bluuebunny/crossref_metadata_2025 huggingface dataset:
Optimization of Shielding- Collimator Parameters for ING-27 Neutron Generator Using MCNP5
Authors: Hegazy Aya Hamdy , Skoy V.R. , Hossny K.
Published: April 2018

Neutron generators are now used in various fields. They produce only fast neutrons; D-D neutron generator produces 2.45 MeV neutrons and D-T produces 14.1 MeV neutrons. In order to optimize shielding-collimator parameters to achieve higher neutron flux at the investigated sample (The signal) with lower neutron and gamma rays flux at the area of the detectors, design iterations are widely used. This work was applied to ROMASHA setup, TANGRA project, FLNP, Joint Institute for Nuclear Research. The studied parameters were; (1) shielding-collimator material, (2) Distance between the shielding-collimator assembly first plate and center of the neutron beam, and (3) thickness of collimator sheets. MCNP5 was used to simulate ROMASHA setup after it was validated on the experimental results of irradiation of Carbon-12 sample for one hour to detect its 4.44 MeV characteristic gamma line. The ratio between the signal and total neutron flux that enters each detector was calculated and plotted, concluding that the optimum shielding-collimator assembly is Tungsten of 5 cm thickness for each plate, and a distance of 2.3 cm. Also, the ratio between the signal and total gamma rays flux was calculated and plotted for each detector, leading to the previous conclusion but the distance was 1 cm.
The Unified Database for BM@N experiment data handling
Authors: Gertsenberger Konstantin , Rogachevsky Oleg
Published: April 2018

The article describes the developed Unified Database designed as a comprehensive relational data storage for the BM@N experiment at the Joint Institute for Nuclear Research in Dubna. The BM@N experiment, which is one of the main elements of the first stage of the NICA project, is a fixed target experiment at extracted Nuclotron beams of the Laboratory of High Energy Physics (LHEP JINR). The structure and purposes of the BM@N setup are briefly presented. The article considers the scheme of the Unified Database, its attributes and implemented features in detail. The use of the developed BM@N database provides correct multi-user access to actual information of the experiment for data processing. It stores information on the experiment runs, detectors and their geometries, different configuration, calibration and algorithm parameters used in offline data processing. An important part of any database - user interfaces are presented.
ESIS ions injection, holding and extraction control system
Authors: Donets E.D. , Donets E.E. , Donets D.E. , Lyuosev D.A. , Ponkin D.O. , Ramsdorf A.Yu. , Boytsov A.Yu. , Salnikov V.V. , Shirikov I.V.
Published: April 2018

Electron string ion source (ESIS) KRION-6T is one of the main parts of the NICA injection complex [1]. During the work on creation of a new ion source for the NICA/MPD project the new ion motion control system was developed, produced and successfully put into operation. Modules development process and operation results are described.
Some Applications of Holography to Study Strongly Correlated Systems
Authors: Bhatnagar Neha
Published: April 2018

In this work, we study the transport coefficients of strongly coupled condensed matter systems using gauge/gravity duality (holography). We consider examples from the real world and evaluate the conductivities from their gravity duals. Adopting the bottom-up approach of holography, we obtain the frequency response of the conductivity for (1+1)-dimensional systems. We also evaluate the DC conductivities for non-relativistic condensed matter systems with hyperscaling violating geometry.
Adaptive particle filter for localization problem in service robotics
Authors: Heilig Alexander , Mamaev Ilshat , Hein Björn , Malov Dmitrii
Published: April 2018

In this paper we present a statistical approach to the likelihood computation and adaptive resampling algorithm for particle filters using low cost ultrasonic sensors in the context of service robotics. This increases the efficiency of the particle filter in the Monte Carlo Localization problem by means of preventing sample impoverishment and ensuring it converges towards the most likely particle and simultaneously keeping less likely ones by systematic resampling. Proposed algorithms were developed in the ROS framework, simulation was done in Gazebo environment. Experiments using a differential drive mobile platform with 4 ultrasonic sensors in the office environment show that our approach provides strong improvement over particle filters with fixed sample sizes.
Gaz Diffusion Layers from functional carbon materials for fuel cells used in energy installations
Authors: Kiseleva Elena , Vasilenko Anna
Published: April 2018

Gas Diffusion Layers (GDL) for fuel cells are two-dimensional carbon materials designed to obtain a smaller thickness, greater bending stiffness, lower residual deformation and lower compressibility compared to analogs. To produce it, functional carbon materials were used: activated carbon of own production, from vegetable raw materials, acetylene black and single-walled Tuball nanotubes. Dependence on the amount of binder is shown, as are the properties of electrodes made by calendering. The resistance of the rolled electrodes is much lower than that of the sputtered electrodes. There are proposed 4 variants of electrodes, which can be used in fuel cells and are used in power energy installations.
Impact of the face angle to traveling trajectory during the riding standing-type personal mobility device
Authors: Kim Jeyeon , Sato Kenta , Hashimoto Naohisa , Kashevnik Alexey , Tomita Kohji , Miyakoshi Seiichi , Takinami Yusuke , Matsumoto Osamu , Boyali Ali
Published: April 2018

In this paper, we investigate the impact of face direction during traveling by Standing-Type Personal Mobility Device (PMD). The use of PMD devices has been a popular choice for recreational activities in the developed countries such as in the USA and the countries in Europe. These devices are not completely risk free and various accidents have been reported. Since that, the risk factors leading to accidents have to be investigated. Unfortunately, the research studies on the risk factors on riding PMD devices have not been matured as much as the studies on driving cars. In this paper, we evaluate the impacts of face angle on travelling trajectory during travelling in a PMD. We showed by experiments that, the face direction is an important factor in risk assessment for traveling by a PMD.
Filling the gaps: shaping lighting. Education for the future
Authors: Bech-Larsen P. , Linnebjerg S. , Mullins M.F.
Published: April 2018

