, clinical data is unavailable in China. To describe clinical features and identify difficulties in the diagnosis of pregnancy-related TB, we performed a retrospective study of 28 TB inpatients at Beijing Chest Hospital. The results were presented in terms of interquartile range (IQR) for age, and medians and percentages with respect to the categorical variables. One patient (3.6%) was immediately diagnosed; for 27 patients (96.4%), the median interval from the initial onset of symptoms to diagnosis was five weeks. Eight cases (28.6%) were microbiologically confirmed. 22 (78.6%) were pulmonary TB (PTB), while six (21.4%) were extrapulmonary TB (EPTB). In addition, eight (28.6%) were miliary TB and six (21.4%) were cerebral TB. 27 (96.4%) were cured and one (3.6%) died. 15 neonates were identified, nine of which were healthy. Two were small for the gestational age (SGA) and one was a stillbirth. Three had neonatal TB, one of which died. Nine were legal abortions and four were spontaneous abortions. Indeed, there was a substantial delay in the diagnosis of TB in the pregnant women and a high incidence of both miliary and cerebral TB was evident. With timely treatment, prognosis is positive.
Synthetic hydrophobic peptides derived from MgtR weaken Salmonella pathogenicity and work with a different mode of action than endogenously produced peptides
Authors: Olvera Mariana Rosas , Garai Preeti , Mongin Grégoire , Vivès Eric , Gannoun-Zaki Laila , Blanc-Potard Anne-Béatrice 
Published: October 2019

AbstractDue to the antibiotic resistance crisis, novel therapeutic strategies need to be developed against bacterial pathogens. Hydrophobic bacterial peptides (small proteins under 50 amino acids) have emerged as regulatory molecules that can interact with bacterial membrane proteins to modulate their activity and/or stability. Among them, the Salmonella MgtR peptide promotes the degradation of MgtC, a virulence factor involved in Salmonella intramacrophage replication, thus providing the basis for an antivirulence strategy. We demonstrate here that endogenous overproduction of MgtR reduced Salmonella replication inside macrophages and lowered MgtC protein level, whereas a peptide variant of MgtR (MgtR-S17I), which does not interact with MgtC, had no effect. We then used synthetic peptides to evaluate their action upon exogenous addition. Unexpectedly, upon addition of synthetic peptides, both MgtR and its variant MgtR-S17I reduced Salmonella intramacrophage replication and lowered MgtC and MgtB protein levels, suggesting a different mechanism of action of exogenously added peptides versus endogenously produced peptides. The synthetic peptides did not act by reducing bacterial viability. We next tested their effect on various recombinant proteins produced in Escherichia coli and showed that the level of several inner membrane proteins was strongly reduced upon addition of both peptides, whereas cytoplasmic or outer membrane proteins remained unaffected. Moreover, the α-helical structure of synthetic MgtR is important for its biological activity, whereas helix-helix interacting motif is dispensable. Cumulatively, these results provide perspectives for new antivirulence strategies with the use of peptides that act by reducing the level of inner membrane proteins, including virulence factors.
Far-UV photoluminescence microscope for impurity domain in hexagonal-boron-nitride single crystals by high-pressure, high-temperature synthesis
Authors: Watanabe Kenji , Taniguchi Takashi 
Published: October 2019

AbstractHexagonal-boron-nitride single crystals grown by high-pressure, high-temperature (HPHT) synthesis are commonly used as the insulated substrate dielectric for two-dimensional (2D) atomic-layered materials like graphene and transition metal dichalcogenides (TMDs) to improve the flatness of the 2D materials atomically without disturbing the 2D electronic characteristics. However, HPHT single crystals often contain impure regions, which can hold subtle clues in regard to the 2D atomic-layered materials for new discoveries in the physics of 2D materials. To identify the position of the impure domains and to avoid them when the 2D devices are prepared, a far-ultraviolet photoluminescence microscope was developed. This microscope makes it possible to visualize the impure-growth region with ease in a no-contact and non-destructive manner.
Dynamic covalent chemistry steers synchronizing nanoparticle self-assembly with interfacial polymerization
Authors: Zhang Fenghua , Yang Zhijie , Hao Jinjie , Zhao Kaixuan , Hua Mingming , Yang Yanzhao , Wei Jingjing 
Published: October 2019

AbstractPrecise organization of matter across multiple length scales is of particular interest because of its great potential with advanced functions and properties. Here we demonstrate a simple yet versatile strategy that enables the organization of hydrophobic nanoparticles within the covalent organic framework (COF) in an emulsion droplet. The interfacial polymerization takes place upon the addition of Lewis acid in the aqueous phase, which allows the formation of COF after a crystallization process. Meanwhile, the interaction between nanoparticles and COF is realized by the use of amine-aldehyde reactions in the nearest loci of the nanoparticles. Importantly, the competition between the nanoparticle self-assembly and interfacial polymerization allows control over the spatial distribution of nanoparticles within COF. As a general strategy, a wide variety of COF-wrapped nanoparticle assemblies can be synthesized and these hybridized nanomaterials could find applications in optoelectronics, heterogeneous catalysis and energy chemistry.
Efficiently reconstructing compound objects by quantum imaging with higher-order correlation functions
Authors: Mikhalychev A. B. , Bessire B. , Karuseichyk I. L. , Sakovich A. A. , Unternährer M. , Lyakhov D. A. , Michels D. L. , Stefanov A. , Mogilevtsev D. 
Published: October 2019

