bluuebunny/crossref_metadata_2025 huggingface dataset:
Impact of completion of primary biliary procedure on outcome of endoscopic retrograde cholangiopancreatographic related perforation
Authors: Srivastava S. , Sharma B. , Puri A. , Sachdeva S. , Jain L. , Jindal A.
Published: August 2017

Background and aims Perforation is one of the worst complications of therapeutic endoscopic retrograde cholangiopancreatography (ERCP). We aimed to study the epidemiology of ERCP related perforation and the impact of completion of intended procedure on the outcome of this complication.

Methods ERCP records from January 2007 to April 2012 were independently evaluated by two investigators for the occurrence of procedure related perforations. A total of 11 500 patients underwent therapeutic ERCP during the study period. The case records of 171 (1.5 %) patients with ERCP related perforations were reviewed to analyze the epidemiology and risk factors associated with poor outcome.

Results Of the 171 patients included in this study, the majority of perforations (n = 129, 75.4 %) were related to use of the needle-knife precut technique. Female gender (1.9 % vs 0.7 %, P < 0.001), age > 40 years (1.7 % vs 1.1 %, P < 0.01), and benign disease (1.7 % vs. 1.1 %, P < 0.01) were risk factors for ERCP related perforation. Most of the perforations (n = 135, 79 %) were detected during the procedure. The majority of patients were managed conservatively (n = 164, 96 %). Although 159 patients recovered, 12 patients (7 %) did not survive. Completion of intended biliary procedure for primary disease was associated with low risk of mortality (2 % vs 15.4 %, P < 0.001).

Conclusions ERCP related perforation is uncommon. The majority of patients can be managed conservatively. The risk of mortality is low and completion of the intended biliary procedure decreases the risk of mortality.
Die Weiterbildungssituation junger Ärztinnen und Ärzte in der Pneumologie: Facharztwahl und Einschätzung karriererelevanter Aspekte vergleichend nach Geschlecht und beruflicher Funktion
Authors: Christians Lucia , Prenzel Regina
Published: August 2017

Die Pneumologie gehört zu den Fächern, die sehr stark unter dem ärztlichen Nachwuchsmangel zu leiden haben. Demgegenüber steht eine fachgebietsübergreifend zunehmend hohe Zahl an weiblichem Nachwuchs, der aufgrund von internalen wie externalen Faktoren in einer erfolgreichen medizinischen Laufbahn blockiert wird.

Um jene karrierehinderlichen, aber auch karriereförderliche Faktoren sowie relevante Aspekte der Fachgebietswahl Pneumologie zu erfassen, wurde auf dem 56. Kongress der DGP eine Teilnehmerbefragung mit 358 Pneumologinnen und Pneumologen durchgeführt. Die Befragung erfolgte anhand eines strukturierten Fragebogens mit Fragen zur Mehrfachauswahl, entwickelt basierend auf Studienergebnissen von Buddeberg-Fischer et al. Dabei wurde verglichen, ob Frauen und Männer einerseits und Weiterzubildende und leitende Ärztinnen und Ärzte andererseits in ihren Einschätzungen divergieren.

Es zeigten sich dabei einige Hinweise auf einen Generationswandel in der Pneumologie: Weiterzubildende berücksichtigten häufiger eine „gute Vereinbarkeit mit einer eigenen Familie“ bei der Facharztwahl als Ober- und Chefärztinnen bzw. -ärzte. Sie empfanden auch die „Möglichkeit zur Teilzeitarbeit“ häufiger karriereförderlich, wohingegen leitende Ärztinnen und Ärzte den Fokus mehr auf den persönlichen Einsatz legten. Weiterhin scheinen Frauen auch in der Pneumologie eine Doppelbelastung von Familie und Beruf zu erleben. So waren für sie „Elternzeit, Kinder, Familie“ signifikant häufiger ein Hindernis in der eigenen Laufbahn. Anderseits erachteten sie die „Möglichkeit zur Teilzeitarbeit“ und eine proaktive Persönlichkeit häufiger als karriereförderlich.

Mehr Präsenz im Studium, flexible Arbeitszeiten und bedarfsgerechtes Mentoring, auch bezogen auf eine gute Kompatibilität von Familie und Beruf, erscheinen gute Strategien zu sein, um das Interesse des Nachwuchses an der Pneumologie zu fördern.
A feasibility study of photoacoustic imaging of ex vivo endoscopic mucosal resection tissues from Barrett’s esophagus patients
Authors: Lim Liang , Streutker Catherine , Marcon Norman , Cirocco Maria , Lao Alexandra , Iakovlev Vladimir , DaCosta Ralph , Wilson Brian
Published: August 2017

Background and study aims Accurate endoscopic detection of dysplasia in patients with Barrett’s esophagus (BE) remains a major clinical challenge. The current standard is to take multiple biopsies under endoscopic image guidance, but this leaves the majority of the tissue unsampled, leading to significant risk of missing dysplasia. Furthermore, determining whether there is submucosal invasion is essential for proper staging. Hence, there is a clinical need for a rapid in vivo wide-field imaging method to identify dysplasia in BE, with the capability of imaging beyond the mucosal layer. We conducted an ex vivo feasibility study using photoacoustic imaging (PAI) in patients undergoing endoscopic mucosal resection (EMR) for known dysplasia. The objective was to characterize the esophageal microvascular pattern, with the long-term goal of performing in vivo endoscopic PAI for dysplasia detection and therapeutic guidance.

