bluuebunny/crossref_metadata_2025 huggingface dataset:
All-polymer Planar Photonic Crystals as an Innovative Tool for the Analysis of Air
Authors: Lova Paola , Megahd Heba , Comoretto Davide
Published: March 2020

The possibility to evaluate the molecular diffusivity in polymer thin films used for packaging and device encapsulation directly in-situ would represent a paradigm changer in the assesment of barrier properties and of air quality. Indeed, employing the packaging itself as a smart sensor could lead to waste reduction and mitigate food poisoning effects. In this work, we demonstrate a new technique that exploits simple UV-Vis reflectance spectroscopy to identify the kinetic of diffusion of small molecules in the vapor phase through polymer thin films and polymer multilayered structures. The new method allows then to assess the presence of the analyte in air and its diffusion coefficient in agreement with gravimetric data reported in literature.
A variational mean-field study of clusterization in a zero-temperature system of soft-core bosons
Authors: Prestipino Santi , Sergi Alessandro , Bruno Ezio , Giaquinta Paolo V.
Published: March 2020

We work out the ground-state diagram of weakly-repulsive penetrable bosons, using mean-field theory with a Gaussian ansatz on the single-particle wave function. Upon compression, the fluid transforms into a cluster supersolid, whose structure is characterized for various choices of the embedding space. In Euclidean space, the stable crystals are those with the most compact structure, i.e., triangular and fcc in two and three dimensions, respectively. For particles confined in a spherical surface, as the sphere radius increases we observe a sequence of transitions between different cluster phases, all having a regular or semiregular polyhedron as supporting frame for the clusters. The present results are relevant for the behavior of ultracold bosons weakly coupled to a Rydberg state.
Toward a quantum-enhanced strontium optical lattice clock at INRIM
Authors: Tarallo Marco G.
Published: March 2020

The new strontium atomic clock at INRIM seeks to establish a new frontier in quantum measurement by joining state-of-the-art optical lattice clocks and the quantized electromagnetic field provided by a cavity QED setup. The goal of our experiment is to apply advanced quantum techniques to state-of-the-art optical lattice clocks, demonstrating enhanced sensitivity while preserving long coherence times and the highest accuracy. In this paper we describe the current status of the experiment and the prospected sensitivity gain for the designed cavity QED setup.
Neutrons production on the IPHI accelerator for the validation of the design of the compact neutron source SONATE
Authors: Tran Hoang Ngoc , Ott Frédéric , Darpentigny Jacques , Marchix Anthony , Letourneau Alain , Chauvin Nicolas , Prunes Fabien , Homatter Benoît , Annighöfer Burkhard , Menelle Alain , Schwindling Jérôme
Published: March 2020

We aim at building a compact accelerator-based neutron source (CANS) which would provide a thermal neutron flux on the order of 4x1012 n.s-1.cm-2.sr-1. Such a brilliance would put compact neutron sources on par with existing medium flux neutron research reactors for neutron scattering experiments. We performed the first neutron production tests on the IPHI proton accelerator at Saclay at a proton energy of 3 MeV. The thermal neutron flux were measured using gold foil activation and 3He detectors. The measured flux were compared with GEANT4 Monte Carlo simulations (10.4) in which the whole experimental setup was modelled. There is a good agreement between the experimental measurements and the Monte-Carlo simulations. The available modelling tools will allow us to optimize the whole Target Moderator Reflector assembly together with the neutron scattering spectrometer geometries for the design of the neutron scattering facility SONATE.
Development of new small-angle neutron scattering geometry with ring-shaped collimated beam for compact neutron source
Authors: Funama Fumiaki , Adachi Yuya , Tasaki Seiji , Abe Yutaka
Published: March 2020

