bluuebunny/crossref_metadata_2025 huggingface dataset:
The human duodenal mucosa harbors all components for a local renin angiotensin system
Authors: Spak Emma , Hallersund Peter , Edebo Anders , Casselbrant Anna , Fändriks Lars
Published: April 2019

The renin-angiotensin system (RAS) is present in the gastrointestinal (GI) tract but remains to be fully characterized, particularly in man. The duodenum plays a role in both the upper and lower GI regulation, as well as in distant organs. The present study investigates the presence and functional potential of RAS in the human duodenal mucosa of healthy individuals. Endoscopically acquired mucosal biopsies from healthy volunteers were examined using western blot, immunohistochemistry, and ELISA. Functionality was examined by using Ussing chambers and recording duodenal transmucosal potential difference (PD) and motility in vivo. Angiotensinogen, Angiotensin II (AngII) and its receptors (AT1R, AT2R) as well as to the RAS associated enzymes renin, ACE, and neprylisin were detected in all samples of duodenal mucosa. Migrating motility complex induced elevations of transmucosal PD were significantly larger after per-oral administration of the AT1R receptor antagonist candesartan. Fasting duodenal motility per se was not influenced by candesartan. The epithelial current produced by duodenal mucosae mounted in Ussing chambers increased significantly after addition of AngII to specimens where the AT1R was blocked using losartan. The epithelial current also increased after addition of the AT2R-selective agonist C21. Immunostaining and pharmacological data demonstrate the presence of a local RAS in the human duodenal mucosa with capacity to influence epithelial ion transport by way of particulary the AT2R.
Evaluation of an Explicit Instructional Approach to Teach Grammatical Forms to Children With Low-Symptom Severity Autism Spectrum Disorder
Authors: Bangert Katherine J. , Halverson Danneka M. , Finestack Lizbeth H.
Published: April 2019

Purpose

Weaknesses in the use of grammatical forms may reduce the functional use of language for verbally expressive children with autism spectrum disorder (ASD) and exacerbate difficulties with academic and social skill development. This early efficacy study evaluated a combined explicit–implicit instructional approach to teach novel grammatical forms to children with ASD.

Method

Seventeen children with ASD between the ages of 4 and 10 years who demonstrated weaknesses in expressive grammatical language completed 2 tasks, each targeting a different novel grammatical form. One form was a gender marking, which required the child to modify the verb if the sentence subject was a boy. The other form was a person marking, which required the child to modify the verb if the sentence subject was the 1st person, “I.” Each form was targeted using implicit-only instruction or combined explicit–implicit instruction. With implicit-only instruction, the examiner presented models and recasts of the targeted form. With explicit–implicit instruction, the examiner presented the rule guiding the form as well as models and recasts. Learning was assessed during each of 4 treatment sessions and after a 1-week delay in 2 contexts.

Results

For the gender target form, significantly more children reliably produced the target form with explicit–implicit instruction (χ
2
= 4.10,
p =
.04). For the person target form, the difference in instruction was not statistically significant. Task performance revealed a positive association with receptive language skills, but not age, nonverbal intelligence, or severity of autism-related behaviors for the person form.

Conclusion

This study provides preliminary evidence that expressively verbal children with low-symptom severity ASD can successfully learn novel grammatical forms with intervention that comprises both explicit and implicit instruction.
Six‐phase dual‐interleaved buck‐boost converter for high power‐density automotive applications
Authors: Velázquez‐Elizondo P. E. , Araujo‐Vargas I. , Villarruel‐Parra A. , Gómez‐Olguín F. J. , Cano‐ Pulido K. , Granados‐Luna T. R.
Published: April 2019

This study presents a 30 kW, six‐phase dual‐interleaved buck‐boost converter which uses an interphase transformer together with six buck‐boost switching arms hard switched at 75 kHz for electric/hybrid vehicle applications. Parameters and construction details of the interphase transformer and common inductors are provided together with a description of the selection of semiconductor devices. Weight, power losses, and temperature rise are evaluated at rated power conditions showing experimental results with a 7 kW/kg gravimetric power density achieved with the converter prototype.
Flux concentrated doubly salient linear permanent magnet machine
Authors: Almoraya Ahmed A. , Baker Nick J. , Smith Kristopher J. , Raihan Mohammad A. H.
Published: April 2019

Different topologies of Vernier permanent magnet (PM) machines have been proposed for direct drive low‐speed applications due to their high thrust and power density. However, this type of machine can suffer from low power factor (PF). In this study, a flux concentrated doubly salient linear permanent magnet machine with V‐shape PM arrays is proposed and compared to a consequent pole (CP) type machine. Using the configuration of V‐shaped PMs allows the flux to be concentrated in iron spacers located between two pieces of PMs. This feature is shown to result in an improvement of the airgap flux density, which allows a reduction in electrical loading and hence an improvement in power factor. In order to achieve a fair comparison, two doubly salient linear permanent magnet machines with different PMs’ configurations have been analysed and compared using transient FEA. The investigated machines have the same overall machine and, crucially, magnet volume. The results confirm that the proposed V‐shape machine is capable of higher thrust force, higher no‐load back EMF and can achieve a higher PF of 42% compared to the consequent pole machine, while it consumes the same amount of the PM material.
Investigation of Sheltering Effect on Global Solar Radiation Data Measured by Weather Stations
Authors: Chang Keh-Chin , Chen Hung-Hsun
Published: April 2019