Materials and methods EMR tissues were mounted luminal side up. The tissues were scanned over a field of view of 14 mm (width) by 15 mm (depth) at 680, 750, and 850 nm (40 MHz acoustic central frequency). Ultrasound and photoacoustic images were simultaneously acquired. Tissues were then sliced and fixed in formalin for histopathology with hematoxylin and eosin staining. A total of 13 EMR specimens from eight patients were included in the analysis, which consisted of co-registration of the photoacoustic images with corresponding pathologist-classified histological images. We conducted mean difference test of the total hemoglobin distribution between tissue classes.

Results Dysplastic and nondysplastic BE can be distinguished from squamous tissue in 84 % of region-of-interest comparisons (42/50). However, the ability of intrinsic PAI to distinguish dysplasia from NDBE, which is the clinically important challenge, was only about 33 % (10/30).

Conclusion We demonstrated the technical feasibility of this approach. Based on our ex vivo data, changes in total hemoglobin content from intrinsic PAI (i. e. without exogenous contrast) can differentiate BE from squamous esophageal mucosa. However, most likely intrinsic PAI is unable to differentiate dysplastic from nondysplastic BE with adequate sensitivity for clinical translation.
Wie sich Bewegung entwickeln kann
Authors: Eppler Sonja , Brutscher Petra
Published: August 2017

Taktile Wahrnehmung als Grundlage kindlicher Entwicklungs- und Entfaltungs­möglichkeiten Bei der Bewegungs- und entwicklungsfördernden
Pflege von Früh- und Neugeborenen sind Pflegende und vor allem Eltern wichtige Interaktionspartner. Hierzu wurden in den letzten Jahren
verschiedene Konzepte entwickelt, dazu gehören Kinästhetik Infant Handling, Basale Stimulation® und das NIDCAP®-Konzept. Dabei stellen sich
immer wieder folgende Fragen: Welche Bedeutung hat Bewegung und Entwicklung in der Interaktion mit den Kleinsten? Wann und wie lernen Kinder
sich zu bewegen? Welche Erfahrungen machen sie vor der Geburt? Was verändert sich mit der Geburt? Wie bedeutend sind diese Erfahrungen für
die Entwicklung? Und was sollten Eltern und Pflegende darüber wissen? – Der dritte Teil unserer Reihe über Kinästhetik soll ­einen kleinen
Einblick in die Bewegungsentwicklung geben.
Inklusion ist Teamwork
Authors: Strecker Dirk
Published: August 2017

Gemeinsamer Schulunterricht mit einem Intensivkind Linn ist schwerstmehrfachbehindert und braucht zudem Intensivpflege. Trotzdem geht
sie in eine Regelschule und nimmt gemeinsam mit gesunden Kindern am Unterricht teil. Möglich wird das durch die Zusammenarbeit aller
Beteiligten – von der Schule über den Pflegedienst und die Pflegefachkräfte bis hin zu Linns Mutter und Vater. Der ist selbst lange in der
Pflegedienstleitung eines ambulanten Kinderkrankenpflegedienstes tätig gewesen. Am Beispiel seiner Tochter berichtet er, wie Inklusion
gelingen kann.
Sommer, Sonne – und was nun?
Authors: Tiedke Barbara E.
Published: August 2017

Schutz von Kindern mit kardiologischen Erkrankungen Weder Alt noch Jung sollte im Sommer ungeschützt in die Sonne gehen. Denn zu viel
Sonne ist nicht nur gefährlich für die Haut, die Hitze belastet auch Herz und Kreislauf. Das gilt im besonderen Maße für Menschen mit
Herzerkrankungen. Wie sich Kinder mit angeborenen Herzfehlern im Sommer am besten schützen, fasst der folgende Beitrag zusammen.
Effects of Fatigue on Voluntary Electromechanical and Relaxation Electromechanical Delay
Authors: Smith Cory , Housh Terry , Hill Ethan , Keller Joshua , Johnson Glen , Schmidt Richard
Published: August 2017

The purposes of the present study were to examine: 1) the effects of fatigue on electromechanical delay from the onsets of the electromyographic signal to force production (EMDE-F), the onsets of the electromyographic to mechanomyographic signals (EMDE-M), the onsets of the mechanomyographic signal to force production (EMDM-F), as well as the cessations of the electromyographic to force production (R-EMDE-F), cessation of the electromyographic to mechanomyographic signals (R-EMDE-M), and cessations of the mechanomyographic signal to force production (R-EMDM-F); and 2) the relative contributions from EMDE-M and EMDM-F to EMDE-F as well as R-EMDE-M and R-EMDM-F to R-EMDE-F from the vastus lateralis in non-fatigued and fatigued states. The values EMDE-F, EMDE-M, EMDM-F, R-EMDE-F, R-EMDE-M and R-EMDM-F were calculated during maximal voluntary isometric contractions, before and after 70% 1-repetition maximum leg extensions to failure. There were significant pretest to posttest increases in EMDE-F (73%;p<0.01), EMDE-M (99%;p<0.01), EMDM-F (60%;p<0.01), R-EMDE-F (101%;p<0.01) and R-EMDM-F (368%;p<0.01), but no significant change in R-EMDE-M (25%;p=0.46). Fatigue-induced increase in EMDE-F indicated excitation-contraction coupling failure (EMDE-M) and increases in the compliance of the series elastic component (EMDM-F). Increases in R-EMDE-F were due to increases in relaxation time for the series elastic component (R-EMDM-F), but not changes in the reversal of excitation-contraction coupling (R-EMDE-M).
Permanent magnetic properties of NdFe12Nx sputtered films epitaxially grown on V buffer layer
Authors: Sato T. , Ohsuna T. , Yano M. , Kato A. , Kaneko Y.
Published: August 2017

