bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian Classification of Vasculitis: A Simulation Study
Authors: Heller I. , Isakov A. , Blinder-Weiner S. , Topilsky M.
Published: March 2018

New classification criteria for vasculitic disorders have recently been proposed by the American College of Rheumatology. These classification criteria have limitations inherent to the method employed in their development. We propose a different approach to the quantitative analysis of the manifestations of vasculitis, which may improve the precision of classification criteria in this domain. Bayesian classifiers were developed for six vasculitides using literature-derived quantitative descriptions of these syndromes. These clinical data were also used in computer programs designed to generate simulations of vasculitis and control cases. The performance of Bayesian classifiers of vasculitis was then compared to that of the American College of Rheumatology criteria, using series of computer-simulated vasculitis cases. Bayesian classifiers identified simulated vasculitis cases with greater accuracy than those of the corresponding American College of Rheumatology 1990 vasculitis criteria in all six diseases studied. As predicted by theoretical considerations, Bayesian classifiers have the potential to identify vasculitis cases more accurately than the proposed American College of Rheumatology 1990 criteria.
Development and Evaluation of Fuzzy Criteria for the Diagnosis of Rheumatoid Arthritis
Authors: Adlassnig K.-P. , Kolarz G. , Leitich H.
Published: March 2018

In 1987, the American Rheumatism Association issued a set of criteria for the classification of rheumatoid arthritis (RA) to provide a uniform definition of RA patients. Fuzzy set theory and fuzzy logic were used to transform this set of criteria into a diagnostic tool that offers diagnoses at different levels of confidence: a definite level, which was consistent with the original criteria definition, as well as several possible and superdefinite levels. Two fuzzy models and a reference model which provided results at a definite level only were applied to 292 clinical cases from a hospital for rheumatic diseases. At the definite level, all models yielded a sensitivity rate of 72.6% and a specificity rate of 87.0%. Sensitivity and specificity rates at the possible levels ranged from 73.3% to 85.6% and from 83.6% to 87.0%. At the superdefinite levels, sensitivity rates ranged from 39.0% to 63.7% and specificity rates from 90.4% to 95.2%. Fuzzy techniques were helpful to add flexibility to preexisting diagnostic criteria in order to obtain diagnoses at the desired level of confidence.
A Problem-Oriented Patient Management Scheme
Authors: Hearn Catherine Rhys , Young D. W.
Published: March 2018

Inefficient patient care may occur not because of lack of medical skills or limitation of resources, but because of inconsistent or deficient application of current medical knowledge. Conventional recording of patient information in the traditional record makes it difficult to assess, for a group of patients with similar problems, the effectiveness of any particular management plan.

The ›Problem-Oriented Patient Management Scheme‹ has been developed to overcome these two difficulties. In essence it is a method of organising management plans for handling of patient problems. As the plans are prespecified they should reflect current medical opinion, as they are written down they can be applied consistently, and as the data needed is itemized the resulting patient record should be analysable to assess the effectiveness of the particular management scheme.
Ein Computerprogramm zur Fehlerentdeckungim „Allgemeinen Krankenblattkopf”
Authors: Thurmayr R. , Dirlich G. , Ruland G.
Published: March 2018

Für die Fehlerentdeckung in der laufenden Basisdokumentation haben wir in unserer Klinik ein Computerprogramm entwickelt und hier detailliert dargestellt. Dieses Programm vereint die verschiedenen Qualitätskontrollarten: Kontrolle der Einzelwerte auf formale unci faktische Fehler und Prüfung des Kollektivs auf Plausibilität. Das Programm wurde in mehrere Schritte zerlegt, in denen sich die Fehlersuche mit Hilfe einer datenverarbeitenden Anlage und die manuelle Fehlerkorrektur abwechseln. Die Reihenfolge dieser Einzelschritte wurde so aufgebaut, daB fortschreitend kompliziertere Methoden zur Fehlerentdeckung eingesetzt werden. Ebenso setzt die Fehlerverbesserung von Stufe zu Stufe mehr Wissen voraus, so daß die späteren Korrekturschritte nicht von den »leichteren« Fehlern mitbelastet werden.
Ein nicht-parametrischer Zweistichproben-F-Test auf Randomisierungsbasis
Authors: Lienert G. A. , Schulz H.
Published: March 2018

Es wird eine Übersicht über derzeit verfügbare verteilungsfreie Dispersionstests gegeben. Da bisher noch kein voll effizienter Zwei-Stichproben-Dispersionstest auf Randomisierungsbasis — entsprechend dem Randomisierungstest von Fisher für Lokationsunterschiede —• vorliegt, wurde ein solcher entwikkelt und an einem Beispiel demonstriert.

Das Rationale beruht darauf, daß die Meßwerte eines Zwei-Stichproben-Vergleiches — nach den Regeln der Kombinatorik — in allen möglichen Kombinationen angeordnet werden und für jede Kombination der zugehörige Varianzquotient (F-Bruch) berechnet wird. Auf diese Weise erhält man eine stichprobenspezifische Prüfverteilung. Die Prüfgröße ergibt sich aus der Zahl der F-Werte, die den beobachteten F-Wert erreichen oder übersteigen. Die Alternativhypothese kann einoder zweiseitig formuliert werden.

