bluuebunny/crossref_metadata_2025 huggingface dataset:
Photospheric magnetic topology of a north polar region
Authors: Pastor Yabar A. , Martínez González M. J. , Collados M.
Published: March 2020

Aims. We aim to characterise the magnetism of a large fraction of the north polar region close to a maximum of activity, when the polar regions are reversing their dominant polarity.

Methods. We make use of full spectropolarimetric data from the CRisp Imaging Spectro-Polarimeter installed at the Swedish Solar Telescope. The data consist of a photospheric spectral line, which is used to infer the various physical parameters of different quiet Sun regions by means of the solution of the radiative transfer equation. We focus our analysis on the properties found for the north polar region and their comparison to the same analysis applied to data taken at disc centre and low-latitude quiet Sun regions for reference. We also analyse the spatial distribution of magnetic structures throughout the north polar region.

Results. We find that the physical properties of the polar region (line-of-sight velocity, magnetic flux, magnetic inclination and magnetic azimuth) are compatible with those found for the quiet Sun at disc centre and are similar to the ones found at low latitudes close to the limb. Specifically, the polar region magnetism presents no specific features. The structures for which the transformation from a line-of-sight to a local reference frame was possible harbour large magnetic fluxes (>1017 Mx) and are in polarity imbalance with a dominant positive polarity, the largest ones (>1019 Mx) being located below 73° latitude.
Insect parasites in multicomponent systems and development of new bioinsecticides
Authors: Glupov Viktor , Martemyanov Vyacheslav , Kryukov Vadim
Published: March 2020

Stable and dynamic interactions among plants, herbivorous insects, parasites and associated microbes are formed in natural habitats. The study of these interactions in multicomponent models is required to develop integrated methods for the management of insect pest populations. In this work, we summarize our studies on the influence of different factors, such as hygrothermal conditions, host development, host microbiota, plant quality, and concomitant infections, on interactions between insects and their parasites, such as fungi, bacteria, viruses and parasitoids. Some approaches for developing complex products for biocontrol are also discussed. For example, the use of natural compounds with immunosuppressive effects may enhance the efficacy of microbial agents toward pest insects.
Assessing phytosanitary risks of growing agricultural crops in Russia and neighboring countries by a complex of phytophagous insects
Authors: Grichanov Igor , Ovsyannikova Elena , Saulich Mikhail
Published: March 2020

The relevance of the study is determined by the need to improve the monitoring of agricutural crop pest distribution. The aim of the research is to identify zones of different phytosanitary risks within the area of crop cultivation in Russia and neighboring countries. Maps characterizing the distribution and harmfulness zones of phytophagous species were used as the primary material for integrated computer analysis. It was necessary to adjust and update a number of maps taking into account research data published over the last 10 years. The analysis resulted in the creation of maps characterizing phytosanitary risk zones for the cultivation of fruit and grain crops by a corresponding complex of specialized phytophagous insects, as well as of agricultural crops in general by a complex of polyphagous pests. Three zones of phytosanitary risk have been outlined, as a consequence of the total harmfulness of phytophagous complex. The combined geoinformation system for agricultural crop pests is included in the “Phytosanitary Risks” cartographical database, which is a set of vector files for all major phytophagous species, distribution and harmfulness zone layers for these species. Outlined zones with low, medium and high phytosanitary risks can be used in the development of integrated pest management.
Use of a hardware-software complex for phytosanitary monitoring and chemical treatments of the Sosnowski hogweed
Authors: Kornilov Timur , Terentev Anton , Kekelidze Valeriy
Published: March 2020

A new technology for the detection and chemical treatment of the Sosnowski hogweed using neural networks and ground and air robotic systems was tested. Confirmation is obtained of the possibility of detecting invasive weeds and their state using satellite imagery and UAVs. The features of the chemical treatment of dicotyledonous plants using UAVs are investigated. The effectiveness of the weed control by chemical pesticides sprayed with UAVs was confirmed by the example of the “Graund” herbicide.
Some aspects of seasonal dynamics of ground beetles in the agrarian landscapes of Kuban Region (Coleoptera, Carabidae)
Authors: Zamotajlov Alexandr S. , Khomitskiy Eugeniy E. , Belyi Alexandr I.
Published: March 2020

The paper discusses influence of some elements of the organic farming and organic fertilizers on carabids dynamics in the foothill zone of the Krasnodar Territory. Species realizing their life cycles in the greenhouses conditions are also identified. Structure of the winter fauna during the warm periods of winter as well as during the snowy and frosty periods is revealed.
A mathematical model of solid-state dewetting of barium thin films on W(112)
Authors: Knavel S.A. , Savina T.V. , Mroz M.V. , Kordesch M.E. , Eads C.N. , Sadowski J.T. , Tenney S.A.
Published: March 2020

Solid state dewetting occurs when a thin solid film is heated. The temperature of dewetting depends on the thickness of the film; dewetting can be observed in the range of 1∕3 to 1∕2 of the bulk melting temperature. While remaining solid, the film behaves in a manner similar to liquids dewetting and agglomerating to forming islands or droplets. One of the possible mechanisms is the conversion of a metastable thin film geometry into a more stable form. Heating the metastable film gives the film atoms higher mobility, and the films retract, dewetting the surface. This atomic motion can be restricted due to surface anisotropy. We present in situ emission microscopy observations of barium thin films deposited onto W(112) by thermal evaporation. From the modeling viewpoint, the evolution of the film in this system could be divided in four stages: (i) the nucleation and growth of the thin film as a simply connected region; (ii) formation of droplets/islands/hillocks; (iii) nucleation of holes; (iv) evolution of the components of the disconnected film to their equilibrium state. We present a continuum model that is qualitatively consistent with the evolution of the film observed at the initial stage of the experiment and discuss the later stages of the evolution of surface structures.
Large deviations of the exit measure through a characteristic boundary for a Poisson driven SDE
Authors: Pardoux Etienne , Samegni-Kepgnou Brice
Published: March 2020