Training and knowledge of lighting is an increasingly sought-after professional quality in Denmark and Sweden. However, technological development in the lighting field has been in recent years extremely rapid, not least in Scandinavia. This has led to a situation, where users, designers, specifiers, buyers and installers are often neither in possession, nor have access to, the knowledge about lighting that they need. The aim of the study is to map and analyze the existing offer and demand for competencies within lighting related fields. That is to say, the study has looked at the existing educational programs within a broad field of lighting and compared this ‘supply’ to the current ‘demand’ by local employers. The paper presents the results from a statistical analysis of data collected from a series of surveys, expert interviews and focus groups, involving more than 250 participants in Sweden and Denmark. Based on the findings, the paper presents recommendations for the design of educational curricula.
The impact of restorative audio-visual environment learning on the stress
Authors: Matveev Nikolai , Shamritskiy Kirill
Published: April 2018

The experiment, conducted in the laser theater Lux Aeterna on the basis of the ITMO University, was aimed at testing the hypothesis about the positive effect of dynamic audio-visual content on the psycho-emotional state of a person and her academic progress after a long period of exposure. Both groups underwent a lengthy Bourdon test and a Shcherbatyh test for the learning stress. Only the participants who passed the laser theater session improved their productivity in the performance of monotonous work in the further passage of the test and showed a significant decrease in the level of general learning stress at the end of the experiment. Correlations between the level of learning stress and academic progress were not found. The use of sessions of dynamic audio-visual content based on the laser theater Lux Aeterna can be considered as an alternative relaxation method that allows changing the level of learning stress in people, increasing productivity in the performance of monotonous work and improve general well-being.
Step-up training for colorectal and gastric ESD and the challenge of ESD training in the proximal colon: results from a German Center
Authors: Ebigbo Alanna , Probst Andreas , Römmele Christoph , Messmann Helmut
Published: April 2018

Background and study aims The endoscopic submucosal dissection (ESD) of cancerous and precancerous lesions in the gastrointestinal (GI) tract is an effective but difficult-to-learn procedure, especially for Western endoscopists. We developed a step-up training protocol and evaluated its outcome on a single endoscopist using specific performance measures.

Patients and methods The training protocol included a 12-month period of 50 observational and supervised ESD cases as well as 24 animal procedures. After completion of the protocol, ESD competency was evaluated in the first 30 independent ESD cases. Majority of lesions were located in the stomach and rectum. Performance measures included R0-resection rate, complication rate and resection speed.

Results R0 resection rate was 93 %, complication rate was 7 % and median resection speed was 6,77 cm2/h. 1 case of delayed perforation with subsequent hemicolectomy occurred in the descending colon.

Conclusion The ESD step-up training protocol used in this study on a single endoscopist showed excellent outcomes for lesions in the rectum and stomach. However, ESD training in the upper colon remains a challenge.
Risk Factors for Systemic Reduced Bone Mineral Density in
Premenopausal Female Patients with Early Untreated Rheumatoid
Arthritis
Authors: Ahmed Hamada S. , Farrag Sherif E. , Okasha Amr E. , Othman Gamal , Shady Ibrahim
Published: April 2018

Background Systemic osteoporosis (OP) is evident among patients with
early rheumatoid arthritis (ERA). This study aimed to investigate the OP risk
factors in patients with ERA and who was treatment-naïve at
inclusion.

Subjects and Methods Systemic bone mineral density (BMD) of the lumbar
spine (LS), femoral neck (FN) and total hip (TH) was measured in 135
treatment-naïve premenopausal females with early Rheumatoid Arthritis
(ERA). For all patients, demographic data, vitamin D status, and the specific
parameters of the disease, including disease activity, serum levels of
rheumatoid factor and anti-citrullinated protein antibodies (ACPA) were
evaluated.

Results T score was<−1.0 in the LS in 16.2%, in
the FN in 22.2% and in the TH in 23.7%. Among our patients,
29.6% had below normal T score at any site. Demographic characteristics,
RA duration, diseases activity did not significantly impact BMD. However,
patients with decreased BMD were more prevalent ACPA- and rheumatoid factor
(RF)-positive than patients with normal BMD. Also, high titer ACPA or RF is
associated with more marked reduction in BMD. In regression analysis, after
adjustment for possible confounders, patient stratification according to ACPA
status and RF status (into negative, low-positive and high positive) still a
significant independent variable associated with lower BMD values.