Small-angle neutron scattering (SANS) is an important tool to investigate material properties in nanometer to micrometer scale. The opportunity to conduct SANS experiments is, however, limited because of the low number of available SANS beam lines. Compact neutron sources are expected to play a significant role to increase neutron scattering facilities including SANS beam lines. The problem is that the flux of compact neutron sources can be very low, which makes it difficult to measure scattered neutrons from a sample. A SANS geometry with ring-shaped collimated beam (r-SANS) is developed to conduct SANS experiments at very low flux neutron sources. By using ring-shaped collimated neutrons to hit a large sample, the scattered neutron flux becomes high on the ring center line because the scattered neutrons with each scattered angle overlaps on each point of the ring center line. By setting a 3He point detector on the center line and shielding the surrounding of the small detection area well, high signal to noise ratio experiments are possible. In this paper, we show the concept of this new geometry and a preliminary experimental result of a glassy carbon sample taken with the r-SANS geometry constructed at Kyoto University proton Accelerator Neutron Source (KUANS).
Neutron spectroscopy from 1 to 15 MeV with Mimac-FastN, a mobile and directional fast neutron spectrometer and an active phantom for BNCT and PFBT
Authors: Santos Daniel , Sauzet Nadine , Guillaudin Olivier , Muraz Jean-François
Published: March 2020

In the frame of direct dark matter search, the fast neutrons producing elastic collisions on the nuclei of the active volume are the ultimate background. The MIMAC (MIcro-tpc MAtrix Chambers) project has developed a directional detector providing the directional signature to discriminate them from the searched events based on 3D nuclear tracks reconstruction. The MIMAC team of the LPSC has adapted one MIMAC chamber as a mobile fast neutron spectrometer, the Mimac-FastN detector, having a wide neutron energy range (10 keV – 600 MeV) working with different gas mixtures and pressures. This presentation will be focused on the MeV range with 4He + 5% CO2 gas mixture at 700 mbar. A boron coating inside the active volume used for calibration purpose opens the possibility to use the active volume as an active phantom for Boron Neutron Capture Therapy (BNCT) and Proton Fusion Boron Therapy (PFBT).
Reconstruction on fast neutron CT for concrete structure inspection with a pixel-type detector by applying linear scanning method
Authors: Yan Mingfei , Wakabayashi Yasuo , Otake Yoshie , Ikeda Yujiro , Taketani Atsushi , Hashiguchi Takao , Wang Sheng , Tian Binbin , Takanashi Takaoki , Kobayashi Tomohiro , Ma Baolong
Published: March 2020

Concrete structure has been widely used in bridges and highways, however, its performance will be deteriorated after long term serving or suffering disaster. Since fast neutron has strong transmission ability and is sensitive to water content in the concrete structure, it can provide an effective probe to inspect the inner structure of concrete with non-destructive way. Thus, we propose a fast neutron imaging and reconstruction system of 3D CT for concrete structure inspection with Riken accelerator-driven compact neutron source (RANS) using a fast neutron pixel-type detector, which has 8×8 pixels. To have a good space resolution on the reconstructed image, a rotation + linear scanning method is devised and is used to collect the projection data from experiment or calculation. In this paper, reconstruction for a concrete object containing both iron bars and acrylic bars for simulation of water has been conducted. As a result, 3D image of 1cm diameter bar is reconstructed by the sparse reconstruction algorithm.
Metastasiertes kolorektales Karzinom
Authors: Krome Susanne
Published: March 2020

Patienten mit fortgeschrittenen kolorektalen Karzinomen und RAS-Wildtyp erhalten nach der Induktionschemotherapie eine Erhaltungstherapie aus EGFR- Inhibition und 5-Fluorouracil/Leucovorin. In der Valentino-Studie wurde überprüft, ob sich der Verzicht auf das Zytostatikum auf das progressionsfreie Überleben (PFS) und das Gesamtüberleben (OS) auswirkt.
DGHO 2019: Tumorkachexie
Authors: Bubenzer Rainer
Published: March 2020

