bluuebunny/crossref_metadata_2025 huggingface dataset:
Delayed Aortic Stent Collapse in Blunt Traumatic Aortic Injury Repair
Authors: Alhaizaey Abdullah , Aljabri Badr , Alghamdi Musaad , AlAhmari Ali , Abulyazied Ahmed , Asiry Mohammed , Al-Omran Mohammed
Published: February 2020

Background Endovascular stent grafting has emerged as an option to treat traumatic aorta injuries with reported significantly low mortality and morbidity. Stent collapse is one of the complications that can occur in this type of treatment. The aim of this article is to analyze the expected cause of stent collapse and to draw attention to the importance of the surveillance follow-up, as this phenomenon may occur late postdeployment.

Methods A retrospectively collected dataset from the two highest volume trauma centers in Saudi Arabia was analyzed between April 2007 and October 2012. A total of 66 patients received stent grafts for traumatic aortic injury and were included in the study. We apply Ishimaru's anatomical aortic arch zones and Benjamin's aortic injury grading systems. There were 35 patients with aortic injury at zone 2, 26 patients in zone 3, and 5 patients in zone 4. About 96% (63) of the injuries were grades 2 and 3, including large intimal flap or aortic wall pseudoaneurysm with change in wall contour. The technical success rate, as defined by complete exclusion of lesions without leaks, stroke, arm ischemia or stent-related complications, was 90%.

Results Proximal stent collapse occurred in 4.5% of patients (3 of 66 inserted stents) during follow-up of 4 to 8 years (mean, 6 years). Patients with stent collapse tended to have an acute aortic arch angle with long-intraluminal stent lip, when compared with patients with noncollapsed stents. Intraluminal lip protrusion more than 10-mm increased collapse (p < 0.001). Stent-grafts sizes larger than 28 mm also demonstrated a higher collapse rate (p < 0.001).

Conclusions The risk of stent collapse appears related to poor apposition of the stent due to severe aortic arch angulation in young patients and to large stent sizes (>28 mm). Such age groups may have more anatomical and aortic size changes during the growth. Clinical and radiological surveillance is essential in follow-up after stent-graft treatment for traumatic aortic injury.
Visual Outcomes after Endoscopic Endonasal Transsphenoidal Resection of Pituitary Adenomas: Our Institutional Experience
Authors: van Essen Max J. , Muskens Ivo S. , Lamba Nayan , Belunek Stephan F.J. , van der Boog Arthur T.J. , Amelink G. Johan , Gosselaar Peter H. , van Doormaal Tristan P.C. , Stades Aline M.E. , Verhoeff Joost J.C. , van Genderen Maria M. , Eenhorst Christine A.E. , Broekman Marike L.D.
Published: February 2020

Objectives Visual dysfunction in patients with pituitary adenomas is a clear indication for endoscopic endonasal transsphenoidal surgery (EETS). However, the visual outcomes vary greatly among patients and it remains unclear what tumor, patient, and surgical characteristics contribute to postoperative visual outcomes.

Methods One hundred patients with pituitary adenomas who underwent EETS between January 2011 and June 2015 in a single institution were retrospectively reviewed. General patient characteristics, pre- and postoperative visual status, clinical presentation, tumor characteristics, hormone production, radiological features, and procedural characteristics were evaluated for association with presenting visual signs and visual outcomes postoperatively. Suprasellar tumor extension (SSE) was graded 0 to 4 following a grading system as formulated by Fujimoto et al.

Results Sixty-six (66/100) of all patients showed visual field defects (VFD) at the time of surgery, of whom 18% (12/66) were asymptomatic. VFD improved in 35 (35%) patients and worsened in 4 (4%) patients postoperatively. Mean visual acuity (VA) improved from 0.67 preoperatively to 0.84 postoperatively (p = 0.04). Nonfunctioning pituitary adenomas (NFPAs) and Fujimoto grade were independent predictors of preoperative VFD in the entire cohort (p = 0.02 and p < 0.01 respectively). A higher grade of SSE was the only factor independently associated with postoperative improvement of VFD (p = 0.03). NFPA and Fujimoto grade 3 were independent predictors of VA improvement (both p = 0.04).

Conclusion EETS significantly improved both VA and VFD for most patients, although a few patients showed deterioration of visual deficits postoperatively. Higher degrees of SSE and NFPA were independent predictors of favorable visual outcomes.
A high power capacity Ka-band radial transit time oscillator with one-gap extraction cavity
Authors: Wang Haitao , Zhang Jun , Dang Fangchao , Qian Baoliang , Ge Xingjun
Published: February 2020

The radial transit time oscillator (RTTO) is promising to realize high power output of millimeter-waves. Although the radial structure can enhance the power capacity, less cavities and small radial dimension make it difficult to improve the power capacity in RTTOs, especially in the extraction cavity. A one-gap extraction cavity in the Ka-band RTTO is proposed in this paper to improve the power capacity. Without electrons, taking the TM011 cavity as an example, the radial reversal resonant electric field can intersect with radial electrons. By choosing the sizes of the cavity, the synchronization of the electrons and the electric field can be realized to achieve effective energy exchange. In particle-in-cell simulation, the RTTO with the TM011 extraction cavity can output 1.0 GW high power microwaves (HPMs) at 31.2 GHz, and the beam-wave conversion efficiency is 31.6%. The maximum electric field in the TM011 cavity is only 800 kV/cm, which is less than one third that in the TM010 extraction cavities. In addition, the TM012 extraction cavity is employed to improve the efficiency to 35.4%. At the same time, because of the increase in the output power, the maximum radial electric field in the TM012 cavity increases to 850 kV/cm. Therefore, the one-gap extraction cavity can realize multiple energy exchanges to get high beam-wave conversion efficiency and enhance the power capacity in the extraction cavity significantly.
Monitoring the safety status of a blast furnace hearth using cooling stave heat flux
Authors: Li Yang , Chen Liangyu , Wang Lei , Ma Jiaocheng
Published: February 2020