AbstractQuantum imaging has a potential of enhancing the precision of objects reconstruction by exploiting quantum correlations of the imaging field, in particular for imaging with low-intensity fields up to the level of a few photons. However, it generally leads to nonlinear estimation problems. The complexity of these problems rapidly increases with the number of parameters describing the object and the correlation order. Here we propose a way to drastically reduce the complexity for a wide class of problems. The key point of our approach is to connect the features of the Fisher information with the parametric locality of the problem, and to reconstruct the whole set of parameters stepwise by an efficient iterative inference scheme that is linear on the total number of parameters. This general inference procedure is experimentally applied to quantum near-field imaging with higher-order correlated light sources, resulting in super-resolving reconstruction of grey compound transmission objects.
180 Gbit/s 4:1 power multiplexer for NRZ‐OOK signals with high output voltage swing in SiGe BiCMOS technology
Authors: Uhl C. , Hettrich H. , Möller M. 
Published: October 2019

A 4:1 multiplexer (MUX) circuit in SiGe BiCMOS technology intended to directly drive a plasmonic Mach–Zehnder modulator for transmitter applications is presented. To achieve the highest data rates at a high output voltage swing, a power MUX concept is applied that maps the high‐speed performance of the final clock signal onto the output data. In the clock tree a novel wideband clock phase shifter circuit is utilised for timing adjustment and frequency doubling. Electrical measurements of the chip demonstrate open eye diagrams for non‐return‐to‐zero on‐off‐keying (NRZ‐OOK) signals up to 180 Gbit/s, which is record speed for Si‐based technologies. A differential output voltage swing of was measured that corresponds to an output voltage swing of more than without the bandwidth limit of the measurement equipment.
Energy calibration and performance testing of LEGe detector
Authors: Hou Dongjie , Wu Chong , Li Chengze , Guo Siming , Wu Jinjie 
Published: October 2019

The low energy germanium detector (LEGe) is in all aspects optimised for performance at low and moderate energies. It has specific advantages over conventional planar or coaxial detectors. LEGe is a kind of semiconductor detector commonly used in X‐ray detection. It can display the spectrum of X‐ray and record photon counts. Photon fluence is used to describe the radiation field by recording the number of incident photons. In order to take full advantage of the low energy response of this intrinsically thin window detector, LEGe cryostats are usually equipped with a beryllium window, thin front and side contact allowing spectroscopy from 3 keV and above. The rear contact is of less than full area which gives a lower detector capacitance compared to a planar device of similar size. It is widely used in low energy gamma spectroscopy, X‐ray absorption spectroscopy, nuclear safeguards or X‐ray fluorescence spectrometer and X‐ray diffraction. Spectrum is an intuitional and accurate description of X‐ray radiation. In this work, experiment was carried out to calibrate the detector and test the spectrum, and then to calculate the energy resolution. The experiment results about energy resolution (full width at half maximum) are 222 eV (@5.9 keV) and 519 eV (@122 keV).
Der erste Eindruck zählt!
Authors: Friedrich Anja 
Published: October 2019

ZusammenfassungDer erste Arbeitstag ist entscheidend, um neues Personal erfolgreich zu integrieren und somit langfristig an die Klinik zu binden. Denn 80 % der Mitarbeiter, die in der Probezeit kündigen, fassen diesen Entschluss bereits am ersten Tag. 1 Damit der Start in den neuen Job glückt, haben wir die wichtigsten Onboarding-Maßnahmen für Sie zusammengestellt.
Da Vinci-assistierte Prostatektomie
Authors: Weber Sarah-Kathrin 
Published: October 2019

ZusammenfassungAls kurative Therapie bei einem Prostatakarzinom ist die radikale Prostatektomie oftmals das Mittel der Wahl. Sie bietet nachweislich einen Überlebensvorteil 1. Durch das da Vinci®-Operationssystem konnte die Operationstechnik zum Wohle der Patienten präzisiert werden.
ATA im OP
Authors: Scheumann Jeannine 
Published: October 2019

ZusammenfassungIn unserer Serie „Berufsbilder“ haben wir die 27-jährige Anästhesietechnische Assistentin (ATA) Jenny Wlecke von der Medizinischen Hochschule Hannover unter anderem gefragt, welche Aufgaben sie im OP erledigt, wie die Arbeitsbedingungen sind und wie sie die finanziellen und beruflichen Perspektiven der ATA einschätzt.