Auf dem DGHO-Kongress beschäftigte sich ein Symposium anhand ausgewählter Studien und Konzepte zur erkrankungsgemäßen Ernährung von Tumorpatienten sowie zur Vermeidung einer Tumorkachexie. Während grundsätzliche Rahmenbedingungen allgemein akzeptiert sind, wie auch in dem jüngst erschienenen Fachbuch zum Thema des Sitzungsvorsitzenden Dr. Jann Arends, Freiburg, eindringlich dargestellt, bestehen vor allem zu therapeutischen Aspekten der Tumorkachexie ausgeprägte Unsicherheiten und erheblicher Klärungsbedarf.
SITC 2019: Bemcentinib plus Pembrolizumab beim NSCLC
Authors: Kretzschmar Alexander
Published: March 2020

Bei Patienten mit Platintherapie-refraktärem nicht-kleinzelligem Lungenkarzinom (NSCLC) Stadium IV und schlechter Prognose führt die Kombination von Pembrolizumab und Bemcentinib (BGB324 oder R428), einem oralen Hemmer der AXL-Kinase bei fast jedem 4. Fall (23 %) doch noch zu einer Gesamtresponse, berichtete Prof. Matthew Krebs, Manchester, kürzlich auf der SITC-Jahrestagung.
ECC 2019: Kolorektales Karzinom
Authors: Heim Thomas M.
Published: March 2020

Gegenüber der systemischen Chemotherapie allein scheint die zusätzliche Behandlung mit zytoreduktiver Chirurgie (CRS) in Kombination mit hyperthermer intraperitonealer Chemotherapie (HIPEC) in der Behandlung von Peritonealkarzinosen kolorektalen Ursprungs von Vorteil zu sein. Ob die HIPEC dabei überhaupt als wirksame Komponente notwendig ist, wurde durch neuere Studien in Frage gestellt. Dr. Vic Verwaal, Aarhus/Dänemark, plädierte auf dem European Colorectal Congress (ECC) jedoch für die Kombination von CRS und HIPEC.
DGHO 2019: Psychoonkologie
Authors: Bubenzer Rainer
Published: March 2020

Es ist nicht bekannt, wann die DGHO einen „Science Slam“ auf ihrer Jahrestagung veranstalten wird. Ganz unverhofft wurde jedoch auf der DGHO-Jahrestagung 2019 in der wissenschaftlichen Sitzung zu „Patient Reported Outcome (PRO) – in Wissenschaft und Praxis“ von Pia Heußner, München, ein preiswürdiger Kurzvortrag zum Thema Lebensqualitäts-Erfassung für Onkologen gehalten (für einen kurzfristig ausgefallenen Vortrag). Und zwar aus dem Stand, voller Engagement, emotional – was bei Science Slams die eigentliche Kunst sein sollte.
SITC 2019: Immun-Konsolidierung beim NSCLC Stadium-III
Authors: Kretzschmar Alexander
Published: March 2020

Eine der interessanten Neuentwicklungen beim NSCLC Stadium III ist die Konsolidierung mit den Checkpoint-Inhibitoren Durvalumab und Pembrolizumab nach vorausgegangener simultaner Radiochemotherapie (cCRT). Einer deutschlandweiten Umfrage der Deutsche Gesellschaft für Radioonkologie (DEGRO) e. V. zur Implementierung einer Konsolidierung mit PD-L1-Immuntherapeutika zeigte, dass die PD-L1-Konsolidierung zwar als Option bei der deutlichen Mehrzahl der befragten Zentren vorgehalten wird. Als wichtige Barriere für die Integration dieser Therapie erwies sich weiterhin, dass nur bei einer Minderheit von Betroffenen eine PD-L1-Testung durchgeführt wird.
Paliperidone LAI and Aripiprazole LAI Plasma Level Monitoring in the
Prophylaxis of Bipolar Disorder Type I with Manic Predominance
Authors: Mauri Massimo Carlo , Reggiori Alessandra , Minutillo Alessandro , Franco Gemma , Pace Chiara Di , Paletta Silvia , Cattaneo Dario
Published: March 2020

Introduction The objective of this study was the evaluation of utility of
plasma level monitoring in the clinical stabilizing efficacy and tolerability of
paliperidone palmitate (PP) vs. aripiprazole monohydrate (AM) in bipolar
disorder I (BD I) with manic predominance.