In instalment of pyranometers at the weather stations for measuring global solar radiation, it often cannot avoid appearance of obstacles in their surroundings. Investigation of sheltering effect on measurement of global solar radiation is performed through introducing the shelter view factor. Evaluation of the shelter view factor is made by means of a fisheye-lens photograph together with the calculation method developed by Steyn (1980). Taitung weather station (TWS) is chosen for the study. The shelter view factor for the pyranometer installed at TWS is estimated to be 11.8%. Measurements of global solar radiation are conducted at a place where is located nearby TSW but with the condition of zero shelter view factor. Comparison of the data measured at these two sites indicates 4% - 25% deviations of global solar radiation observed in different months of 2017. It suggests a need of the correction to the sheltering effect in the measuring process of global solar radiation at the weather stations except those who are not subject to surrounding obstacles in the sky dome.
Architectural conjectural mapping: two examples
Authors: Boca Silvia , Korolija Aleksa
Published: April 2019

Mapping is a key research tool to understand the relationship between specific geographical features and territorial transformations (settlement patterns, hydraulic works, new rail and road infrastructure, land-use change). Starting from the Italian academic tradition (Muratori, Caniggia, Rossi) that focused mainly on the urban context we have developed mapping for fringe-areas at various scales: from city and countryside to expanding rural areas that mark the shifting boundaries(using the agricultural Behera-Region/Alexandria in Egypt and the Belgrade urban evolution in Serbia). Mapping should envision not only the geomorphological features but also the complexity of the landscape structure, as a repository of layers, questioning what are we looking for through mapping and constructing the legend accordingly: selecting which elements need to be highlighted or remain latent and which additional elements need to be identified with the help of complementary sources. GIS holds potential for showing key physical features, their extent, quantity and position in a single glance but is mapping the same as tracing? Is it capable of showing the space-time whirl in landscape transformations?
Landscapes and national imagination: The role of national parks in the formation of national belonging in Turkey
Authors: Uzmay Asya Ece
Published: April 2019

When the concept of a national park idea was first established in the USA, it was promoted as the ownership of the landscape for the use of the people while emphasizing national identity through nature. As a latecomer to this movement, this paper describes part of the journey of the establishment of national parks in Turkey, with a focus on the period between 1950 and 1975. In this paper I argue that the national parks were a means of constructing a national identity through the transformative power of modernism on the countryside. Focusing on different national parks from Turkey, I interrogated the role of these so-called pristine and primitive lands in the construction of national identity through different forms. Under the threat of neoliberal economic policies and new approaches to understanding of nature these protected and reserved pieces of “nature” deserve more attention.
Hepatitis C – von der individuellen Heilung zur weltweiten Elimination?
Authors: Boettler Tobias , Lohmann Volker , Bartenschlager Ralf
Published: April 2019

With the implementation of highly effective direct acting antivirals (DAAs), global control or even elimination of chronic hepatitis C virus (HCV) infection might have come into reach. In fact, DAA therapy leads to complete virus elimination, defined as sustained viral response (SVR), in the vast majority of patients. Moreover, in patients without cirrhosis, the risk of developing HCC after DAA therapy is significantly reduced. For viremic patients who have already received DAA therapy, a distinction must be made between relapse and reinfection. The rate of new infections remains high and many infected individuals are undiagnosed. In order to come closer to the WHO goal of eliminating HCV worldwide by 2030, programs are needed to identify and treat all HCV-infected individuals. Strategies are missing in most countries to achieve this goal. Generic DAA therapies are available in some countries and appear to have similar cure rates compared to those obtained with the original drugs. The high variability of HCV, the numerous strategies of the virus to escape the immune response, and the lack of a suitable small animal model are key hurdles for vaccine development. Currently, the efficacy of two vaccine candidates is being investigated in clinical trials. The development of a protective vaccine is important, despite available therapy, to sustainably reduce the rate of new infections both in developing countries and in people with risk behavior.
Keine falsche Angst – HIV-Infektion
Authors: Baumgärtner Martina
Published: April 2019

Physiotherapeuten sind verpflichtet, auch Menschen mit infektiösen Krankheiten zu behandeln. Was auf den ersten Blick beunruhigt, ist mit den richtigen Vorsichtsmaßnahmen ungefährlich. Da der Patient seine Krankheit in der Physiotherapie nicht angeben muss, sind entsprechende Hygienemaßnahmen grundsätzlich wichtig. physiopraxis stellt in den kommenden Ausgaben sechs relevante Infektionskrankheiten vor.
Endoscopic full-thickness transoral outlet reduction with semicircumferential endoscopic submucosal dissection
Authors: Hollenbach Marcus , Selig Lars , Lellwitz Sylvia , Beer Sebastian , Feisthammel Jürgen , Rosendahl Jonas , Schaumburg Tiffany , Mössner Joachim , Hoffmeister Albrecht
Published: April 2019

Background Endoscopic full-thickness transoral outlet reduction (efTOR) is a therapeutic option to reduce a dilated gastrojejunal anastomosis (GJA) after Roux-en-Y gastric bypass (RYGB). Mucosal ablation with argon plasma coagulation (APC) is usually performed to achieve tissue adaptation. However, rupture of sutures before scarring can lead to recurrent dilatation of the GJA. Here, we describe efTOR with a semicircumferential endoscopic submucosal dissection (ESD-efTOR) as an alternative to APC-efTOR.

