bluuebunny/crossref_metadata_2025 huggingface dataset:
Transversality enforced Newton–Raphson algorithm for fast calculation of maximum loadability
Authors: Ali Mazhar , Dymarsky Anatoly , Turitsyn Konstantin
Published: December 2017

The authors propose a novel modification of the conventional Newton–Raphson load flow solver for characterisation of the maximal system loadability. Within the proposed approach, the standard power flow equations are extended with (i) an algebraic representation of maximal and minimal voltage level conditions and (ii) with the so‐called transversality condition restricting the set of solutions to the boundary of the solvability region. Solutions to this extended system of equation characterise the maximal load levels for which the solution of power flow equations exists and satisfies the standard feasibility constraints on voltage levels. The resulting system of equations is non‐singular and can be solved with just a few standard Newton–Raphson type iterations. Different possible choices of transversality conditions are discussed together with fast algorithms for evaluating the transversality conditions and their gradients. Implementation of the algorithm is described in detail, and its performance is validated on several IEEE cases.
Multiple antenna channel characterisation for wearable devices in an indoor stairwell environment
Authors: Catherwood Philip A. , Scanlon William G.
Published: December 2017

Any building with more than one floor will have stairwells of some form, yet this area is often neglected in channel characterisation studies. The authors present fading channel models and examine attainable spatial diversity gains at 90% signal reliability for an off‐body multiple‐antenna system at frequencies of 3, 4, and 5 GHz in an indoor stairwell. Additionally, they investigate received power, mutual coupling and channel cross‐correlation, signal combining modelling, and antenna spatial diversity; the authors believe this is a valuable advancement beyond current knowledge to understand wearable multiple‐input multiple‐output technology in stairwell environments. Results reveal that two‐branch spatial diversity techniques offer signal gains over individual single channels in the range of 1.7–3.3 dB for line of sight (LOS) and 1.8–3.4 dB for non‐LOS (NLOS) for each of the three investigated frequencies, while three‐channel diversity combining appears to offer no significant additional gain over the two‐branch combinations. Furthermore, for NLOS cases the best‐fit statistical distribution channel models were found to change when spatial diversity was utilised; this highlights mitigated channel fading and increased signal reliability.
Hierarchical loop‐flower basis for solving electric field integral equation
Authors: Wen Dingbang , Nie Zaiping , Wang Yiling , Liu Lu
Published: December 2017

A novel kind of hierarchical loop‐flower bases is presented for solving electric field integral equation. Compared with conventional hierarchical loop‐tree‐based method, the total bases for proposed hierarchical loop‐flower‐based method can be reduced a third. Thus, the memory and time cost can be largely reduced. The hierarchical loop‐flower basis function is defined on a hierarchical mesh which can be generated by a mesh refinement algorithm. By expanding the current with the hierarchical loop‐flower bases, the solenoidal and non‐solenoidal current are separated and thus the EFIE low‐frequency breakdown issue can be remedied. In addition to that a multiresolution preconditioner technology is also introduced to fast up the iterative convergence speed. Some examples show that the basis number is largely reduced.
Compact three‐way filtering Bagley polygon power divider based on composite right/left‐handed transmission lines
Authors: Song Kaijun , Xu Boqiang , Guo Song , Ren Xue , Zhang Fan
Published: December 2017

This study presents a compact three‐way Bagley Polygon power divider integrated with bandpass response. Two compact filters are embedded into the power divider to replace the conventional quarter‐wavelength transmission lines (TLs). Moreover, the zero‐degree TLs are utilised to realise the miniaturisation, meanwhile, the power divider's intrinsic isolation performance is maintained. Analysis and guided equations are given. For verification, a Bagley Polygon power divider integrates with good filtering response and wide stopband is fabricated. Good agreement between the prediction and measurement validated the proposed method.
Effective implicit finite‐difference method for sensitivity analysis of stiff stochastic discrete biochemical systems
Authors: Morshed Monjur , Ingalls Brian , Ilie Silvana
Published: December 2017

Simulation of cellular processes is achieved through a range of mathematical modelling approaches. Deterministic differential equation models are a commonly used first strategy. However, because many biochemical processes are inherently probabilistic, stochastic models are often called for to capture the random fluctuations observed in these systems. In that context, the Chemical Master Equation (CME) is a widely used stochastic model of biochemical kinetics. Use of these models relies on estimates of kinetic parameters, which are often poorly constrained by experimental observations. Consequently, sensitivity analysis, which quantifies the dependence of systems dynamics on model parameters, is a valuable tool for model analysis and assessment. A number of approaches to sensitivity analysis of biochemical models have been developed. In this study, the authors present a novel method for estimation of sensitivity coefficients for CME models of biochemical reaction systems that span a wide range of time‐scales. They make use of finite‐difference approximations and adaptive implicit tau‐leaping strategies to estimate sensitivities for these stiff models, resulting in significant computational efficiencies in comparison with previously published approaches of similar accuracy, as evidenced by illustrative applications.
The distribution of stars around the Milky Way’s central black hole
Authors: Baumgardt H. , Amaro-Seoane P. , Schödel R.
Published: December 2017

Context. The distribution of stars around a massive black hole (MBH) has been addressed in stellar dynamics for the last four decades by a number of authors. Because of its proximity, the centre of the Milky Way is the only observational test case where the stellar distribution can be accurately tested. Past observational work indicated that the brightest giants in the Galactic centre (GC) may show a density deficit around the central black hole, not a cusp-like distribution, while we theoretically expect the presence of a stellar cusp.