Hearths are an accident-prone component in blast furnaces. Accidents, especially hearth burnthrough, cause substantial economic losses and even casualties. Ensuring safe operations is a challenging task as it is impossible to directly observe the internal state of a hearth. Measured data from thermocouples arranged in the hearth lining are often used to evaluate the furnace safety status. However, thermocouples are easily damaged due to their long-term operation at high temperatures. This paper proposes an approach to assist in the safety monitoring of a hearth using heat flux from cooling staves. The method is proposed through a series of finite element simulations to construct the heat flux monitoring calculation model. The No. 3 blast furnace of an iron making plant is taken as an example. The three-dimensional finite element simulation method to calculate the monitoring value of the cooling stave heat flux is described in detail. The simulation results demonstrate that the heat flux monitoring of different cooling staves can vary. Even for the same cooling stave, the monitoring value varies with the increased lining erosion. To ensure safe operations, the monitoring value should be updated when the erosion profile of the lining changes significantly.
Hot plasma electrons exhibit counterintuitive cooling behavior
Authors: Bandari Anashe
Published: February 2020

The cooling rate of energetic electrons within a plasma unexpectedly terminates with the creation of phase-space buckets that retain heat.
Urokinase plasminogen activator detector helps monitor cancer
Authors: Mandel Savannah
Published: February 2020

A quick and flexible urokinase plasminogen activator detector leads to inexpensive detection and monitoring of cancer.
Remarkable nucleation and growth of ultrafine particles from vehicular exhaust
Authors: Guo Song , Hu Min , Peng Jianfei , Wu Zhijun , Zamora Misti L. , Shang Dongjie , Du Zhuofei , Zheng Jing , Fang Xin , Tang Rongzhi , Wu Yusheng , Zeng Limin , Shuai Shijin , Zhang Wenbin , Wang Yuan , Ji Yuemeng , Li Yixin , Zhang Annie L. , Wang Weigang , Zhang Fang , Zhao Jiayun , Gong Xiaoli , Wang Chunyu , Molina Mario J. , Zhang Renyi
Published: February 2020

Significance

High concentrations of ultrafine particles (UFPs), approaching 1 million/cm
3
, are frequently produced from new particle formation under urban environments, but the fundamental mechanisms regulating nucleation and growth for UFPs are poorly understood. From simultaneous ambient and environmental chamber measurements, we demonstrate remarkable formation of UFPs from urban traffic emissions. By replicating ambient conditions using an environmental chamber method, we elucidate the roles of existing particles, photochemistry, and synergy of multipollutant photooxidation in nucleation and growth of UFPs. Our results reveal that synergetic oxidation of vehicular exhaust leads to efficient formation of UFPs under urban conditions. Recognition of this large urban source for UFPs is essential to accurately assessing their impacts and to effectively developing mitigation policies.
Animal-related concepts across languages and cultures from a cognitive linguistic perspective
Authors: Belkhir Sadia
Published: February 2020

This paper investigates the use of animal-related concepts in the proverbs of English, French, Arabic, and Kabyle. Research in cognitive linguistics has highlighted the important role played by cultural influences in conceptual metaphor variation (Kövecses 2005). Animal-related proverbs constitute interesting examples of cultural influences upon conceptual metaphor and its instantiation in language (Belkhir 2014,2012). The principle of hierarchy underlying the Great Chain Metaphor Theory has been questioned. It has been demonstrated that in addition to the ranking ofhumanandanimalconcepts on a hierarchical scale,animalconcepts were also ranked on the scale (Belkhir 2014). The present article attempts to show that there exists another type of ranking that seems to have never been explored to date; that is, the ranking of concepts within the same animal species. Therefore, this paper offers a cross-cultural cognitive study of some animal-related concepts’ use in a sample of English, French, Arabic, and Kabyle proverbs. Its aim is to explore the influence of cultural contexts and cultural models upon the main meaning foci characterizing the conceptsdog, lion,ass, horse, camel,andoxleading to, not only a hierarchical classification of these animals, but to a classification of animals within one animal species as a result of the influences of cultural contexts and cultural models. The conclusion is that sociocultural contexts determine the main meaning foci characterizing the animal source domain concepts involved in thehuman is animalmetaphor resulting in animal-animal rankings within different species, and animal-animal rankings within the same species.
An integrated study of visual metaphors in Chinese editorial cartoons
Authors: Niu Peipei
Published: February 2020

