bluuebunny/crossref_metadata_2025 huggingface dataset:
Demand response measures and its quantitative effects in promoting renewable energy accommodation in high proportional renewable energy scenario
Authors: Li Xiaofei , Huang Yuehui , Yang Shuo
Published: November 2017

The rapid growth of renewable energy generation capacity, including wind power and photovoltaic power, brings greater challenges to its accommodation. Based on the renewable energy power output characteristics, this study analyses the calculation method and optimisation model of renewable energy power accommodation ability, and explores two demand response (DR) measures, including transferable load and electric power alternative, and conducts quantitative analysis on their effects in renewable energy power accommodation. Based on the design scenario of the Northwest Power Grid in 2020, the demand‐side response measures were adopted to enhance the accommodation of renewable energy. The results show that the effectiveness of the model and the two DR measures can improve the ability of renewable energy accommodation. DR is an important direction in the accommodation of renewable energy based on the current load level.
Numerical modeling of the 1840s major eruption of η Carinae as an explosion
Authors: González Ricardo F.
Published: November 2017

In this paper, new two-dimensional hydrodynamical simulations of η Car’s nebulae are performed. In the 1840s, the massive star η Car suffered a major eruption that resulted in the formation of a bipolar structure, which is commonly known as the large Homunculus. During this event, η Car expelled into the circumstellar material a total mass of ~10 M⊙ and released a total energy of Ek ~ 1050 erg over a very short time (≤5 yr). These kinds of explosive events are frequently called supernova impostors due to their resemblance to a type II supernova, but the stars survive the explosion. In the case of η Car, a brief explosion scenario provides a potential explanation for the behavior of the historical light curve of η Car a few years (~10 yr) after the nineteenth century outburst. Here, such an alternative scenario of an explosion is assumed (instead of a super-Eddington wind) in order to investigate whether an explosive event is also able to explain the shape and kinematics of the large Homunculus. I show that the numerical simulations presented here indeed resemble some of the observed features of the nebula, such as the present-day double-shell structure of the Homunculus, with a thin outer dense shell and a thicker inner layer, as well as thermal instabilities (Rayleigh-Taylor and Kelvin-Helmholtz) along the dense shell that may lead to the current mottled appearance of the large Homunculus. Nonetheless, the explosion model for the 1840s major eruption of η Car is not able to account for the estimated age of the large Homunculus.
Combining low- to high-resolution transit spectroscopy of HD 189733b
Authors: Pino Lorenzo , Ehrenreich David , Wyttenbach Aurélien , Bourrier Vincent , Nascimbeni Valerio , Heng Kevin , Grimm Simon , Lovis Christophe , Malik Matej , Pepe Francesco , Piotto Giampaolo
Published: November 2017

Space-borne low- to medium-resolution (ℛ ~ 102–103) and ground-based high-resolution spectrographs (ℛ ~ 105) are commonly used to obtain optical and near infrared transmission spectra of exoplanetary atmospheres. In this wavelength range, space-borne observations detect the broadest spectral features (alkali doublets, molecular bands, scattering, etc.), while high-resolution, ground-based observations probe the sharpest features (cores of the alkali lines, molecular lines). The two techniques differ by several aspects. (1) The line spread function of ground-based observations is ~103 times narrower than for space-borne observations; (2) Space-borne transmission spectra probe up to the base of thermosphere (P ≳ 10−6 bar), while ground-based observations can reach lower pressures (down to ~10−11 bar) thanks to their high resolution; (3) Space-borne observations directly yield the transit depth of the planet, while ground-based observations can only measure differences in the apparent size of the planet at different wavelengths. These differences make it challenging to combine both techniques. Here, we develop a robust method to compare theoretical models with observations at different resolutions. We introduce πη, a line-by-line 1D radiative transfer code to compute theoretical transmission spectra over a broad wavelength range at very high resolution (ℛ ~ 106, or Δλ ~ 0.01 Å). An hybrid forward modeling/retrieval optimization scheme is devised to deal with the large computational resources required by modeling a broad wavelength range ~0.3–2 μm at high resolution. We apply our technique to HD 189733b. In this planet, HST observations reveal a flattened spectrum due to scattering by aerosols, while high-resolution ground-based HARPS observations reveal sharp features corresponding to the cores of sodium lines. We reconcile these apparent contrasting results by building models that reproduce simultaneously both data sets, from the troposphere to the thermosphere. We confirm: (1) the presence of scattering by tropospheric aerosols; (2) that the sodium core feature is of thermospheric origin. When we take into account the presence of aerosols, the large contrast of the core of the sodium lines measured by HARPS indicates a temperature of up to ~10 000K in the thermosphere, higher than what reported in the literature. We also show that the precise value of the thermospheric temperature is degenerate with the relative optical depth of sodium, controlled by its abundance, and of the aerosol deck.
Broadband study of blazar 1ES 1959+650 during flaring state in 2016
Authors: Patel S. R. , Shukla A. , Chitnis V. R. , Dorner D. , Mannheim K. , Acharya B. S. , Nagare B. J.
Published: November 2017

Aims. The nearby TeV blazar 1ES 1959+650 (z = 0.047) was reported to be in flaring state during June–July 2016 by Fermi-LAT, FACT, MAGIC and VERITAS collaborations. We studied the spectral energy distributions (SEDs) in different states of the flare during MJD 57530–57589 using simultaneous multiwaveband data with the aim of understanding the possible broadband emission scenario during the flare.