Aims. We here present a solution to this long-standing problem.

Methods. We performed direct-summation N-body simulations of star clusters around massive black holes and compared the results of our simulations with new observational data of the GC’s nuclear cluster.

Results. We find that after a Hubble time, the distribution of bright stars as well as the diffuse light follow power-law distributions in projection with slopes of Γ ≈ 0.3 in our simulations. This is in excellent agreement with what is seen in star counts and in the distribution of the diffuse stellar light extracted from adaptive-optics (AO) assisted near-infrared observations of the GC.

Conclusions. Our simulations also confirm that there exists a missing giant star population within a projected radius of a few arcsec around Sgr A*. Such a depletion of giant stars in the innermost 0.1 pc could be explained by a previously present gaseous disc and collisions, which means that a stellar cusp would also be present at the innermost radii, but in the form of degenerate compact cores.
Organocatalytic Asymmetric Synthesis of Pentasubstituted Tetrahydrothiopyrans Bearing a Quaternary Centre through a Double Michael Reaction
Authors: Pan Subhas , Mondal Buddhadeb
Published: December 2017

An organocatalytic, asymmetric, double-Michael strategy has been developed employing trans-α-cyano-α,β-unsaturated ketones for the synthesis of pentasubstituted tetrahydrothiopyrans bearing a quaternary center. A proline-derived bifunctional thiourea was found to be the most effective catalyst for this reaction. With 10 mol% of catalyst, good yields and good to high diastereomeric ratios, as well as excellent enantioselectivities, were obtained with a variety of tetrahydrothiopyrans under mild reaction conditions.
Asymmetric Organocatalytic Friedel–Crafts Hydroxyalkylation of Indoles Using Electrophilic Pyrazole-4,5-diones
Authors: Enders Dieter , Vetica Fabrizio , Chauhan Pankaj , Mahajan Suruchi , Raabe Gerhard
Published: December 2017

The electrophilic reactivity of a series of novel pyrazole-4,5-dione derivatives in the organocatalytic Friedel–Crafts reaction with various substituted indoles has been tested. The disclosed procedure catalyzed by a cinchona alkaloid derivative allows the conjugation of two very important aza-heterocyclic scaffolds to generate a new class of indolylpyrazolones bearing a tetrasubstituted stereocenter in excellent yields (up to 99%) and with enantioselectivities of up to 94:6 er.
Validation of a New Web-Based System for Point-of-Care Implant Documentation in Total Knee Arthroplasty
Authors: Ramanathan Deepak , Gad Bishoy , Luckett Matthew , Klika Alison , Spindler Kurt , Higuera Carlos
Published: December 2017

Implant documentation in total knee arthroplasty (TKA) must be both accurate and comprehensive. A new system enables surgeons to complete a secure, web-based operative report for each surgery. This study evaluated implant documentation using this system and hypothesized that it would be as reliable as the current standard. This was a retrospective study of all primary and revision TKA performed at a single academic institution from January 1, 2015 to March 31, 2015, by eight adult reconstruction surgeons who used the web-based system. Electronic medical records and implant logbooks were chosen as a composite standard reference for implant documentation. Cohen's kappa statistic and Pearson's correlation coefficients were used to determine agreement between the system and the standard reference. Mean kappa value for entire system was 0.916 ± 0.152 (p = 0.015) indicating “almost perfect” agreement (as per Landis and Koch's method) with standard reference. Pearson's correlation coefficient was 0.926 ± 0.147 (p = 0.021) further corroborating this excellent agreement. There was “substantial” or “fair” agreement for items pertaining to cement and augments. Overall, sensitivity was 0.98 (95% confidence interval: 0.71–0.98) and specificity 0.93 (95% confidence interval: 0.53–0.98) indicating that the system was very effective at documenting whether or not an implant was placed. The system exhibited significantly greater sensitivity than specificity (p = 0.027). This study demonstrated excellent performance of this novel system in point-of-care TKA implant documentation. Further research is needed to validate its use in arthroplasty of other joints and its potential for documentation of biomedical device implantation in other fields such as cardiothoracic surgery and gastroenterology.
Predicting Vaginal Delivery in Nulliparous Women Undergoing Induction of Labor at Term
Authors: Reddy U. M. , Huang C. C. , Auguste T. C. , Bauer D. , Overcash R. T. , Kawakita T.
Published: December 2017

Objective We sought to develop a model to calculate the likelihood of vaginal delivery in nulliparous women undergoing induction at term.

Study Design We obtained data from the Consortium on Safe Labor by including nulliparous women with term singleton pregnancies undergoing induction of labor at term. Women with contraindications for vaginal delivery were excluded. A stepwise logistic regression analysis was used to identify the predictors associated with vaginal delivery by considering maternal characteristics and comorbidities and fetal conditions. The receiver operating characteristic curve, with an area under the curve (AUC) was used to assess the accuracy of the model.

Results Of 10,591 nulliparous women who underwent induction of labor, 8,202 (77.4%) women had vaginal delivery. Our model identified maternal age, gestational age at delivery, race, maternal height, prepregnancy weight, gestational weight gain, cervical exam on admission (dilation, effacement, and station), chronic hypertension, gestational diabetes, pregestational diabetes, and abruption as significant predictors for successful vaginal delivery. The overall predictive ability of the final model, as measured by the AUC was 0.759 (95% confidence interval, 0.749–0.770).