Let O be the basin of attraction of a given equilibrium of a dynamical system, whose solution is the law of large numbers limit of the solution of a Poissonian SDE as the size of the population tends to +∞. We consider the law of the exit point from O of that Poissonian SDE. We adapt the approach of Day [J. Math. Anal. Appl. 147 (1990) 134–153] who studied the same problem for an ODE with a small Brownian perturbation. For that purpose, we will use the large deviations principle for the Poissonian SDE reflected at the boundary of O, studied in our recent work Pardoux and Samegni [Stoch. Anal. Appl. 37 (2019) 836–864]. The main motivation of this work is the extension of the results concerning the time of exit from the set O established in Kratz and Pardoux [Vol. 2215 of Lecture Notes in Math.. Springer (2018) 221–327] and Pardoux and Samegni [J. Appl. Probab. 54 (2017) 905–920] to unbounded open sets O. This is done in sections 4.2.5 and 4.2.7 of Britton and Pardoux [Vol. 2255 of Lecture Notes in Math. Springer (2019) 1–120], see also The SIR model with demography subsection below.
Kinderwunsch bei Multipler Sklerose
Authors: Hellwig Kerstin , Wilkening Wibke
Published: March 2020

Eine Multiple Sklerose (MS) tritt meist im reproduktionsfähigen Alter auf. Deshalb ist die Frage der Familienplanung bei Patienten mit MS von großer Bedeutung. Die Datenlage zu den krankheitsmodifizierenden Therapien (DMT) im Hinblick auf Familienplanung, Schwangerschaft und Stillzeit wächst, auch wenn viele Fragen nicht eindeutig beantwortet werden können.
Therapie der hochaktiven Multiplen Sklerose
Authors: Pul Refik , Kleinschnitz Christoph
Published: March 2020

Immuntherapien bei Multipler Sklerose müssen sich nach randomisiert kontrollierten klinischen Studien auch in der klinischen Routine bewähren. Dazu werden Register- und Kohortenstudien durchgeführt. Eine große Kohortenstudie an den Universitätskliniken Essen-Duisburg und Münster untersucht Wirksamkeit und Sicherheit von Cladribin-Tabletten im klinischen Alltag. Erste Analysen scheinen die Ergebnisse der Zulassungsstudie CLARITY in einer breiter gefassten Patientenpopulation zu bestätigen.
Partial Capitate with/without Hamate Osteotomy in the Treatment of Kienböck's Disease: Influence of the Stage of the Disease on the Midterm Outcome
Authors: Atiyya Ahmed Naeem , Nabil Amr , El Lattif Aly Ibrahim Abd , El Saied Mohamed Nabil , Soliman Ramy Ahmed
Published: March 2020

Objective Moritomo et al introduced partial capitate osteotomy as a treatment modality for early stages of Kienböck's disease. This technique maintains articular contact between the capitate and the scaphoid. We added hamate-shortening osteotomy in addition to partial capitate shortening in cases of lunate type II. The purpose of this study was to evaluate intermediate-term results of partial capitate shortening, investigate the influence of the stage of the disease on the outcome, and assess the clinical and radiological outcomes of adding hamate osteotomy in cases of type II lunate.

Patients and Methods A total of 17 consecutive patients (3 women, 14 men) with early stages of Kienböck's disease were prospectively reviewed using the aforementioned technique. Eight patients were in stage II and nine patients were in stage IIIA according to the Lichtman classification system. Clinical outcome measures included pain visual analog score, grip strength and range of motion as a percentage of the unaffected side, and assessment using the Patient-Rated Hand and Wrist Evaluation (PRHWE) and the modified Wrightington Hospital Wrist Score (MWHWS). Radiological outcome measures included healing of the osteotomy site, Stahl index, radioscaphoid angle, and progression of the disease.

Results Follow-up period averaged 72 months. All cases of isolated capitate osteotomy and combined capitate and hamate osteotomies united fully. Clinical results revealed significant improvement in pain, grip strength and extension, and PRHWE and MWHWS values. Wrist flexion did not change postoperatively. Patients with stage II showed better overall results and significant MWHWS improvement.

Conclusion At the intermediate term, partial capitate with/without hamate shortening is an effective modality for the treatment of patients with early stage Kienböck's disease. Stage II patients showed better results than stage IIIA patients in terms of pain, flexion, grip, PRHWE, and MWHWS. Adding hamate osteotomy may improve the functional results for type II lunate; however, a larger sample is needed to elicit statistical significance.