Conceptual metaphor theory highlights that metaphor is a matter of thinking. This assumption indicates that metaphors exist not only in language, but also in other modes. This study examines uses of visual and visual-verbal metaphors in 50 Chinese editorial cartoons conceptualizing serious haze problem, with the intention of eliciting implicit meaning conveyed by visual signs alone or together with verbal texts. Both conceptual and critical discourse analysis of the metaphors are conducted. The study finds that the way a metaphor is realized visually and verbally in a cartoon determines the features mapped onto the topic, and further implicitly expresses a critical stance toward the topic under discussion. The metaphors in the cartoons evoke a general understanding of haze problem by activating the war scenario and familiar cultural or social context in viewers. It is found in this corpus that visual fusion and visual replacement are the most frequent kinds of visual metaphors. The study further affirms that visual metaphors are better in conveying rich and implicit conceptual and affective meaning, and can be direct manifestation of the conceptual metaphor without the mediation of language. In sum the study suggests the need for an integrated approach to visual metaphoric representation in multimodal analysis.
Coating of lightweight wool fabric with nano clay for fire retardancy
Authors: Jose Seiko , Shanmugam Nachimuthu , Das Sekhar , Kumar Ajay , Pandit Pintu
Published: February 2020

Nano-kaolinite was applied to lightweight wool fabric for imparting fire retardant finish using pad batch as well as exhaust method. The effect of fire retardant treatments on the physico-mechanical properties of wool fabric was studied in detail. Nano-kaolinite incorporated fire retardant
formulations showed high fire retardant performance in terms of inclined flammability test, limiting oxygen index (LOI) and thermogravimetric analysis. The characterization of nanoparticles was performed using various analytical instruments. The results inferred that nano-kaolinite treatment
by both application methods is effective for improving the fire resistance of wool fabric. The treatment resulted up to 32% enhancement in fire retardant properties.
Identification of a multi-component berberine 11-hydroxylase from Burkholderia sp. strain CJ1
Authors: Yoshida Hinaka , Takeda Hisashi , Wakana Daigo , Sato Fumihiko , Hosoe Tomoo
Published: February 2020

Berberine (BBR) is a protoberberine alkaloid extracted from plants such as Coptis japonica (Ranunculaceae). In a previous report, we demonstrated the existence of a 11-hydroxylation pathway employed by BBR-utilizing bacteria for metabolism of BBR. In the present study, we report the identification of the genes brhA, brhB, and brhC as encoding a multicomponent BBR 11-hydroxylase in Burkholderia sp. strain CJ1. BrhA is belonging to the Rieske non-heme iron oxygenase (RO) family, a class of enzymes known to catalyze the first step in bacterial aromatic-ring hydroxylation. We further demonstrate that BrhA activity requires BrhB (ferredoxin reductase) and BrhC (ferredoxin) as electron transport chain components. A BLAST search revealed that BrhA exhibits 38% and 33% sequence identity to dicamba O-demethylase (DdmC; AY786443) and chloroacetanilide herbicides N-dealkylase (CndA; KJ461679), respectively. To our knowledge, this work represents the first report of a bacterial oxygenase catalyzing the metabolism of a polycyclic aromatic-ring alkaloid.

Abbreviations: BBR: berberine; D-BBR: demethyleneberberine; H-BBR: 11-hydroxyberberine; HD-BBR: 11-hydroxydemethyleneberberine; HDBA: 2-hydroxy-3,4-dimethoxybenzeneacetic acid; PAL: palmatine; H-PAL: 11-hydroxypalmatine; BRU: berberrubine; Fd: ferredoxin; FdR: ferredoxin reductase; ETC: electron transport chain
Induction of 2-cyanoethyl-isoxazolin-5-one as an antifeedant against the tobacco cutworm (Spodoptera litura) by jasmonic acid in sweet pea leaf
Authors: Tebayashi Shinichi , Moriyama Ruri , Arakawa Ryo , Sato Masashi
Published: February 2020

Although sweet pea (Lathyrus odoratus) beans contain toxic β-aminopropionitrile, the plant itself is readily attacked by insects and is, therefore, protected through the use of pesticides. Consequently, the induction of L. odoratus resistance to insect attack via exogenous treatment is promising for pest control development. Screening of inducible elicitor effects showed that treatment of sweet pea foliage with jasmonic acid (JA) can induce antifeeding-based resistance to tobacco cutworm (Spodoptera litura) larvae. Spectroscopic analysis identified 2-cyanoethyl-isoxazolin-5-one (2-CEIX) as the antifeedant with a half-maximal effective concentration of 33.6 µmol/g fr. wt., i.e., exogenous JA treatment induced antifeeding activity due to the accumulation of 2-CEIX. Moreover, 2-CEIX-induced mortality of S. litura larvae was evaluated by a dipping test and the half-maximal lethal dose was determined to be 5.9 mg/mL. Therefore, 2-CEIX was concluded to be a suitable induced resistance target for elicitors or a lead compound for insecticide development.
Heavy hadronic molecules with pion exchange and quark core couplings: a guide for practitioners
Authors: Yamaguchi Yasuhiro , Hosaka Atsushi , Takeuchi Sachiko , Takizawa Makoto
Published: February 2020

We discuss selected and important features of hadronic molecules as one of several promising forms of exotic hadrons near thresholds. Using examples of