Methods. The UV-optical and X-ray data from UVOT and XRT respectively on board Swift and high energy γ-ray data from Fermi-LAT were used to generate multiwaveband lightcurves as well as to obtain high flux states and quiescent state SEDs. The correlation and lag between different energy bands was quantified using discrete correlation function. The synchrotron self-Compton (SSC) model was used to reproduce the observed SEDs during flaring and quiescent states of the source.

Results. A good correlation is seen between X-ray and high energy γ-ray fluxes. The spectral hardening with increase in the flux is seen in X-ray band. The power law index vs. flux plot in γ-ray band indicates the different emission regions for 0.1–3 GeV and 3–300 GeV energy photons. Two zone SSC model satisfactorily fits the observed broadband SEDs. The inner zone is mainly responsible for producing synchrotron peak and high energy γ-ray part of the SED in all states. The second zone is mainly required to produce less variable optical-UV and low energy γ-ray emission.

Conclusions. Conventional single zone SSC model does not satisfactorily explain broadband emission during observation period considered. There is an indication of two emission zones in the jet which are responsible for producing broadband emission from optical to high energy γ-rays.
GALACTICNUCLEUS: A high angular resolutionJHKsimaging survey of the Galactic centre
Authors: Nogueras-Lara F. , Gallego-Calvente A. T. , Dong H. , Gallego-Cano E. , Girard J. H. V. , Hilker M. , de Zeeuw P. T. , Feldmeier-Krause A. , Nishiyama S. , Najarro F. , Neumayer N. , Schödel R.
Published: November 2017

Context.The Galactic centre (GC) is of fundamental astrophysical interest, but existing near-infrared surveys fall short covering it adequately, either in terms of angular resolution, multi-wavelength coverage, or both. Here we introduce the GALACTICNUCLEUS survey, aJHKsimaging survey of the centre of the Milky Way with a 0.2″ angular resolution.Aims.The purpose of this paper is to present the observations of Field 1 of our survey, centred approximately on SgrA* with an approximate size of 7.95′ × 3.43′. We describe the observational set-up and data reduction pipeline and discuss the quality of the data. Finally, we present the analysis of the data.

Methods.The data were acquired with the near-infrared camera High Acuity Wide field K-band Imager (HAWK-I) at the ESO Very Large Telescope (VLT). Short readout times in combination with the speckle holography algorithm allowed us to produce final images with a stable, Gaussian PSF (point spread function) of 0.2″ FWHM (full width at half maximum). Astrometric calibration is achieved via the VISTA Variables in the Via Lactea (VVV) survey and photometric calibration is based on the SIRIUS/Infrared Survey Facility telescope (IRSF) survey. The quality of the data is assessed by comparison between observations of the same field with different detectors of HAWK-I and at different times.

Results.We reach 5σdetection limits of approximatelyJ= 22,H= 21, andKs= 20. The photometric uncertainties are less than 0.05 atJ≲ 20,H≲ 17, andKs≲ 16. We can distinguish five stellar populations in the colour-magnitude diagrams; three of them appear to belong to foreground spiral arms, and the other two correspond to high- and low-extinction star groups at the GC. We use our data to analyse the near-infrared extinction curve and find some evidence for a possible difference between the extinction index betweenJ−HandH−Ks. However, we conclude that it can be described very well by a power law with an index ofαJHKs= 2.30 ± 0.08. We do not find any evidence that this index depends on the position along the line of sight, or on the absolute value of the extinction. We produce extinction maps that show the clumpiness of the ISM (interstellar medium) at the GC. Finally, we estimate that the majority of the stars have solar or super-solar metallicity by comparing our extinction-corrected colour-magnitude diagrams with isochrones with different metallicities and a synthetic stellar model with a constant star formation.
Aluminum(III) Chloride Promoted Oxygen Transfer: Selective
Oxidation of Sulfides to Sulfoxides
Authors: Li Zhengming , Xie Yongtao , Li Yuxin , Zhou Sha , Zhou Shaa , Zhang Yan , Chen Minggui
Published: November 2017

An efficient selective oxidation of sulfides to sulfoxides has been developed by means of AlCl3-promoted oxygen transfer from phenyliodine diacetate [PhI(OAc)2]. AlCl3 proved to be the optimal ­Lewis acid for the activation of PhI(OAc)2. Various substituted sulfides were selectively transformed into the corresponding sulfoxides in good to excellent yields (≤99%). The high efficiency, excellent functional-group compatibility, broad substrate scope, and mild conditions render the current transformation useful for the synthesis of sulfoxides.
Local and Lower Limb Complications during and after Femoral Cannulation for Extracorporeal Life Support
Authors: Kreibich Maximilian , Benk Christoph , Leitner Sophie , Beyersdorf Friedhelm , Morlock Julia , Scherer Christian , Rylski Bartosz , Trummer Georg
Published: November 2017

Objective The extracorporeal life support system (ECLS) system is a lifesaving option for patients in pulmonary and/or cardiac failure. We reviewed our data on local complications in the leg and groin during and after ECLS explantation.