Vorteile des Tests: Er spricht nur auf Unterschiede der Dispersion zweier Stichproben an, und seine relative asymptotische Effizienz ist gleich eins. Nachteilig wirkt sich der erhebliche Rechenaufwand aus, wenn keine Rechenanlage zur Verfügung steht.
Die Erfassung qualitativer medizinischer Angaben mit Hilfe von Endlosmarkierungsbelegen (EMB)
Authors: Grabner H. , Neumann H.
Published: March 2018

Es wird über ein Verfahren berichtet, welches es ermöglicht, unter Verwendung von Endlosmarkierungsbelegen auch mit einer kleinen elektronischen Datenverarbeitungsanlage einen Großteil der qualitativen Daten im Krankenhaus zu erfassen.
Experimental Compound Letter Designations
Authors: Engelbert Herbert
Published: March 2018

Most companies use a system of letters and numbers to identify their experimental compounds before they have a name. A list of over 250 of the letter designations used by various companies is presented.
Automatic Method for Processing Mass Data in Clinical Medicine (FOSDIC)
Authors: Volk M. , Greenough M. L. , Pipberger H. V. , Cosma J.
Published: March 2018

1. The need for automatic data processing techniques in investigative medicine is briefly-stated and stresse’d.

2. Among the more widely used methods for collection, storage and analysis of large scale data, the punch cards, although suitable for direct computer input, leave a limited input speed.

3. A new system developed jointly by the Bureau of the Census and the National Bureau of Standards, called FOSDIC is described.

4. FOSDIC is basically an analog scanner actuated by a digital computer. It automatically reads, recodes and transcribes the information on magnetic tape in binary language.

5. FOSDIC. consists of four parts: a scanning unit, a program unit, a tape unit and a console.

6. Printed documents of suitable size and format are used for data collection; they are microfilmed” and the information contained therein is automatically scanned and recorded on digital magnetic tape, suitable for direct input to a digital electronic computer.

7. Some of the advantages offered by this system are stressed: they are speed and versatility in the scanning and transcribing process, flexibility in the size and format of the printed document and space saving in the storage of microfilmed documents.

8. FOSDIC system is being used in several research projects in progress; in one project reduction of clinical information is the aim, in other ones correlation between analog records such as the electrocardiogram with clinical information is pursued. Since the clinical information is collected from more than one hospital, uniformity in the collected documents is an important factor.
Design of a Computer Supported Clinical Study
Authors: Lemlich A. , Ziffer H.
Published: March 2018

A computer supported clinical study concerning the natural history and prognosis of heart disease was carried out. The use of automated data processing system facilitated the collection of clinical data and permitted the use of advanced statistical- procedures in the evaluation of these data. Clinical shock was found to be the most important factor in the prognosis of this disease. Other important clinical and laboratory features of this disease were investigated statistically. Further studies concerning the application of computer systems and techniques to clinical diagnosis are in progress and will be reported upon in the future.
Untersuchungen über die Ernährung als Krankheitsursache )
Authors: Lang K.
Published: March 2018

Neben die bekannten Untersuchungen über Mangel- und Überernährung sowie über die Imba-lanz von Nahrungsmitteln tritt heute das weltweite Problem der Nahrungsmittelumstellung, teils zivilisatorisch, teils durch die starke Bevölkerungszunahme bedingt. Die Industrialisierung von Erzeugung, Verarbeitung und Verteilung führt zu einer Veränderung der Qualität der Lebensmittel.

Die Möglichkeiten der Kontamination der Lebensmittel mit allerlei Fremdstoffen haben zugenommen, außerdem finden — allerdings in gesetzlich geregeltem Umfange — Lebensmittelzusatzstoffe zwecks Konservierung, Färbung, Aromatisierung u. dgl. Verwendung. Außerdem bedingt die Zubereitung der Nahrung das Entstehen neuer Substanzen mit teilweise nur imgenügend bekannter biologischer Wirkung.

Die Behauptungen, daß die gegenwärtige Ernährung die Ursache der sogenannten ,,Zivilisationskrankheiten” sei, sind weitgehend spekulativ. Dies wird an den 3 Beispielen Arteriosklerose, Krebs und Karies im Einzelnen ausgeführt.

Zur Zeit stehen keine einwandfreien Unterlagen darüber zur Verfügung, wie sich die qualitativen und quantitativen Veränderungen der Ernährung für den Menschen auswirken.

Voraussetzung für die Klärung dieser schwerwiegenden Fragen kann nur eine systematische, statistisch auswertbare Materialsammlung sein; deren Realisierung wird aber wegen der zu hohen Aufwendigkeit des Projektes in absehbarer Zeit vermutlich nicht möglich sein.
Lymphfisteln an der unteren Extremität
Authors: Piza-Katzer H. , Schoeller T. , Wechselberger G. , Del Frari B.
Published: March 2018