Level of Evidence This is a Level IV, therapeutic study.
Infantile Spasms: Opportunities to Improve Care
Authors: Messer Ricka , Knupp Kelly G.
Published: March 2020

Infantile spasm (IS) is a distinct epilepsy syndrome characterized by epileptic spasms (the clinical seizure type) and hypsarrhythmia (the electrographic abnormality). IS is frequently accompanied by impaired neurodevelopment and is often associated with structural, genetic, or metabolic etiologies. Prompt treatment of this severe epileptic encephalopathy improves long-term outcomes but remains elusive in many situations. Despite common misconceptions, even patients with identified etiologies or preexisting developmental delay benefit from proven standard therapies, including adrenocorticotropic hormone (ACTH), oral corticosteroids, or vigabatrin. Treatment efficacy should be assessed with electroencephalography at 2 weeks, and an alternative therapy is indicated if epileptic spasms or hypsarrhythmia have not resolved. Collaboration with primary care providers is critical to mitigate the potentially serious adverse effects of standard treatments and also to provide developmental interventions. Although new approaches are on the horizon, addressing current challenges and opportunities now can dramatically improve patient outcomes.
Sugammadex: Applications in Pediatric Critical Care
Authors: Tobias Joseph D.
Published: March 2020

Sugammadex is a novel pharmacologic agent, which reverses neuromuscular blockade with a mechanism that differs from acetylcholinesterase inhibitors such as neostigmine. There is a growing body of literature demonstrating its efficacy in pediatric patients of all ages. Prospective trials have demonstrated a more rapid and more complete reversal of rocuronium-induced neuromuscular blockade than the acetylcholinesterase inhibitor, neostigmine. Unlike the acetylcholinesterase inhibitors, sugammadex effectively reverses intense or complete neuromuscular blockade. It may also be effective in situations where reversal of neuromuscular blockade is problematic including patients with neuromyopathic conditions or when acetylcholinesterase inhibitors are contraindicated. This article reviews the physiology of neuromuscular transmission as well as the published literature, regarding the use of sugammadex in pediatric population including the pediatric intensive care unit population. Clinical applications are reviewed, adverse effects are discussed, and dosing algorithms are presented.
Umbilical Cord Blood Lead Level Disparities between Flint and Detroit
Authors: Hanna-Attisha Mona , Gonuguntla Ashweena , Peart Nadine , LaChance Jenny , Taylor D. Kay , Chawla Sanjay
Published: March 2020

Objective The lead-in-water impact of the Flint water crisis on the youngest and most neurodevelopmentally vulnerable population was largely unknown. The objective of this study was to investigate and compare cord blood lead levels (CBLLs) in newborns in Flint, Michigan, after the Flint water crisis, to a group of Detroit newborns.

Study Design Mothers of 99 Flint newborns were surveyed about potential lead exposures. These neonates were born after the recognition of population-wide lead-in-water contamination. CBLLs were measured and maternal–fetal metrics were reviewed. CBLLs and maternal–fetal metrics were then compared with those of a retrospective cohort of 116 Detroit newborns who previously shared the same water source. Analysis involved descriptive statistics, independent t-test, and χ
2 analysis.

Results CBLLs greater than or equal to 1 μg/dL (0.05 μmol/L) were more prevalent among Flint newborns (14%), as compared with Detroit newborns (2%; p = 0.001). This was a sevenfold disparity between Flint and Detroit newborns. No statistically significant differences were found in birth weight, head circumference, small for gestational age status, gestational age, or preterm status among the two groups.

Conclusion The Flint water crisis potentially exposed newborns to lead in utero, implicating maternal–fetal outcomes and future health and development. Primary prevention efforts, including identification and mitigation of lead exposure before conception and during pregnancy, are needed. New environmental exposure detection methods and long-term neurodevelopmental follow-up will complement the findings of this study.
Lanthanum(III) Trifluoromethanesulfonate Catalyzed Direct Synthesis of Ureas from N-Benzyloxycarbonyl-, N-Allyloxycarbonyl-, and N-2,2,2-Trichloroethoxycarbonyl-Protected Amines
Authors: Kim Hee-Kwon , Bui Tien Tan
Published: March 2020

A novel lanthanum triflate mediated conversion of N-benzyl­oxycarbonyl-, N-allyloxycarbonyl-, and N-trichloroethoxycarbonyl-­protected amines into nonsymmetric ureas was discovered. In this study, lanthanum triflate was found to be an effective catalyst for preparing various nonsymmetric ureas from protected amines. A variety of protected aromatic and aliphatic carbamates reacted readily with various amines in the presence of lanthanum triflate to generate the desired ureas in high yields. This result demonstrated that this novel lanthanum triflate catalyzed preparation of ureas from Cbz, Alloc, and Troc carbamates can be employed for the formation of various urea structures.
Limiting absorption principle and scattering matrix for Dirac operators with δ-shell interactions
Authors: Behrndt Jussi , Holzmann Markus , Mantile Andrea , Posilicano Andrea
Published: March 2020

We provide a limiting absorption principle for self-adjoint realizations of Dirac operators with electrostatic and Lorentz scalar δ-shell interactions supported on regular compact surfaces. Then, we show completeness of the wave operators and give a representation formula for the scattering matrix.
Tribometer for measuring coefficients of friction of uneven surfaces like articular cartilage
Authors: Schütte Andy , Mack Michael , Behler Helmut , Ruland Michael , Weiß Christel , Schwarz Markus L. R.
Published: March 2020