Methods Fifty-six outpatients of both sexes, age ranging from 18 to 65
years, affected by BD I with manic predominance, orally treated and stabilized
after acute episode for at least 2 weeks with paliperidone or aripiprazole
(n=31, paliperidone; n=25, aripiprazole) underwent a prospective
observational study of switching to the corresponding long-acting injection
(LAI) on the basis of clinical evaluation. The efficacy and tolerability of the
2 treatments were assessed by BPRS, PANSS, HAMD21, and MRS rating scales and a
check list every month for 12 months. Drug plasma levels determinations (PLs)
were performed at the same times.

Results A good clinical stability and tolerability of both drugs were
reported. Lower mean PLs of PP showed a positive effect on depressive symptoms.
AM PLs variability was associated with greater instability of manic symptoms
whereas intermediate PLs seem to have more influence on depressive
symptomatology.

Discussion PLs drug monitoring has been proven to be useful, and further
investigations to identify optimal therapeutic ranges for LAI formulations are
needed.
Influence of Tranexamic Acid on Inflammatory Signaling in Trauma
Authors: Barrett Christopher D. , Kong Yi Wen , Yaffe Michael B.
Published: March 2020

Plasmin generation in trauma patients has wide-ranging effects, from breakdown of clots to remodeling the extracellular matrix. An evolving recognition of plasmin as a critical effector molecule in various inflammatory signals and pathways has rendered the study of plasmin(ogen) and its regulation by upstream activators and downstream targets and inhibitors key to understanding the inflammatory responses to trauma. Tranexamic acid, a widely available lysine analogue medication on the World Health Organization's list of essential medicines, has rapidly become one of the most commonly implemented adjunct treatments for bleeding after traumatic injury in clinical practice. In this article, we review the effects, both anti- and proinflammatory, of tranexamic acid, with a focus on the injured trauma patient.
Whole Blood for Civilian Urban Trauma Resuscitation: Historical, Present, and Future Considerations
Authors: Walsh Mark , Fries Dietmar , Moore Ernest , Moore Hunter , Thomas Scott , Kwaan Hau C. , Marsee Mathew K. , Grisoli Anne , McCauley Ross , Vande Lune Stefani , Chitta Swetha , Vyakaranam Sudhir , Waxman Dan , McCurdy Michael T. , Zimmer Donald , Patel Bhavesh , Thachil Jecko
Published: March 2020

Whole blood (WB) has been used for more than a century for far-forward combat resuscitation. Following the Iraq/Afghanistan combat, maritime, and austere environment use of WB for the resuscitation of severely hemorrhaging patients, there has been an increasing use of WB for the civilian urban resuscitation environment population. The impetus for this was not just improved outcomes in far-forward hospitals, which had different populations and different needs than the civilian urban population, but also an application of the lessons suggested by recent 1:1:1 plasma:platelets:packed red cells fixed-ratio studies for patients with massive transfusion needs. Mechanistic, logistic, and standardization concerns have been addressed and are evolving as the WB project advances. A small number of studies have been published on WB in the civilian urban trauma population. In addition, European experience with viscoelastic testing and resuscitation with fibrinogen and prothrombin complex concentrate has provided another viewpoint regarding the choice of resuscitation strategies for severely bleeding trauma patients in urban civilian environments. There are randomized controlled trials in process, which are testing the hypothesis that WB may be beneficial for the civilian urban population. Whether WB will improve mortality significantly is now a matter of intense study, and this commentary reviews the history, mechanistic foundations, and logistical aspects for the use of WB in the civilian trauma population.
Superconductivity in La and Y hydrides: Remaining questions to experiment and theory
Authors: Struzhkin Viktor , Li Bing , Ji Cheng , Chen Xiao-Jia , Prakapenka Vitali , Greenberg Eran , Troyan Ivan , Gavriliuk Alexander , Mao Ho-kwang
Published: March 2020