Conclusion We identified independent risk factors that can be used to predict vaginal delivery among nulliparas undergoing induction at term. Our predictor provides women with additional information when considering induction.
Radiographic Morphology and Method for Localization of the Adductor Tubercle on Anterior–Posterior Knee Radiographs
Authors: Liu Kuan-Lin , Wang Chen-Chie , Chen Ing-Ho , Chang Chia-Ming , Wu Wen-Tien , Yeh Kuang-Ting
Published: December 2017

The adductor tubercle (AT) is a landmark for joint line identification in knee arthroplasty. Up to now, there has not been a dedicated study to define its morphology on an anterior–posterior (AP) radiograph. As a result, radiographic localization of the AT has been inconsistent and confusing. Ten bone specimens, each with the AT labeled with a metal marker, were radiographed to demonstrate the AT appearance on AP radiographs. Based on this knowledge, a method to locate the AT was developed. A total of 200 clinical radiographs were examined to further confirm the observed radiographic morphology with emphasis on the visibility of the AT and its association with the rotational status of the knee on radiographs. One hundred of them were used to test the reliability of this method of AT identification. Of the 200 ATs, 153 (76%) were clearly visible on radiographs as a faint pyramid-shaped shadow protruding outward from the inflexion point of the concave–convex silhouette over the femoral shaft-condylar junction, allowing direct identification. For invisible ATs (24%), this inflexion point was found to be a useful surrogate landmark for their identification. Locating the AT using this technique showed a good intra- and interobserver reliabilities. The proposed method may be valuable for the consistent use of this landmark in joint line identification on radiographs.
Kryptogener Schlaganfall: Rhythmusdetektion versus pragmatische orale Antikoagulation
Authors: Jilek Clemens , Lewalter Thorsten
Published: December 2017

Der kryptogene Schlaganfall betrifft 20 – 25% der ischämischen Schlaganfälle und wird vom Mechanismus als embolisch angesehen. Zur Identifikation von rhythmogenen Ursachen stehen implantierbare Event-Recorder zur Verfügung, die in der CRYSTAL-AF-Studie bei bis zu 30% der Patienten mit kryptogenem Schlaganfall innerhalb von 3 Jahren Vorhofflimmern nachweisen konnten. Event-Recorder sind effektiv und im britischen Gesundheitssystem kostendeckend. Studien zur pragmatischen oralen Antikoagulation mit Warfarin konnten dagegen keinen Vorteil bez. Verhinderung ischämischer Schlaganfälle zeigen und gingen überwiegend mit hohem Blutungsrisiko einher. Lediglich Sub-Subgruppen zeigten einen geringen Vorteil. Nicht-Vitamin-K-abhängige orale Antikoagulanzien (nOAK) zeigen im Vergleich zu Vitamin-K-Antagonisten ein besseres Effektivitäts- und Sicherheitsprofil. Drei randomisierte Studien rekrutieren aktuell Patienten, um den Wert der pragmatischen oralen Antikoagulation in der Vermeidung von Schlaganfällen bei Patienten mit stattgehabtem kryptogenem Schlaganfall zu evaluieren. Zusammengefasst liegt eine Klasse-IB-Indikation für das Rhythmusmonitoring nach kryptogenem Schlaganfall vor. Für eine pragmatische orale Antikoagulation fehlen bisher überzeugende Daten. Ergebnisse der nOAK-Studien sollten ab Ende 2018 verfügbar sein.
Strain Elastography - How To Do It?
Authors: Dietrich Christoph , Barr Richard , Farrokh André , Dighe Manjiri , Hocke Michael , Jenssen Christian , Dong Yi , Saftoiu Adrian , Havre Roald
Published: December 2017

Tissue stiffness assessed by palpation for diagnosing pathology has been used for thousands of years. Ultrasound elastography has been developed more recently to display similar information on tissue stiffness as an image. There are two main types of ultrasound elastography, strain and shear wave. Strain elastography is a qualitative technique and provides information on the relative stiffness between one tissue and another. Shear wave elastography is a quantitative method and provides an estimated value of the tissue stiffness that can be expressed in either the shear wave speed through the tissues in meters/second, or converted to the Young’s modulus making some assumptions and expressed in kPa. Each technique has its advantages and disadvantages and they are often complimentary to each other in clinical practice. This article reviews the principles, technique, and interpretation of strain elastography in various organs. It describes how to optimize technique, while pitfalls and artifacts are also discussed.
Agreement between endoscopic ultrasound-guided fine-needle aspiration and endobiliary brush cytology in suspected pancreaticobiliary malignancies
Authors: Sullivan Matthew , Kincaid Hope , Shah Shashin , Shah Hiral
Published: December 2017

Background and study aims For suspected pancreaticobiliary malignancies, endobiliary brush cytology during endoscopic retrograde cholangiopancreatography (ERCP) remains the diagnostic test of choice despite historically poor and variable sensitivity. This has led to increased use of endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) as an initial test. Recently, our institution began using a cytology brush that was designed specifically to collect a more substantial and higher-quality sample. The aim of this study was to investigate whether this brush design would provide more adequate samples and have high agreement with EUS-FNA in patients who underwent both procedures.