Conclusion Presence of ACPA or RF is associated with increased risk for
development of reduced systemic BMD from very early stage of rheumatoid
arthritis. Furthermore, this risk increases more with higher levels of ACPA or
RF. Measurement of BMD should be performed for ACPA- or RF-positive patients
with early RA.
Peroxisomal Disorders: Experience from a Genetic Center in North India
Authors: Angurana Suresh Kumar , Suthar Renu , Panigrahi Inusha
Published: April 2018

Diagnosis of peroxisomal disorders (PDs) is often delayed because of unfamiliarity with the characteristic features of PDs and their genetic heterogeneity. Aim of this study was to describe clinical profiles of six children with PDs. This is a retrospective study involving six children with PDs. The patients included three males, one female, and a fetus. Three patients were diagnosed with Zellweger's syndrome, two with rhizomelic chondrodysplasia punctata, and one with X-linked adrenoleukodystrophy. These diagnoses were established based on clinical, radiological, and biochemical features (elevated very long chain fatty acids levels). Parents of all cases have been provided genetic counseling and advised of prenatal diagnosis. Diagnosis of PDs requires knowledge of characteristic clinicoradiological features, and clinical confirmation is possible with simple imaging and biochemical investigations. Molecular diagnosis is possible for selected cases.
Apolipoprotein M Protects Lipopolysaccharide-Treated Mice from Death and Organ Injury
Authors: Kurano Makoto , Tsuneyama Koichi , Morimoto Yuki , Shimizu Tomo , Jona Masahiro , Kassai Hidetoshi , Nakao Kazuki , Aiba Atsu , Yatomi Yutaka
Published: April 2018

Objective High-density lipoprotein (HDL) has been epidemiologically shown to be associated with the outcome of sepsis. One potential mechanism is that HDL possesses pleiotropic effects, such as anti-apoptosis, some of which can be ascribed to sphingosine 1-phosphate (S1P) carried on HDL via apolipoprotein M (apoM). Therefore, the aim of this study was to elucidate the roles of apoM/S1P in the consequent lethal conditions of sepsis, such as multiple organ failure caused by severe inflammation and/or disseminated intravascular coagulation.

Methods and Results In mice treated with lipopolysaccharide (LPS), both plasma apoM levels and the expression of apoM in the liver and kidney were suppressed. The overexpression of apoM improved the survival rate and ameliorated the elevated plasma alanine aminotransferase (ALT) and creatinine levels, while the knockout or knockdown of apoM deteriorated these parameters in mice treated with LPS. Treatment with VPC23019, an antagonist against S1P receptor 1 and 3, or LY294002, a PI3K inhibitor, partially reversed these protective properties arising from the overexpression of apoM. The overexpression of apoM inhibited the elevation of plasma plasminogen activator inhibitor-1, restored the phosphorylation of Akt, and induced anti-apoptotic changes in the liver, kidney and heart.

Conclusion These results suggest that apoM possesses protective properties against LPS-induced organ injuries and could potentially be introduced as a novel therapy for the severe conditions that are consequent to sepsis.
Characterisation and Some Properties of the Protein C Activator from Agkistrodon Contortrix Contortrix Venom
Authors: Exner Thomas , Vaasjoki Riita
Published: April 2018

The protein C activator (PCA) detectable in the venom of Agkistrodon Contortrix Contortrix (ACCV, Southern Copperhead) by specific immunochromometric assay and anticoagulant activity has been isolated and partially characterized. Chromatog raphy of the crude venom on SP-Sephadex followed by Con A Sepharose and finally on hydroxylapatite was necessary to achieve an electrophoretically – pure product. The isolated PCA is a single chain glycoprotein with strong positive charge and an apparent molecular weight of 36,000.

It had an immediate-inhibiting effect on the activated partial thromboplastin time (APTT) of normal plasma with no noticeable eilect Oii the piOtliiumbm time, its piolonging eifect oil the APTT was dependent on protein C and il appeared to interfere with the contact mechanism rather than with factors V and VIII. It had enzymatic activity on some tripeptide chromogenic substrates sensitive to thrombin and kallikrein. When mixed with normal plasma it generated activity on substrates sensitive to activated protein C and should be useful for studies of protein C.
Thrombosis Associated with Antiphospholipid Antibodies Cannot Be Explained by Effects on Endothelial and Platelet Prostanoid Synthesis
Authors: Hasselaar Paula , Derksen Ronald H W M , Blokzijl Laya , de Groot Philip G
Published: April 2018

The effect of 23 antiphospholipid antibody positive SLE sera, 4 antiphospholipid antibody negative SLE sera and 17 control sera on endothelial prostacyclin and platelet thromboxane A? production was studied. Endothelial cells and platelets were stimulated with different agonists. Depending on the stimulus used, 4-19% of the SLE sera inhibited the prostacyclin release, whereas 4-28% enhanced prostacyclin production. Our data suggest that the pathophysiological mechanisms underlying decreased prostacyclin production are heterogeneous. Follow-up of two patients showed that prostacyclin inhibitory activity was variable in time. Platelet thromboxane production was normal nr increased, but never decreased in the presence of the SLE sera. An imbalance in thromboxane A2/prostacyclin ratio was present in some patients, but did not correlate with a history of thrombosis. We conclude that, in general, interference of antiphospholipid antibodies with endoihelial or platelet prostanoid synthesis does not explain the occurrence of thromboembolic manifestations in antiphospholipid antibody positive SLE patients.
Regulation of Arachidonic Acid-Dependent Ca++ Influx in Human Platelets
Authors: Bosia Amalia , Losche Wolfgang , Pannocchia Antonella , Treves Silvia , Ghigo Dario , Till Uwe , Pescarmona Gianpiero
Published: April 2018