Methods Patients were included when an ECLS was cannulated in the groin and the ECLS was successfully weaned and explanted. Data were collected retrospectively in patients from January 2013 to January 2016.

Results In this study, 90 patients were included; 39 (43%) ECLS were implanted with surgical cut down and 51 (57%) ECLS were implanted percutaneously. Most patients needed ECLS support following cardiac surgery: cut down: 25 (64%) versus percutaneous: 28 (55%) (p = 0.40). A distal leg perfusion cannula was implanted simultaneously in 61 (68%) patients (cut down: 25 [64%] vs. percutaneous: 36 [71%], p = 0.36). Distal leg ischemia was diagnosed in a total of 10 (11%) patients (cut down: 2 [5%] vs. percutaneous: 8 [16%], p = 0.18). Of those 10 patients, 5 patients had leg ischemia despite a distal leg perfusion cannula in place (cut down: 1 [3%] vs. percutaneous: 4 [8%], p = 0.38). Revascularization was successfully achieved in all patients and no amputations had to be performed. Similar rates of wound healing disorders were observed in both groups: cut down: 11 (28%) versus percutaneous: 10 (20%) patients (p = 0.45).

Conclusion Surgical and percutaneous implantation and explantation of ECLS are safe and feasible with comparable complication rates, including wound healing disorders. We recommend that a lower limb perfusion cannula should be placed to prevent leg ischemia. Surgical cut-down placement of the distal leg perfusion cannula may reduce the incidence of distal leg ischemia compared with percutaneous distal leg cannula implantation. Correct placement of the cannula should be controlled.
Complications of Implanted Nonbiologic Devices—An Overview
Authors: Kwaan Hau
Published: November 2017

Under physiologic conditions, blood is contained within the vascular space lined with smooth endothelial cells. When various devices made of nonbiologic material are implanted, blood will be exposed to a foreign surface. A series of events ensue and may lead to many complications, including thrombosis, hemolysis, thrombocytopenia, bleeding, infection, and malfunction of the device. The incidence, manifestations, and special characteristics of these complications vary with different types of implanted devices. However, they have in common an important pathogenic pathway that of an exposure to a foreign surface. Despite the development of improved versions of these devices, more research on the causative factors of these complications is needed to take preventive and corrective measures, particularly those that enhance the process of healing by re-endothelialization of the foreign surface. This article is a brief review of the complications encountered in blood-contacting devices.
Nuklearmedizinische Verfahren zur Diagnostik der Spondylodiszitis
Authors: Davis K. , Happel C. , Heller M. , Vogl T. , Rauschmann M. , Grünwald F.
Published: November 2017

Es existieren zahlreiche nuklearmedizinische Verfahren zur Detektion einer Spondylodiszitis (SP), welche sich in ihrer diagnostischen Wertigkeit teils deutlich unterscheiden. Während sich die Leukozyten- beziehungsweise Antikörperszintigrafie aufgrund mangelnder Sensitivität und Spezifität nicht bewährt hat, zeigt die Skelettszintigrafie gute Ergebnisse und kommt insbesondere bei Kontraindikationen zur MRT zum Einsatz. Die 18F-FDG-PET hat sich inzwischen als führende Diagnostik der SP in der nuklearmedizinischen Bildgebung durchgesetzt. Insbesondere im Vergleich zur MRT, welche bis dato den Gold-Standard der morphologisch-diagnostischen Bildgebung der SP darstellt, liefert die 18F-FDG-PET deutliche Vorteile. So zeigt sich die 18F-FDG-PET bezüglich der Differenzierung zwischen degenerativen und entzündlichen Veränderungen, der frühen Detektion der Erkrankung sowie der Evaluation des Therapieansprechens überlegen. Insgesamt liefert die Kombination aus 18F-FDG-PET und MRT eine nahezu 100 %ig korrekte Detektion infektiöser SP.
Die konservative und operative Therapie der unspezifischen Spondylodiszitis
Authors: Bogert Jochen , Tateen Aimen , Hempfing Axel
Published: November 2017

Die pyogene Spondylodiszitis entsteht meist endogen durch eine Bakteriämie, aber auch exogene Ursachen wie etwa wirbelsäulennahe Infiltrationen können sie hervorrufen. Es besteht eine zunehmende Inzidenz der Erkrankung, die noch immer mit einer signifikanten Mortalität der in vielen Fällen immunsupprimierten und hochbetagten Patienten einhergeht. Eine frühzeitige Diagnosestellung durch Bildgebung und Erregerisolierung ist entscheidend für ein gutes Behandlungsergebnis. Die überwiegende Zahl der Patienten kann konservativ behandelt werden, wichtig sind ein frühzeitiger Beginn der antibiotischen Therapie sowie eine adäquate Ruhigstellung. Operative Therapieziele sind neben der Dekompression und Infektsanierung die Stabilisation und Deformitätenkorrektur. Es kommen rein dorsale offene Verfahren, ggf. mit Ausräumung der Bandscheibe und TLIF, sowie minimalinvasive Stabilisierungen zur Anwendung. Bei ausgeprägten ventralen Destruktionen, Fehlstellungen und Abszedierungen muss durch einen separaten ventralen Zugang debridiert und stabilisiert werden. In der überwiegenden Zahl der Fälle können gute Behandlungsergebnisse erreicht werden, in Einzelfällen bestehen jedoch große therapeutische Herausforderungen. Individuelle Therapieentscheidungen sind notwendig, da einerseits die Literatur keine eindeutigen Behandlungsleitlinien vorgibt und es sich andererseits um teils hochbetagte und multimorbide Patienten handelt.
Prostatakarzinom imitiert metastasiertes Bronchialkarzinom – Ein Fallbericht
Authors: Drosos Konstantinos , Höfner Klaus
Published: November 2017