Patients and methods A retrospective chart review was conducted of all patients who underwent both EUS-FNA and endobiliary brush cytology for suspicion of pancreaticobiliary malignancy from January 2013 to May 2015. A total of 41 patients met the inclusion criteria. Initially, sample quality was evaluated. Final cytology results were then assessed for agreement with EUS-FNA using Cohen’s kappa. The effect of considering atypical cytology as negative was also uniquely evaluated by running separate analyses.

Results Brush cytology provided an adequate sample in 95.1 % of cases. Cohen’s Kappa demonstrated moderate agreement between brush cytology and EUS-FNA: κ = 0.42 (P = 0.001). When atypical results were excluded, agreement increased: κ = 0.60 (P = 0.02), but remained moderate. If atypical results were considered “positive,” the two procedures demonstrated equal cancer detection rates of 80.8 %.

Conclusions The studied brush provided more adequate samples compared with historical rates for brush cytology and had moderate agreement with EUS-FNA. If this brush truly increases sample adequacy, it could potentially provide results comparable to EUS-FNA at lower cost.
Seitwärtsbewegung auf einer Unterstützungsfläche
Authors: Muesse André , Vehma Stefanie , Brutscher Petra , Eppler Sonja
Published: December 2017

Auf vielen Wegen zur Fortbewegung Aufbauend auf den Transfer aus der Rücken- in die Seitenlage erläutern die Autoren hier die Bewegung
seitwärts auf einer Unterstützungsfläche – beispielsweise im Bett – und stellen ihre Anwendbarkeit im pflegerischen Kontext dar. Wie schon
in den vorangegangenen Artikeln dieser Serie wird es auch hierbei die Unterscheidung der Anwendung beim Früh-/Neugeborenen und der beim
älteren Kind geben. Das zugrundeliegende Bewegungsmuster ist in beiden Fällen dasselbe, bedarf jedoch individuell unterschiedlicher
Unterstützung durch die Pflegekraft oder eine andere helfende Person.
Besuche mit Struktur
Authors: Thielmann Susanna
Published: December 2017

Geschwisterkinder auf der interdisziplinären pädiatrischen Intensivstation Jedes Kind reagiert anders, wenn es zum ersten Mal sein
krankes Geschwister auf einer Intensivstation besucht. Eine Begleitung dieser Kinder sollte daher individuell und dem Alter und der
Situation angemessen sein. Wie Pflegende diese Begleitung professionell gestalten können, zeigt dieser Beitrag.
Demenzielle Syndrome: die Grundlagen
Authors: Zemke Jens
Published: December 2017

Neurodegeneration In westlichen Industrienationen leiden mehr als 8 % der über 65-Jährigen unter mittelschweren oder schweren
Demenzformen. Der Begriff demenzielles Syndrom steht für eine heterogene Gruppe von Erkrankungen mit der gemeinsamen Endstrecke des
allgemeinen intellektuellen Abbaus. Häufig wird das demenzielle Syndrom gleichbedeutend mit dem Begriff Demenz verwendet.
Konfundierungen und Störfaktoren in rehabilitationswissenschaftlichen Beobachtungs- und Interventionsstudien
Authors: Wirtz Markus
Published: December 2017

Um Effekte von Rehabilitationsmaßnahmen prüfen zu können, muss das Studiendesign so gewählt werden, dass Veränderungen der Zielvariablen (z. B. Gesundheitszustand) möglichst eindeutig auf die Interventionsmaßnahme zurückgeführt werden können. Bei Beobachtungsstudien muss davon ausgegangen werden, dass konfundierende Merkmale den Einfluss der Maßnahme auf die Zielvariable systematisch überlagern und Effektschätzungen verzerren. Die Präferenz für eine Behandlungsalternative, die Behandlungsmotivation sowie das Ausmaß der initialen Beeinträchtigung der Rehabilitanden sind typische Konfundierungen, die insbesondere bei freiwilliger Behandlungsauswahl oder bei Teilnahme nach Behandlungsempfehlung berücksichtigt werden müssen (programmexterne Störfaktoren). Bei gut kontrollierten Interventionsstudien (insb. randomisiert kontrollierte Studien, RCT), bei denen die Inanspruchnahme der Behandlung systematisch kontrolliert erfolgt, können diese Fehlerquellen vermieden werden. Aber auch bei gut kontrollierten Interventionsstudien kann die Studiendurchführung (z. B. aufgrund der Stichprobenauswahl, des Einsatzes von Messinstrumenten, des Austauschs zwischen Vergleichsgruppen; Designeffekte, Treatmentkontaminationen) die eindeutige Interpretierbarkeit der Studienbefunde beeinträchtigen. In diesem Beitrag wird gezeigt, welche Konfundierungen und Störeinflüsse typischerweise die Validität der Schlussfolgerungen aus empirischen Zusammenhängen verringern können. Es wird verdeutlicht, wie potenziell verzerrende Konfundierungen und Effekte von Störfaktoren durch die Gestaltung der Untersuchung vermieden oder bestmöglich kontrolliert werden können.
Visual assessment of colorectal flat and depressed lesions by using narrow band imaging
Authors: Nakamura Hiroshi , Ikematsu Hiroaki , Osera Shozo , Ito Renma , Sato Daiki , Minamide Tatsunori , Okamoto Naoki , Yamamoto Yoichi , Hombu Takuya , Takashima Kenji , Nakajo Keiichiro , Kadota Tomohiro , Yoda Yusuke , Hori Keisuke , Oono Yasuhiro , Yano Tomonori
Published: December 2017

Background and study aims Visual assessment of laterally spreading tumors non-granular type (LST-NG) and depressed lesions by narrow band imaging (NBI) without magnification has not been studied. We investigated the role of non-magnifying NBI in detecting LST-NG and type IIc lesions on colonoscopy.