Methods We enrolled 41 patients with comparable baseline characteristics (APC-efTOR 26; ESD-efTOR 15). The main objectives were reduction in the GJA diameter and in ruptured sutures. Technical success, complications, total weight loss (TWL), and percentage of total and excess weight loss (%TWL and %EWL) at 3 and 12 months, were assessed.

Results ESD-efTOR resulted in significantly fewer ruptured sutures (20 % vs. 69 %; P = 0.004) and a greater reduction in the GJA (major 20 % vs. 0 %; minor 54 % vs. 37 %; no reduction 13 % vs. 58 %; P = 0.02) after 3 months. Technical efficacy, examination time, and rate of complications were comparable.

Conclusions ESD-efTOR resulted in a significantly greater reduction in the GJA diameter and a lower risk of ruptured sutures compared with APC-efTOR.
Schwerelosigkeit, Biodiversität und Umwelt
Authors: Ullrich Oliver
Published: April 2019

Forschung und Innovation bekommen Flügel: Im Jahr 2018 führte das Innovationscluster Luft- und Raumfahrt der Universität Zürich (UZH Space Hub) mehrere größere Forschungsflugkampagnen vom Militärflugplatz Dübendorf durch: Die „3rd Swiss Parabolic Flight Campaign“ (Abb. 1) zur Forschung in Schwerelosigkeit mit dem Airbus A310 ZERO-G, Messflüge in der Biodiversitätsforschung mit einem King Air B200 in Zusammenarbeit mit der NASA und ein Flugeinsatz des Zeppelin NT zur Testung von Technologien zur Plastikmülldetektion.
One-Pot Approach for SNAr Reaction of Fluoroaromatic Compounds with Cyclopropanol
Authors: Jin Hao , Gao Zhuo , Zhou Shaodong , Qian Chao
Published: April 2019

A novel method for preparing aromatic compounds containing cyclopropoxy via nucleophilic aromatic substitution reaction (SNAr) of fluoroaromatic compounds with cyclopropanol under relatively mild conditions is presented. As compared to the approaches reported previously for preparing 1-(cyclopropyloxy)-2-nitrobenzene, the one proposed in this work is simplified without sacrificing the yields: When the reaction was performed at 75 °C with Cs2CO3 as the base and DMF as solvent, after 6 h the yield was up to 90%. Finally, various fluoroaromatic compounds were employed as substrates for a test that proves a wide application scope of the method.
The Chemical Syntheses of Nannocystins
Authors: Wang Zhang
Published: April 2019

The broad and potent anticancer activity of the nannocystin family of natural products has attracted significant efforts toward their total syntheses. Currently, seven total syntheses of different members of the nannocystins have been reported. In this Short Review, different synthetic approaches are highlighted. The reported structure-activity relationship (SAR) studies will also be highlighted.
Practical Gram-Scale Synthesis of Either α- or β-Anomer of C-Vinyl Glycosides
Authors: Rouzier Florian , Sillé Rosanne , Nourry Arnaud , Tessier Arnaud , Pipelier Muriel , Guillarme Stéphane
Published: April 2019

The synthesis C-vinyl glycosides, useful intermediates for the synthesis of C-glycoconjugates, was carried out on gram-scale by controlled reduction of the corresponding ethynyl derivatives in good to excellent yields in different carbohydrate series.
Incidence and Risk Factors for Clostridium Difficile-Associated Diarrhea Following Revision Total Hip Arthroplasty
Authors: Curtis Gannon L. , Yokhana Sanar S. , Samuel Linsen T. , Higuera-Rueda Carlos A. , Little Bryan E. , Darwiche Hussein L.
Published: April 2019

Clostridium difficile-associated diarrhea (CDAD) is a well-known cause of complications and increased hospital cost following surgery. As CDAD rates continue to be adopted as a quality metric by institutions, it is important to detect high-risk patients prior to surgery, including revision total hip arthroplasty (rTHA). This study was performed to identify the incidence and risk factors of CDAD within 30 days of rTHA. The American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) was accessed from 2015 to 2016 to identify rTHA procedures. Overall, 4,178 patients were included. Preoperative and perioperative variables were analyzed as potential risk factors for the development of CDAD. To compare categorical variables, Chi-square and Fisher's exact tests were used, while t-tests were used to detect differences in continuous variables. Independent risk factors for CDAD were identified using stepwise logistic regression. The rate of CDAD was found to be 0.5% (20/4,178) within 30 days of rTHA. Preoperative functional dependence (odds ratio [OR] = 3.34; p = 0.035) and dyspnea (OR = 3.80; p = 0.019), were statistically significant risk factors for the development of CDAD after rTHA. Septic revision was not a significant risk factor for CDAD (OR = 2.50; p = 0.082). The incidence of CDAD after rTHA in the United States is approximately 0.5%. Independent risk factors for CDAD include preoperative functional dependence and dyspnea. High-risk patients must be identified prior to surgery and antibiotic selection for other infections should be managed judiciously.
Atomic layer deposition of stoichiometric In2O3 films using liquid ethylcyclopentadienyl indium and combinations of H2O and O2 plasma
Authors: Mizutani Fumikazu , Higashi Shintaro , Inoue Mari , Nabatame Toshihide
Published: April 2019