To clarify the magnetic properties of the NdFe12Nx compound, which shows promise as a high-performance permanent magnet material, NdFe12Nx epitaxial films fabricated by using a V underlayer on MgO (100) single-crystalline substrates were investigated. Nd-Fe films deposited on a V underlayer consist of NdFe12 grains, which have a c-axis orientation perpendicular to the film plane, as well as α-Fe and Nd2Fe17 phases. In the Nd-Fe-N film obtained by subsequent nitridation of the Nd-Fe film, NdFe12Nx grains grew as the dominant phase, and the volume fractions of α-Fe phases dropped below 5%. A Nd-Fe-N film with a thickness of 50 nm exhibits a saturation magnetization (Ms) of 1.7 T, an anisotropy field (HA) of ∼60 kOe, a magnetocrystalline anisotropy energy (K1) of ∼4.1 MJ/m3, and a coercivity (Hc) of 1.7 kOe. The Hc of a Nd-Fe-N film with a thickness of 25 nm is 4.3 kOe. These results indicate that NdFe12Nx compounds have a superior Ms compared to Nd-Fe-B magnets, while the enhancement in Hc is indispensable.
Note: Development of a cryocooler based high efficiency cryosorption pump
Authors: Verma Ravi , Chatterjee Aritra , Kasthurirengan Srinivasan , Shivaprakash N. C. , Behera Upendra
Published: August 2017

In this communication, we report the development of a cryosorption pump, whose pumping speeds are higher at least by a factor of 1.5 compared to the commercial pumps in specific pressure ranges. This uses a material of high adsorbing capacity along with an adhesive of high thermal conductivity. The measured pumping speeds of these pumps for different gases such as nitrogen, argon, hydrogen, and helium are higher than the commercial cryopumps in the pressure range from 5 × 10−6 mbar to 5 × 10−5 mbar. The developed pump will be quite useful for fusion applications.
Laboratory study of collisionless coupling between explosive debris plasma and magnetized ambient plasma
Authors: Bondarenko A. S. , Schaeffer D. B. , Everson E. T. , Clark S. E. , Lee B. R. , Constantin C. G. , Vincena S. , Van Compernolle B. , Tripathi S. K. P. , Winske D. , Niemann C.
Published: August 2017

The explosive expansion of a localized plasma cloud into a relatively tenuous, magnetized, ambient plasma characterizes a variety of astrophysical and space phenomena. In these rarified environments, collisionless electromagnetic processes rather than Coulomb collisions typically mediate the transfer of momentum and energy from the expanding “debris” plasma to the surrounding ambient plasma. In an effort to better understand the detailed physics of collisionless coupling mechanisms, compliment in situ measurements of space phenomena, and provide validation of previous computational and theoretical work, the present research jointly utilizes the Large Plasma Device and the Raptor laser facility at the University of California, Los Angeles to study the super-Alfvénic, quasi-perpendicular expansion of laser-produced carbon (C) and hydrogen (H) debris plasma through preformed, magnetized helium (He) ambient plasma via a variety of diagnostics, including emission spectroscopy, wavelength-filtered imaging, and a magnetic flux probe. Doppler shifts detected in a He1+ ion spectral line indicate that the ambient ions initially accelerate transverse to both the debris plasma flow and the background magnetic field. A qualitative analysis in the framework of a “hybrid” plasma model (kinetic ions and inertia-less fluid electrons) demonstrates that the ambient ion trajectories are consistent with the large-scale laminar electric field expected to develop due to the expanding debris. In particular, the transverse ambient ion motion provides direct evidence of Larmor coupling, a collisionless momentum exchange mechanism that has received extensive theoretical and numerical investigation. In order to quantitatively evaluate the observed Doppler shifts, a custom simulation utilizing a detailed model of the laser-produced debris plasma evolution calculates the laminar electric field and computes the initial response of a distribution of ambient test ions. A synthetic Doppler-shifted spectrum constructed from the simulated test ion velocities excellently reproduces the experimental measurements, verifying that the observed ambient ion motion corresponds to collisionless coupling through the laminar electric field.
Energy spectrum of a generalized Scarf potential using the asymptotic iteration method and the tridiagonal representation approach
Authors: Al-Buradah Sadig A. , Bahlouli Hocine , Alhaidari Abdulaziz D.
Published: August 2017

The well-known trigonometric Scarf potential is generalized by adding a sinusoidal term and then treated using the Asymptotic Iteration Method (AIM) and the Tridiagonal Representation Approach (TRA). The energy spectrum of the associated bound states is computed. For the AIM, we have improved convergence of the quantization condition that terminates the iterations asymptotically. This is accomplished by looking for the range of initial values of the space variable in the terminating condition that produces stable results (plateau of convergence). We have shown that with increasing iteration, this plateau of convergence grows up rapidly to an optimal iteration number and then shrinks slowly to a point. The value of this point (or points) may depend on the physical parameters. The numerical results have been compared favorably with those resulting from the TRA.
Optically active dilute-antimonide III-nitride nanostructures for optoelectronic devices
Authors: Chowdhury F. A. , Sadaf S. M. , Shi Q. , Chen Y.-C. , Guo H. , Mi Z.
Published: August 2017