Es wird über den Fall eines PSA-negativen und lokal fortgeschrittenen azinären Prostatakarzinoms berichtet, das bei thyroid transcription factor-1 (TTF-1) Expression eine Metastase eines bereits behandelten Bronchialkarzinoms imitierte. Unseres Wissens ist ein TTF-1 positiv azinäres Prostatakarzinom bisher nur ein Mal in der Literatur dokumentiert. Die Bestimmung des Immunophänotyps des Karzinoms mit Napsin A, CK7 und CK20 in Kombination mit der Beurteilung des gesamten Krankheitsverhaltens waren für die definitive Diagnose eines primären Prostatakarzinoms entscheidend.
Die konservative und operative Therapie bei kindlichen Spondylodiszitiden und der spezifischen Spondylitis
Authors: Ruf Michael , Drumm Jörg , Berthold Christophe , Gregor Ostrowski , Pitzen Tobias
Published: November 2017

In diesem Artikel werden die Besonderheiten der konservativen und operativen Therapie bei der kindlichen Spondylodiszitis und der spezifischen, tuberkulösen Spondylitis besprochen. Beides sind seltene Erkrankungen, bei beiden gibt es sinnvolle konservative Therapieansätze und bei beiden stellen Deformitäten im weiteren Verlauf häufige und ernsthafte Komplikationen dar.
Schädel-Hirn-Trauma
Authors: Clauberg Ralf , Hattingen Elke
Published: November 2017

Ein Schädel-Hirn-Trauma ist im jungen und mittleren Alter in erster Linie Folge eines Unfalls mit Auto, Motorrad, Fahrrad oder anderen Transportmitteln. Bei älteren Menschen ist dagegen häufiger ein Sturz die Ursache. Im folgenden Beitrag werden das diagnostische Vorgehen und typische Verletzungen im Rahmen eines Schädel-Hirn-Traumas dargestellt.
Public Health: Gesundheit für alle
Authors: Wildner Manfred , Kurth Bärbel-Maria , Wieler Lothar
Published: November 2017

Public Health – mit diesem Begriff verbinden sich Hoffnungen auf Gesundheit für alle, auf Vernunft und Evidenz-gestützte Rationalität im Gesundheitswesen, auf eine Landes- und Sprachgrenzen überwindende, internationale bzw. globale Anstrengung im Dienst an der Gesundheit und dem Wohlergehen der Menschen (siehe z. B. auch das Ziel 3 für nachhaltige Entwicklung der Vereinten Nationen). Die Suche nach einer allgemein anerkannten deutschen Bezeichnung für Public Health ist bisher noch offen. Dabei steht nach Ansicht von William Henry Welch und Wickliff Rose, Autoren des einflussreichen Welch-Rose-Reports von 1915, die Wiege moderner Public Health auch in Deutschland 1. Ihr Bericht führte zur Gründung der traditionsreichen Johns Hopkins Bloomberg School of Public Health in Baltimore (USA). Welch und Rose bezogen sich dabei auf das Pettenkofersche Hygiene-Institut in München, damals weltweit einzigartig. Bezeichnenderweise wird im Welch-Rose-Report auf die „doppelte“ Natur einer in den Naturwissenschaften verankerten, hygienebasierten Public-Health-Bewegung in Deutschland und einer sozialwissenschaftlich-verwaltungspraktisch ausgerichteten, in ihrem Gebiet ebenfalls führenden, Public-Health-Kultur in Großbritannien hingewiesen. Die naheliegende Chance für die Zukunft wurde damals in einer Verbindung beider Ansätze gesehen.
The economic impact of using single-operator cholangioscopy for the treatment of difficult bile duct stones and diagnosis of indeterminate bile duct strictures
Authors: Deprez Pierre , Garces Duran Rodrigo , Moreels Tom , Furneri Gianluca , Demma Federica , Verbeke Len , Van der Merwe Schalk , Laleman Wim
Published: November 2017

Background and study aim Conventional endoscopic retrograde cholangiopancreatography (ERCP) combines endoscopy and radiography to diagnose and treat pathological conditions of the bile duct. The aim of the present analysis was to evaluate the clinical and economic impact of the use of single-operator intraductal cholangioscopy (IDC), which allows for direct visualization of the bile duct, as an alternative to ERCP for the treatment of difficult bile duct stones and the diagnosis of bile duct strictures.

Patients and methods The clinical and economic consequences of single-operator IDC use were evaluated using two decision-tree models, one for management of difficult-to-remove stones and one for stricture diagnosis. A hospital perspective was adopted. Data to populate the models were derived from two Belgian hospitals that specialize in endoscopic procedures of the bile duct. Overall, the examined population consisted of 62 patients with difficult stones and 49 patients with indeterminate strictures.