Quin2 was used to study the rise in cytoplasmic free calcium ([Ca++]i) and the role of prostaglandin (PG) endoperoxides/thromboxane A2 (TxA2), reduced glutathione (GSH), ADP and the glycoprotein (GP) Ilb IIIa complex in mediating [Ca++]i rise during àiachidonic acid(AA)induced platelet aggregation. Ca++mobilization, mostly due to an influx across the plasma membrane, is completely inhibited by aspirin and persists after selective blockade of TxA2 synthase by dazoxiben. GSH total depletion causes a complete aggregation block and 90% inhibition of the transient: U-46619, a stable analog of cyclic endoperoxide PGH2, stimulates [Ca++]i transient in aspirintreated or in GSH depleted platelets. ADPscavengers, ATP (which competes for the ADP receptor), and monoclonal antibodies against the GP Ilb IIIa complex reduce AAinduced Ca++ influx. Therefore, PG endoperoxides alone or a PGH2/TxA2 mimetic stimulate Ca++ influx. Synthesis of PGH2 and TxA2 depends on the availability of GSH, which acts as the reducing cofactor for the PG peroxidase activity. ADP and GP II b ill a are regulating factors of AA mediated Ca++ influx during platelet activation.
Hypopituitarism Secondary to an Arachnoid Cyst — Case Report
Authors: Cunha Eliezer , Souza Anderson , Teixeira Manoel , Figueireido Eberval
Published: April 2018

Arachnoid cysts (ACs) are a rare condition of mass effect injury and are usually found in the Sylvian fissure. However, rarely, they can appear in the sellar area, causing symptoms of compression. Due to the mass effect, the sellar arachnoid cyst (SAC) may cause headaches, visual disturbances, hypopituitarism, precocious puberty, and the “bobble-head doll” syndrome.

We present the case of JNS, 61 years old, male. The patient presented with hypotestosteronism, hypothyroidism, hypocortisolism and bitemporal hemianopsia. The magnetic resonance imaging scans revealed a mass above the pituitary gland, compatible with a SAC. A surgical excision was performed with removal of the capsule and fenestration within the subarachnoid spaces for emptying the cyst. After the procedure, the patient presented great clinical improvement. The rarity of the case calls attention to the fact that SACs should be thought of as a differential diagnosis in cases of hypopituitarism.
Determination of Human Thrombin-Antithrombin III Complex in Plasma with an Enzyme-Linked Immunosorbent Assay
Authors: Pelzer Hermann , Schwarz Angela , Heimburger Norbert
Published: April 2018

An enzyme-linked immunosorbent assay (ELISA) was developed for the determination of thrombin-antithrombin III complex (TAT) in human plasma. The test system follows the sandwich principle and uses two different antibodies directed against human thrombin and human antithrombin III, respectively. The antibodies bind selectively to the corresponding antigen moieties of TAT. The assay was calibrated with definite concentrations of preformed purified TAT added to TAT-poor plasma. The lower limit of sensitivity of the assay was 0.5 μg/1. Mean coefficients of variation of 4.2% (intraassay) and 3.5% (interassay) were found for TAT concentrations between 2 and 60 μg/1. A reference range from 0.85 to 3.2 μg/1 was calculated from TAT concentration in plasma samples from 88 healthy donors (mean value ± SD: 1.45 ± 0.4 μg/I). In plasma samples from patients with pulmonary embolism (n = 17), TAT concentrations between 3 and 25 μg/1 were measured. In 15 patients with deep vein thrombosis, TAT was found up to 3 to 25 μg/1. From these data we conclude that measurement of TAT can be a sensitive parameter for specific detection of a latent activation of the clotting pathway.
Decreased Platelet Number and Function and Increased Fibrinolysis Contribute to Postoperative Bleeding in Cardiopulmonary Bypass Patients
Authors: Holloway D Scott , Summaria Louis , Sandesara Jyoti , Paul Vagher J , Alexander John C , Caprini Joseph A
Published: April 2018

We simultaneously evaluated platelet and fibrinolytic parameters to assess their individual and combined contributions to postoperative blood loss in cardiopulmonary (CP) bypass patients. Platelet count, platelet aggregability, hematocrit, plasminogen (PLG) concentration, alpha2-antiplasmin (AP) concentration, free protease activity (fPA), and antithrombin-III (AT-III) were measured in nine patients undergoing surgery using cardiopulmonary bypass. Chest tube drainage was used as the measure of postoperative blood loss. Hematocrit, platelet count, PT .G , AP and AT-TTT all decreased during CP bypass, with PLG and AT-III decreasing much more than dilution. During CP bypass, platelet aggregability to A DP did not change significantly from pre-bypass, but aggregability to arachidonic acid (AA) decreased significantly. Following protamine administration there was a large increase (83%) in fPA, the platelet count showed a further drop (from 61 % to 50% of pre-bypass levels) . and platelet aggregability decreased significantly (from 95% to 34% of prebypass levels for ADP, and from 55% to 11.9% for A A). Chest tube drainage during the first four postoperative hours correlated positively (p <0.05) with the combination of increase in free protease activity and decrease in platelet count. The total chest tube drainage correlated significantly with the combination of decrease in platelet count and the decrease in platelet aggregability. These combinations of changes correlated significantly with postoperative blood loss whereas the individual changes did not. These data indicate that during the early postoperative period the increased fibrinolytic activity and the decreased platelet count together contribute toward postoperative blood loss in CP bypass patients, and that during the entire first 24 hour period postoperatively the decreased platelet number and decreased platelet function are important contributors to blood loss.
Need for Quantitative Measurement Methods for Posterior Uveitis: Comparison of Dual FA/ICGA Angiography, EDI-OCT Choroidal Thickness and SUN Vitreous Haze Evaluation in Stromal Choroiditis
Authors: Fabro Filippo , Herbort Carl
Published: April 2018

Background/Purpose Quantitative methods for posterior uveitis are necessary for precise appraisal and follow-up of inflammation in practice and in clinical trials. The aim of this study was to assess fluorescein angiography (FA), indocanine green angiography (ICGA), and enhanced depth imaging optical coherence tomography choroidal thickness (EDI-OCT CT) in two stromal choroiditis entities, birdshot retinochoroiditis (BRC), and Vogt-Koyanagi-Harada disease (VKH), as well as to determine (1) disease patterns, (2) respective response to therapy, and (3) their potential utility in clinical trials in comparison to vitreous haze, the present standard outcome used in clinical trials.