Patients and methods This retrospective study examined consecutive patients diagnosed as having LST-NG and/or type IIc lesions in our hospital between August 2011 and July 2013. These lesions were classified as “Brownish area (BA),” “Brown only in the margins (O-ring sign),” “Same color as the normal mucosa (SC),” and “Whitish area (WA)” based on their appearance on non-magnifying NBI, and their appearance were compared with their histopathological findings.

Results A total of 18 type IIc and 180 LST-NG lesions were analyzed. Among the type IIc lesions, 5 (28 %), 12 (67 %), and 1 (5 %) were classified as BA, O-ring sign, and SC, respectively. Among the LST-NG lesions, 126 (70 %), 26 (14 %), and 28 lesions (16 %) were classified as BA, O-ring sign, and SC, respectively. The IIc lesions were found to have 1 lesion (20 %) with high-grade dysplasia (HGD) in the BA, and 2 lesions (17 %) with invasive cancer (IC) in the O-ring sign group. Among the LST-NG lesions, 27 (21 %) were found to have IC and 49 (39 %), HGD in the BA group; 8 lesions (31 %) had IC and 4 (15 %) had HGD in the O-ring sign group; and 1 lesion (4 %) had IC and 4 (14 %) had HGD in the SC group.

Conclusions Most flat and depressed colorectal lesions were seen on non-magnifying NBI as brown lesions with the exception of some flat lesions that were indistinguishable in color from the adjacent normal mucosa. Some of these flat lesions were also found to have HGD or IC.
Systematischer Review zur Krankheitslast durch Campylobacter spp.
Authors: Lackner Julia , Schlichting Daniela , Müller-Graf Christine , Greiner Matthias
Published: December 2017

Campylobacter spp. sind Bakterien, die weltweit als einer der häufigsten Auslöser für eine Gastroenteritis gelten und zu schwerwiegenden Folgeerkrankungen führen können. Die Krankheitslast durch Campylobacterbakterien wurde bereits in mehreren Studien mithilfe der quantitativen Maßzahl disability-adjusted life years (DALY) für ausgewählte Länder berechnet. Ziel der Übersichtsarbeit ist es zu evaluieren, ob die berechneten DALYs in den betrachten Ländern und Zeiträume vergleichbar sind und wenn nicht, welche Faktoren die Schätzungen beeinflussen. Da als wichtigster Übertragungsweg für Campylobacter spp. Lebensmittel gelten, wurden auch Publikationen in die Suche einbezogen, die nur die lebensmittelbedingte Krankheitslast abbildeten. Mithilfe einer systematischen Literatursuche, wurden 21 länderspezifische Publikationen und eine Studie der Weltgesundheitsorganisation im Suchzeitraum 1/1996–6/2016 gefunden. Durch unterschiedliche Methoden bei der Berechnung der Krankheitslast sowie die Qualitätsunterschiede der Daten schwanken die Ergebnisse der Schätzungen der Gesamtkrankheitslast in den länderspezifischen Publikationen von 0,4 DALYs in Frankreich bis 109 DALY pro 100000 Einwohner in Polen. Da die Berechnung des attributablen Risikos auf Grundlage der mit Unsicherheiten behafteten Schätzungen der Inzidenzen der campylobacterbedingten Erkrankungen erfolgt, zeigen sich auch bei der lebensmittelbedingten Krankheitslast große Spannweiten von 0,5 DALYs pro 100000 Einwohner in Griechenland bis 21,2 DALY pro 100000 Einwohner in Neuseeland, welche nicht ausschließlich auf die länderspezifischen Variabilität in der Produktion, dem Verzehrsverhalten und dem Vorkommen von Campylobacter spp. zurückzuführen sind.
Theoretical approaches for treating non-valence correlation-bound anions
Authors: Voora Vamsee K. , Kairalapova Arailym , Sommerfeld Thomas , Jordan Kenneth D.
Published: December 2017

In this work, we use a model (H2O)4 cluster, the bent CO2 molecule, and tetracyanoethylene as systems to explore the applicability of various electronic structure methods for characterizing non-valence correlation-bound anion states. The methods examined include the algebraic diagrammatic construction, various equation-of-motion coupled cluster methods, orbital-optimized MP2, and Brueckner coupled cluster doubles with perturbative triples. We demonstrate that the key to treating this challenging class of anions is the use of methods that include adequate orbital relaxation in response to long-range dispersion-like correlation effects.
Effect of particle shape and slip mechanism on buoyancy induced convective heat transport with nanofluids
Authors: Joshi Pranit Satish , Mahapatra Pallab Sinha , Pattamatta Arvind
Published: December 2017