Wir berichten über die intraoperative Darstellung von postoperativ entstandenen Lymphfisteln an der unteren Extremität durch intrakutane Injektion von Methylenblau und deren chirurgische Therapie. Zusätzlich werden alternative Behandlungsmethoden der Lymphfisteln diskutiert. Patienten, Material, Methoden: Von März 2005 bis November 2006 wurde bei drei Patienten eine intraoperative Fisteldarstellung durch eine interdigitale intrakutane Injektion von Methylenblau durchgeführt und anschließend das dargestellte Lymphgefäß ligiert. Ergebnisse: Der unmittelbare postoperative Verlauf war komplikationsfrei. In einem durchschnittlichen Nachuntersuchungszeitraum von 11 Monaten trat kein Rezidiv auf. Schlussfolgerung: Die intraoperative Fisteldarstellung mit Methylenblau ist eine kostenarme Methode zur Diagnose und Behandlung einer externen Lymphfistel an der unteren Extremität.
Spectral simplicity of apparent complexity. II. Exact complexities and complexity spectra
Authors: Riechers Paul M. , Crutchfield James P.
Published: March 2018

The meromorphic functional calculus developed in Part I overcomes the nondiagonalizability of linear operators that arises often in the temporal evolution of complex systems and is generic to the metadynamics of predicting their behavior. Using the resulting spectral decomposition, we derive closed-form expressions for correlation functions, finite-length Shannon entropy-rate approximates, asymptotic entropy rate, excess entropy, transient information, transient and asymptotic state uncertainties, and synchronization information of stochastic processes generated by finite-state hidden Markov models. This introduces analytical tractability to investigating information processing in discrete-event stochastic processes, symbolic dynamics, and chaotic dynamical systems. Comparisons reveal mathematical similarities between complexity measures originally thought to capture distinct informational and computational properties. We also introduce a new kind of spectral analysis via coronal spectrograms and the frequency-dependent spectra of past-future mutual information. We analyze a number of examples to illustrate the methods, emphasizing processes with multivariate dependencies beyond pairwise correlation. This includes spectral decomposition calculations for one representative example in full detail.
Interplay between morphological and shielding effects in field emission via Schwarz-Christoffel transformation
Authors: Marcelino Edgar , de Assis Thiago A. , de Castilho Caio M. C.
Published: March 2018

It is well known that sufficiently strong electrostatic fields are able to change the morphology of Large Area Field Emitters (LAFEs). This phenomenon affects the electrostatic interactions between adjacent sites on a LAFE during field emission and may lead to several consequences, such as: the emitter's degradation, diffusion of absorbed particles on the emitter's surface, deflection due to electrostatic forces, and mechanical stress. These consequences are undesirable for technological applications, since they may significantly affect the macroscopic current density on the LAFE. Despite the technological importance, these processes are not completely understood yet. Moreover, the electrostatic effects due to the proximity between emitters on a LAFE may compete with the morphological ones. The balance between these effects may lead to a non trivial behavior in the apex-Field Enhancement Factor (FEF). The present work intends to study the interplay between proximity and morphological effects by studying a model amenable for an analytical treatment. In order to do that, a conducting system under an external electrostatic field, with a profile limited by two mirror-reflected triangular protrusions on an infinite line, is considered. The FEF near the apex of each emitter is obtained as a function of their shape and the distance between them via a Schwarz-Christoffel transformation. Our results suggest that a tradeoff between morphological and proximity effects on a LAFE may provide an explanation for the observed reduction of the local FEF and its variation at small distances between the emitter sites.
Electron parallel closures for the 3 + 1 fluid model
Authors: Ji Jeong-Young , Joseph Ilon
Published: March 2018

Linear closures are obtained for arbitrary collisionality for the 3 + 1 fluid model which includes the evolution of density, flow velocity, and pressure both parallel and perpendicular to a preferred direction, usually a magnetic field. A large set of 6400 moment equations is solved to provide closures that are accurate in the collisional regime and well into the collisionless regime. The closures in the collisionless limit are determined by solving the kinetic equation with a model collision operator. Simple fits for the kernel functions that define the closures are obtained for arbitrary collisionality in wave number space. The results are linearly accurate to within 3% across the entire range of collisionality.
Conformational effects on the torsional barriers in m-methylanisole studied by microwave spectroscopy
Authors: Ferres Lynn , Stahl Wolfgang , Nguyen Ha Vinh Lam
Published: March 2018

The microwave spectrum of m-methylanisole (also known as 3-methylanisole, or 3-methoxytoluene) was measured using a pulsed molecular jet Fourier transform microwave spectrometer operating in the frequency range of 2–26.5 GHz. Quantum chemical calculations predicted two conformers with the methoxy group in trans or cis position related to the ring methyl group, both of which were assigned in the experimental spectrum. Due to the internal rotation of the ring methyl group, all rotational transitions introduced large A-E splittings up to several GHz, which were analyzed with a newly developed program, called aixPAM, working in the principal axis system. There are significant differences in the V3 potential barriers of 55.7693(90) cm−1 and 36.6342(84) cm−1 determined by fitting 223 and 320 torsional components of the cis and the trans conformer, respectively. These values were compared with those found in other m-substituted toluenes as well as in o- and p-methylanisole. A comparison between the aixPAM and the XIAM code (using a combined axis system) was also performed.
Non-parametric wall model and methods of identifying boundary conditions for moments in gas flow equations
Authors: Liao Meng , To Quy-Dong , Léonard Céline , Monchiet Vincent
Published: March 2018