We have studied the epitaxy, energy bandgap, and structural and optical properties of GaSbN nanostructures in the dilute antimony (Sb) limit (Sb concentration < 1%). GaSbN nanowire structures are grown on a Si substrate by plasma-assisted molecular beam epitaxy. It is observed, both theoretically and experimentally, that the incorporation of a very small amount of Sb (<1%) in GaN can substantially reduce the energy bandgap of GaN from 3.4 eV to ∼2 eV. We have further demonstrated that emission wavelengths of GaSbN nanowires can be tuned from ∼365 nm to 600 nm at room-temperature by varying the Sb incorporation. Functional GaSbN nanowire light-emitting diodes are also demonstrated, which exhibit strong emission in the deep-visible spectral range.
A novel current injection device for harmonic reduction of three-phase controlled converters in renewable energy utility interfacing
Authors: Eltamaly Ali M.
Published: August 2017

Three-phase controlled/uncontrolled converters have been used in renewable energy applications such as photovoltaic and wind energy as rectifiers and inverters. The main drawback of these converters is the high THD (Total Harmonic Distortion) in their line currents. Many techniques have been used to remedy this problem. Third harmonic current injection is one of the best solutions for the harmonic reduction in line currents of these converters. Injecting third harmonic current from the dc-bus to the line currents reduces its harmonic contents. Minimum THD for any firing angle of the controlled converter is a function of the phase-angle and amplitude of harmonic injection current that can be controlled by a single-phase controlled converter and a boost converter, respectively. This scheme is used with a zigzag transformer to circulate the harmonic injection current to the line currents. A novel mathematical analysis for the proposed scheme and state of the art scheme is introduced. The mathematical analysis introduces the optimum values for components on the harmonic injection path at minimum THD and the corresponding efficiency. The scheme under study has been simulated using the PSIM program. A lab prototype for this scheme has been implemented. Mathematical, simulation, and experimental results for this scheme have been introduced, compared, and discussed. The results show the superiority of the proposed scheme.
Numerical simulation of quantized current generated by a quantum dot pump
Authors: Ahn Ye-Hwan , Chung Yunchul
Published: August 2017

The quantized current generated by a quantum dot pump is calculated numerically. The numerical simulation is done by dividing the time varying potential into many static potentials with a short time interval and calculating the electron capture and pumping rate with the time independent Schrödinger equation. The simulation results show good agreement with reported experimental results qualitatively. The calculated 2D pump current map and the plateau width dependence on the modulation gate voltage show good agreement with the experimental results. From the simulation results, it is explained how the back-tunneling process affects the accuracy of the current plateaus quantitatively. Also, the energy distribution of the pumped electron is calculated, which can be measured experimentally. Finally, it is found that the pump current accuracy can be enhanced by increasing the entrance gate width, which is important to realize the quantum current standard.
Patterns of dissolved organic matter across the Patagonian landscape: a broad-scale survey of Chilean and Argentine lakes
Authors: Zagarese Horacio E. , Ferraro Marcela , Queimaliños Claudia , Diéguez María del Carmen , Suárez Diego Añón , Llames María Eugenia
Published: August 2017

Dissolved organic matter (DOM) is a complex mixture of carbon compounds from autochthonous and allochthonous sources. Dissolved organic carbon (DOC) concentrations and optical metrics of DOM provide clues as to the sources and processes affecting the DOM pool. Herein we provide the first broad-scale characterisation of DOM from Patagonian lakes across a strong west–east precipitation gradient. Fifty-eight lakes from Northern Patagonia (Argentina and Chile) plus six lakes from the Antarctic Peninsula were sampled during summer 2000–01. Six DOM metrics were evaluated: DOC absorbance at 254nm (a254) and 350nm (a350), DOC-specific absorbance at 254nm (a254/DOC) and 350nm (a350/DOC) and spectral slope between 275 and 295nm (S275–295). The DOM of Chilean maritime lakes and shallow (<15m) Andean lakes exhibited terrestrial signatures and a pattern of variation consistent with their occurrence across the longitudinal precipitation gradient (i.e. S275–295 increased, whereas a350/DOC decreased from west to east). The contribution of allochthonous DOM was smaller in deep (>15m) Andean lakes, which is consistent with their longer water retention time. Steppe lakes, mostly from endorheic basins, made up the most heterogeneous group with regard to DOM characteristics.
Nitrogen: the historical progression from ignorance to knowledge, with a view to future solutions
Authors: Galloway James N. , Leach Allison M. , Erisman Jan Willem , Bleeker Albert
Published: August 2017

Once upon a time there was enough naturally occurring nitrogen (N) to provide food for the world’s peoples. Then there was not in the western regions. Now there is due to industrially produced NH3. But this transition from plenty, to scarcity, to plenty has come with a tremendous environmental cost. This paper provides an historical overview of the growth of knowledge about N and about its impacts, both positive and negative. The paper also explores three scenarios of what might have been, if in 1700 the world had the N-knowledge that we have now. The paper then projects N use to feed the world’s people in 2050 under three scenarios of per-capita protein consumption: increasing, constant and decreasing relative to nutritional guidelines. The three projected results for 2050 annual N use from producing and consuming food are 320, 230 and 170 Tg N respectively. The latter is equivalent to 1970 levels. Given that the first scenario (increasing protein) is most likely without utilising our N-knowledge, the paper ends with suggestions for improvements in N use and management.
Towards an Improved System for Sampling New England Groundfish Using Video Technology
Authors: Stokesbury Kevin D. E. , Cadrin Steven X. , Calabrese Nick , Keiley Emily , Lowery Travis M. , Rothschild Brian J. , DeCelles Gregory R.
Published: August 2017