To examine coefficients of friction (COFs) of articular cartilage, it is necessary to use cartilage as a friction partner. Irregularities of surfaces require special tribometers and calculation methods. The aim of this study was to establish a tribometer system for measuring a low COF of cartilage and to develop and validate an algorithm that takes the irregularities into consideration. We used a pin-on-plate tribometer that allows a vertical displacement of the pin to follow the surface of the plate and developed an algorithm that takes these irregularities into account. We were, thus, able to take into consideration a forward and backward movement, an upward and downward movement, and different force ratios. The algorithm was validated using a spherical POM (polyoxymethylene) pin against a stainless steel plate at slope angles up to 24°. First examinations with articular cartilage against articular cartilage samples of a stifle joint of a pig were then performed. The newly developed tribometer worked well when POM against a stainless steel hump was examined. The COF increased for slope angles steeper than ±15°. There was an interaction between the COF and the slope angle, but not for the range within ±15°. Cartilage examinations revealed COFs as published in the literature. The tribometer and the algorithm were suitable for the detection of low COF of irregular surfaces of the plate within a range of ±15°. The COF resulting from the forward and backward movements should be averaged.
Control of current waveform of laser ion source using pulsed magnetic field
Authors: Takahashi Kazumasa , Kuzumoto Masayuki , Matsumoto Yuki , Sasaki Toru , Kikuchi Takashi
Published: March 2020

We investigated plasma behavior with a solenoid-generated static and pulsed magnetic field by measuring time evolution in a transverse ion current profile to control the ion current waveform of a laser ion source. The results showed that static magnetic fields cannot enhance the ion current in the slow region of time of flight (TOF). However, a pulsed magnetic field whose magnetic flux density is rising while a plasma passes through the solenoid can enhance the ion current in the same TOF region. The results showed that applying a pulsed magnetic field to a laser-produced plasma is an effective way to control an ion current waveform in a laser ion source to produce an ion beam with a flat-top-shaped pulse. By using a pulsed magnetic field, the ion current waveform peak was held for ∼50 µs.
Vapor-deposited Au thin films modified by plasma etching for surface-enhanced Raman scattering active substrates
Authors: Kondo Takahiro , Tomida Akira , Morishita Nanaka , Saito Yuika
Published: March 2020

Surface-enhanced Raman scattering (SERS) has been used in many fields as a high sensitivity spectroscopic technique. SERS involves local amplification of the electromagnetic field in close proximity to metal nanostructures. Therefore, the morphology of nanoscale structures greatly affects SERS spectroscopy. We carried out modification of the morphology of vapor-deposited Au thin films by plasma etching to form islandlike structures for the development of SERS-active substrates. The modified Au films were evaluated by atomic force microscopy and finite-difference time-domain simulation. The islands on plasma-etched Au films had finer structures because of the collisions of high-energy ions. Furthermore, the island size on the plasma-etched films was almost independent of the film thickness from 5 to 30 nm. When the film thickness decreased below ∼5 nm, many small islands were generated. Due to small islands, active sites where the electric field was enhanced significantly increased. From the results of SERS spectroscopy, it was found that SERS intensities by the film, which had a large number of small islands, are strongly enhanced. We concluded that the thinner Au film with thickness below ∼5 nm was the most suitable for SERS spectroscopy.
Complement C1q mediates the expansion of periportal hepatic progenitor cells in senescence-associated inflammatory liver
Authors: Ho Tung-Ching , Wang Er-Yea , Yeh Kun-Huei , Jeng Yung-Ming , Horng Jau-Hau , Wu Li-Ling , Chen Yi-Tzu , Huang Hsuan-Cheng , Hsu Chia-Lang , Chen Pei-Jer , Yeh Shiou-Hwei , Chen Ding-Shinn
Published: March 2020

Significance

This study has identified C1q in the chronic hepatitis liver as an unorthodox signal for activating the essential β-catenin pathway in hepatic progenitor cells (HPCs) and liver tumors, which is critical for their proliferation and dedifferentiation. Inhibition of C1q not only effectively suppressed the expansion, but also facilitated the differentiation of HPCs and liver tumors. However, it spared the orthodox β-catenin function in pericentral normal hepatocytes. C1q thus becomes a potential therapeutic target for liver tumors derived from HPCs in patients with chronic hepatitis.
Distinct signaling and transcriptional pathways regulate peri-weaning development and cold-induced recruitment of beige adipocytes
Authors: Wu Yixuan , Kinnebrew Melissa A. , Kutyavin Vassily I. , Chawla Ajay
Published: March 2020

Adipose tissue provides a defense against starvation and environmental cold. These dichotomous functions are performed by three distinct cell types: energy-storing white adipocytes, and thermogenic beige and brown adipocytes. Previous studies have demonstrated that exposure to environmental cold stimulates the recruitment of beige adipocytes in the white adipose tissue (WAT) of mice and humans, a process that has been extensively investigated. However, beige adipose tissue also develops during the peri-weaning period in mice, a developmental program that remains poorly understood. Here, we address this gap in our knowledge using genetic, imaging, physiologic, and genomic approaches. We find that, unlike cold-induced recruitment in adult animals, peri-weaning development of beige adipocytes occurs in a temperature- and sympathetic nerve-independent manner. Instead, the transcription factor B cell leukemia/lymphoma 6 (BCL6) acts in a cell-autonomous manner to regulate the commitment but not the maintenance phase of beige adipogenesis. Genome-wide RNA-sequencing (seq) studies reveal that BCL6 regulates a core set of genes involved in fatty acid oxidation and mitochondrial uncoupling, which are necessary for development of functional beige adipocytes. Together, our findings demonstrate that distinct transcriptional and signaling mechanisms control peri-weaning development and cold-induced recruitment of beige adipocytes in mammals.
A photosynthetic antenna complex foregoes unity carotenoid-to-bacteriochlorophyll energy transfer efficiency to ensure photoprotection
Authors: Niedzwiedzki Dariusz M. , Swainsbury David J. K. , Canniffe Daniel P. , Hunter C. Neil , Hitchcock Andrew
Published: March 2020