In this paper, we use the molecular dynamics simulation method to study gas-wall boundary conditions. Discrete scattering information of gas molecules at the wall surface is obtained from collision simulations. The collision data can be used to identify the accommodation coefficients for parametric wall models such as Maxwell and Cercignani-Lampis scattering kernels. Since these scattering kernels are based on a limited number of accommodation coefficients, we adopt non-parametric statistical methods to construct the kernel to overcome these issues. Different from parametric kernels, the non-parametric kernels require no parameter (i.e. accommodation coefficients) and no predefined distribution. We also propose approaches to derive directly the Navier friction and Kapitza thermal resistance coefficients as well as other interface coefficients associated with moment equations from the non-parametric kernels. The methods are applied successfully to systems composed of CH4 or CO2 and graphite, which are of interest to the petroleum industry.
Characteristics of GaN-based 500 nm light-emitting diodes with embedded hemispherical air-cavity structure
Authors: Zhang Minyan , Li Yufeng , Li Qiang , Su Xilin , Wang Shuai , Feng Lungang , Tian Zhenhuan , Guo Maofeng , Zhang Guowei , Ding Wen , Yun Feng
Published: March 2018

GaN-based 500 nm light-emitting diodes (LEDs) with an air-cavity formed on a laser-drilled hemispherical patterned sapphire substrate (HPSS) were investigated. The cross-section transmission electron microscopy image of the HPSS-LED epilayer indicated that most of the threading dislocations were bent towards the lateral directions. It was found that in InGaN/GaN multiple quantum wells (MQWs) of HPSS-LEDs, there were fewer V-pits and lower surface roughness than those of conventional LEDs which were grown on flat sapphire substrates (FSSs). The high-resolution x-ray diffraction showed that the LED grown on a HPSS has better crystal quality than that grown on a FSS. Compared to FSS-LEDs, the photoluminescence (PL) intensity, the light output power, and the external quantum efficiency at an injected current of 20 mA for the HPSS-LED were enhanced by 81%, 65%, and 62%, respectively, such enhancements can be attributed to better GaN epitaxial quality and higher light extraction. The slightly peak wavelength blueshift of electroluminescence for the HPSS-LED indicated that the quantum confined Stark effect in the InGaN/GaN MQWs has been reduced. Furthermore, it was found that the far-field radiation patterns of the HPSS-LED have smaller view angles than that of the FSS-LED. In addition, the scanning near field optical microscope results revealed that the area above the air-cavity has a larger PL intensity than that without an air-cavity, and the closer to the middle of the air-cavity the stronger the PL intensity. These nano-light distribution findings were in good agreement with the simulation results obtained by the finite difference time domain method.
Nano-structuring of multi-layer material by single x-ray vortex pulse with femtosecond duration
Authors: Kohmura Yoshiki , Zhakhovsky Vasily , Takei Dai , Suzuki Yoshio , Takeuchi Akihisa , Inoue Ichiro , Inubushi Yuichi , Inogamov Nail , Ishikawa Tetsuya , Yabashi Makina
Published: March 2018

A narrow zero-intensity spot arising from an x-ray vortex has huge potential for future applications such as nanoscopy and nanofabrication. We here present an X-ray Free Electron Laser (XFEL) experiment with a focused vortex wavefront which generated high aspect ratio nanoneedles on a Cr/Au multi-layer (ML) specimen. A sharp needle with a typical width and height of 310 and 600 nm was formed with a high occurrence rate at the center of a 7.71 keV x-ray vortex on this ML specimen, respectively. The observed width exceeds the diffraction limit, and the smallest structures ever reported using an intense-XFEL ablation were fabricated. We found that the elemental composition of the nanoneedles shows a significant difference from that of the unaffected area of Cr/Au ML. All these results are well explained by the molecular dynamics simulations, leading to the elucidation of the needle formation mechanism on an ultra-fast timescale.
Density functional theory study of atomic and electronic properties of defects in reduced anatase TiO2 nanocrystals
Authors: Morita Kazuki , Yasuoka Kenji
Published: March 2018

Anatase TiO2 nanocrystals have received considerable attention owing to their promising applications in photocatalysis, photovoltaics, and fuel cells. Although experimental evidence has shown that the performance of nanocrystals can be significantly improved through reduction, the mechanistic basis of this enhancement remains unclear. To shed a light on the chemistry of reduced anatase TiO2 nanocrystals, density functional theory were used to investigate the properties of defects and excess electrons. We demonstrated that oxygen vacancies are stable both on the surface and at the sub-surface of the nanocrystal, while titanium interstitials prefer sub-surface sites. Different defect locations possessed different excess electron structures, which contributed to deep and shallow states in the band gap of the nanocrystals. Furthermore, valence band tailing was observed, resulting in band gap narrowing. The theoretical results presented here deepen our understanding, and show the potential of defects to considerably change the macroscopic properties of anatase TiO2 nanocrystals.
Does the professional attitude of physicians always affect their professional behaviour? A survey in tertiary hospitals in Nanchang City, China
Authors: Wang Xuan , Du Xin , Liu Chenxi , Zhang Xinping
Published: March 2018