There is considerable controversy regarding abundance estimates of New England groundfish. Federal surveys sample randomly but are restricted to short tow lengths and minimal area covered at high daily expense. Working collaboratively with fishermen, we developed a video system that can be deployed in a commercial trawl net to improve the information on the abundance and distribution of groundfish stocks (focusing on Atlantic Cod Gadus morhua and Yellowtail Flounder Limanda ferruginea) by increasing the amount of sea floor sampled per sea day without killing more fish. Rather than being hauled to the surface for counting, fish are counted as they pass through the net. This results in continuous transect data that can be processed into sampling units, randomized, and used to estimate abundance. High-intensity sampling of important habitats can complement existing multispecies random and stratified random survey designs to reduce uncertainty, presenting a clearer picture of the resource.
Use of Gifu Anaerobic Medium for culturing 32 dominant species of human gut microbes and its evaluation based on short-chain fatty acids fermentation profiles
Authors: Gotoh Aina , Nara Misaki , Sugiyama Yuta , Sakanaka Mikiyasu , Yachi Hiroyuki , Kitakata Aya , Nakagawa Akira , Minami Hiromichi , Okuda Shujiro , Katoh Toshihiko , Katayama Takane , Kurihara Shin
Published: August 2017

Recently, a “human gut microbial gene catalogue,” which ranks the dominance of microbe genus/species in human fecal samples, was published. Most of the bacteria ranked in the catalog are currently publicly available; however, the growth media recommended by the distributors vary among species, hampering physiological comparisons among the bacteria. To address this problem, we evaluated Gifu anaerobic medium (GAM) as a standard medium. Forty-four publicly available species of the top 56 species listed in the “human gut microbial gene catalogue” were cultured in GAM, and out of these, 32 (72%) were successfully cultured. Short-chain fatty acids from the bacterial culture supernatants were then quantified, and bacterial metabolic pathways were predicted based on in silico genomic sequence analysis. Our system provides a useful platform for assessing growth properties and analyzing metabolites of dominant human gut bacteria grown in GAM and supplemented with compounds of interest.
Comparing state pension reforms in EU countries before and after 2008
Authors: Grech Aaron George
Published: August 2017

Many EU countries have been carrying out substantial state pension reforms since the mid-1990s. This article studies whether the reforms that were carried out in ten EU countries before and after the 2008 financial crisis are different. This is done through an analysis of the different elements of these reforms and also by comparing pension entitlements after each set of reforms. The main conclusion is that the pre-crisis reforms were much stronger and had a more negative impact on women than the post-crisis reforms. It is harder to determine whether this represents a temporary break in the reform process or a permanent change in the orientation of pension reforms in these ten countries.
Impaired JIP3-dependent axonal lysosome transport promotes amyloid plaque pathology
Authors: Gowrishankar Swetha , Wu Yumei , Ferguson Shawn M.
Published: August 2017

Lysosomes robustly accumulate within axonal swellings at Alzheimer’s disease (AD) amyloid plaques. However, the underlying mechanisms and disease relevance of such lysosome accumulations are not well understood. Motivated by these problems, we identified JNK-interacting protein 3 (JIP3) as an important regulator of axonal lysosome transport and maturation. JIP3 knockout mouse neuron primary cultures accumulate lysosomes within focal axonal swellings that resemble the dystrophic axons at amyloid plaques. These swellings contain high levels of amyloid precursor protein processing enzymes (BACE1 and presenilin 2) and are accompanied by elevated Aβ peptide levels. The in vivo importance of the JIP3-dependent regulation of axonal lysosomes was revealed by the worsening of the amyloid plaque pathology arising from JIP3 haploinsufficiency in a mouse model of AD. These results establish the critical role of JIP3-dependent axonal lysosome transport in regulating amyloidogenic amyloid precursor protein processing and support a model wherein Aβ production is amplified by plaque-induced axonal lysosome transport defects.
Phosphoinositide-mediated ring anchoring resists perpendicular forces to promote medial cytokinesis
Authors: Snider Chloe E. , Willet Alaina H. , Chen Jun-Song , Arpağ Göker , Zanic Marija , Gould Kathleen L.
Published: August 2017

Many eukaryotic cells divide by assembling and constricting an actin- and myosin-based contractile ring (CR) that is physically linked to the plasma membrane (PM). In this study, we report that Schizosaccharomyces pombe cells lacking efr3, which encodes a conserved PM scaffold for the phosphatidylinositol-4 kinase Stt4, build CRs that can slide away from the cell middle during anaphase in a myosin V–dependent manner. The Efr3-dependent CR-anchoring mechanism is distinct from previously reported pathways dependent on the Fes/CIP4 homology Bin-Amphiphysin-Rvs167 (F-BAR) protein Cdc15 and paxillin Pxl1. In efr3Δ, the concentrations of several membrane-binding proteins were reduced in the CR and/or on the PM. Our results suggest that proper PM lipid composition is important to stabilize the central position of the CR and resist myosin V–based forces to promote the fidelity of cell division.
Commodity Price Comovement and Financial Speculation: The Case of Cotton
Authors: Janzen Joseph P. , Smith Aaron , Carter Colin A.
Published: August 2017