Experiments and numerical simulation of natural convection heat transfer with nanosuspensions are presented in this work. The investigations are carried out for three different types of nanosuspensions: namely, spherical-based (alumina/water), tubular-based (multi-walled carbon nanotube/water), and flake-based (graphene/water). A comparison with in-house experiments is made for all the three nanosuspensions at different volume fractions and for the Rayleigh numbers in the range of 7 × 105–1 × 107. Different models such as single component homogeneous, single component non-homogeneous, and multicomponent non-homogeneous are used in the present study. From the present numerical investigation, it is observed that for lower volume fractions (∼0.1%) of nanosuspensions considered, single component models are in close agreement with the experimental results. Single component models which are based on the effective properties of the nanosuspensions alone can predict heat transfer characteristics very well within the experimental uncertainty. Whereas for higher volume fractions (∼0.5%), the multi-component model predicts closer results to the experimental observation as it incorporates drag-based slip force which becomes prominent. The enhancement observed at lower volume fractions for non-spherical particles is attributed to the percolation chain formation, which perturbs the boundary layer and thereby increases the local Nusselt number values.
The fractal geometry of Hartree-Fock
Authors: Theel Friethjof , Karamatskou Antonia , Santra Robin
Published: December 2017

The Hartree-Fock method is an important approximation for the ground-state electronic wave function of atoms and molecules so that its usage is widespread in computational chemistry and physics. The Hartree-Fock method is an iterative procedure in which the electronic wave functions of the occupied orbitals are determined. The set of functions found in one step builds the basis for the next iteration step. In this work, we interpret the Hartree-Fock method as a dynamical system since dynamical systems are iterations where iteration steps represent the time development of the system, as encountered in the theory of fractals. The focus is put on the convergence behavior of the dynamical system as a function of a suitable control parameter. In our case, a complex parameter λ controls the strength of the electron-electron interaction. An investigation of the convergence behavior depending on the parameter λ is performed for helium, neon, and argon. We observe fractal structures in the complex λ-plane, which resemble the well-known Mandelbrot set, determine their fractal dimension, and find that with increasing nuclear charge, the fragmentation increases as well.
Applied axial magnetic field effects on laboratory plasma jets: Density hollowing, field compression, and azimuthal rotation
Authors: Byvank T. , Banasek J. T. , Potter W. M. , Greenly J. B. , Seyler C. E. , Kusse B. R.
Published: December 2017

We experimentally measure the effects of an applied axial magnetic field (Bz) on laboratory plasma jets and compare the experimental results with numerical simulations using an extended magnetohydrodynamics code. A 1 MA peak current, 100 ns rise time pulse power machine is used to generate the plasma jet. On application of the axial field, we observe on-axis density hollowing and a conical formation of the jet using interferometry, compression of the applied Bz using magnetic B-dot probes, and azimuthal rotation of the jet using Thomson scattering. Experimentally, we find densities ≲5 × 1017 cm−3 on-axis relative to jet densities of ≳3 × 1018 cm−3. For aluminum jets, 6.5 ± 0.5 mm above the foil, we find on-axis compression of the applied 1.0 ± 0.1 T Bz to a total 2.4 ± 0.3 T, while simulations predict a peak compression to a total 3.4 T at the same location. On the aluminum jet boundary, we find ion azimuthal rotation velocities of 15–20 km/s, while simulations predict 14 km/s at the density peak. We discuss possible sources of discrepancy between the experiments and simulations, including surface plasma on B-dot probes, optical fiber spatial resolution, simulation density floors, and 2D vs. 3D simulation effects. This quantitative comparison between experiments and numerical simulations helps elucidate the underlying physics that determines the plasma dynamics of magnetized plasma jets.
A long-range ordered array of copper tetrameric units embedded in an on-surface metal organic framework
Authors: Lo Cicero Matteo , Della Pia Ada , Riello Massimo , Colazzo Luciano , Sedona Francesco , Betti Maria Grazia , Sambi Mauro , De Vita Alessandro , Mariani Carlo
Published: December 2017

We report on the assembly of a highly ordered array of copper tetrameric clusters, coordinated into a metal-organic network. The ordered cluster array has been achieved by the deposition of tetrahydroxyquinone molecules on the Cu(111) surface at room temperature, and subsequent thermally activated dehydrogenation with the formation of tetraoxyquinone tetra-anions with a 4 × 4 periodicity. The supramolecular organic network acts as a spacer for the highly ordered two-dimensional network of copper tetramers at the very surface.
Analysis of interlocking performances on non-oriented electrical steels
Authors: Liu Li-Hsiang , Liu Lee-Cheng
Published: December 2017

In order to reduce energy loss in motor, applications of high-efficiency non-oriented electrical steel sheets and optimal laminating process are both important elements. The motor core loss deterioration is influenced by a number of factors, such as flux distribution, stress and strain, space harmonics, temperature, and short circuits between lamination. In conventional clamping method, steel sheets are laminated via interlocking or welding in general manner. The measured energy loss by welding was much larger than that by interlocking. Therefore, interlocking is well known and usually employed with benefit of easy conducting. The protuberance shapes affected the fastening strength. Generally, the intensity of rectangular type is stronger than the circular counterparts. However, the circular interlocking has better magnetic characteristics. To clarify the method effectiveness, interlocking performances regarding fastened strength and magnetic deterioration by lamination were investigated. The key parameters of protuberance shape and forming depth were designed. Precisely manufacturing operation was applied to avoid interlocking failure. Magnetic properties largely influenced by clamping method are crucial to minimizing the magnetic deterioration during laminating procedure. Several experiments for various processing conditions were undertaken, and the quantification results showed the rectangular interlocking had better fastened strength but worsened iron loss comparing with the circular arrangement. To acquire the comprehensive mechanical and electrical identities for electrical steel lamination, deliberate producing conditions regarding minimizing the magnetic deterioration should be adopted prudently.
Spatial and directional control of self-assembled wrinkle patterns by UV light absorption
Authors: Kortz C. , Oesterschulze E.
Published: December 2017