Methods This retrospective study included newly diagnosed patients with BRC and VKH, seen at the Centre for Ophthalmic Specialized Care, Lausanne, Switzerland. Angiographic signs were quantified using an established dual FA/ICGA scoring system for uveitis at presentation and on follow-up. FA/ICGA score ratios were compared between diseases to determine disease patterns. EDI-OCT CT was determined using a spectral domain instrument. Vitreous haze was determined using the SUN (Standardization of Uveitis Nomenclature) method.

Results Among 1872 uveitis patients seen from 1995 to 2016, 8 newly diagnosed BRC patients (16 eyes) and 6 newly diagnosed VKH patients (12 eyes) had sufficient data for study inclusion. Patients with BRC and VKH at initial onset had mean FA scores of 16.1 ± 7.0 vs. 4.6 ± 2.1 (p < 0.0001), respectively, while mean ICGA scores were similarly high in the two diseases, 18.9 ± 3.6 (BRC) vs. 20.8 ± 7.5 (VKH). After therapy, FA and ICGA scores decreased significantly for both entities (− 60% of FA score and 55% of ICGA score in BRC vs. − 72% of FA score and − 87% for ICGA score in VKH). EDI-OCT CT decreased significantly in the two entities. Vitreous haze was almost absent in VKH and low in BRC.

Conclusion Dual FA/ICGA scoring showed the diverse disease patterns of BRC and VKH; both the retina and choroid were involved at onset in BRC, whereas VKH was a pure choroidal disease with later spillover into the retina. Dual FA/ICGA allowed for the precise measurement of inflammation at onset and upon follow-up. EDI-OCT CT responded to therapy in both diseases but was found to be of limited use in this early/subacute disease phase because it lacked sensitivity to detect subclinical recurrences and was therefore only useful for long-term follow-up. Vitreous haze was low in both entities and thus useless as an inflammatory parameter.
Cataract Surgery in High Hyperopia
Authors: Waldmann Nicolas , Gerber Nadine , Hill Warren , Goldblum David
Published: April 2018

Background Although cataract surgery is a well-established and standardised procedure, it can be demanding and associated with higher complication rates in high hyperopia. We present clinical data for highly hyperopic patients who underwent cataract surgery over a 12-year period (2005 – 2016) and at a single centre.

Patients and Methods Out of a total of 11 434 cataract operations, 41 highly hyperopic eyes (SN60AT ≥ 31 dpt) were included for analysis. We compared the target spherical equivalent to the final postoperative spherical equivalent for five different formulas. We also reviewed the best corrected distance visual acuity (BCDVA) before and after surgery and any complications.

Results LogMAR BCDVA increased significantly from a mean of 0.5 before to 0.37 after surgery (p = 0.02). The main reasons for the reduced final BCDVA were glaucoma, Fuchs corneal endothelial dystrophy, and age-related macular degeneration. One eye suffered a radial capsule tear and received a sulcus implanted intraocular lens (IOL). There was no statistically significant difference between formulas with respect to aberration of the final spherical equivalent.

Conclusions Patients with high hyperopia often have ocular comorbidities. Such eyes may be surgically challenging, resulting in reduced benefits from cataract surgery compared to normal eyes.
A fast low-to-high confinement mode bifurcation dynamics in the boundary-plasma gyrokinetic code XGC1
Authors: Ku S. , Chang C. S. , Hager R. , Churchill R. M. , Tynan G. R. , Cziegler I. , Greenwald M. , Hughes J. , Parker S. E. , Adams M. F. , D'Azevedo E. , Worley P.
Published: April 2018

A fast edge turbulence suppression event has been simulated in the electrostatic version of the gyrokinetic particle-in-cell code XGC1 in a realistic diverted tokamak edge geometry under neutral particle recycling. The results show that the sequence of turbulent Reynolds stress followed by neoclassical ion orbit-loss driven together conspire to form the sustaining radial electric field shear and to quench turbulent transport just inside the last closed magnetic flux surface. The main suppression action is located in a thin radial layer around ψN≃0.96–0.98, where ψN is the normalized poloidal flux, with the time scale ∼0.1 ms.
Numerical solution of the unsteady diffusion-convection-reaction equation based on improved spectral Galerkin method
Authors: Zhong Jiaqi , Zeng Cheng , Yuan Yupeng , Zhang Yuzhe , Zhang Ye
Published: April 2018

The aim of this paper is to present an explicit numerical algorithm based on improved spectral Galerkin method for solving the unsteady diffusion-convection-reaction equation. The principal characteristics of this approach give the explicit eigenvalues and eigenvectors based on the time-space separation method and boundary condition analysis. With the help of Fourier series and Galerkin truncation, we can obtain the finite-dimensional ordinary differential equations which facilitate the system analysis and controller design. By comparing with the finite element method, the numerical solutions are demonstrated via two examples. It is shown that the proposed method is effective.
Advanced photonic filters based on cascaded Sagnac loop reflector resonators in silicon-on-insulator nanowires
Authors: Wu Jiayang , Moein Tania , Xu Xingyuan , Moss David J.
Published: April 2018