Liquid ethylcyclopentadienyl indium (InEtCp) was synthesized, and this compound exhibited superior characteristics, including a relatively high vapor pressure and thermal stability up to 250 °C. In2O3 thin films were subsequently deposited by atomic layer deposition (ALD) using the InEtCp as a precursor together with combinations of oxidants: H2O followed by O2 plasma (WpO), H2O followed by O2 (WO), O2 plasma alone (pO), and O2 plasma followed by H2O (pOW). The growth rates for In2O3 thin films using the pO and pOW processes were much smaller than those using the WO and WpO processes. A self-limiting surface reaction during the WpO process was observed with no delay in nucleation when the pulse times for InEtCp, H2O, and O2 plasma were 0.1, 2.0, and 14 s, respectively, at a growth temperature of 200 °C. For the WO and WpO processes, the In2O3 films are considered to be formed by quite different mechanisms, due to oxidation or lack thereof in the presence or absence of the -O-In-OH* intermediate product. This is due to the difference in the oxidation strength of O2 gas and O2 plasma during the oxidation step in the ALD process. As a result, In2O3 thin films deposited by WpO were obtained with a stoichiometric O/In ratio of 1.5 and a negligibly low residual carbon concentration of around TOF-SIMS detection limit, below 1 ppm. Therefore, InEtCp is one of the promising candidate precursors to form a high quality In2O3 film.
Measurement system for adhesion force on single particles with microelectromechanical-based actuated tweezers
Authors: Yamaguchi D.
Published: April 2019

A system for measuring the adhesion force of a single particle using microelectromechanical-system-based actuated tweezers (nanotweezers) and an atomic force microscope (AFM) cantilever was developed. In the proposed technique, a particle picked up with nanotweezers is brought into contact with and separated from the cantilever. The adhesion force is determined by measuring the deflection of the cantilever at the instant of separation from the particle. The throughput of measurement is much improved compared with that of a colloid probe AFM because the particle is picked up and held only by gripping with the nanotweezers, rather than sample preparation by manual cantilever mounting. A measurement apparatus was designed to realize the proposed system, and a force–displacement curve was successfully obtained. In addition, decreases in the adhesion force due to external coating added to particles were measured using the prototype apparatus.
Comparison of longitudinal and transverse smoothing by spectral dispersion on stimulated Brillouin backscattering in inertial confinement fusion plasmas
Authors: Duluc M. , Penninckx D. , Loiseau P. , Riazuelo G. , Bourgeade A. , Chatagnier A. , D'humières E.
Published: April 2019

In the context of inertial confinement fusion, optical smoothing is a technique used to provide laser irradiation as homogeneous as possible. It is required for limiting the development of laser-plasma instabilities, in particular, stimulated Brillouin backscattering (SBS). Here, we carefully compare longitudinal and transverse smoothing by spectral dispersion in an ideal smoothing configuration for each case. With 3D codes, we have simulated SBS in a gold plasma. We show that, as opposed to common belief, the time evolution of the SBS reflectivity exhibits some differences between both smoothing schemes. First, the asymptotic values of the saturation levels are not quite the same. With a simple ray description and computing the SBS gain for each ray, we were able to explain this difference. Moreover, the dynamics of SBS are also somewhat different. We have shown that SBS dynamics are driven by the time evolution of speckle properties and in particular by the effective interaction length between the Brillouin backscattered light and the hot-spots. This effective interaction length depends both on the longitudinal velocity and on the length of the hot-spots. As a matter of fact, synchronizing the effective interaction lengths of both smoothing schemes also synchronizes the backscattering curves before reaching the saturation level.
Modifications to the gradient schemes on unstructured cell centered grids for the accurate determination of gradients near conductivity changes
Authors: Trautmann M. , Spaniol E. , Hertel M. , Füssel U.
Published: April 2019

Gradient schemes for the cell centered finite volume method on unstructured grids, namely, the divergence theorem and the least squares schemes, have been widely adopted because they have reached a high precision for most applications. These schemes assume continuously differentiable fields for the calculation of the gradients. However, this assumption is violated in the vicinity of conductivity jumps between cells. It is shown that this deficiency leads to a wrong calculation of the gradients and thus the flux density in cells near conductivity changes. For large conductivity jumps, the error of the flux density can exceed several orders of magnitude. Based on theoretical considerations, flux conservative versions of the schemes are derived for the central gradient scheme and extended to the divergence theorem and least squares schemes. The modified schemes named flux conservative divergence theorem and flux conservative least squares take the nonlinearity of a conservation variable near conductivity changes into account and eliminate the error made by the assumption of a continuously differentiable field. The schemes are demonstrated on Cartesian and highly skewed grids with different grid resolutions with a large conductivity jump. The error of the flux density is shown to be reduced by several orders of magnitude up to machine precision for Cartesian grids.
Electric field influences on the initial electron temperature of ultracold plasmas
Authors: Jiang Puchang , Roberts Jacob L.
Published: April 2019