Objective Understanding the effect of professional attitude on professional behaviour is conducive to the development of targeted measures to promote professionalism. The aim of the present study was to explore the effect of professional attitude on professional behaviour. Methods Using a self-reported questionnaire, 212 physicians were surveyed using quota sampling in six tertiary hospitals in Nanchang City. The effect of professional attitude on professional behaviour was analysed through logistic regression analysis. Results Providing necessary care regardless of a patient’s ability to pay, working on quality improvement initiatives, informing patients of medical errors and reporting incompetent colleagues had significant positive effects on corresponding professional behaviour (odds ratios (95% confidence intervals) 11.06 (3.78, 32.40), 9.42 (1.93, 46.01), 4.04 (1.29, 12.63) and 5.51 (1.26, 24.08) respectively). However, attitudes towards minimising disparities in care, undergoing periodic recertification examinations and reporting medical errors did not significantly affect corresponding professional behaviour. Conclusions Professional attitude affects professional behaviour, but such an effect varies with different professional norms. These findings imply that improving the professional attitude is useful but insufficient to promote medical professionalism. A management system conducive to the conversion of professional attitude to professional behaviour should be established. What is known about the topic? Several studies have affirmed that Chinese physicians accept most areas of medical professionalism embodied in the Charter on Medical Professionalism. However, only a few published studies have examined the effect of professional attitude on professional behaviour. Understanding the effect of professional attitude on professional behaviour is conducive to the development of targeted measures to promote professionalism. The present study attempted to fill the current knowledge gaps. What does this paper add? The study surveyed professional attitudes and behaviour of Chinese physicians and explored the effects of the former on the latter. The study found that professional attitude affects professional behaviour, but such an effect varies with different professional norms. The results may help establish fundamental problems in the professionalism of physicians and in measures to promote professional behaviour not only in China, but also in other countries. What are the implications for practitioners? The implications for hospital managers and policy makers are that improving professional attitude is useful but insufficient to promote medical professionalism. A management system conducive to the conversion of professional attitude to professional behaviour should be established.
Trafficking to the seed protein storage vacuole
Authors: Ashnest Joanne R. , Gendall Anthony R.
Published: March 2018

The processing and subcellular trafficking of seed storage proteins is a critical area of physiological, agricultural and biotechnological research. Trafficking to the lytic vacuole has been extensively discussed in recent years, without substantial distinction from trafficking to the protein storage vacuole (PSV). However, despite some overlap between these pathways, there are several examples of unique processing and machinery in the PSV pathway. Moreover, substantial new data has recently come to light regarding the important players in this pathway, in particular, the intracellular NHX proteins and their role in regulating lumenal pH. In some cases, these new data are limited to genetic evidence, with little mechanistic understanding. As such, the implications of these data in the current paradigm of PSV trafficking is perhaps yet unclear. Although it has generally been assumed that the major classes of storage proteins are trafficked via the same pathway, there is mounting evidence that the 12S globulins and 2S albumins may be trafficked independently. Advances in identification of vacuolar targeting signals, as well as an improved mechanistic understanding of various vacuolar sorting receptors, may reveal the differences in these trafficking pathways.
Rlip depletion prevents spontaneous neoplasia in TP53 null mice
Authors: Awasthi Sanjay , Tompkins Joshua , Singhal Jyotsana , Riggs Arthur D. , Yadav Sushma , Wu Xiwei , Singh Sharda , Warden Charles , Liu Zheng , Wang Jinhui , Slavin Thomas P. , Weitzel Jeffrey N. , Yuan Yate-Ching , Awasthi Meenakshi , Srivastava Satish K. , Awasthi Yogesh C. , Singhal Sharad S.
Published: March 2018

Significance

Mice that have homozygous deletion of the p53 tumor suppressor protein universally die of malignancy, generally before 6 months of age. We show that hemizygous deficiency of RALBP1 (RLIP76 or Rlip) confers a degree of protection from spontaneous malignancy that has never previously been observed. This discovery introduces a paradigm for p53 function, in which Rlip plays a central role as an effector that appears necessary for the cancer susceptibility of p53 null mice. Because p53 loss has a powerful effect on genomic instability that contributes to the initiation and promotion of cancers and to drug and radiation resistance in humans, our findings provide a method for prevention and therapy of p53-deficient cancer.
How an intrinsic ligand tunes the activity of a potassium channel
Authors: Khoo Keith K. , Pless Stephan A.
Published: March 2018

Khoo and Pless examine new work that provides mechanistic insight into the role of the intrinsic ligand in KCNH ion channels.​
Research on the Precision Control Technology of Short - line Segmental Prefabricated Assembly Bridge
Authors: Dai Xihua , Wu Xingfa , Zhang Taike
Published: March 2018

Short-line prestressed assembly bridge construction method has been widespread used for more than 10 years in China, unlike the “wysiwyg” cast-in-place beam, prefabrication and assembling construction process control is more important, especially for the virtual segment assembly. Due to the short line method commonly used in the large-scale bridge project, it is necessary to research intensive construction control, and improve the level of short line method. This article studied in two ways: the precast assembling error processing and precision control based on parametric analysis of the structure deformation.
3. Making sense of genes and genomes
Authors: Archibald John
Published: March 2018

While DNA sequencing is faster and cheaper than ever before, genome assembly remains a significant challenge. ‘Making sense of genes and genomes’ explores how laboratory and computational methods are used in combination to elucidate the true physical nature of DNA molecules inside living cells, and how genes are identified among the vast quantities of chemical letters making up an organism’s genome. It begins with shotgun sequencing—a method that has stood the test of time in balancing efficiency and accuracy. It then considers the problems and solutions of genome assembly; gene finding with transcriptomics; the BLAST algorithm; how to find where proteins carry out their functions; and genome re-sequencing.
5. Evolutionary genomics
Authors: Archibald John
Published: March 2018