D

D

¯

*

systems such as X(3872) and Z

c
, emphasis is put on the roles of the one pion exchange interaction between them and their coupling to intrinsic quark states. Thus hadronic molecules emerge as admixtures of the dominant long-range hadron structure and short-range quark structure. For the pion exchange interaction, properties of the tensor force are analyzed in detail. More coupled channels supply more attractions, and heavier constituents suppress kinetic energies, providing more chances to form hadronic molecules of heavy hadrons. Throughout this article, we show details of basic ideas and methods.
Status of the SPES Exotic Beam Facility
Authors: Comunian M , Andrighetto A , Antonini P , Baltador C , Bellan L , Benini D , Bermudez J , Bisoffi G , Bortolato D , Calderolla M , Cavenago M , Corradetti S , de Ruvo L , Facco A , Fagotti E , Favaron P , Ferrari L , Galatà A , Galtarossa F , Giacchini M , Gramegna F , Lombardi A , Maggiore M , Manzolaro M , Marcato D , Marchi T , Mastinu P , Modanese P , Moisio M F , Monetti A , Montis M , Palmieri A , Pavinato S , Pedretti D , Pisent A , Poggi M , Prete G , Roncolato C , Rossignoli M , Sarchiapone L , Scarpa D , Zafiropoulos D , Bellato M
Published: February 2020

At Legnaro National Laboratories of INFN is under construction a Rare Isotope Facility called “Selective Production of Exotic Species” (SPES) based on a 35-70 MeV proton cyclotron, able to deliver two beams with a total current up to 0.75 mA, an ISOL fission target station and an existing ALPI superconducting accelerator as a post accelerator (up to 10 MeV/u for A/q=7). The paper will cover notably: the high-resolution mass separator, the CW RFQ (80 MHz, 727 keV/u, with internal bunching), the 1+ low energy transfer line and the injection line from Charge Breeder to ALPI under installation.
New method to design magnetic channels with 2D optimization tools and using permendur vanadium
Authors: Neri L. , Calabretta L. , Rifuggiato D. , Karamyshev O.
Published: February 2020

Magnetic channels are used in almost all cyclotrons to focus radially the beam along the extraction path through the coils and yoke region, where the rapid fall off of the magnetic field produces a strong vertical focusing and radial defocusing of the beam. These magnetic channels consist generally of three iron bars. The current sheet approximation has been generally used to evaluate quickly the performance of magnetic channels.

For the new magnetic channels to be used in the upgrade of the LNS-INFN k800 Superconducting Cyclotron, a new method was developed to investigate complex configurations and to achieve higher magnetic gradients in a larger area. The optimization procedure is based on a genetic algorithm implemented on MATLAB code and using the COMSOL code to perform the 2D magnetic field simulations.

Moreover, the use of permendur vanadium in alternative to iron allows to reduce the volume of the bars and mainly the magnetic force.

The results of our simulations are here presented.
High-Brilliance Neutron Source Project
Authors: Zakalek P , Cronert T , Baggemann J , Doege P-E , Rimmler M , Voigt J , Mauerhofer E , Rücker U , Gutberlet T , Podlech H , Meusel O , Schwarz M , Li J , Böhm S , Brückel Th
Published: February 2020

The High-Brilliance Neutron Source (HBS) project aims to design a scalable compact accelerator driven neutron source (CANS) which is competitive and cost-efficient. The concept allows one to optimize the whole facility including accelerator, target, moderators and neutron optics to the demands of individual neutron instruments. Particle type, energy, timing, and pulse structure of the accelerator are fully defined by the requirements of a given neutron instrument. In the following, we present the current status of the HBS project.
High resolution mass separator dipole design studies for SPES project
Authors: Baltador C , Comunian M , Bellan L , Cavenago M , De Lorenzi A , Galatà A , Ferrari L , Mosio F , Pisent A
Published: February 2020

The purposes of the SPES (Selective Production of Exotic Species) project at INFN laboratory in Legnaro (Italy) is to study nuclei close to the drip lines. Therefore, a High-Resolution Mass Separator (HRMS) must provide full separation of the ions with a resolution 1/20000, to be sensible to the proton-neutron mass difference in the fission products. SPES HRMS consists of: two 90° magnet dipoles, one electrostatic multipole in between them, six electrostatic quadrupoles, two electrostatic hexapoles and two electrostatic triplets before and after the slits on the object and image point. All these components will be installed on a high voltage platform with a maximum operating voltage of -240 kV. Before entering the HRMS, a 40 keV energy beam go through an RFQ Cooler, designed to have an output energy spread of 1 eV. Mass separation within target resolution is the most critical part: dipoles must provide a magnetic field homogeneity of 4 10−5 throughout beam occupancy (half magnet pole surface), at a field intensity of 0.562 T for the reference ion 132 Sn. Therefore, a very accurate dipole design is mandatory. This contribute will show the studies which lead to a possible dipole design.
NEW TYPE OF INJECTOR FOR CANCER THERAPY1
Authors: Xing Chaochao , Lu Liang , Yang Lei , He Tao , Xu Xianbo , Li Jia , Xia Qianxu
Published: February 2020

We performed a compact design for a 100 MHz Hybrid Single Cavity (HSC) for an injector of cancer therapy. The proposed designs are conventional four-rod structure and Drift Tube Linac (DTL) in a single Inter-digital H-mode (IH) cavity. This compact linac injector, running at frequency of 100 MHz, accelerates C6+ beams with 20 mA from 0.02 MeV/u up to 4 MeV/u. The total length of HSC is designed to be less than 4 meters.
Evolution of a paleolake on Russian Island (Sea of Japan) in middle-late Holocene: record of sea-level oscillations, extreme storms and tsunami
Authors: Grebennikova T , Razjigaeva N , Ganzey L , Ganzei K , Arslanov Kh , Maksimov F , Petrov A , Kharlamov A
Published: February 2020