One of the properties of ultracold plasmas that make them interesting objects of study is that they are cold enough that strong coupling effects can be made manifest at their typical densities. In order to study strong coupling effects, sufficiently low temperatures need to be obtained. In turn, this means that the limitations to the lowest achievable temperatures for the electrons and ions in ultracold plasmas are worth investigating as they determine the degree to which strong coupling can be achieved. In addition, understanding these limitations also illuminates the basic physics of ultracold plasmas. A DC electric field applied during ultracold plasma formation can result in significant heating of the electron component. In the work presented here, we use molecular dynamics simulations to study this heating process and determine its impact as a function of ultracold plasma parameters such as electron temperature and density. We find that this heating can have a significant impact on the lowest achievable temperatures for lower-density ultracold plasmas in particular.
Kinetic modeling of ELM-induced tungsten transport in a tokamak plasma
Authors: van Vugt D. C. , Huijsmans G. T. A. , Hoelzl M. , Loarte A. ,   ASDEX Upgrade Team,   EUROfusion MST1 Team
Published: April 2019

Impurity accumulation in the core plasma leads to fuel dilution and higher radiative losses that can lead to loss of the H-mode, to thermal collapse of the plasma, and eventually even to a disruption in tokamaks. In present experiments, it has been shown that Edge Localized Modes (ELMs) at sufficiently high frequency are required to prevent W accumulation in the core, by expelling impurities from the edge plasma region, thus preventing their penetration into the plasma core. We present a full-orbit particle extension of the MHD code JOREK suitable for simulating impurity transport during ELMs. This model has been applied to the simulation of an ELM crash in ASDEX Upgrade, where we have quantified the displacement of W particles across flux surfaces. The transport mechanism is shown to be the particle E × B-drifts due to the electric field created by the MHD instability underlying the ELM. In- and outward transport is observed as a series of interchange motions, leading to a superdiffusive behavior. This causes not only the particles near the plasma pedestal to move outwards but also the particles outside of the pedestal to move inwards. This has important consequences for operation with W in ITER, where it is expected to be screened in the pedestal, and ELMs are shown here to increase the core W density. A comparison with existing diffusive modeling is made, showing a qualitative agreement and the limitations of this simplified modeling approach.
Relaxation processes in carbon dioxide
Authors: Kustova E. , Mekhonoshina M. , Kosareva A.
Published: April 2019

The present study is aimed in providing a framework for applying different continuum models of relaxation processes in carbon dioxide flows. Kinetic equations for the distribution function are written taking into account the CO2 structure and various mechanisms of vibrational relaxation; collision operators for different internal energy transitions are derived. For weak non-equilibrium conditions, a one-temperature model is developed with emphasis to the bulk viscosity phenomenon. For strong non-equilibrium conditions, multi-temperature models are introduced, and their advantages and limitations are discussed. A general algorithm for calculating vibrational relaxation time in polyatomic molecules is proposed. Bulk viscosity coefficients are studied in the temperature range 200–2500 K; it is shown that uncoupling rotational and vibrational modes results in essentially overpredicted values of the bulk viscosity coefficient at low temperatures. The shock wave structure in CO2 is studied using the continuum models and compared with the solution obtained in the frame of the model kinetic approach; the effect of bulk viscosity on the shock wave width and temperature profile is evaluated. It is concluded that well justified choice of the model extends considerably the range of applicability of the continuum approach for non-equilibrium flow simulations.
Review of Scientific Instruments New Products
Authors: Mandelis Andreas
Published: April 2019

In order to supplement manufacturers’ information, this department will welcome the submission by our readers of brief communications reporting measurements on the physical properties of materials which supersede earlier data or suggest new research applications.
Vigna unguiculata seed priming is related to redox status of plumule, radicle and cotyledons
Authors: Boucelha Lilya , Djebbar Réda , Abrous-Belbachir Ouzna
Published: April 2019

Pre-germination treatments represent the physiological methods that improve plant production by modulating the metabolic activities of germination before the emergence of the radicle. It was suggested that reactive oxygen species (ROS) play a crucial role in signalling seed germination. Our work consisted in studying changes in the redox status in the embryonic axis (radicle and plumule) and in cotyledons of Vigna unguiculata (L.) Walp. non-primed, osmoprimed (30% PEG6000), hydroprimed or twice hydroprimed seeds, by estimating antioxidant activities and production of ROS. Some antioxidant enzymatic activities as well as total non-enzymatic antioxidant capacity were measured. The production of hydrogen peroxide (H2O2) and superoxide anion (O2–) was also assessed by 3,3′-diaminobenzidine (DAB) and nitroblue tetrazolium (NBT) respectively. The results obtained showed, on the one hand, that priming allows activation of antioxidant enzymes, especially in the plumule. On the other hand, these results showed that priming caused an accumulation of ROS in embryonic tissues. This may explain the improvement of seed germination performance according to the oxidative window model. Priming induced changes in the redox environment at the seed level. These changes were closely related to the pre-germination treatments. Indeed, a double cycle of hydration-rehydration induced the broadest spectrum of modifications of the redox status, which would explain the improvement of the seed vigour.
Improved functional oocyte enucleation by actinomycin D for bovine somatic cell nuclear transfer
Authors: Moura Marcelo T. , Badaraco Jeferson , Sousa Regivaldo V. , Lucci Carolina M. , Rumpf Rodolfo
Published: April 2019