Significance

Photosynthesis uses carotenoids as light-harvesting pigments and for photoprotective energy dissipation. The carbon–carbon double bond conjugation length of carotenoids (
N
) affects the carotenoid-to-(bacterio)chlorophyll energy transfer efficiency, but the photoprotective capability was considered to be independent of
N
. Using light-harvesting complex 2 from the model photosynthetic bacterium
Rhodobacter sphaeroides
containing ζ-carotene (
N
= 7) or neurosporene (
N
= 9), we demonstrate that decreasing the conjugation length increases the carotenoid-to-bacteriochlorophyll energy transfer efficiency, in the case of ζ-carotene to ∼100%. However, unity quantum efficiency comes at the cost of photoprotection, suggesting that naturally evolved photosynthesis tolerates some energetic loss to allow essential energy dissipation, explaining why longer-conjugation length carotenoids are utilized in native pigment–protein complexes.
Navigating graduate school and academia
Authors: Mackey Alison
Published: March 2020

This chapter takes the form of short answers to questions
posed by graduate students. I lay out some of the questions that I have
encountered most frequently during my two decades working with graduate
students as an advisor, as a Director of Graduate Studies, and as an
instructor of a number of classes, including, currently, a Graduate
Professionalization seminar. I also include some of the questions that are
often asked of me by newly graduated students, in their first faculty
positions. I first provide my own answers to these questions, and then point
to the much more complete and focused information that can be found in many
of the other chapters contained in the current volume.
Towards achieving work-life balance in academia
Authors: Larsson Tove , Loewen Shawn , Oliver Rhonda , Sasaki Miyuki , Tracy-Ventura Nicole , Plonsky Luke
Published: March 2020

The competing demands of teaching, research, and service seem
to never end. Consequently, as academics, we often find ourselves feeling
unable to realize our professional goals while also maintaining a life
outside of work. Recognizing that there is no one-size-fits-all way to
achieve or approximate work-life balance, this chapter presents essays on
this topic by five applied linguists with a range of backgrounds. Each is
personal and introspective, providing concrete guidance on what they have
found to be true and helpful in an effort to achieve satisfaction in their
professional as well as personal lives. The chapter also includes an
introduction that brings together five of the main themes found throughout
of the chapter.
Navigating the academic job market
Authors: Long Avizia Y. , Kyle Kristopher , Crookes Graham
Published: March 2020

An important goal for most PhD students is to procure gainful
employment. Although PhD students receive a great deal of training in the
areas of critiquing, conducting, and publishing research, the process of
searching, applying for, and securing an academic job is one that is often
shrouded in mystery. This chapter attempts to shed some light on this
arduous and stressful task, and in doing so make it less mysterious.
Although the chapter is written with PhD students in mind, it may also be
helpful for early career scholars with limited experience on the job market.
Regardless of your individual background/circumstance, training, and
previous job-searching experiences (or lack thereof), the goal is a shared
one: To navigate the academic job market effectively and obtain one or more
job offers. In this chapter, we cover three key phases in the job search
process, including preparing for the job market (as early as possible),
starting the search (approximately one year before one hopes to be
employed), and excelling in job interviews. In each section, we highlight
key aspects of the preparation stage, and provide specific steps an aspiring
academic can take. It is our experience that few reasonably comprehensive
resources exist that provide insight into the entire process of securing an
academic job (see Kelsky, 2015).
Furthermore, few resources offer the joint perspective(s) of new (i.e.,
Avizia and Kris) and seasoned (i.e., Graham) scholars who have successfully
obtained academic jobs in the field. A particular goal of this chapter is to
provide such a resource within the particular context of the field of
applied linguistics.
Antioxidant activity and absorption of cyanidin-3-O-glucoside liposomes in GES-1 cells in vitro
Authors: Quan Zhao , Guan Rongfa , Huang Haizhi , Yang Kai , Cai Ming , Meng Xianghe
Published: March 2020

The use of anthocyanins are limited by their chemical properties. Recent evidence suggests Cyanidin-3-O-glucoside (C3 G) liposomes via the ethanol injection method exhibit improved stability. In the current study, the characterization and cell absorption of C3 G liposomes were explored via transmission electron microscopy and flow cytometry. The internalization of the C3 G liposomes across the gastric epithelial cell monolayer (GES-1 cells) were investigated. Results showed that the particle size and encapsulation efficiency were 234 ± 9.35 nm and 75.0% ± 0.001, respectively. The total antioxidant capacity (T-AOC) and malondialdehyde (MDA) content were used to evaluate the antioxidant activity of C3 G liposomes. The C3 G liposomes can obviously increased T-AOC and decreased the MDA content.Collectively, C3 G liposomes protected human GES-1 cells from gastric mucosal injury induced by H2O2 by activating the related antioxidant pathway. Our research could provide a new effective treatment strategy for the absorption of stomach drugs.