Recent booms and busts in commodity prices have generated concerns that financial speculation causes excessive commodity‐price comovement, driving prices away from levels implied by supply and demand under rational expectations. We develop a structural vector autoregression model of a commodity futures market and use it to explain two recent spikes in cotton prices. In doing so, we make two contributions to the literature on commodity price dynamics. First, we estimate the extent to which cotton price booms and busts can be attributed to comovement with other commodities. Finding such comovement would be necessary but would not be sufficient evidence to establish that broad‐based financial speculation drives commodity prices. Second, after controlling for aggregate demand and comovement, we develop a new method to point identify shocks to precautionary demand for cotton separately from shocks to current supply and demand. To do so, we use differences in volatility across time implied by the rational expectations competitive storage model. We find limited evidence that financial speculation caused cotton prices to spike in 2008 or 2011. We conclude that the 2008 price spike was driven mostly by precautionary demand for cotton, and the 2011 spike was caused by a net supply shortfall.
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization
Authors: Katoh Kazutaka , Rozewicki John , Yamada Kazunori D
Published: August 2017

This article describes several features in the MAFFT online service for multiple sequence alignment (MSA). As a result of recent advances in sequencing technologies, huge numbers of biological sequences are available and the need for MSAs with large numbers of sequences is increasing. To extract biologically relevant information from such data, sophistication of algorithms is necessary but not sufficient. Intuitive and interactive tools for experimental biologists to semiautomatically handle large data are becoming important. We are working on development of MAFFT toward these two directions. Here, we explain (i) the Web interface for recently developed options for large data and (ii) interactive usage to refine sequence data sets and MSAs.
Metagene projection characterizes GEN2.2 and CAL-1 as relevant human plasmacytoid dendritic cell models
Authors: Carmona-Sáez Pedro , Varela Nieves , Luque María José , Toro-Domínguez Daniel , Martorell-Marugan Jordi , Alarcón-Riquelme Marta E , Marañón Concepción
Published: August 2017

Motivation

Plasmacytoid dendritic cells (pDC) play a major role in the regulation of adaptive and innate immunity. Human pDC are difficult to isolate from peripheral blood and do not survive in culture making the study of their biology challenging. Recently, two leukemic counterparts of pDC, CAL-1 and GEN2.2, have been proposed as representative models of human pDC. Nevertheless, their relationship with pDC has been established only by means of particular functional and phenotypic similarities. With the aim of characterizing GEN2.2 and CAL-1 in the context of the main circulating immune cell populations we have performed microarray gene expression profiling of GEN2.2 and carried out an integrated analysis using publicly available gene expression datasets of CAL-1 and the main circulating primary leukocyte lineages.

Results

Our results show that GEN2.2 and CAL-1 share common gene expression programs with primary pDC, clustering apart from the rest of circulating hematopoietic lineages. We have also identified common differentially expressed genes that can be relevant in pDC biology. In addition, we have revealed the common and differential pathways activated in primary pDC and cell lines upon CpG stimulatio.

Availability and implementation

R code and data are available in the supplementary material.

Supplementary information

Supplementary data are available at Bioinformatics online.
3. Producing a persuasive presentation
Authors: Snape John , Watt Gary
Published: August 2017

This chapter provides guidance on producing a persuasive presentation. It provides answers to the following questions: Is it always necessary to prepare for a moot presentation? What form should a presentation take? When is a submission outside the ground of appeal? How long should the presentation be? How should submissions be presented logically? How should one prepare for a moot presentation? Should the speech be written out? Should it be read out or should it be learnt by heart?
4. Choice and use of authorities
Authors: Snape John , Watt Gary
Published: August 2017

This chapter focuses on the main tool of the mooter's trade — case authorities. It provides answers to the following questions: What is ‘exchange of authorities’ and is it appropriate to rely on the opponent's authorities? How should authorities be chosen? How should authorities be cited? Should research be delegated to others? Can other people's ideas be used? Should help be sought from tutors? In what ways can the law library be used in preparing for a moot presentation? What is the difference between square and round brackets in a case citation? How should electronic information resources be used? When and how should overseas authorities be referred to? What does the Latin mean in a law report? How can old cases be obtained? Is an authority ever too old to use? In addition to reading a report of a judgment of a case, should counsels' arguments also be read?
6. Professional practice
Authors: Snape John , Watt Gary
Published: August 2017

This chapter demonstrates the relevance of mooting for professional practice. It shows that mooting insists upon exacting standards of behaviour, dress, personal presentation, research, preparation, information management, time management, and communication. Mooting provides students with a set of skills than can make them better lawyers. At the very least it will equip students to work within a team, and to a deadline, and to present the fruits of teamwork in a robust, attractive, and memorable way. The chapter provides answers to the following questions: How should colleagues be liaised with and should their arguments be known? Are there any rules of fair play to be observed in mooting? Should the original law reports be produced in front of the moot court? When should skeleton arguments be used and what form should skeleton arguments, if permitted, take? Should Latin be used in the moot presentation? Is a professional courtroom manner important? What is the dress code for a moot? How should colleagues and opponents be addressed and referred to?
Fast, robust and precise 3D localization for arbitrary point spread functions
Authors: Li Yiming , Mund Markus , Hoess Philipp , Matti Ulf , Nijmeijer Bianca , Sabinina Vilma Jimenez , Ellenberg Jan , Schoen Ingmar , Ries Jonas
Published: August 2017