Somatic cell nuclear transfer (SCNT) allows animal cloning but remains technically challenging. This study investigated limitations to functional oocyte enucleation by actinomycin D (AD) as a means of making SCNT easier to perform. Denuding oocytes or inhibiting transcription before AD treatment revealed that the toxicity of this compound during bovine oocyte maturation is mediated by cumulus cells. Exposure of denuded oocytes to higher concentrations of AD (5–20μgmL−1) and stepwise reductions of the incubation period (from 14.0 to 0.25h) led to complete inhibition of parthenogenetic development. Bovine SCNT using this improved AD enucleation protocol (NT(AD)) restored cleavage rates compared with rates in the parthenogenetic and SCNT controls (P(CTL) and NT(CTL) respectively). However, NT(AD) was associated with increased caspase-3 activity in cleavage stage embryos and did not recover blastocyst rates. The removal of AD-treated oocyte spindle before reconstruction (NT(AD+SR)) improved embryo development and reduced caspase-3 activity to levels similar to those in the P(CTL) and NT(CTL) groups. Furthermore, mid-term pregnancies were achieved using NT(AD+SR) blastocysts. In conclusion, improvements in AD functional enucleation for bovine SCNT circumvents most cellular roadblocks to early embryonic development and future investigations must focus on restoring blastocyst formation.
Biggish data: Friedrich Engels, material ecology, and Victorian data
Authors: Parham John
Published: April 2019

Through Friedrich Engels’ The Condition of the Working Class in England (1845), this article examines two prominent themes in environmental humanities – vital ecological materialism and ‘big data’. Engels’ vivid descriptions of factories, houses, and environment shared the central tenets of ‘material ecology’ – ‘thing power’ (Jane Bennett); ‘intra-actions’ of social and material agency (Karen Barad); ‘trans-corporeality’ (Stacy Alaimo) – and met Bennett’s call to align vital and historical materialism. The main body of the paper connects his analysis both to current debates about integrating ‘big data’ into social science and the humanities and to comparable nineteenth-century developments in statistics and data visualisation. Engels articulated the working-class condition by blending four distinct modes of investigation: big data; qualitative survey research; literary thick description; and theory (the nascent critique of capitalist political economy). Such a mix remains rich with possibilities for sociology and humanities not only in communicating but in generating knowledge about complex ecologies.
A Study about Principle Component Analysis and Eigenface for Facial Extraction
Authors: Erwin  , Azriansyah M , Hartuti N , Fachrurrozi Muhammad , Adhi Tama Bayu
Published: April 2019

Facial recognition is one of the most successful applications of image analysis and understanding. This paper presents a Principal Component Analysis (PCA) and eigenface method for facial feature extraction. Several performance metrics, i.e. accuracy, precision, and recall are taken into account as a baseline of experiment. Furthermore, two public data sets, namely SOF (Speech on faces) and MIT CBCL Facerec are incorporated in the experiment. Based on our experimental result, it can be revealed that PCA has performed well in terms of accuracy, precision, and recall metrics by 0.598, 0.63, and 0.598, respectively.
The Critical Study of Mutual Coherence Properties on Compressive Sensing Framework for Sparse Reconstruction Performance: Compression vs Measurement System
Authors: Andryani Nur Afny C. , Dwi Pradnyana Kadek , Gunawan Dadang
Published: April 2019

Compressive Sensing (CS) framework becomes well known since its ability to recover signal only by using less sampling required by Shanon-Nyquist theorem. The lack of required sampling is no longer constraint for having good reconstruction performance. The load is shifted to the reconstruction procedure instead of the sampling acquisition process. As long as the signal can be guaranteed sparse, the CS based method is able to provide high reconstruction accuracy. One of the CS principle is incoherence property, which can be represented by mutual coherence value. It represents the coherence between the sensing matrix and the sparse base dictionary. The theory said the less coherence between those two parameters, the more precise the reconstruction is. In fact, it is not consistently applied. The research presented on this paper find that, the theory is consistent for reconstruction on compression system, while it is not applied on the reconstruction of measurement system. Other properties are found to be more representative on assigning necessary condition for reconstruction performance on measurement system.
Design and preliminary performance tests of the IFMIF-LIPAc Cryoplant
Authors: Renard B. , Machefel A. , Maebara S. , Phillips G. , Pruneri G. , Brédy Ph. , Riquelme A. , Vincent B. , Legrand J. , Gire C. , Ebisawa T. , Wanner M.
Published: April 2019

Special features of this Cryoplant are first given with operating purpose, main constraints, design choices for this cryoplant which will cool down a superconductive module (SRF Linac) of an accelerator currently under installation in Japan. The relationship between compliance with Japanese regulations and the successful hydraulic, electric and instrumentation tests are discussed. Measurements of refrigeration power and liquefaction rate were achieved inside the Dewar, and margin power was measured. Further functional and performance tests were conducted in order to demonstrate the correct operation of the cryogenic lines and distribution systems. These tests were performed successfully without the cryomodule, in anticipation to its installation and operation.
Nonmuscle myosin IIA and IIB differentially modulate migration and alter gene expression in primary mouse tumorigenic cells
Authors: Halder Debdatta , Saha Shekhar , Singh Raman K. , Ghosh Indranil , Mallick Ditipriya , Dey Sumit K. , Ghosh Arijit , Das Benu Brata , Ghosh Somiranjan , Jana Siddhartha S.
Published: April 2019