We demonstrate advanced integrated photonic filters in silicon-on-insulator (SOI) nanowires implemented by cascaded Sagnac loop reflector (CSLR) resonators. We investigate mode splitting in these standing-wave (SW) resonators and demonstrate its use for engineering the spectral profile of on-chip photonic filters. By changing the reflectivity of the Sagnac loop reflectors (SLRs) and the phase shifts along the connecting waveguides, we tailor mode splitting in the CSLR resonators to achieve a wide range of filter shapes for diverse applications including enhanced light trapping, flat-top filtering, Q factor enhancement, and signal reshaping. We present the theoretical designs and compare the CSLR resonators with three, four, and eight SLRs fabricated in SOI. We achieve versatile filter shapes in the measured transmission spectra via diverse mode splitting that agree well with theory. This work confirms the effectiveness of using CSLR resonators as integrated multi-functional SW filters for flexible spectral engineering.
Trophic relationships among animals associated with drifting wrack
Authors: Baring Ryan J. , Lester Rebecca E. , Fairweather Peter G.
Published: April 2018

Wrack accumulates commonly in surf zones of sandy beaches and can be a semipermanent feature. Very few studies have investigated the trophic pathways associated with wrack accumulations in sandy beach surf zones, despite their potential importance to nearshore food webs. In the present study, we were specifically interested in determining the fish–wrack trophic associations in the nearshore. Macrophytes, macroinvertebrates and fish were sampled from drifting wrack at two sites with different macrophyte compositions (i.e. algae v. an algae–seagrass mix) in South Australia. The gut contents of fish were sampled, and the δ13C and δ15N stable isotope signatures of fish, macroinvertebrates and macrophytes were analysed. Using both the stable isotope and diet data, we identified that fish are feeding among wrack accumulations, but some unexplained trophic pathways suggest that fish are also likely to be foraging over multiple habitats elsewhere for food. In contrast, there was more evidence that grazing macroinvertebrates may be feeding on and around macrophytes within the accumulations, as well as using them as habitat. Thus, the present study established some baseline trophic pathways associated with wrack accumulations in sandy beach surf zones. Given the modest evidence for use of wrack as a food source, the lower trophic levels of the food webs identified remain unknown and should be an area for future research.
Origin, antigenicity, and function of a secreted form of ORF2 in hepatitis E virus infection
Authors: Yin Xin , Ying Dong , Lhomme Sébastien , Tang Zimin , Walker Christopher M. , Xia Ningshao , Zheng Zizheng , Feng Zongdi
Published: April 2018

Significance

Hepatitis E virus (HEV) is a main cause of acute hepatitis worldwide. Recent evidence suggests that HEV-infected cells release a secreted form of ORF2 protein (ORF2
S
) but its origin and function are unknown. Here we demonstrate that ORF2
S
and ORF2
C
(the actual capsid protein) are different translation products and that ORF2
S
is not essential for the HEV life cycle but inhibits antibody-mediated neutralization of HEV. Our results have important implications for understanding the HEV replication cycle and immune evasion mechanisms. The identified internal start codon in this study is highly conserved in most HEV strains, suggesting that the production of ORF2
S
is an evolutionary conserved function for HEV.
Practical reasoning and practical knowledge
Authors: Stout Rowland
Published: April 2018

The judgement that provides the content of intention and coincides with the conclusion of practical reasoning is a normative judgement about what to do, and not, as Anscombe and McDowell argue, a factual judgement about what one is doing. Treating the conclusion of practical reasoning as expressing a recommendation rather than a verdict undermines McDowell’s argument; the special nature of practical reasoning does not preclude its conclusions being normative. Anscombe’s and McDowell’s claim that practical self-knowledge is productive of action may be accommodated by identifying the content of practical knowledge not with the conclusion but with a premise of practical reasoning – a kind of practical reasoning that occurs within rather than before action.
Effects of Sn on microstructure and mechanical properties of as-rolled Mg–5Zn–1Mn alloy
Authors: Zou Jiankun , Yan Hongge , Chen Jihua , Xia Weijun , Su Bin , Lei Yi , Wu Qin
Published: April 2018

Effects of Sn on microstructure and mechanical properties of Mg–5Zn–1Mn alloy subjected to high strain rate rolling (9.1 s-1), 300°C and 80% pass reduction are investigated. With higher Sn content, the dynamic recrystallisation (DRX) grain size gradually decreases due to the stronger pinning of nano-scale precipitates at grain boundaries and the DRX fraction first increases due to the enhanced effect on DRX by decreasing stacking fault energy and then decreases due to more precipitates at grain boundaries. Ultimate tensile strength ( UTS) and elongation to rupture ( Er) of as-rolled alloys increase and then decrease. Alloy with 0.9 mass% Sn exhibits the highest DRX fraction (95 vol.-%), the finer DRX grain size (1.22 µm), UTS of 358 MPa and Er of 20.4%.
Non-symmetric convex polytopes and Gabor orthonormal bases
Authors: Chung Randolf , Lai Chun-kit
Published: April 2018

In this paper, we show that non-symmetric convex polytopes cannot serve as a window function to produce a Gabor orthonormal basis by any time-frequency sets.
The Associations Between Mental Health Status, Hypertension, and Hospital Inpatient Visits in Women in the United States
Authors: Rozario Sylvia S , Masho Saba W
Published: April 2018

BACKGROUND

Poor mental health status is more prevalent in women and may be related to poor hypertension outcomes and increased hospital inpatient visits. This study aims to find the association between mental health status and hypertension in women and the combined effect of mental health status and hypertension on hospital inpatient visits in women in the United States.