Wrinkle formation on surfaces is a phenomenon that is observed in layered systems with a compressed elastic thin capping layer residing on a viscoelastic film. So far, the properties of the viscoelastic material could only be changed replacing it by another material. Here, we propose to use a photosensitive material whose viscoelastic properties, Young's modulus, and glass transition temperature can easily be adjusted by the absorption of UV light. Employing UV lithography masks during the exposure, we gain additionally spatial and directional control of the self-assembled wrinkle pattern formation that relies on a spinodal decomposition process. Inspired by the results on surface wrinkling and its dependence on the intrinsic stress, we also derive a method to avoid wrinkling locally by tailoring the mechanical stress distribution in the layered system choosing UV masks with convex patterns. This is of particular interest in technical applications where the buckling of surfaces is undesirable.
Quantum ballistic transport in strained epitaxial germanium
Authors: Gul Y. , Holmes S. N. , Newton P. J. , Ellis D. J. P. , Morrison C. , Pepper M. , Barnes C. H. W. , Myronov M.
Published: December 2017

Large scale fabrication using Complementary Metal Oxide Semiconductor compatible technology of semiconductor nanostructures that operate on the principles of quantum transport is an exciting possibility now due to the recent development of ultra-high mobility hole gases in epitaxial germanium grown on standard silicon substrates. We present here a ballistic transport study of patterned surface gates on strained Ge quantum wells with SiGe barriers, which confirms the quantum characteristics of the Ge heavy hole valence band structure in 1-dimension. Quantised conductance at multiples of 2e2/h is a universal feature of hole transport in Ge up to 10 × (2e2/h). The behaviour of ballistic plateaus with finite source-drain bias and applied magnetic field is elucidated. In addition, a reordering of the ground state is observed.
Effects of pH and mineralisation on nitrification in a subtropical acid forest soil
Authors: Zhao Wei , Zhang Jin-bo , Müller Christoph , Cai Zu-cong
Published: December 2017

Effects of pH on nitrification have been explored widely; however, few researchers have investigated the compound effects of pH and mineralisation on nitrification and responsible nitrifiers in subtropical forest soils. An acid subtropical forest soil was subjected to pH treatments by liming for 40 days at 25°C and 60% water holding capacity. After 40 days, gross N transformation rates in the samples were evaluated using the 15N tracing technique and model. Ammonia-oxidising bacteria (AOB) and ammonia-oxidising archaea (AOA) were quantified by quantitative polymerase chain reaction. The results showed that gross rates of mineralisation (P < 0.01), NH4+ oxidation to NO3− (P < 0.01), and dissimilatory NO3− reduction to ammonium (DNRA, P < 0.05) significantly increased with elevated soil pH. The NH4+ oxidation to NO3− rates and N mineralisation rates were significantly correlated (P < 0.05). The abundance of AOB (P < 0.05) but not AOA amoA genes dramatically increased in the elevated pH treatments after 40 days. We suggest that the N mineralisation was sensitive to elevated pH in the subtropical acid forest soil, which increased the supply rate of nitrification substrate and the favourable pH microsites for nitrifiers. Interactions between elevated pH and mineralisation have a synergistic and stimulatory effect on development of AOB and their associated nitrifying activity.
Accurate mapping of tRNA reads
Authors: Hoffmann Anne , Fallmann Jörg , Vilardo Elisa , Mörl Mario , Stadler Peter F , Amman Fabian
Published: December 2017

Motivation

Many repetitive DNA elements are transcribed at appreciable expression levels. Mapping the corresponding RNA sequencing reads back to a reference genome is notoriously difficult and error-prone task, however. This is in particular true if chemical modifications introduce systematic mismatches, while at the same time the genomic loci are only approximately identical, as in the case of tRNAs.

Results

We therefore developed a dedicated mapping strategy to handle RNA-seq reads that map to tRNAs relying on a modified target genome in which known tRNA loci are masked and instead intronless tRNA precursor sequences are appended as artificial ‘chromosomes’. In a first pass, reads that overlap the boundaries of mature tRNAs are extracted. In the second pass, the remaining reads are mapped to a tRNA-masked target that is augmented by representative mature tRNA sequences. Using both simulated and real life data we show that our best-practice workflow removes most of the mapping artefacts introduced by simpler mapping schemes and makes it possible to reliably identify many of chemical tRNA modifications in generic small RNA-seq data. Using simulated data the FDR is only 2%. We find compelling evidence for tissue specific differences of tRNA modification patterns.

Availability and implementation

The workflow is available both as a bash script and as a Galaxy workflow from https://github.com/AnneHoffmann/tRNA-read-mapping.

Supplementary information

Supplementary data are available at Bioinformatics online.
LitPathExplorer: a confidence-based visual text analytics tool for exploring literature-enriched pathway models
Authors: Soto Axel J , Zerva Chrysoula , Batista-Navarro Riza , Ananiadou Sophia
Published: December 2017

Motivation

Pathway models are valuable resources that help us understand the various mechanisms underpinning complex biological processes. Their curation is typically carried out through manual inspection of published scientific literature to find information relevant to a model, which is a laborious and knowledge-intensive task. Furthermore, models curated manually cannot be easily updated and maintained with new evidence extracted from the literature without automated support.