Results In the model for difficult stone management, the use of IDC determined a decrease in the number of procedures (– 27 % relative reduction) and costs (– €73 000; – 11 % relative reduction) when compared with ERCP. In the model for stricture diagnosis, the use of IDC determined a decrease in the number of procedures (– 31 % relative reduction) and costs (– €13 000; – 5 % relative variation) when compared with ERCP.

Conclusions The single-operator IDC system performed better than ERCP for the treatment of difficult bile duct stones and the diagnosis of bile duct strictures, and reduced the overall expenditure in hospitals in Belgium.
How to communicate effectively with policymakers: combine insights from psychology and policy studies
Authors: Cairney Paul , Kwiatkowski Richard
Published: November 2017

To communicate effectively in policymaking systems, actors need to understand how policymakers process evidence and the environment in which they operate. Therefore, we combine psychology and policy studies to produce a three-step strategy. First, do not bombard people with evidence. Human beings have too much information to process, and they use heuristics to filter information to make decisions quickly. Synthesise and frame evidence to help you tailor it to the ways in which policymakers demand and understand information. Second, find the right time to act. Timing matters during key individuals’ patterns of thinking and the alignment of conditions in political systems. Third, engage with real world policymaking rather than waiting for a ‘rational’ and orderly process to appear. To present evidence during mythical stages of a ‘policy cycle’ is misguided, and to ‘speak truth to power’ without establishing legitimacy and building trust may be counterproductive. Our overall message is pragmatic, not Machiavellian: effective communication requires the suppliers of evidence to see the world from the perspective of their audience and understand the policy process in which they engage.
Moral discourse in the Twitterverse
Authors: Sterling Joanna , Jost John T.
Published: November 2017

We analyzed Twitter language to explore hypotheses derived from moral foundations
theory, which suggests that liberals and conservatives prioritize different
values. In Study 1, we captured 11
million tweets from nearly 25,000 U.S. residents and observed that liberals
expressed fairness concerns more often than conservatives, whereas conservatives
were more likely to express concerns about group loyalty, authority, and purity.
Increasing political sophistication exacerbated ideological differences in
authority and group loyalty. At low levels of sophistication, liberals used more
harm language, but at high levels of sophistication conservatives referenced
harm more often. In Study 2, we
analyzed 59,000 tweets from 388 members of the U.S. Congress. Liberal
legislators used more fairness- and harm-related words, whereas conservative
legislators used more authority-related words. Unexpectedly, liberal legislators
used more language pertaining to group loyalty and purity. Follow-up analyses
suggest that liberals and conservatives in Congress use similar words to
emphasize different policy priorities.
Student perspectives on assessment for learning
Authors: DeLuca Christopher , Chapman-Chin Allison E. A. , LaPointe-McEwan Danielle , Klinger Don A.
Published: November 2017

Assessment for learning (AfL) has become a widespread approach across many educational systems. To date, AfL research has emphasized teachers’ knowledge, skills, and practices, with few studies examining students’ responses to an AfL pedagogical approach. The purpose of this research was to focus directly on students’ perspectives on their use and value of AfL approaches through a survey of 1079 K–12 students and portfolio‐based interviews with 12 purposefully selected students. Survey data were analyzed through descriptive and inferential statistics across grade levels. Interview data were analyzed using standard thematic coding processes. Students most frequently used and valued teacher feedback and success criteria to support their learning. Peer feedback was the least valued AfL approach for all students. Some significant differences between grade levels were noted. Our results suggest that using AfL approaches is a learned behaviour; students need to be explicitly taught about AfL concepts, terminology, and use over time. This study also highlights that AfL implementation requires sustained focus, research, and support in schools and classrooms for students to value and fully benefit from assessment‐based teaching.
Cpf1-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cpf1
Authors: Park Jeongbin , Bae Sangsu
Published: November 2017

Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5′-TTTN-3′ at the 5′ ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale. One can easily access the data using a straightforward web interface, and using the powerful collections feature one can easily design gRNAs for thousands of genes in short time.

Availability and implementation

Free access at http://www.rgenome.net/cpf1-database/.
3dRPC: a web server for 3D RNA–protein structure prediction
Authors: Huang Yangyu , Li Haotian , Xiao Yi
Published: November 2017

RNA–protein interactions occur in many biological processes. To understand the mechanism of these interactions one needs to know three-dimensional (3D) structures of RNA–protein complexes. 3dRPC is an algorithm for prediction of 3D RNA–protein complex structures and consists of a docking algorithm RPDOCK and a scoring function 3dRPC-Score. RPDOCK is used to sample possible complex conformations of an RNA and a protein by calculating the geometric and electrostatic complementarities and stacking interactions at the RNA–protein interface according to the features of atom packing of the interface. 3dRPC-Score is a knowledge-based potential that uses the conformations of nucleotide-amino-acid pairs as statistical variables and that is used to choose the near-native complex-conformations obtained from the docking method above. Recently, we built a web server for 3dRPC. The users can easily use 3dRPC without installing it locally. RNA and protein structures in PDB (Protein Data Bank) format are the only needed input files. It can also incorporate the information of interface residues or residue-pairs obtained from experiments or theoretical predictions to improve the prediction.