METHODS

The household component of 2014 Medical Expenditure Panel Surveys (MEPS) was analyzed (N = 9,137). Kessler (K6) scale for mental health status (poor, good/excellent), hypertension (yes, no), and hospital inpatient visits (yes, no) were examined. A combined effect variable for mental health status and hypertension was created. Multiple logistic regression analysis was conducted and adjusted odds ratios (AORs) with corresponding 95% confidence intervals (CIs) were calculated.

RESULTS

After adjusting for confounders, women who reported poor mental health had significantly higher odds of hypertension compared to women who reported good/excellent mental health (AOR = 1.39, 95% CI = 1.16, 1.68). Further, women who reported hypertension coupled with poor mental health had higher odds of having hospital inpatient visits compared to women who reported no hypertension coupled with good/excellent mental health in the adjusted analysis (AOR = 3.03, 95% CI = 1.96, 4.69).

CONCLUSIONS

There is a significant association between mental health status and hypertension in women. Further, poor mental health status coupled with hypertension leads to increase hospital inpatient visits for women. It is important that health professionals focus on utilizing available screening tools to assess mental health status of women for early detection and to manage the disorder.
Dissecting newly transcribed and old RNA using GRAND-SLAM
Authors: Jürges Christopher , Dölken Lars , Erhard Florian
Published: April 2018

Summary: Global quantification of total RNA is used to investigate steady state levels of gene expression. However, being able to differentiate pre-existing RNA (that has been synthesized prior to a defined point in time) and newly transcribed RNA can provide invaluable information e.g. to estimate RNA half-lives or identify fast and complex regulatory processes. Recently, new techniques based on metabolic labeling and RNA-seq have emerged that allow to quantify new and old RNA: Nucleoside analogs are incorporated into newly transcribed RNA and are made detectable as point mutations in mapped reads. However, relatively infrequent incorporation events and significant sequencing error rates make the differentiation between old and new RNA a highly challenging task. We developed a statistical approach termed GRAND-SLAM that, for the first time, allows to estimate the proportion of old and new RNA in such an experiment. Uncertainty in the estimates is quantified in a Bayesian framework. Simulation experiments show our approach to be unbiased and highly accurate. Furthermore, we analyze how uncertainty in the proportion translates into uncertainty in estimating RNA half-lives and give guidelines for planning experiments. Finally, we demonstrate that our estimates of RNA half-lives compare favorably to other experimental approaches and that biological processes affecting RNA half-lives can be investigated with greater power than offered by any other method. GRAND-SLAM is freely available for non-commercial use at http://software.erhard-lab.de; R scripts to generate all figures are available at zenodo (doi: 10.5281/zenodo.1162340).
Ultra-fast global homology detection with Discrete Cosine Transform and Dynamic Time Warping
Authors: Raimondi Daniele , Orlando Gabriele , Moreau Yves , Vranken Wim F
Published: April 2018

Motivation

Evolutionary information is crucial for the annotation of proteins in bioinformatics. The amount of retrieved homologs often correlates with the quality of predicted protein annotations related to structure or function. With a growing amount of sequences available, fast and reliable methods for homology detection are essential, as they have a direct impact on predicted protein annotations.

Results

We developed a discriminative, alignment-free algorithm for homology detection with quasi-linear complexity, enabling theoretically much faster homology searches. To reach this goal, we convert the protein sequence into numeric biophysical representations. These are shrunk to a fixed length using a novel vector quantization method which uses a Discrete Cosine Transform compression. We then compute, for each compressed representation, similarity scores between proteins with the Dynamic Time Warping algorithm and we feed them into a Random Forest. The WARP performances are comparable with state of the art methods.

Availability and implementation

The method is available at http://ibsquare.be/warp.

Supplementary information

Supplementary data are available at Bioinformatics online.
A highly sensitive trap vector system for isolating reporter cells and identification of responsive genes
Authors: Ishikawa Kosuke , Kobayashi Yuta , Wakabayashi Yutaro , Watanabe Shinya , Semba Kentaro
Published: April 2018

We devised a versatile vector system for efficient isolation of reporter cells responding to a certain condition of interest. This system combines nontoxic GAL4-UAS and piggyBac transposon systems, allowing application to mammalian cells and improved expression of a fluorescent reporter protein for cell sorting. Case studies under conditions of c-MYC gene induction or endoplasmic reticulum (ER) stress with thapsigargin on mouse or human cell lines confirmed easy and efficient isolation of responsive reporter cells. Sequence analyses of the integrated loci of the thapsigargin-responsive clones identified responsive genes including BiP and OSBPL9. OSBPL9 is a novel ER stress-responsive gene and we confirmed that endogenous mRNA expression of OSBPL9 is upregulated by thapsigargin, and is repressed by IRE1α inhibitors, 4μ8C and toyocamycin, but not significantly by a PERK inhibitor, GSK2656157. These results demonstrate that this approach can be used to discover novel genes regulated by any stimuli without the need for microarray analysis, and that it can concomitantly produce reporter cells without identification of stimuli-responsive promoter/enhancer elements. Therefore, this system has a variety of benefits for basic and clinical research.
Ascending aortic aneurysm repair 44 years after Starr–Edwards caged-ball aortic valve replacement
Authors: Hatton Gabrielle E , Tanaka Akiko , Estrera Anthony L
Published: April 2018