The diatom algae from sediments of a paleolake serve as records of changes to environments over the last 7500 cal yr. The lagoon lake formed when the sea level approximately corresponded to the present-day position. Evolution of the paleolake was controlled by sea-level oscillations and humidity changes. Eight stages have been distinguished. During a dry episode in 7330–7090 cal yr BP the lake size decreased. The salinity reached maximal values at the Holocene transgression peak. Three stages of a higher salinity are recognized (6750–6500, 6080–5830, 5420–5090 cal yr BP). A severe flood occurred in 6080–6000 cal yr BP. The brackish-water lake existed in ∼5090 cal yr BP and the freshwater lake in ∼4090 cal yr BP. A prolonged phase of decreasing humidity, associated with a weakening of summer monsoons, led to a drop in sedimentation rates in ∼3510 cal yr BP. Peat accumulation started at the Little Ice Age. The lake was transformed into a swamp during drop in precipitations in ∼270 cal yr BP. Presence of marine diatoms typical in bay and deep-water forms are evidence of influence of extreme storms and tsunami. The age of the paleotsunami coincides well with the regional data.
Foraminiferal and dinocyst associations as indicators of the Holocene environmental changes at the Cambridge Strait, Franz Josef Land
Authors: Ivanova E V , Novichkova E A , Kozhanova D A
Published: February 2020

Herein we report the first decadal to centennial–scale resolution data on foraminiferal and dinocyst assemblages from core AMK-5454 collected in the hard-to-reach Cambridge Strait, Franz Josef Land, and on corresponding paleoenvironments over the last 9.2 ka. The dinocyst and foraminiferal assemblages from the core are rather diverse through the Holocene and represented by 24 and 33 taxa, respectively. The most active hydrodynamics and probably Atlantic Water (AW) inflow are suggested by the enhanced values of autotrophic dinocysts and epibenthic species, as well as Melonis barleeanus, from 9.2 to 6.3 cal ka BP. Specific benthic assemblages indicate high-productivity frontal conditions at site location from 6.3 to 4.1 cal ka BP. AW influx from the Franz Victoria Trough to the Cambridge Strait in subsurface to bottom layer, below the very cold Arctic Water and dense sea ice, is documented by enhanced % Cassidulina teretis over the last 4.5 ka.
The Early Holocene vegetation changes in the vicinity of the Gorbunovo peat bog in the Middle Urals (Russia)
Authors: Lapteva E G , Korona O M , Zhilin M G
Published: February 2020

The paper presents the results of a comprehensive palaeobotanical research of lacustrine and peat deposits of archaeological Mesolithic sites discovered at the Gorbunovo peat bog (Middle Urals). Pollen and plant macrofossil data, as well as a biome model were used to describe the vegetation changes in the study area in the Early Holocene. It was found out that in the second half of the Pre-Boreal and the first half of the Boreal periods of the Early Holocene (approximately to 9,800–9,600 cal BP), the vicinity of the Gorbunovo peat bog was dominated by cold deciduous forests. Larch, spruce-larch and birch forests and meadow communities with periglacial elements were widespread. Various aquatic plants could be found in the pond, though it started to turn into swamp. In the second half of the Boreal period (approximately at 9,600–9,500 cal BP), the taiga biome, including pine and birch-pine forests with occurrence of spruce started to prevail. Periglacial communities became degraded. Aggressive water logging led to the formation of a peat bog.
Landscapes, paleosols and climate in the north of Mongolia during the Holocene
Authors: Timireva S N , Batkhishig O , Sycheva S A , Kononov Yu M , Simakova A N , Byambaa G , Telmen T , Samdandorj M , Filippova K G , Konsnantinov E A
Published: February 2020

Integrated paleogeographic studies have been performed on the loess and soil sequence in the lower reaches of the Orkhon R., northern Mongolia. The samples were taken continuously through the sequence and studied using a broad assortment of field and laboratory analyses. There are five paleosols exposed in the section under study crowned with the present-day soil and separated from each other by loess horizons or proluvial-deluvial deposits. The dating by radiocarbon proved the soil development beginning from the early Holocene. The two lower soils (PS4 and PS5) formed at that interval are noted for the minimum salinity and a considerable content of carbonates. The soils dated to the middle Holocene (PS3 and PS2) contain the least proportion of organic matter and increased salinity, which may be attributed to a dryer climate (even at optimum intervals) than in the early and late Holocene. In common with the present-day soil, the PS1 buried soil is characterized by negligible (or absent) salinity, and a noticeable accumulation of organic matter and carbonates indicative of favorable warm and relatively wet conditions. All the pollen assemblages indicate the dominance of grass vegetation; it may be safely suggested that open meadow and steppe landscapes, occasionally replaced by semi-deserts, prevailed in the considered region during the Holocene.
Latent tracks of swift Bi ions in Si3N4
Authors: van Vuuren A Janse , Ibrayeva A , Rymzhanov R A , Zhalmagambetova A , O’Connell J H , Skuratov V A , Uglov V V , Zlotski S V , Volkov A E , Zdorovets M
Published: February 2020

Parameters such as track diameter and microstruture of latent tracks in polycrystalline Si3N4 induced by 710 MeV Bi ions were studied using TEM and XRD techniques, and MD simulation. Experimental results are considered in terms of the framework of a ‘core–shell’ inelastic thermal spike (i-TS) model. The average track radius determined by means of electron microscopy coincides with that deduced from computer modelling and is similar to the track core size predicted by the i-TS model using a boiling criterion. Indirect (XRD) techniques give a larger average latent track radius which is consistent with the integral nature of the signal collected from the probed volume of irradiated material.
Schiller on Freedom and Aesthetic Value: Part I
Authors: Matherne Samantha , Riggle Nick
Published: February 2020