Availability and implementation

The address of 3dRPC web server is http://biophy.hust.edu.cn/3dRPC.
Identifying simultaneous rearrangements in cancer genomes
Authors: Oesper Layla , Dantas Simone , Raphael Benjamin J
Published: November 2017

Motivation

The traditional view of cancer evolution states that a cancer genome accumulates a sequential ordering of mutations over a long period of time. However, in recent years it has been suggested that a cancer genome may instead undergo a one-time catastrophic event, such as chromothripsis, where a large number of mutations instead occur simultaneously. A number of potential signatures of chromothripsis have been proposed. In this work, we provide a rigorous formulation and analysis of the ‘ability to walk the derivative chromosome’ signature originally proposed by Korbel and Campbell. In particular, we show that this signature, as originally envisioned, may not always be present in a chromothripsis genome and we provide a precise quantification of under what circumstances it would be present. We also propose a variation on this signature, the H/T alternating fraction, which allows us to overcome some of the limitations of the original signature.

Results

We apply our measure to both simulated data and a previously analyzed real cancer dataset and find that the H/T alternating fraction may provide useful signal for distinguishing genomes having acquired mutations simultaneously from those acquired in a sequential fashion.

Availability and implementation

An implementation of the H/T alternating fraction is available at https://bitbucket.org/oesperlab/ht-altfrac.

Supplementary information

Supplementary data are available at Bioinformatics online.
glactools: a command-line toolset for the management of genotype likelihoods and allele counts
Authors: Renaud Gabriel
Published: November 2017

Motivation

Research projects involving population genomics routinely need to store genotyping information, population allele counts, combine files from different samples, query the data and export it to various formats. This is often done using bespoke in-house scripts, which cannot be easily adapted to new projects and seldom constitute reproducible workflows.

Results

We introduce glactools, a set of command-line utilities that can import data from genotypes or population-wide allele counts into an intermediate representation, compute various operations on it and export the data to several file formats used by population genetics software. This intermediate format can take two forms, one to store per-individual genotype likelihoods and a second for allele counts from one or more individuals. glactools allows users to perform operations such as intersecting datasets, merging individuals into populations, creating subsets, perform queries (e.g. return sites where a given population does not share an allele with a second one) and compute summary statistics to answer biologically relevant questions.

Availability and implementation

glactools is freely available for use under the GPL. It requires a C ++ compiler and the htslib library. The source code and the instructions about how to download test data are available on the website (https://grenaud.github.io/glactools/).

Supplementary information

Supplementary data are available at Bioinformatics online.
Mapping-free variant calling using haplotype reconstruction from k-mer frequencies
Authors: Audano Peter A , Ravishankar Shashidhar , Vannberg Fredrik O
Published: November 2017

Motivation

The standard protocol for detecting variation in DNA is to map millions of short sequence reads to a known reference and find loci that differ. While this approach works well, it cannot be applied where the sample contains dense variants or is too distant from known references. De novo assembly or hybrid methods can recover genomic variation, but the cost of computation is often much higher. We developed a novel k-mer algorithm and software implementation, Kestrel, capable of characterizing densely packed SNPs and large indels without mapping, assembly or de Bruijn graphs.

Results

When applied to mosaic penicillin binding protein (PBP) genes in Streptococcus pneumoniae, we found near perfect concordance with assembled contigs at a fraction of the CPU time. Multilocus sequence typing (MLST) with this approach was able to bypass de novo assemblies. Kestrel has a very low false-positive rate when applied to the whole genome, and while Kestrel identified many variants missed by other methods, limitations of a purely k-mer based approach affect overall sensitivity.

Availability and implementation

Source code and documentation for a Java implementation of Kestrel can be found at https://github.com/paudano/kestrel. All test code for this publication is located at https://github.com/paudano/kescases.

Supplementary information

Supplementary data are available at Bioinformatics online.
Classifying next-generation sequencing data using a zero-inflated Poisson model
Authors: Zhou Yan , Wan Xiang , Zhang Baoxue , Tong Tiejun
Published: November 2017

Motivation

With the development of high-throughput techniques, RNA-sequencing (RNA-seq) is becoming increasingly popular as an alternative for gene expression analysis, such as RNAs profiling and classification. Identifying which type of diseases a new patient belongs to with RNA-seq data has been recognized as a vital problem in medical research. As RNA-seq data are discrete, statistical methods developed for classifying microarray data cannot be readily applied for RNA-seq data classification. Witten proposed a Poisson linear discriminant analysis (PLDA) to classify the RNA-seq data in 2011. Note, however, that the count datasets are frequently characterized by excess zeros in real RNA-seq or microRNA sequence data (i.e. when the sequence depth is not enough or small RNAs with the length of 18–30 nucleotides). Therefore, it is desired to develop a new model to analyze RNA-seq data with an excess of zeros.

Results

In this paper, we propose a Zero-Inflated Poisson Logistic Discriminant Analysis (ZIPLDA) for RNA-seq data with an excess of zeros. The new method assumes that the data are from a mixture of two distributions: one is a point mass at zero, and the other follows a Poisson distribution. We then consider a logistic relation between the probability of observing zeros and the mean of the genes and the sequencing depth in the model. Simulation studies show that the proposed method performs better than, or at least as well as, the existing methods in a wide range of settings. Two real datasets including a breast cancer RNA-seq dataset and a microRNA-seq dataset are also analyzed, and they coincide with the simulation results that our proposed method outperforms the existing competitors.