Abbreviations: C3G: Cyanidin-3-O-glucoside; LP: Liposome; GES-1 cells: Human gastric epithelial cell lines; FBS: Fetal Bovine Serum; PBS: Phosphate-buffered saline; PC: Phosphatidylcholine; CH: Cholesterol; MDA: Malondialdehyde; TEM: Transmission electron microscope; FCM: Flow cytometry; FITC: Fluorescein isothiocyanate; DAPI: 4′, 6-diamidino-2phenylidole; FT-IR: Fourier Transform infrared spectroscopy; PFA: Paraformaldehyde
Comparison of CBCT based synthetic CT methods suitable for proton dose calculations in adaptive proton therapy
Authors: Thummerer Adrian , Zaffino Paolo , Meijers Arturs , Marmitt Gabriel Guterres , Seco Joao , Steenbakkers Roel J H M , Langendijk Johannes A , Both Stefan , Spadea Maria F , Knopf Antje C
Published: March 2020

In-room imaging is a prerequisite for adaptive proton therapy. The use of onboard cone-beam computed tomography (CBCT) imaging, which is routinely acquired for patient position verification, can enable daily dose reconstructions and plan adaptation decisions. Image quality deficiencies though, hamper dose calculation accuracy and make corrections of CBCTs a necessity. This study compared three methods to correct CBCTs and create synthetic CTs that are suitable for proton dose calculations. CBCTs, planning CTs and repeated CTs (rCT) from 33 H&N cancer patients were used to compare a deep convolutional neural network (DCNN), deformable image registration (DIR) and an analytical image-based correction method (AIC) for synthetic CT (sCT) generation. Image quality of sCTs was evaluated by comparison with a same-day rCT, using mean absolute error (MAE), mean error (ME), Dice similarity coefficient (DSC), structural non-uniformity (SNU) and signal/contrast-to-noise ratios (SNR/CNR) as metrics. Dosimetric accuracy was investigated in an intracranial setting by performing gamma analysis and calculating range shifts. Neural network-based sCTs resulted in the lowest MAE and ME (37/2 HU) and the highest DSC (0.96). While DIR and AIC generated images with a MAE of 44/77 HU, a ME of −8/1 HU and a DSC of 0.94/0.90. Gamma and range shift analysis showed almost no dosimetric difference between DCNN and DIR based sCTs. The lower image quality of AIC based sCTs affected dosimetric accuracy and resulted in lower pass ratios and higher range shifts. Patient-specific differences highlighted the advantages and disadvantages of each method. For the set of patients, the DCNN created synthetic CTs with the highest image quality. Accurate proton dose calculations were achieved by both DCNN and DIR based sCTs. The AIC method resulted in lower image quality and dose calculation accuracy was reduced compared to the other methods.
Characteristics of ion beams generated in the interaction of ultra-short laser pulses with ultra-thin foils
Authors: McIlvenny A , Ahmed H , Scullion C , Doria D , Romagnani L , Martin P , Naughton K , Sgattoni A , Symes D R , Macchi A , McKenna P , Zepf M , Kar S , Borghesi M
Published: March 2020

Experiments investigating ion acceleration from laser-irradiated ultra-thin foils on the GEMINI laser facility at the Rutherford appleton laboratory indicate a transition to ‘light sail’ radiation pressure acceleration when using circularly polarised, high contrast laser pulses. This paper complements previously published results with additional data and modelling which provide information on the multispecies dynamics taking place during the acceleration, and provides an indication on expected scaling of these processes at higher laser intensities.
Representation of low-tropospheric temperature inversions in ECMWF reanalyses over Europe
Authors: Palarz Angelika , Luterbacher Jürg , Ustrnul Zbigniew , Xoplaki Elena , Celiński-Mysław Daniel
Published: March 2020

Despite the fact that tropospheric temperature inversions are thought to be an important feature of climate as well as a significant factor affecting air quality, low-level cloud formation, and the radiation budget of the Earth, a quantitative assessment of their representation in atmospheric reanalyses is yet missing. Here, we provide new evidence of the occurrence of low-tropospheric temperature inversions and associated uncertainties in their parameters existing among reanalyses produced by the European Centre for Medium-Range Weather Forecasts (ECMWF) and upper-air soundings for Europe covering the period 2001–2010. The reanalyses utilized here include (1) surface-input reanalyses represented by ERA-20C and CERA-20C as well as (2) full-input reanalyses represented by ERA-Interim and ERA5. The upper-air soundings were derived from the Integrated Global Radiosonde Archive (IGRA), version 2. The data consists mainly of air temperature and geopotential height from the model levels (ModLev) and pressure levels (PresLev) of ECMWF reanalyses. The results show that the frequency of surface-based inversions (SBI) and elevated inversions (EI) is largely in agreement among the reanalyses. The quality of their representation depends, however, on the inversion type, season, and region. Over the vast majority of IGRA upper-air stations, SBI frequency is overestimated and EI frequency is underestimated by ECMWF reanalyses. Substantially larger uncertainties arise from the selection between the data of ModLev and PresLev of the reanalyses—the differences in the frequency of the temperature inversions are particularly large for summertime SBI suggesting that PresLev are not capable of resolving the main features of shallow and weak SBI.
Machine learning for the solution of the Schrödinger equation
Authors: Manzhos Sergei
Published: March 2020