We present a fitter for 3D single-molecule localization of arbitrary, experimental point spread functions (PSFs) that reaches minimum uncertainty for EMCCD and sCMOS cameras, and achieves more than 105fits/s. We provide tools to robustly model experimental PSFs and correct for depth induced aberrations, which allowed us to achieve an unprecedented 3D resolution with engineered astigmatic PSFs, and acquire high quality 3D superresolution images even on standard microscopes without 3D optics.
Fear extinction requires infralimbic cortex projections to the basolateral amygdala
Authors: Bloodgood Daniel W. , Sugam Jonathan A. , Holmes Andrew , Kash Thomas L.
Published: August 2017

Fear extinction involves the formation of a new memory trace that attenuates fear responses to a conditioned aversive memory, and extinction impairments are implicated in trauma- and stress-related disorders. Previous studies in rodents have found that the infralimbic prefrontal cortex (IL) and its glutamatergic projections to the basolateral amygdala (BLA) and basomedial amygdala (BMA) instruct the formation of fear extinction memories. However, it is unclear whether these pathways are exclusively involved in extinction, or whether other major targets of the IL, such as the nucleus accumbens (NAc) also play a role. To address this outstanding issue, the current study employed a combination of electrophysiological and chemogenetic approaches in mice to interrogate the role of IL-BLA and IL-NAc pathways in extinction. Specifically, we used patch-clamp electrophysiology coupled with retrograde tracing to examine changes in neuronal activity of the IL and prelimbic cortex (PL) projections to both the BLA and NAc following fear extinction. We found that extinction produced a significant increase in the intrinsic excitability of IL-BLA projection neurons, while extinction appeared to reverse fear induced changes in IL-NAc projection neurons. To establish a causal counterpart to these observations, we then used a pathway-specific Designer Receptors Exclusively Activated by Designer Drugs (DREADD) strategy to selectively inhibit PFC-BLA projection neurons during extinction acquisition. Using this approach, we found that DREADD-mediated inhibition of PFC-BLA neurons during extinction acquisition impaired subsequent extinction retrieval. Taken together, our findings provide further evidence for a critical contribution of the IL-BLA neural circuit to fear extinction.
Human hippocampal replay during rest prioritizes weakly-learned information and predicts memory performance
Authors: Schapiro Anna C. , McDevitt Elizabeth A. , Rogers Timothy T. , Mednick Sara C. , Norman Kenneth A.
Published: August 2017

There is now extensive evidence that the hippocampus replays experiences during quiet rest periods, and that this replay benefits subsequent memory. A critical open question is how memories are prioritized for replay during these offline periods. We addressed this question in an experiment in which participants learned the features of 15 objects and then underwent fMRI scanning to track item-level replay in the hippocampus using pattern analysis during a rest period. Objects that were remembered less well were replayed more during the subsequent rest period, suggesting a prioritization process in which weaker memories—memories most vulnerable to forgetting—are selected for wake replay. Participants came back for a second session, either after a night of sleep or a day awake, and underwent another scanned rest period followed by a second memory test. In the second session, more hippocampal replay of a satellite during the rest period predicted better subsequent memory for that satellite. Only in the group with intervening sleep did rest replay predict improvement from the first to second session. Our results provide the first evidence that replay of individual memories occurs during rest in the human hippocampus and that this replay prioritizes weakly learned information, predicts subsequent memory performance, and relates to memory improvement across a delay with sleep.
MSPminer: abundance-based reconstitution of microbial pan-genomes from shotgun meta-genomic data
Authors: Oñate Florian Plaza , Le Chatelier Emmanuelle , Almeida Mathieu , Cervino Ales-sandra C. L. , Gauthier Franck , Magoulès Frédéric , Ehrlich S. Dusko , Pichaud Matthieu
Published: August 2017

Motivation

Analysis toolkits for shotgun metagenomic data achieve strain-level characterization of complex microbial communities by capturing intra-species gene content variation. Yet, these tools are hampered by the extent of reference genomes that are far from covering all microbial variability, as many species are still not sequenced or have only few strains available. Binning co-abundant genes obtained fromde novoassembly is a powerful reference-free technique to discover and reconstitute gene repertoire of microbial species. While current methods accurately identify species core parts, they miss many accessory genes or split them into small gene groups that remain unassociated to core clusters.

Results

We introduce MSPminer, a computationally efficient software tool that reconstitutes Metagenomic Species Pan-genomes (MSPs) by binning co-abundant genes across metagenomic samples. MSPminer relies on a new robust measure of proportionality coupled with an empirical classifier to group and distinguish not only species core genes but accessory genes also. Applied to a large scale metagenomic dataset, MSPminer successfully delineates in a few hours the gene repertoires of 1 661 microbial species with similar specificity and higher sensitivity than existing tools. The taxonomic annotation of MSPs reveals microorganisms hitherto unknown and brings coherence in the nomenclature of the species of the human gut microbiota. The provided MSPs can be readily used for taxonomic profiling and biomarkers discovery in human gut metagenomic samples. In addition, MSPminer can be applied on gene count tables from other ecosystems to perform similar analyses.