Availability and implementation

The software is available at http://www.math.hkbu.edu.hk/∼tongt.

Supplementary information

Supplementary data are available at Bioinformatics online.
ProphTools: general prioritization tools for heterogeneous biological networks
Authors: Navarro Carmen , Martínez Victor , Blanco Armando , Cano Carlos
Published: November 2017

Background

Networks have been proven effective representations for the analysis of biological data. As such, there exist multiple methods to extract knowledge from biological networks. However, these approaches usually limit their scope to a single biological entity type of interest or they lack the flexibility to analyze user-defined data.

Results

We developed ProphTools, a flexible open-source command-line tool that performs prioritization on a heterogeneous network. ProphTools prioritization combines a Flow Propagation algorithm similar to a Random Walk with Restarts and a weighted propagation method. A flexible model for the representation of a heterogeneous network allows the user to define a prioritization problem involving an arbitrary number of entity types and their interconnections. Furthermore, ProphTools provides functionality to perform cross-validation tests, allowing users to select the best network configuration for a given problem. ProphTools core prioritization methodology has already been proven effective in gene-disease prioritization and drug repositioning. Here we make ProphTools available to the scientific community as flexible, open-source software and perform a new proof-of-concept case study on long noncoding RNAs (lncRNAs) to disease prioritization.

Conclusions

ProphTools is robust prioritization software that provides the flexibility not present in other state-of-the-art network analysis approaches, enabling researchers to perform prioritization tasks on any user-defined heterogeneous network. Furthermore, the application to lncRNA-disease prioritization shows that ProphTools can reach the performance levels of ad hoc prioritization tools without losing its generality.
Long-read sequence assembly of the firefly Pyrocoelia pectoralis genome
Authors: Fu Xinhua , Li Jingjing , Tian Yu , Quan Weipeng , Zhang Shu , Liu Qian , Liang Fan , Zhu Xinlei , Zhang Liangsheng , Wang Depeng , Hu Jiang
Published: November 2017

Background

Fireflies are a family of insects within the beetle order Coleoptera, or winged beetles, and they are one of the most well-known and loved insect species because of their bioluminescence. However, the firefly is in danger of extinction because of the massive destruction of its living environment. In order to improve the understanding of fireflies and protect them effectively, we sequenced the whole genome of the terrestrial firefly Pyrocoelia pectoralis.

Findings

Here, we developed a highly reliable genome resource for the terrestrial firefly Pyrocoelia pectoralis (E. Oliv., 1883; Coleoptera: Lampyridae) using single molecule real time (SMRT) sequencing on the PacBio Sequel platform. In total, 57.8 Gb of long reads were generated and assembled into a 760.4-Mb genome, which is close to the estimated genome size and covered 98.7% complete and 0.7% partial insect Benchmarking Universal Single-Copy Orthologs. The k-mer analysis showed that this genome is highly heterozygous. However, our long-read assembly demonstrates continuousness with a contig N50 length of 3.04 Mb and the longest contig length of 13.69 Mb. Furthermore, 135 589 SSRs and 341 Mb of repeat sequences were detected. A total of 23 092 genes were predicted; 88.44% of genes were annotated with one or more related functions.

Conclusions

We assembled a high-quality firefly genome, which will not only provide insights into the conservation and biodiversity of fireflies, but also provide a wealth of information to study the mechanisms of their sexual communication, bio-luminescence, and evolution.
Diagnostic Importance of Hyphae on Heart Valve Tissue in Histoplasma Endocarditis and Treatment With Isavuconazole
Authors: Wiley Zanthia , Woodworth Michael H , Jacob Jesse T , Lockhart Shawn R , Rouphael Nadine G , Gullett Jonathan C , Guarner Jeannette , Workowski Kimberly
Published: November 2017

A patient who never resided in an endemic area for dimorphic fungi was diagnosed with Histoplasma capsulatum endocarditis. His diagnosis was suggested by yeast and hyphae on cardiac valve tissue pathology. Isavuconazole was an optimal therapeutic option due to renal dysfunction and anticoagulation with warfarin for mechanical valve replacement.
Transcriptomic Analysis of Arabidopsis Seedlings in Response to an Agrobacterium-Mediated Transformation Process
Authors: Duan Kaixuan , Willig Christopher J. , De Tar Joann R. , Spollen William G. , Zhang Zhanyuan J.
Published: November 2017

Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease. This pathogen is capable of transferring the T-DNA from its Ti plasmid to the host cell and, then, integrating it into the host genome. To date, this genetic transformation ability has been harnessed as the dominant technology to produce genetically modified plants for both basic research and crop biotechnological applications. However, little is known about the interaction between Agrobacterium tumefaciens and host plants, especially the host responses to Agrobacterium infection and its associated factors. We employed RNA-seq to follow the time course of gene expression in Arabidopsis seedlings infected with either an avirulent or a virulent Agrobacterium strain. Gene Ontology analysis indicated many biological processes were involved in the Agrobacterium-mediated transformation process, including hormone signaling, defense response, cellular biosynthesis, and nucleic acid metabolism. RNAseq and quantitative reverse transcription-polymerase chain reaction results indicated that expression of genes involved in host plant growth and development were repressed but those involved in defense response were induced by Agrobacterium tumefaciens. Further analysis of the responses of transgenic Arabidopsis lines constitutively expressing either the VirE2 or VirE3 protein suggested Vir proteins act to enhance plant defense responses in addition to their known roles facilitating T-DNA transformation.
Development of a Real-Time RT-PCR for the Universal Detection of LChV1 and Study of the Seasonal Fluctuation of the Viral Titer in Sweet Cherry Cultivars
Authors: Katsiani Asimina T. , Pappi Polyxeni , Olmos Antonio , Efthimiou Konstantinos E. , Maliogka Varvara I. , Katis Nikolaos I.
Published: November 2017