In his Letters on the Aesthetic Education of Man, Friedrich Schiller draws a striking connection between aesthetic value and individual and political freedom, claiming that, ‘it is only through beauty that man makes his way to freedom’. However, contemporary ways of thinking about freedom and aesthetic value make it difficult to see what the connection could be. Through a careful reconstruction of the Letters, we argue that Schiller’s theory of aesthetic value serves as the key to understanding not only his view of aesthetic engagement, but also his distinctive account of individual and political freedom. In Part I, we develop a reconstruction of Schiller's view that aesthetic value is the only path to individual freedom and in Part II we analyze how Schiller connects aesthetic value to political freedom. In the end, we show that Schiller defends a non-hedonic, action-oriented, communitarian theory of aesthetic value and a theory of freedom that makes the aesthetic not just supererogatory but fundamental for any fully autonomous life. Although we have lost touch with this way of thinking about aesthetic value and freedom, we submit that it is illuminating for contemporary thinking about both.
A survey of gene expression meta-analysis: methods and applications
Authors: Toro-Domínguez Daniel , Villatoro-García Juan Antonio , Martorell-Marugán Jordi , Román-Montoya Yolanda , Alarcón-Riquelme Marta E , Carmona-Sáez Pedro
Published: February 2020

The increasing use of high-throughput gene expression quantification technologies over the last two decades and the fact that most of the published studies are stored in public databases has triggered an explosion of studies available through public repositories. All this information offers an invaluable resource for reuse to generate new knowledge and scientific findings. In this context, great interest has been focused on meta-analysis methods to integrate and jointly analyze different gene expression datasets. In this work, we describe the main steps in the gene expression meta-analysis, from data preparation to the state-of-the art statistical methods. We also analyze the main types of applications and problems that can be approached in gene expression meta-analysis studies and provide a comparative overview of the available software and bioinformatics tools. Moreover, a practical guide for choosing the most appropriate method in each case is also provided.
FluPhenotype—a one-stop platform for early warnings of the influenza A virus
Authors: Lu Congyu , Cai Zena , Zou Yuanqiang , Zhang Zheng , Chen Wenjun , Deng Lizong , Du Xiangjun , Wu Aiping , Yang Lei , Wang Dayan , Shu Yuelong , Jiang Taijiao , Peng Yousong
Published: February 2020

Motivation

Newly emerging influenza viruses keep challenging global public health. To evaluate the potential risk of the viruses, it is critical to rapidly determine the phenotypes of the viruses, including the antigenicity, host, virulence and drug resistance.

Results

Here, we built FluPhenotype, a one-stop platform to rapidly determinate the phenotypes of the influenza A viruses. The input of FluPhenotype is the complete or partial genomic/protein sequences of the influenza A viruses. The output presents five types of information about the viruses: (i) sequence annotation including the gene and protein names as well as the open reading frames, (ii) potential hosts and human-adaptation-associated amino acid markers, (iii) antigenic and genetic relationships with the vaccine strains of different HA subtypes, (iv) mammalian virulence-related amino acid markers and (v) drug resistance-related amino acid markers. FluPhenotype will be a useful bioinformatic tool for surveillance and early warnings of the newly emerging influenza A viruses.

Availability and implementation

It is publicly available from: http://www.computationalbiology.cn : 18888/IVEW.

Supplementary information

Supplementary data are available at Bioinformatics online.
Polar labeling: silver standard algorithm for training disease classifiers
Authors: Wagholikar Kavishwar B , Estiri Hossein , Murphy Marykate , Murphy Shawn N
Published: February 2020

Motivation

Expert-labeled data are essential to train phenotyping algorithms for cohort identification. However expert labeling is time and labor intensive, and the costs remain prohibitive for scaling phenotyping to wider use-cases.

Results

We present an approach referred to as polar labeling (PL), to create silver standard for training machine learning (ML) for disease classification. We test the hypothesis that ML models trained on the silver standard created by applying PL on unlabeled patient records, are comparable in performance to the ML models trained on gold standard, created by clinical experts through manual review of patient records. We perform experimental validation using health records of 38 023 patients spanning six diseases. Our results demonstrate the superior performance of the proposed approach.

Availability and implementation

We provide a Python implementation of the algorithm and the Python code developed for this study on Github.

Supplementary information

Supplementary data are available at Bioinformatics online.
InterLig: improved ligand-based virtual screening using topologically independent structural alignments
Authors: Mirabello Claudio , Wallner Björn
Published: February 2020

Motivation

In the past few years, drug discovery processes have been relying more and more on computational methods to sift out the most promising molecules before time and resources are spent to test them in experimental settings. Whenever the protein target of a given disease is not known, it becomes fundamental to have accurate methods for ligand-based virtual screening, which compares known active molecules against vast libraries of candidate compounds. Recently, 3D-based similarity methods have been developed that are capable of scaffold hopping and to superimpose matching molecules.

Results

Here, we present InterLig, a new method for the comparison and superposition of small molecules using topologically independent alignments of atoms. We test InterLig on a standard benchmark and show that it compares favorably to the best currently available 3D methods.

Availability and implementation

The program is available from http://wallnerlab.org/InterLig.