Machine learning (ML) methods have recently been increasingly widely used in quantum chemistry. While ML methods are now accepted as high accuracy approaches to construct interatomic potentials for applications, the use of ML to solve the Schrödinger equation, either vibrational or electronic, while not new, is only now making significant headway towards applications. We survey recent uses of ML techniques to solve the Schrödinger equation, including the vibrational Schrödinger equation, the electronic Schrödinger equation and the related problems of constructing functionals for density functional theory (DFT) as well as potentials which enter semi-empirical approximations to DFT. We highlight similarities and differences and specific difficulties that ML faces in these applications and possibilities for cross-fertilization of ideas.
Reporting of Benign Endometrial Cells in Papanicolaou Tests
Authors: Hernandez Andrea , Schatz-Siemers Nina , Zhou Fang , Brandler Tamar C , Negron Raquel , Modi Lopa , Elgert Paul A , Simsir Aylin
Published: March 2020

Objectives

The 2014 Bethesda System (TBS 2014) guidelines for reporting cervical cytology revised the age for reporting benign endometrial cells (BECs) from 40 years or older to age 45 years or older. We evaluated this change and further investigated if extending the reporting age to 50 years or older may be acceptable.

Methods

We reviewed cases with BECs reported on Papanicolaou tests in women age 40 years or older and 45 years or older before and after implementation of TBS 2014. Follow-up endometrial biopsy/curettage results were categorized as benign, endometrial hyperplasia with or without atypia, or malignant. Hyperplasia and malignant follow-up were considered clinically significant. Clinical data were documented. Results were compared for women age 40 to 44, 45 to 49, and 50 years or older.

Results

Follow-up in 15 (100%) women age 40 to 44 years was benign. In women age 45 to 49 years, 61 (96.8%) had benign follow-up, one (1.6%) had atypical hyperplasia, and one (1.6%) had malignant follow-up. In women age 50 years or older, 57 (86.5%) had benign follow-up, four (6%) had malignant follow-up, and seven (7.5%) had atypical or nonatypical hyperplasia. There was a significant difference in follow-up between the age groups of 40 to 49 and 50 or older (P = .023).

Conclusions

We conclude that the TBS 2014 revision was justified. Our data suggest that age 50 years or older rather than age 45 years or older may be an acceptable cutoff for reporting BECs.
Economic Imperception; or, Reading Capital on the Beach with Thoreau
Authors: Moskowitz Alex
Published: March 2020

This essay argues that throughout his oeuvre, Henry David Thoreau develops a theory of sensory perception that comes to its literary culmination in Cape Cod (1865). I argue that Thoreau’s thinking on the senses demonstrates that the senses are a product of historical development. In Cape Cod, Thoreau is particularly interested in how economic interest has trained the senses to become structurally incapable of sensing the death that is a necessary part of the commodity form and social life in general—similar to what Karl Marx in Capital (1867) would describe as “dead labor.” This essay explores how in Cape Cod, Thoreau offers his reader a method of reading that seeks to make legible through literary form—specifically through puns, metaphor, and juxtaposition—the point at which the senses fail. Thoreau’s method in Cape Cod therefore differs from his more well-known works such as Walden (1854), where he only explicitly tells his readers about that to which they are blind. Ultimately, I claim that Thoreau’s political message throughout his career remains much the same, but the way in which he mobilizes literary form to convey that message marks an important change in how we might make sense of—and make sensible—political economy.
immuneSIM: tunable multi-feature simulation of B- and T-cell receptor repertoires for immunoinformatics benchmarking
Authors: Weber Cédric R , Akbar Rahmad , Yermanos Alexander , Pavlović Milena , Snapkov Igor , Sandve Geir K , Reddy Sai T , Greiff Victor
Published: March 2020

B- and T-cell receptor repertoires of the adaptive immune system have become a key target for diagnostics and therapeutics research. Consequently, there is a rapidly growing number of bioinformatics tools for immune repertoire analysis. Benchmarking of such tools is crucial for ensuring reproducible and generalizable computational analyses. Currently, however, it remains challenging to create standardized ground truth immune receptor repertoires for immunoinformatics tool benchmarking. Therefore, we developed immuneSIM, an R package that allows the simulation of native-like and aberrant synthetic full-length variable region immune receptor sequences by tuning the following immune receptor features: (i) species and chain type (BCR, TCR, single and paired), (ii) germline gene usage, (iii) occurrence of insertions and deletions, (iv) clonal abundance, (v) somatic hypermutation and (vi) sequence motifs. Each simulated sequence is annotated by the complete set of simulation events that contributed to its in silico generation. immuneSIM permits the benchmarking of key computational tools for immune receptor analysis, such as germline gene annotation, diversity and overlap estimation, sequence similarity, network architecture, clustering analysis and machine learning methods for motif detection.

Availability and implementation

The package is available via https://github.com/GreiffLab/immuneSIM and on CRAN at https://cran.r-project.org/web/packages/immuneSIM. The documentation is hosted at https://immuneSIM.readthedocs.io.

Contact

sai.reddy@ethz.ch or victor.greiff@medisin.uio.no

Supplementary information

Supplementary data are available at Bioinformatics online.
A multitask multiple kernel learning formulation for discriminating early- and late-stage cancers
Authors: Rahimi Arezou , Gönen Mehmet
Published: March 2020

Motivation

Genomic information is increasingly being used in diagnosis, prognosis and treatment of cancer. The severity of the disease is usually measured by the tumor stage. Therefore, identifying pathways playing an important role in progression of the disease stage is of great interest. Given that there are similarities in the underlying mechanisms of different cancers, in addition to the considerable correlation in the genomic data, there is a need for machine learning methods that can take these aspects of genomic data into account. Furthermore, using machine learning for studying multiple cancer cohorts together with a collection of molecular pathways creates an opportunity for knowledge extraction.