Little cherry virus 1 (LChV1) is a sweet cherry pathogen which has lately been reported in other Prunus spp. LChV1 variability makes reliable detection a challenging undertaking. The objective of this work was to develop a rapid, sensitive, and reliable one-tube, real-time reverse-transcription polymerase chain reaction (RT-PCR) for the detection and quantification of LChV1. Primers and a TaqMan probe were designed, using conserved regions of the capsid protein gene. Detection range was evaluated using several divergent viral isolates. The amplification efficiency of the method was estimated at 96.7%, whereas the detection limit was about 100 RNA copies. The protocol was applied in the study of virus fluctuation within leaves and phloem tissue throughout the year and the best periods to test and plant tissues to sample were determined. Comparative analysis of this method with a previously published nested RT-PCR revealed the higher analytical and diagnostic sensitivity of the new test, making it a reliable tool that can be used in routine testing and certification programs.
A new standard for crustacean genomes: the highly contiguous, annotated genome assembly of the clam shrimp Eulimnadia texana reveals HOX gene order and identifies the sex chromosome
Authors: Baldwin-Brown James G. , Weeks Stephen C. , Long Anthony D.
Published: November 2017

Vernal pool clam shrimp (Eulimnadia texana) are a promising model system due to their ease of lab culture, short generation time, modest sized genome, a somewhat rare stable androdioecious sex determination system, and a requirement to reproduce via desiccated diapaused eggs. We generated a highly contiguous genome assembly using 46X of PacBio long read data and 216X of Illumina short reads, and annotated using Illumina RNAseq obtained from adult males or hermaphrodites. 85% of the 120Mb genome is contained in the largest 8 contigs, the smallest of which is 4.6Mb. The assembly contains 98% of transcripts predicted via RNAseq. This assembly is qualitatively different from scaffolded Illumina assemblies: it is produced from long reads that contain sequence data along their entire length, and is thus gap free. The contiguity of the assembly allows us to order the HOX genes within the genome, identifying two loci that contain HOX gene orthologs, and which approximately maintain the order observed in other arthropods. We identified a partial duplication of the Antennapedia gene adjacent to the few genes homologous to the Bithorax locus. Because the sex chromosome of an androdioecious species is of special interest, we used existing allozyme and microsatellite markers to identify theE. texanasex chromosome, and find that it comprises nearly half of the genome of this species. Linkage patterns indicate that recombination is extremely rare and perhaps absent in hermaphrodites, and as a result the location of the sex determining locus will be difficult to refine using recombination mapping.
Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples
Authors: Xue Katherine S. , Greninger Alexander L. , Pérez-Osorio Ailyn , Bloom Jesse D.
Published: November 2017

The high mutation rates of RNA viruses lead to rapid genetic diversification, which can enable cooperative interactions between variants in a viral population. We previously described two distinct variants of H3N2 influenza virus that cooperate in cell culture. These variants differ by a single mutation, D151G, in the neuraminidase protein. The D151G mutation reaches a stable frequency of about 50% when virus is passaged in cell culture. However, it is unclear whether selection for the cooperative benefits of D151G is a cell-culture phenomenon, or whether the mutation is also sometimes present at appreciable frequency in virus populations sampled directly from infected humans. Prior work has not detected D151G in unpassaged clinical samples, but these studies have used methods like Sanger sequencing and pyrosequencing that are relatively insensitive to low-frequency variation. We identified nine samples of human H3N2 influenza collected between 2013 to 2015 in which Sanger sequencing had detected a high frequency of the D151G mutation following one to three passages in cell culture. We deep-sequenced the unpassaged clinical samples to identify low-frequency viral variants. The frequency of D151G did not exceed the frequency of library preparation and sequencing errors in any of the sequenced samples. We conclude that passage in cell culture is primarily responsible for the frequent observations of D151G in recent H3N2 influenza strains.

IMPORTANCE

Viruses mutate rapidly, and recent studies of RNA viruses have shown that related viral variants can sometimes cooperate to improve each other’s growth. We previously described two variants of H3N2 influenza virus that cooperate in cell culture. The mutation responsible for cooperation is often observed when human samples of influenza virus are grown in the lab before sequencing, but it is unclear whether the mutation also exists in human infections or is exclusively the result of lab passage. We identified nine human isolates of influenza that had developed the cooperating mutation after being grown in the lab, and performed highly sensitive deep-sequencing of the unpassaged clinical samples to determine whether the mutation existed in the original human infections. We found no evidence of the cooperating mutation in the unpassaged samples, suggesting that the cooperation primarily arises in laboratory conditions.