Availability

The binary is freely available for non-commercial users at enterome.fr/site/downloads/ Contact:florian.plaza-onate@inra.fr

Supplementary information

Available in the file namedSupplementary Information.pdf
Functional limb muscle innervation prior to cholinergic transmitter specification during early metamorphosis inXenopus
Authors: Lambert F. M. , Cardoit L. , Courty E. , Bougerol M. , Thoby-Brisson M. , Simmers J. , Tostivint H. , Le Ray D.
Published: August 2017

In vertebrates, functional motoneurons are defined as differentiated neurons that are connected to a central premotor network and activate peripheral muscle using acetylcholine. Generally, motoneurons and muscles develop simultaneously during embryogenesis. However, duringXenopusmetamorphosis, developing limb motoneurons must reach their target muscles through the already established larval cholinergic axial neuromuscular system. Here, we demonstrate that at metamorphosis onset, spinal neurons retrogradely labeled from the emerging hindlimbs initially express neither choline acetyltransferase nor vesicular acetylcholine transporter. Nevertheless, they are positive for the motoneuronal transcription factor Islet1/2 and exhibit intrinsic and axial locomotor-driven electrophysiological activity. Moreover, the early appendicular motoneurons activate developing limb musclesvianicotinic antagonist-resistant, glutamate antagonist-sensitive, neuromuscular synapses. Coincidently, the hindlimb muscles transiently express glutamate, but not nicotinic receptors. Subsequently, both pre- and postsynaptic neuromuscular partners switch definitively to typical cholinergic transmitter signaling. Thus, our results demonstrate a novel context-dependent re-specification of neurotransmitter phenotype during neuromuscular system development.
FastID: Extremely Fast Forensic DNA Comparisons
Authors: Ricke Darrell O.
Published: August 2017

Rapid analysis of DNA forensic samples can have a critical impact on time sensitive investigations. Analysis of forensic DNA samples by massively parallel sequencing is creating the next gold standard for DNA forensic analysis. This technology enables the expansion of forensic profiles from the current 20 short tandem repeat (STR) loci to tens of thousands of single nucleotide polymorphism (SNP) loci. A forensic search scales by the product of the number of loci and the number of profile comparisons. This paper introduces a method (FastID) to address the need for rapid scalable analysis of DNA forensic samples (patent pending)[1]. FastID can search a profile of 2,500 SNP loci against 20 million profiles in 5.08 seconds using a single computational thread on a laptop (Intel i7 4.0 GHz).
Fast P(RMNE): Fast Forensic DNA Probability of Random Man Not Excluded Calculation
Authors: Ricke Darrell O. , Schwartz Steven
Published: August 2017

High throughput sequencing (HTS) of DNA forensic samples is expanding from the sizing of short tandem repeats (STRs) to massively parallel sequencing (MPS). HTS panels are expanding from the FBI 20 core Combined DNA Index System (CODIS) loci to include SNPs. The calculation of random man not excluded, P(RMNE), is used in DNA mixture analysis to estimate the probability that a person is present in a DNA mixture. This calculation encounters calculation artifacts with expansion to larger panel sizes. Increasing the floating-point precision of the calculations allows for increased panel sizes but with a corresponding increase in computation time. The Taylor series higher precision libraries used fail on some input data sets leading to algorithm unreliability. Herein, a new formula is introduced for calculating P(RMNE) that scales to larger SNP panel sizes while being computationally efficient (patent pending)[1].
Flyscan opportunities in medicine: the case of quantum rattle based on gold quantum dots
Authors: Esteve Emmanuel , Reguer Solenn , Boissiere Cédric , Chanéac Corinne , Lugo Gustavo , Jouanneau Chantal , Mocuta Cristian , Thiaudière Dominique , Leclercq Nicolas , Leyh Bernard , Greisch Jean-François , Berthault Julien , Daudon Michel , Ronco Pierre , Bazin Dominique
Published: August 2017

The new rapid scan method, Flyscan mode, implemented on the DiffAbs beamline at Synchrotron SOLEIL, allows fast micro-X-ray fluorescence data acquisition. It paves the way for applications in the biomedical field where a large amount of data is needed to generate meaningful information for the clinician. This study presents a complete set of data acquired after injection of gold-cluster-enriched mesoporous silica nanospheres, used as potential theranostic vectors, into rats. While classical X-ray fluorescence investigations (using step-by-step acquisitions) are based on a limited number of samples (approximately one per day at the DiffAbs beamline), the Flyscan mode has enabled gathering information on the interaction of nanometer-scale vectors in different organs such as liver, spleen and kidney at the micrometer scale, for five rats, in only a single five-day synchrotron shift. Moreover, numerous X-ray absorption near-edge structure spectra, which are beam-time-consuming taking into account the low concentration of these theranostic vectors, were collected.
Impacts of residential construction defects on customer satisfaction
Authors: Milion Raphael Negri , Alves Thaís da C.L. , Paliari José Carlos
Published: August 2017

Purpose

The purpose of this paper is to investigate the impact of defects on the satisfaction of residential construction customers. Three working hypotheses were tested: first, defects in residential construction impact the customer satisfaction; second, different defects have different impacts on customer satisfaction; and third, interviewing customers about defects in their residential units is not a reliable method to collect data.

Design/methodology/approach

The research investigated correlations between data on defects and customer satisfaction surveys carried out by a construction company on its projects. Data were cross-checked to determine what kinds of defects have the worse impact on customer satisfaction.

Findings

The occurrence of defects does not necessarily jeopardize customer satisfaction, although it appears to be a concern to the customers who responded to the survey. When the occurrence of defects did interfere with customer satisfaction, it was found that the worse impacts resulted from the occurrence of multiple defects in a single unit, the inability of the construction company to communicate with the customer after a claim was filed, and the occurrence of functional defects. Results suggest that interviewing customers about the defect occurrence in their units is not a reliable method to collect data for research purposes.

Practical implications

Results can be used to help companies better define continuous improvement activities and avoid the occurrence of defects that cause the worse impacts to customer satisfaction.

Originality/value

Data availability is a challenge for studies on defects. This study had direct access to data from a construction company, which made the presented analyses possible.