Supplementary information

Supplementary data are available at Bioinformatics online.
Baloxavir: A Novel Antiviral Agent in the Treatment of Influenza
Authors: Abraham George M , Morton Jacob B , Saravolatz Louis D
Published: February 2020

Baloxavir marboxil (formerly S-033188) is a prodrug of baloxavir acid (S-033447) and inhibits cap-dependent endonuclease, an essential protein involved in the initiation of viral transcription by cleaving capped mRNA bound to PB2. Its adverse event profile is comparable to oseltamivir but is still vulnerable to resistance. The single-dose baloxavir marboxil is an appealing antiviral regimen for the treatment of influenza among outpatients when compared with longer, twice-daily regimens of oral and inhaled neuraminidase inhibitors. This review focuses on the mode of action, antiviral activity, pharmacokinetics, clinical indications, and safety profiles of this drug. Considerations for formulary addition and its place in therapy are also discussed.
Moderate but not severe hypothermia causes pro-arrhythmic changes in cardiac electrophysiology
Authors: Dietrichs Erik S , McGlynn Karen , Allan Andrew , Connolly Adam , Bishop Martin , Burton Francis , Kettlewell Sarah , Myles Rachel , Tveita Torkjel , Smith Godfrey L
Published: February 2020

Aims

Treatment of arrhythmias evoked by hypothermia/rewarming remains challenging, and the underlying mechanisms are unclear. This in vitro experimental study assessed cardiac electrophysiology in isolated rabbit hearts at temperatures occurring in therapeutic and accidental hypothermia.

Methods and results

Detailed ECG, surface electrogram, and panoramic optical mapping were performed in isolated rabbit hearts cooled to moderate (31°C) and severe (17°C) hypothermia. Ventricular activation was unchanged at 31°C while action potential duration (APD) was significantly prolonged (176.9 ± 4.2 ms vs. 241.0 ± 2.9 ms, P < 0.05), as was ventricular repolarization. At 17°C, there were proportionally similar delays in both activation and repolarization. These changes were reflected in the QRS and QT intervals of ECG recordings. Ventricular fibrillation threshold was significantly reduced at 31°C (16.3 ± 3.1 vs. 35 ± 3.5 mA, P < 0.05) but increased at 17°C (64.2 ± 9.9, P < 0.05). At 31°C, transverse conduction was relatively unchanged by cooling compared to longitudinal conduction, but at 17°C both transverse and longitudinal conduction were proportionately reduced to a similar extent. The gap junction uncoupler heptanol had a larger relative effect on transverse than longitudinal conduction and was able to restore the transverse/longitudinal conduction ratio, returning ventricular fibrillation threshold to baseline values (16.3 ± 3.1 vs. 36.3 ± 4.3 mA, P < 0.05) at 31°C. Rewarming to 37°C restored the majority of the electrophysiological parameters.

Conclusions

Moderate hypothermia does not significantly change ventricular conduction time but prolongs repolarization and is pro-arrhythmic. Further cooling to severe hypothermia causes parallel changes in ventricular activation and repolarization, changes which are anti-arrhythmic. Therefore, relative changes in QRS and QT intervals (QR/QTc) emerge as an ECG-biomarker of pro-arrhythmic activity. Risk for ventricular fibrillation appears to be linked to the relatively low temperature sensitivity of ventricular transmural conduction, a conclusion supported by the anti-arrhythmic effect of heptanol at 31°C.
A Novel Approach to Investigate the Effect of Tree Reconstruction Artifacts in Single-Gene Analysis Clarifies Opsin Evolution in Nonbilaterian Metazoans
Authors: Fleming James F , Feuda Roberto , Roberts Nicholas W , Pisani Davide
Published: February 2020

Our ability to correctly reconstruct a phylogenetic tree is strongly affected by both systematic errors and the amount of phylogenetic signal in the data. Current approaches to tackle tree reconstruction artifacts, such as the use of parameter-rich models, do not translate readily to single-gene alignments. This, coupled with the limited amount of phylogenetic information contained in single-gene alignments, makes gene trees particularly difficult to reconstruct. Opsin phylogeny illustrates this problem clearly. Opsins are G-protein coupled receptors utilized in photoreceptive processes across Metazoa and their protein sequences are roughly 300 amino acids long. A number of incongruent opsin phylogenies have been published and opsin evolution remains poorly understood. Here, we present a novel approach, the canary sequence approach, to investigate and potentially circumvent errors in single-gene phylogenies. First, we demonstrate our approach using two well-understood cases of long-branch attraction in single-gene data sets, and simulations. After that, we apply our approach to a large collection of well-characterized opsins to clarify the relationships of the three main opsin subfamilies.
Who benefits most from extending financial protection for cataract surgery in Vietnam? An extended cost-effectiveness analysis of small incision surgery
Authors: Essue Beverley M , Jan Stephen , Phuc Huynh Tan , Dodson Sarity , Armstrong Kirsten , Laba Tracey-Lea
Published: February 2020