Though many cancers are known to show up-regulation of nonmuscle myosin (NM) IIA and IIB, the mechanism by which NMIIs aid in cancer development remains unexplored. Here we demonstrate that tumor-generating, fibroblast-like cells isolated from 3-methylcholanthrene (3MC)-induced murine tumor exhibit distinct phospho-dependent localization of NMIIA and NMIIB at the perinuclear area and tip of the filopodia and affect cell migration differentially. While NMIIA-KD affects protrusion dynamics and increases cell directionality, NMIIB-KD lowers migration speed and increases filopodial branching. Strategically located NMIIs at the perinuclear area colocalize with the linker of nucleoskeleton and cytoskeleton (LINC) protein Nesprin2 and maintain the integrity of the nuclear-actin cap. Interestingly, knockdown of NMIIs results in altered expression of genes involved in epithelial-to-mesenchymal transition, angiogenesis, and cellular senescence. NMIIB-KD cells display down-regulation of Gsc and Serpinb2, which is strikingly similar to Nesprin2-KD cells as assessed by quantitative PCR analysis. Further gene network analysis predicts that NMIIA and NMIIB may act on similar pathways but through different regulators. Concomitantly, knockdown of NMIIA or NMIIB lowers the growth rate and tumor volume of 3MC-induced tumor in vivo. Altogether, these results open a new window to further investigate the effect of LINC-associated perinuclear actomyosin complex on mechanoresponsive gene expression in the growing tumor.
Hypertension Contributes to Neuropathy in Patients With Type 1 Diabetes
Authors: Ponirakis Georgios , Petropoulos Ioannis N , Alam Uazman , Ferdousi Maryam , Asghar Omar , Marshall Andrew , Azmi Shazli , Jeziorska Maria , Mahfoud Ziyad R , Boulton Andrew J M , Efron Nathan , Nukada Hitoshi , Malik Rayaz A
Published: April 2019

BACKGROUND

Diabetic peripheral neuropathy (DPN) can lead to foot ulceration and amputation. There are currently no disease-modifying therapies for DPN. The aim of this study was to determine if hypertension contributes to DPN in patients with type 1 diabetes mellitus (T1DM).

METHODS

Subjects with T1DM (n = 70) and controls (n = 78) underwent a comprehensive assessment of DPN.

RESULTS

Hypertension was present in 40 of 70 T1DM subjects and 20 of 78 controls. Hypertension was associated with abnormal nerve conduction parameters (P = 0.03 to <0.001), increased vibration perception threshold (P = 0.01) and reduced corneal nerve fiber density and length (P = 0.02) in subjects with T1DM. However, after adjusting for confounding factors only tibial compound motor action potential and nerve conduction velocity were associated with hypertension (P = 0.03) and systolic blood pressure (P < 0.01 to <0.0001). Hypertension had no effect on neuropathy in subjects without diabetes.

CONCLUSIONS

This study shows that hypertension is associated with impaired nerve conduction in T1DM. It supports previous small trials showing that angiotensin-converting enzyme inhibitors improve nerve conduction and advocates the need for larger clinical trials with blood pressure lowering agents in DPN.
Agreement Between Ambulatory and Home Blood Pressure Monitoring in Detecting Nighttime Hypertension and Nondipping Patterns in the General Population
Authors: Lindroos Annika S , Kantola Ilkka , Salomaa Veikko , Juhanoja Eeva P , Sivén Sam S , Jousilahti Pekka , Jula Antti M , Niiranen Teemu J
Published: April 2019

BACKGROUND

Nighttime blood pressure (BP) and nondipping pattern are strongly associated with hypertensive end-organ damage. However, no previous studies have compared the diagnostic agreement between ambulatory and home monitoring in detecting these BP patterns in the general population.

METHODS

We studied a population-based sample of 180 persons aged 32–80 years. The study protocol included 24-hour ambulatory BP monitoring, home daytime measurements over 7 days, home nighttime measurements (6 measurements over 2 consecutive nights using a timer-equipped home device), and ultrasound measurements for left ventricular mass index (LVMI) and carotid intima-media thickness (IMT). We defined nondipping as a <10% reduction in nighttime BP compared with daytime BP, and nighttime hypertension as BP ≥ 120/70 mm Hg.

RESULTS

The agreement between ambulatory and home monitoring for detecting nighttime hypertension was good (80%, κ = 0.56, P < 0.001). However, their agreement in detecting nondipping status was poor (54%, κ = 0.12, P = 0.09). The magnitude of ambulatory systolic BP dipping percent was 1.7% higher than on home monitoring (P = 0.004), whereas no difference was observed for diastolic BP dipping (difference: 0.7%, P = 0.33). LVMI and IMT were significantly greater among individuals with nighttime hypertension than in normotensive individuals, irrespective of the measurement method. However, only ambulatory nondippers, but not home nondippers, had more advanced end-organ damage than dippers.