We are still learning how to make sense of what genome sequences have to tell us. ‘Evolutionary genomics’ first considers the ‘molecular clock’, a bedrock concept underlying modern comparative genomic research. Molecular clocks can be inferred using both protein (amino acid) and DNA (nucleotide) sequences. It then looks at our understanding of Y-chromosome and mitochondrial DNA evolution before discussing the difficulties of extracting ancient DNA from fossils. Among the most remarkable achievements of ancient DNA research has been the sequencing of nuclear genomes from Neanderthals and other now-extinct human relatives, aiding research into what makes us human. The question of how eukaryotic cells evolved from prokaryotes is also considered.
1. What is geophysics?
Authors: Lowrie William
Published: March 2018

Geophysics is a field of earth sciences that uses the methods of physics to investigate the complex physical properties of the Earth and the natural processes that have determined and continue to govern its evolution. ‘What is geophysics?’ explains how geophysical investigations cover a wide range of research fields—including planetary gravitational and magnetic fields and seismology—extending from surface changes that can be observed from Earth-orbiting satellites to complex behaviour in the Earth’s deep interior. The timescale of processes occurring in the Earth also has a very broad range, from earthquakes lasting a few seconds to the motions of tectonic plates that take place over tens of millions of years.
2. Planet Earth
Authors: Lowrie William
Published: March 2018

Two important physical laws determine the behaviour of the Earth as a planet and the relationship between the Sun and its planets: the law of conservation of energy and the law of conservation of angular momentum. ‘Planet Earth’ explains these laws along with the ‘Big Bang’ theory that describes the formation of the solar system: the Sun; the eight planets divided into the inner, terrestrial planets (Mercury, Venus, the Earth, and Mars) and the outer, giant planets (Jupiter, Saturn, Uranus, and Neptune); and the Trans-Neptunian objects that lie beyond Neptune. Kepler’s laws of planetary motion, the Chandler wobble, the effects of the Moon and Jupiter on the Earth’s rotation, and the Milankovitch cycles of climatic variation are also discussed.
5. Gravity and the figure of the Earth
Authors: Lowrie William
Published: March 2018

‘Gravity and the figure of the Earth’ discusses the measurement of gravity and its variation at the Earth’s surface and with depth. Gravity is about 0.5 per cent stronger at the poles than at the equator and it first increases with depth until the core–mantle boundary and then sinks to zero at the Earth’s centre. Using satellites to carry out geodetic and gravimetric observations has revolutionized geodesy, creating a powerful geophysical tool for observing and measuring dynamic processes on the Earth. The various measurement techniques employed fall in two categories: precise location of a position on the Earth (such as GPS) and accurate determination of the geoid and gravitational field. Bouguer and free-air gravity anomalies and isostasy are explained.
1. Origins
Authors: Ellis Erle C.
Published: March 2018

Overwhelming evidence now confirms that humans are changing Earth in unprecedented ways. With such evidence, the proposal to recognize the Anthropocene as a new interval of geologic time—the Anthropocene epoch—would seem without issue. Yet the opposite is true. The Anthropocene remains highly controversial even among Earth scientists. ‘Origins’ considers different origin stories—from the myths of ancient Greece to the First Copernican Revolution to Darwin’s origins of man. The significance of the Anthropocene resides in its role as a new lens through which age-old narratives and philosophical questions are being revisited and rewritten. It concludes that there are good reasons to accept that a new chapter of Earth history might indeed be unfolding, with humans playing a leading role.
7. Politikos
Authors: Ellis Erle C.
Published: March 2018

The concept of the Anthropocene has travelled far beyond its natural sciences origins. Since it was first proposed, the Anthropocene has inspired a barrage of socially relevant questions, stoked intense debates, and served as a muse for artists and designers. ‘Politikos’ explains that the politics of inequality, environmental ethics, and the challenges of responsible action under conditions of potentially catastrophic global change have all been connected with the Anthropocene proposal. Would scientific recognition of the Anthropocene change public perceptions and actions? What would happen if the Anthropocene was not accepted as a new epoch of geologic time? Despite many interpretations, there appears to be a common thread of the Anthropocene as crisis.
3. History and heroes
Authors: Hutchinson Ben
Published: March 2018

Seen from a Western perspective, the history of comparative literature can be divided into three categories: how European literatures have been compared inside Europe; how European literature has been compared with other cultures outside Europe; and how literatures outside Europe have been compared among themselves. ‘History and heroes’ explains how from the empire building of the 19th century, via the Jewish diaspora of the 20th century, to the postcolonial culture wars of the 21st century, the problems and prejudices of comparative literature have formed a cultural counterpart to the problems and prejudices of modernity. To understand its history, in this spirit, is to understand why it matters.
5. The futures of comparative literature
Authors: Hutchinson Ben
Published: March 2018