Results

We have developed LitPathExplorer, a visual text analytics tool that integrates advanced text mining, semi-supervised learning and interactive visualization, to facilitate the exploration and analysis of pathway models using statements (i.e. events) extracted automatically from the literature and organized according to levels of confidence. LitPathExplorer supports pathway modellers and curators alike by: (i) extracting events from the literature that corroborate existing models with evidence; (ii) discovering new events which can update models; and (iii) providing a confidence value for each event that is automatically computed based on linguistic features and article metadata. Our evaluation of event extraction showed a precision of 89% and a recall of 71%. Evaluation of our confidence measure, when used for ranking sampled events, showed an average precision ranging between 61 and 73%, which can be improved to 95% when the user is involved in the semi-supervised learning process. Qualitative evaluation using pair analytics based on the feedback of three domain experts confirmed the utility of our tool within the context of pathway model exploration.

Availability and implementation

LitPathExplorer is available at http://nactem.ac.uk/LitPathExplorer_BI/.

Supplementary information

Supplementary data are available at Bioinformatics online.
DeepSF: deep convolutional neural network for mapping protein sequences to folds
Authors: Hou Jie , Adhikari Badri , Cheng Jianlin
Published: December 2017

Motivation

Protein fold recognition is an important problem in structural bioinformatics. Almost all traditional fold recognition methods use sequence (homology) comparison to indirectly predict the fold of a target protein based on the fold of a template protein with known structure, which cannot explain the relationship between sequence and fold. Only a few methods had been developed to classify protein sequences into a small number of folds due to methodological limitations, which are not generally useful in practice.

Results

We develop a deep 1D-convolution neural network (DeepSF) to directly classify any protein sequence into one of 1195 known folds, which is useful for both fold recognition and the study of sequence–structure relationship. Different from traditional sequence alignment (comparison) based methods, our method automatically extracts fold-related features from a protein sequence of any length and maps it to the fold space. We train and test our method on the datasets curated from SCOP1.75, yielding an average classification accuracy of 75.3%. On the independent testing dataset curated from SCOP2.06, the classification accuracy is 73.0%. We compare our method with a top profile–profile alignment method—HHSearch on hard template-based and template-free modeling targets of CASP9-12 in terms of fold recognition accuracy. The accuracy of our method is 12.63–26.32% higher than HHSearch on template-free modeling targets and 3.39–17.09% higher on hard template-based modeling targets for top 1, 5 and 10 predicted folds. The hidden features extracted from sequence by our method is robust against sequence mutation, insertion, deletion and truncation, and can be used for other protein pattern recognition problems such as protein clustering, comparison and ranking.

Availability and implementation

The DeepSF server is publicly available at: http://iris.rnet.missouri.edu/DeepSF/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Species-specific residence times in the aft part of a pelagic survey trawl: implications for inference of pre-capture spatial distribution using the Deep Vision system
Authors: Underwood Melanie J , Rosen Shale , Engås Arill , Jørgensen Terje , Fernö Anders
Published: December 2017

In-trawl camera systems promise to improve the resolution of trawl sampling used to ground-truth the interpretation of acoustic survey data. In this study, the residence time of fish in front of the Deep Vision camera system, used to identify, measure and count fish inside the trawl, was analysed to determine the reliability of spatial distribution recorded by the system. Although Atlantic herring (Clupea harengus), haddock (Melanogrammus aeglefinus), and most Atlantic cod (Gadus morhua) moved quickly back through the aft part of the pelagic trawl, saithe (Pollachius virens) spent up to 4 min in front of the system. The residence time increased for saithe and cod when other individuals were present, and cod swimming in the low water flow close to the trawl netting spent longer there than cod at the centre of the trawl. Surprisingly, residence time was not related to the size of the fish, which may be explained by the collective behaviour of shoaling fish. Our findings suggest that while in-trawl images can be used to identify, measure and count most species, when sampling fast-swimming species such as saithe the position inferred from when they were imaged may not reflect the actual spatial distribution prior to capture.
Connectedness of Brill–Noether Loci via Degenerations
Authors: Osserman Brian
Published: December 2017

We show that limit linear series spaces for chains of curves are reduced. Using recent advances in the foundations of limit linear series, we then use degenerations to study the question of connectedness for spaces of linear series with imposed ramification at up to two points. We find that in general, these spaces may not be connected even when they have positive dimension, but we prove a criterion for connectedness which generalizes the theorem previously proved by Fulton and Lazarsfeld in the case without imposed ramification.
Genomics, Epigenetics, and Precision Medicine in Integrative Preventive Medicine
Authors: Casanova Nancy G. , Wang Ting , Chiang Eddie T. , Garcia Joe G. N.
Published: December 2017

This chapter briefly reviews the use of genomewide screening for early detection, treatment, and prevention and the utility of genome-based biomarkers as a tool for precision medicine and its application to population and integrative preventive medicine. Advances in technology have made genomic screening more affordable and widely available, and both our understanding and the value of testing grow as more data is collected. Even more recently, the growing availability of epigenetic testing, methylation and ROS-associated molecular signatures are providing more insight into dynamic aspects of the human genome and how lifestyle and IPM change affect the expression of the genome. Early adoption of precision medicine in oncology offers a model that should be expanded into wider areas of treatment and prevention.