We report a case of ascending aortic aneurysm repair and redo aortic valve replacement with a bioprosthesis 44 years after aortic valve replacement with a Starr–Edwards metal caged-ball prosthesis. The patient presented with a moderately stenotic caged-ball valve and a 50-mm ascending aortic aneurysm on a routine follow-up transthoracic echocardiography. We replaced the valve with a bioprosthesis at the time of aortic repair as the patient wished to stop anticoagulation therapy. Intraoperatively, we found that the cloth covering of the cage was nearly completely destroyed.
Two-scale method for the Monge–Ampère equation: pointwise error estimates
Authors: Nochetto R H , Ntogkas D , Zhang W
Published: April 2018

In this paper we continue the analysis of the two-scale method for the Monge–Ampère equation for dimension d ≥ 2 introduced in the study by Nochetto et al. (2017, Two-scale method for the Monge–Ampère equation: convergence to the viscosity solution. Math. Comput., in press). We prove continuous dependence of discrete solutions on data that in turn hinges on a discrete version of the Alexandroff estimate. They are both instrumental to prove pointwise error estimates for classical solutions with Hölder and Sobolev regularity. We also derive convergence rates for viscosity solutions with bounded Hessians which may be piecewise smooth or degenerate.
A visual analytics approach for pattern-recognition in patient-generated data
Authors: Feller Daniel J , Burgermaster Marissa , Levine Matthew E , Smaldone Arlene , Davidson Patricia G , Albers David J , Mamykina Lena
Published: April 2018

Objective

To develop and test a visual analytics tool to help clinicians identify systematic and clinically meaningful patterns in patient-generated data (PGD) while decreasing perceived information overload.

Methods

Participatory design was used to develop Glucolyzer, an interactive tool featuring hierarchical clustering and a heatmap visualization to help registered dietitians (RDs) identify associative patterns between blood glucose levels and per-meal macronutrient composition for individuals with type 2 diabetes (T2DM). Ten RDs participated in a within-subjects experiment to compare Glucolyzer to a static logbook format. For each representation, participants had 25 minutes to examine 1 month of diabetes self-monitoring data captured by an individual with T2DM and identify clinically meaningful patterns. We compared the quality and accuracy of the observations generated using each representation.

Results

Participants generated 50% more observations when using Glucolyzer (98) than when using the logbook format (64) without any loss in accuracy (69% accuracy vs 62%, respectively, p = .17). Participants identified more observations that included ingredients other than carbohydrates using Glucolyzer (36% vs 16%, p = .027). Fewer RDs reported feelings of information overload using Glucolyzer compared to the logbook format. Study participants displayed variable acceptance of hierarchical clustering.

Conclusions

Visual analytics have the potential to mitigate provider concerns about the volume of self-monitoring data. Glucolyzer helped dietitians identify meaningful patterns in self-monitoring data without incurring perceived information overload. Future studies should assess whether similar tools can support clinicians in personalizing behavioral interventions that improve patient outcomes.
Post-chemoradiation volumetric response predicts survival in newly diagnosed glioblastoma treated with radiation, temozolomide, and bevacizumab or placebo
Authors: Ellingson Benjamin M , Abrey Lauren E , Garcia Josep , Chinot Olivier , Wick Wolfgang , Saran Frank , Nishikawa Ryo , Henriksson Roger , Mason Warren P , Harris Robert J , Leu Kevin , Woodworth Davis C , Mehta Arnav , Raymond Catalina , Chakhoyan Ararat , Pope Whitney B , Cloughesy Timothy F
Published: April 2018

Background

In the current study we used contrast-enhanced T1 subtraction maps to test whether early changes in enhancing tumor volume are prognostic for overall survival (OS) in newly diagnosed glioblastoma (GBM) patients treated with chemoradiation with or without bevacizumab (BV).

Methods

Seven hundred ninety-eight patients (404 BV and 394 placebo) with newly diagnosed GBM in the AVAglio trial (NCT00943826) had baseline MRI scans available, while 337 BV-treated and 269 placebo-treated patients had >4 MRI scans for response evaluation. The volume of contrast-enhancing tumor was quantified and used for subsequent analyses.

Results

A decrease in tumor volume during chemoradiation was associated with a longer OS in the placebo group (hazard ratio [HR] = 1.578, P < 0.0001) but not BV-treated group (HR = 1.135, P = 0.4889). Results showed a higher OS in patients on the placebo arm with a sustained decrease in tumor volume using a post-chemoradiation baseline (HR = 1.692, P = 0.0005), and a trend toward longer OS was seen in BV-treated patients (HR = 1.264, P = 0.0724). Multivariable Cox regression confirmed that sustained response or stable disease was prognostic for OS (HR = 0.7509, P = 0.0127) when accounting for age (P = 0.0002), KPS (P = 0.1516), postsurgical tumor volume (P < 0.0001), O6-methylguanine-DNA methyltransferase status (P < 0.0001), and treatment type (P = 0.7637) using the post-chemoradiation baseline.

Conclusions

The post-chemoradiation timepoint is a better baseline for evaluating efficacy in newly diagnosed GBM. Early progression during the maintenance phase is consequential in predicting OS, supporting the use of progression-free survival rates as a meaningful surrogate for GBM.
Successful Treatment of Cerebral Toxoplasmosis Using Pyrimethamine Oral Solution Compounded From Inexpensive Bulk Powder
Authors: Hodgson Hayley A , Sim Taeyong , Gonzalez Hemil , Aziz Mariam , Rhee Yoona , Lewis Paul O , Jhobalia Neel , Shields Beth , Wang Sheila K
Published: April 2018

A price increase of pyrimethamine tablets in the United States has made the life-saving drug difficult to acquire for hospitalized patients who need it most. We report the successful use of a pyrimethamine oral suspension compounded from an economical bulk powder in a patient with acute toxoplasmic encephalitis.