Comparative literature is both central and marginal to literary studies: central because it draws on almost every discipline in the Humanities; marginal because it is not tied to any single tradition, risking being ignored by all of them. For all its past struggles and present debates, comparative literature has an increasingly central role to play in the Humanities’ future. ‘The futures of comparative literature’ explains that in this age of specialists, generalists continue to play a vital role in shaping and supporting the life of the mind. International, interdisciplinary forms of knowledge remain the very essence of modernity. Now more than ever, the aesthetic education of comparative literature is indispensable.
8. Economics
Authors: Singer Peter
Published: March 2018

‘Economics’ considers Marx’s economic theories as outlined in Capital, which he regarded as his masterpiece. Marx believed that the capitalist economic system, regarded by the classical economists as natural and inevitable, was an alienated form of human life. The importance of economics lay in the explanation it provided of the workings of this alienation and the manner in which it could be overcome. Many of Marx’s theories have been refuted by events, so were the central theses of Capital simply mistaken? We should regard Capital as the work of a critic of capitalist society. Marx wanted to expose the deficiencies of classical economics in order to expose the deficiencies of capitalism.
A survey and evaluation of Web-based tools/databases for variant analysis of TCGA data
Authors: Zhang Zhuo , Li Hao , Jiang Shuai , Li Ruijiang , Li Wanying , Chen Hebing , Bo Xiaochen
Published: March 2018

The Cancer Genome Atlas (TCGA) is a publicly funded project that aims to catalog and discover major cancer-causing genomic alterations with the goal of creating a comprehensive ‘atlas’ of cancer genomic profiles. The availability of this genome-wide information provides an unprecedented opportunity to expand our knowledge of tumourigenesis. Computational analytics and mining are frequently used as effective tools for exploring this byzantine series of biological and biomedical data. However, some of the more advanced computational tools are often difficult to understand or use, thereby limiting their application by scientists who do not have a strong computational background. Hence, it is of great importance to build user-friendly interfaces that allow both computational scientists and life scientists without a computational background to gain greater biological and medical insights. To that end, this survey was designed to systematically present available Web-based tools and facilitate the use TCGA data for cancer research.
Functional annotation of genomic variants in studies of late-onset Alzheimer’s disease
Authors: Butkiewicz Mariusz , Blue Elizabeth E , Leung Yuk Yee , Jian Xueqiu , Marcora Edoardo , Renton Alan E , Kuzma Amanda , Wang Li-San , Koboldt Daniel C , Haines Jonathan L , Bush William S
Published: March 2018

Motivation

Annotation of genomic variants is an increasingly important and complex part of the analysis of sequence-based genomic analyses. Computational predictions of variant function are routinely incorporated into gene-based analyses of rare-variants, though to date most studies use limited information for assessing variant function that is often agnostic of the disease being studied.

Results

In this work, we outline an annotation process motivated by the Alzheimer’s Disease Sequencing Project, illustrate the impact of including tissue-specific transcript sets and sources of gene regulatory information and assess the potential impact of changing genomic builds on the annotation process. While these factors only impact a small proportion of total variant annotations (∼5%), they influence the potential analysis of a large fraction of genes (∼25%).

Availability and implementation

Individual variant annotations are available via the NIAGADS GenomicsDB, at https://www.niagads.org/genomics/ tools-and-software/databases/genomics-database. Annotations are also available for bulk download at https://www.niagads.org/datasets. Annotation processing software is available at http://www.icompbio.net/resources/software-and-downloads/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Deep learning improves antimicrobial peptide recognition
Authors: Veltri Daniel , Kamath Uday , Shehu Amarda
Published: March 2018

Motivation

Bacterial resistance to antibiotics is a growing concern. Antimicrobial peptides (AMPs), natural components of innate immunity, are popular targets for developing new drugs. Machine learning methods are now commonly adopted by wet-laboratory researchers to screen for promising candidates.

Results

In this work, we utilize deep learning to recognize antimicrobial activity. We propose a neural network model with convolutional and recurrent layers that leverage primary sequence composition. Results show that the proposed model outperforms state-of-the-art classification models on a comprehensive dataset. By utilizing the embedding weights, we also present a reduced-alphabet representation and show that reasonable AMP recognition can be maintained using nine amino acid types.

Availability and implementation

Models and datasets are made freely available through the Antimicrobial Peptide Scanner vr.2 web server at www.ampscanner.com.

Supplementary information

Supplementary data are available at Bioinformatics online.
A joint spatial factor analysis model to accommodate data from misaligned areal units with application to Louisiana social vulnerability
Authors: Nethery Rachel C , Sandler Dale P , Zhao Shanshan , Engel Lawrence S , Kwok Richard K
Published: March 2018

With the threat of climate change looming, the public health community has an interest in identifying communities at the highest risk of devastation based not only on geographic features but also on social characteristics. Indices of community social vulnerability can be created by applying a spatial factor analysis to a set of relevant social variables measured for each community; however, current spatial factor analysis methodology is ill-equipped to handle spatially misaligned data. We introduce a joint spatial factor analysis model that can accommodate spatial data from two distinct partitions of a geographic space and identify a common set of latent factors underlying them. By defining the latent factors over the intersection of the two partitions, the model minimizes loss of information. Using simulated data constructed to mimic the spatial structure of our real data, we confirm the reliability of the model and demonstrate its superiority over competing ad hoc methods for dealing with misaligned data in spatial factor analysis. Finally, we construct an index of community social vulnerability for each census tract in Louisiana, a state prone to environmental disasters, which could be exacerbated by climate change, by applying the joint spatial factor analysis model to a set of misaligned social indicator data from the state. To demonstrate the utility of this index, we integrate it with Louisiana flood insurance claims data to identify communities that may be at particularly high risk during natural disasters, based on both social and geographic features.
Seeing through†
Authors: Brander Keith M
Published: March 2018