Results

We studied the problem of discriminating early- and late-stage tumors of several cancers using genomic information while enforcing interpretability on the solutions. To this end, we developed a multitask multiple kernel learning (MTMKL) method with a co-clustering step based on a cutting-plane algorithm to identify the relationships between the input tasks and kernels. We tested our algorithm on 15 cancer cohorts and observed that, in most cases, MTMKL outperforms other algorithms (including random forests, support vector machine and single-task multiple kernel learning) in terms of predictive power. Using the aggregate results from multiple replications, we also derived similarity matrices between cancer cohorts, which are, in many cases, in agreement with available relationships reported in the relevant literature.

Availability and implementation

Our implementations of support vector machine and multiple kernel learning algorithms in R are available at https://github.com/arezourahimi/mtgsbc together with the scripts that replicate the reported experiments.

Supplementary information

Supplementary data are available at Bioinformatics online.
Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
Authors: Sun Kun
Published: March 2020

Motivation

Next-generation sequencing (NGS) data frequently suffer from poor-quality cycles and adapter contaminations therefore need to be preprocessed before downstream analyses. With the ever-growing throughput and read length of modern sequencers, the preprocessing step turns to be a bottleneck in data analysis due to unmet performance of current tools. Extra-fast and accurate adapter- and quality-trimming tools for sequencing data preprocessing are therefore still of urgent demand.

Results

Ktrim was developed in this work. Key features of Ktrim include: built-in support to adapters of common library preparation kits; supports user-supplied, customized adapter sequences; supports both paired-end and single-end data; supports parallelization to accelerate the analysis. Ktrim was ∼2–18 times faster than current tools and also showed high accuracy when applied on the testing datasets. Ktrim could thus serve as a valuable and efficient tool for short-read NGS data preprocessing.

Availability and implementation

Source codes and scripts to reproduce the results descripted in this article are freely available at https://github.com/hellosunking/Ktrim/, distributed under the GPL v3 license.

Contact

sunkun@szbl.ac.cn

Supplementary information

Supplementary data are available at Bioinformatics online.
NLRP3 inflammasome as prognostic factor and therapeutic target in primary progressive multiple sclerosis patients
Authors: Malhotra Sunny , Costa Carme , Eixarch Herena , Keller Christian W , Amman Lukas , Martínez-Banaclocha Helios , Midaglia Luciana , Sarró Eduard , Machín-Díaz Isabel , Villar Luisa M , Triviño Juan Carlos , Oliver-Martos Begoña , Parladé Laura Navarro , Calvo-Barreiro Laura , Matesanz Fuencisla , Vandenbroeck Koen , Urcelay Elena , Martínez-Ginés María-Luisa , Tejeda-Velarde Amalia , Fissolo Nicolás , Castilló Joaquín , Sanchez Alex , Robertson Avril A B , Clemente Diego , Prinz Marco , Pelegrin Pablo , Lünemann Jan D , Espejo Carmen , Montalban Xavier , Comabella Manuel
Published: March 2020

Primary progressive multiple sclerosis is a poorly understood disease entity with no specific prognostic biomarkers and scarce therapeutic options. We aimed to identify disease activity biomarkers in multiple sclerosis by performing an RNA sequencing approach in peripheral blood mononuclear cells from a discovery cohort of 44 untreated patients with multiple sclerosis belonging to different clinical forms and activity phases of the disease, and 12 healthy control subjects. A validation cohort of 58 patients with multiple sclerosis and 26 healthy control subjects was included in the study to replicate the RNA sequencing findings. The RNA sequencing revealed an interleukin 1 beta (IL1B) signature in patients with primary progressive multiple sclerosis. Subsequent immunophenotyping pointed to blood monocytes as responsible for the IL1B signature observed in this group of patients. Functional experiments at baseline measuring apoptosis-associated speck-like protein containing a CARD (ASC) speck formation showed that the NOD-leucine rich repeat and pyrin containing protein 3 (NLRP3) inflammasome was overactive in monocytes from patients with primary progressive multiple sclerosis, and canonical NLRP3 inflammasome activation with a combination of ATP plus lipopolysaccharide was associated with increased IL1B production in this group of patients. Primary progressive multiple sclerosis patients with high IL1B gene expression levels in peripheral blood mononuclear cells progressed significantly faster compared to patients with low IL1B levels based on the time to reach an EDSS of 6.0 and the Multiple Sclerosis Severity Score. In agreement with peripheral blood findings, both NLRP3 and IL1B expression in brain tissue from patients with primary progressive multiple sclerosis was mainly restricted to cells of myeloid lineage. Treatment of mice with a specific NLRP3 inflammasome inhibitor attenuated established experimental autoimmune encephalomyelitis disease severity and improved CNS histopathology. NLRP3 inflammasome-specific inhibition was also effective in reducing axonal damage in a model of lipopolysaccharide-neuroinflammation using organotypic cerebellar cultures. Altogether, these results point to a role of IL1B and the NLRP3 inflammasome as prognostic biomarker and potential therapeutic target, respectively, in patients with primary progressive multiple sclerosis.