Treatment costs remain a barrier for having timely cataract surgery in Vietnam, particularly for females and the poor, despite significant progress in achieving universal health coverage (UHC). This study evaluated the potential impact, on health and financial protection, of eliminating medical and non-medical out-of-pocket costs associated with cataract surgery. An extended cost-effectiveness analysis (ECEA) was conducted with a societal perspective. The ECEA modelled how many more disability-adjusted life years (DALYs) and cases of catastrophic health expenditure (CHE) and medical impoverishment could be averted across income quintiles and between males and females. Two programmes were evaluated: (1) eliminating medical out-of-pocket costs for small incision cataract surgery and (2) Programme A plus a voucher programme covering non-medical out-of-pocket costs. Compared with current, the incremental cost per year of Programme A was estimated to be $833 396 and $1 641 835 for Programme B, each representing <0.01% of total health care spending in 2016. Males and females in the richest income quintiles would avert more DALYs than those in the poorest quintiles. For both programmes, most cases of CHE would be averted by individuals in the poorest income quintile. Programme B would avert the most CHE cases overall and females would have a greater share of benefits. All cases of impoverishing medical expenditure would be averted by individuals in the poorest quintile (A: 115 cases and B: 493 cases) for both programmes. The cost to avert each case of CHE with Programme A ranged from $67 to $292 and $100 to $232 for Programme B. We found a pro-rich health distribution and a pro-poor CHE distribution associated with eliminating out-of-pocket costs of cataract surgery in Vietnam. A programme that addressed both medical and non-medical out-of-pocket costs could have the greatest impact on improving financial protection in this population, particularly among the poorest income quintiles and for females. This study supports the concordance between the objectives of UHC and gender equity.
The Proliferation of Joint Interpretation Clauses in New International Investment Agreements: A Mixed Blessing?
Authors: Marotti Loris
Published: February 2020

Joint interpretation clauses (JICs) are among the most controversial control mechanisms on the interpretative powers of tribunals brought by the current wave of reform of the investor–State dispute settlement system (ISDS). Literally proliferating in the new generation of international investment agreements (IIAs), these clauses give contracting States the power to issue joint interpretations (JIs) that are expressly recognized as binding upon dispute settlement bodies and may even be issued in relation to matters pending before such bodies. This article discusses several issues raised by the ‘authentic interpretation’ enhanced by JICs. In the first part, JICs are assessed against the background of the general rule on treaty interpretation, including, in particular, subsequent agreements under article 31(3)(a) of the 1969 Vienna Convention on the Law of Treaties. The second part of the article addresses the tensions between judicial bodies and treaty parties sharing the interpretative authority over IIAs and investigates whether there are any limitations on the interpretative powers of States under JICs. The third part is devoted to the impact of JIs on the proper conduct of investment arbitration proceedings, considering the participation of private actors (the investors) in the proceedings and the ‘dual role’ of States (as treaty parties and respondents) in this field. The concluding part of the article speculates whether a greater institutionalization of the international investment regime is likely to prompt more frequent forms of judicial reactions against ‘ill-perceived’ JIs and fuel the tension between States and dispute settlement bodies.
Pericardial Adipose Tissue Volume Is Independently Associated With Human Immunodeficiency Virus Status and Prior Use of Stavudine, Didanosine, or Indinavir
Authors: Knudsen Andreas D , Krebs-Demmer Lisanne , Bjørge Natascha I D , Elming Marie B , Gelpi Marco , Sigvardsen Per E , Lebech Anne-Mette , Fuchs Andreas , Kühl Jørgen T , Køber Lars , Lundgren Jens , Nordestgaard Børge G , Kofoed Klaus F , Nielsen Susanne D
Published: February 2020

Background

Increased pericardial adipose tissue is associated with higher risk of cardiovascular disease. We aimed to determine whether human immunodeficiency virus (HIV) status was independently associated with larger pericardial adipose tissue volume and to explore possible HIV-specific risk factors.

Methods

Persons with HIV (PWH) were recruited from the Copenhagen Comorbidity in HIV Infection (COCOMO) Study and matched 1:1 on age and sex to uninfected controls. Pericardial adipose tissue volume was measured using cardiac computed tomography.

Results

A total of 587 PWH and 587 controls were included. Median age was 52 years, and 88% were male. Human immunodeficiency virus status was independently associated with 17 mL (95% confidence interval [CI], 10–23; P < .001) larger pericardial adipose tissue volume. Larger pericardial adipose tissue volume was associated with low CD4+ nadir and prior use of stavudine, didanosine, and indinavir. Among PWH without thymidine analogue or didanosine exposure, time since initiating combination antiretroviral treatment (per 5-year use) was associated with l6 mL (95% CI, −6 to −25; P = .002) lower pericardial adipose tissue volume.

Conclusions

Human immunodeficiency virus status was independently associated with larger pericardial adipose tissue volume. Severe immunodeficiency, stavudine, didanosine, and indinavir were associated with larger pericardial adipose tissue volume. Persons with HIV with prior exposure to these drugs may constitute a distinct cardiovascular risk population.
Image-based extrusion with realistic surface wrinkles
Authors: Ragragui Anouar , Ouazzani Chahdi Adnane , Halli Akram , Satori Khalid
Published: February 2020

Per-pixel extrusion mapping is an image-based modeling and rendering technique that can be used in a large variety of computer graphic applications. This technique makes it possible to create geometries without polygonal meshes by extrusion of a basic form stored in a 2D binary image. It is available in four versions: basic extrusion, outward extrusion, beveled extrusion, and chamfered extrusion, and all allow the production of satisfactory results in terms of interactivity or visual quality. The problem is that the extruded surfaces do not exhibit microrelief effects and have a lack of realistic superficial wrinkles. To solve this problem, we proposed in this paper a combination of the per-pixel extrusion mapping and the bump mapping in order to add a microrelief effect to extruded surfaces without changing the basic geometry. For the real-time synchronization between the depth scaling of the microreliefs and the resulting shading, we proposed to use a scale factor to further disturb the normal in a function of depths.