The title of this paper is intended in the sense of both “seeing through things”, which requires critical, reflexive thinking and also in the sense of “seeing things through”, which requires tenacity and patience. I address some of the concerns that I have about how we think through, structure, and write about science and I introduce three major research areas that I have been involved in: (i) studies of population dynamics of fish in the Irish Sea that lead to work on plankton dynamics and marine ecosystems, but with the problems of marine policy and management in mind, (ii) the ICES/GLOBEC Cod and Climate Change programme, and (iii) global marine food production and the work of the IPCC.
Congenital Dermal Sinus and Limited Dorsal Myeloschisis: “Spectrum Disorders” of Incomplete Dysjuction Between Cutaneous and Neural Ectoderms
Authors: Lee Ji Yeoun , Park Sung-Hye , Chong Sangjoon , Phi Ji Hoon , Kim Seung-Ki , Cho Byung-Kyu , Wang Kyu-Chang
Published: March 2018

BACKGROUND

The existence of tethering tracts in spinal dysraphism, other than congenital dermal sinus (CDS), has been recognized and has been summated into an integrated concept of limited dorsal myeloschisis (LDM).

OBJECTIVE

To elucidate the underlying embryology of LDM in relation to CDS by focusing on the pathological features of special cases of tethering tracts.

METHODS

Out of 389 spinal dysraphism patients who were operated on from 2010 to 2016, 5 patients who had tethering tracts composed of both CDS and LDM (or “probable LDM” if only fibrous tissue was found) were identified. Their clinical presentation, radiological images, operative findings, and pathology were thoroughly reviewed.

RESULTS

Three nonsaccular-type patients harbored stalks in which the squamous epithelial lined sinus (CDS) was found in the distal portion, and fibroneural (LDM) or fibrous (probable LDM) tissue in the proximal part. Two patients had saccular lesions, and a stalk was found inside the sac, connecting a small pit on the skin to the spinal cord. The tracts were pathologically identical to a CDS.

CONCLUSION

This study reports the coexistence of CDS and LDM (or probable LDM) components. These unique cases support the hypothesis that the CDS and LDM are among a spectrum of an anomaly that is caused by failure of complete dysjunction between cutaneous and neural ectoderms. Neurosurgeons should be aware of the possibility of coexisting “CDS” components in cases suggestive of LDM. In such cases, not only untethering but also meticulous removal of the squamous epithelium is critical.
Phage Therapy for a Multidrug-Resistant Acinetobacter baumannii Craniectomy Site Infection
Authors: LaVergne Stephanie , Hamilton Theron , Biswas Biswajit , Kumaraswamy M , Schooley R T , Wooten Darcy
Published: March 2018

In the era of antibiotic resistance, alternative treatment options for multidrug-resistant bacterial infections are being explored. We present a case of multidrug-resistant Acinetobacter baumannii infection treated with bacteriophages. Clinical trials are needed to further investigate bacteriophage therapy as an option to treat multidrug-resistant bacterial infections.
Semi-Automated Visualization and ANalysis of Trends: A “SAVANT” for Facilitating Antimicrobial Stewardship Using Antistaphylococcal Resistance and Consumption as a Prototype
Authors: Clifford Robert J , Chukwuma Uzo , Sparks Michael E , Richesson Douglas , Neumann Charlotte V , Waterman Paige E , Moran-Gilad Jacob , Julius Michael D , Hinkle Mary K , Lesho Emil P
Published: March 2018

Background

Governments and health care regulators now require hospitals and nursing homes to establish programs to monitor and report antimicrobial consumption and resistance. However, additional resources were not provided. We sought to develop an approach for monitoring antimicrobial resistance and consumption that health care systems can implement with minimal added costs or modifications to existing diagnostic and informatics infrastructure.

Methods

Using (1) the electronic laboratory information system of a nationwide managed care network, (2) the 3 most widely used commercial microbiology diagnostic platforms, and (3) Staphylococcus aureus, one of the most common causes of infections worldwide, as a prototype, we validated the approach dubbed “SAVANT” for Semi-Automated Visualization and ANalysis of Trends. SAVANT leverages 3 analytical methods (time series analysis, the autoregressive integrated moving average, and generalized linear regression) on either commercial or open source software to report trends in antistaphylococcal use and resistance.

Results

All laboratory results from January 2010 through December 2015 from an annual average of 9.2 million health care beneficiaries were queried. Inpatient and outpatient prescription rates were calculated for 8 key antistaphylococcal compounds. Trends and relationships of antistaphylococcal consumption and resistance among 81 840 unique S. aureus isolates from >6.5 million cultures were revealed.

Conclusions

Using existing or freely available resources, SAVANT was successfully implemented across a complex and geographically dispersed 280-hospital network, bridging a critical gap between medical informatics, large-scale data analytics, and mandatory reporting of health care quality metrics.