CONCLUSION

We observed a good agreement between ambulatory and home BP monitoring in detecting nighttime hypertension in the general population. Two-night home monitoring could offer an inexpensive and feasible method for the diagnosis of nighttime hypertension.
Variant Score Ranker—a web application for intuitive missense variant prioritization
Authors: Du Juanjiangmeng , Sudarsanam Monica , Pérez-Palma Eduardo , Ganna Andrea , Francioli Laurent , Iqbal Sumaiya , Niestroj Lisa-Marie , Leu Costin , Weisburd Ben , Poterba Tim , Nürnberg Peter , Daly Mark J , Palotie Aarno , May Patrick , Lal Dennis
Published: April 2019

Motivation

The correct classification of missense variants as benign or pathogenic remains challenging. Pathogenic variants are expected to have higher deleterious prediction scores than benign variants in the same gene. However, most of the existing variant annotation tools do not reference the score range of benign population variants on gene level.

Results

We present a web-application, Variant Score Ranker, which enables users to rapidly annotate variants and perform gene-specific variant score ranking on the population level. We also provide an intuitive example of how gene- and population-calibrated variant ranking scores can improve epilepsy variant prioritization.

Availability and implementation

http://vsranker.broadinstitute.org

Supplementary information

Supplementary data are available at Bioinformatics online.
Cell-level somatic mutation detection from single-cell RNA sequencing
Authors: Vu Trung Nghia , Nguyen Ha-Nam , Calza Stefano , Kalari Krishna R , Wang Liewei , Pawitan Yudi
Published: April 2019

Motivation

Both single-cell RNA sequencing (scRNA-seq) and DNA sequencing (scDNA-seq) have been applied for cell-level genomic profiling. For mutation profiling, the latter seems more natural. However, the task is highly challenging due to the limited input materials from only two copies of DNA molecules, while whole-genome amplification generates biases and other technical noises. ScRNA-seq starts with a higher input amount, so generally has better data quality. There exists various methods for mutation detection from DNA sequencing, it is not clear whether these methods work for scRNA-seq data.

Results

Mutation detection methods developed for either bulk-cell sequencing data or scDNA-seq data do not work well for the scRNA-seq data, as they produce substantial numbers of false positives. We develop a novel and robust statistical method—called SCmut—to identify specific cells that harbor mutations discovered in bulk-cell data. Statistically SCmut controls the false positives using the 2D local false discovery rate method. We apply SCmut to several scRNA-seq datasets. In scRNA-seq breast cancer datasets SCmut identifies a number of highly confident cell-level mutations that are recurrent in many cells and consistent in different samples. In a scRNA-seq glioblastoma dataset, we discover a recurrent cell-level mutation in the PDGFRA gene that is highly correlated with a well-known in-frame deletion in the gene. To conclude, this study contributes a novel method to discover cell-level mutation information from scRNA-seq that can facilitate investigation of cell-to-cell heterogeneity.

Availability and implementation

The source codes and bioinformatics pipeline of SCmut are available at https://github.com/nghiavtr/SCmut.

Supplementary information

Supplementary data are available at Bioinformatics online.
Valine increases milk fat synthesis in mammary gland of gilts through stimulating AKT/MTOR/SREBP1 pathway†
Authors: Che Long , Xu Mengmeng , Gao Kaiguo , Zhu Cui , Wang Li , Yang Xuefen , Wen Xiaolu , Xiao Hao , Jiang Zongyong , Wu De
Published: April 2019

Lactating mammary glands are among the most active lipogenic organs and provide a large percentage of bioactive lipids and calories for infant growth. The branched-chain amino acid (BCAA) valine is known to modulate fatty acids synthesis in adipose tissue; however, its effects on fat metabolism and the underlying mechanisms in mammary glands remain to be determined. Valine supplementation during late pregnancy significantly increased the contents of total milk fat, triglyceride, sphingomyelin, and polyunsaturated fatty acids in the colostrum of gilts. Further study in porcine mammary epithelial cells (PMECs) confirmed that valine upregulated the phosphorylation levels of AKT-activated MTOR and subsequently induced the nuclear accumulation of sterol regulatory element binding protein 1 (SREBP1), thus increasing the expression of proteins related to fatty acids synthesis and intracellular triacylglycerol content. Inhibition of AKT/MTOR signaling or silencing of SREBP1 in PMECs downregulates the expression of proteins related to fatty acids synthesis and intracellular triacylglycerol content. Our findings indicated that valine enhanced milk fat synthesis of colostrum in porcine mammary glands via the AKT/MTOR/SREBP1 signaling pathway.
Nonparametric independence testing via mutual information
Authors: Berrett T B , Samworth R J
Published: April 2019

We propose a test of independence of two multivariate random vectors, given a sample from the underlying population. Our approach is based on the estimation of mutual information, whose decomposition into joint and marginal entropies facilitates the use of recently developed efficient entropy estimators derived from nearest neighbour distances. The proposed critical values may be obtained by simulation in the case where an approximation to one marginal is available or by permuting the data otherwise. This facilitates size guarantees, and we provide local power analyses, uniformly over classes of densities whose mutual information satisfies a lower bound. Our ideas may be extended to provide new goodness-of-fit tests for normal linear models based on assessing the independence of our vector of covariates and an appropriately defined notion of an error vector. The theory is supported by numerical studies on both simulated and real data.