Recent reports of the superconductivity in hydrides of two different families (covalent lattice, as in SH3 and clathrate-type H-cages containing La and Y atoms, as in LaH10 and YH6) have revealed new families of high-Tc materials with Tc’s near room temperature values. These findings confirm earlier expectations that hydrides may have very high Tc’s due to the fact that light H atoms have very high vibrational frequencies, leading to high Tc values within the conventional Bardeen–Cooper–Schrieffer phonon mechanism of superconductivity. However, as is pointed out by Ashcroft, it is important to have the metallic hydrogen “alloyed” with the elements added to it. This concept of a metallic alloy containing a high concentration of metal-like hydrogen atoms has been instrumental in finding new high-Tc superhydrides. These new superhydride “room-temperature” superconductors are stabilized only at very high pressures above 100 GPa, making the experimental search for their superconducting properties very difficult. We will review the current experimental and theoretical results for LaH10−x and YH6−x superhydrides.
Enhancing electromagnetic radiations by a pre-ablation laser during laser interaction with solid target
Authors: Xia Yadong , Li Dongyu , Zhang Siyuan , Wu Minjian , Yang Tong , Geng Yixing , Zhu Jungao , Xu Xiaohan , Li Chengcai , Wang Chuanke , Wang Feng , Lin Chen , Li Tingshuai , Yan Xueqing
Published: March 2020

Ultra-short untraintense laser interacting with solid targets can produce significant electromagnetic pulses (EMPs), which are strongly pertinent to laser and target parameters. In this study, EMPs' generation due to pulsed laser (30 fs, 6×1019 W/cm2) irradiating aluminum foils are recorded and analyzed. The experimental results indicate a pre-ablation pulse (200 ps, 1×1012 W/cm2) that tends to enhance the electromagnetic emission inside the target chamber and the diagnostic cavity. The largest EMP signal is obtained when the pre-ablation pulse is incident on the target at 100 ps prior to the main laser beam. Meanwhile, the frequencies of EMPs are broadened up to 2 GHz in the diagnostic cavity in the 100 ps delayed case, indicating that EMPs with higher frequencies can be generated if the most energetic electrons are accelerated. The simulating results verify expansion of the pre-plasmas induced by the pre-ablation laser, which is beneficial to lift both the energy and quantity of hot electrons escaping from the target, accounting for the ehancement of EMPs. The resulting conclusions offer a new avenue to generate intense EMPs, which can be potentially used in nondestructive examination, high-power microwave source, and energy transfer.
Tunable positive magnetoresistance and crossover from weak antilocalization to weak localization transition in half-Heusler compounds RPtBi (R = lanthanide)
Authors: Chen Jie , Li Hang , Ding Bei , Hou Zhipeng , Liu Enke , Xi Xuekui , Wu Guangheng , Wang Wenhong
Published: March 2020

We report the observation of large tunable positive magnetoresistance (MR) effects in magnetic lanthanide half-Heusler compounds RPtBi (R = Tb, Dy, Ho, Er, and Tm). The value of MR shows a great enhancement from 41% to 1740% by replacing R from Tb to Tm at 2 K under a magnetic field of 9 T. Moreover, a transition of MR from weak antilocalization to weak localization is clearly confirmed when the lanthanide R changed from Tm to Tb. We attribute this transition to gradually enhanced spin-dependent scattering in these magnetic lanthanide half-Heusler compounds RPtBi.
Supersonically sprayed carbon nanotubes and silver nanowires as efficient heat spreaders and cooling films
Authors: Kim Tae-Gun , Park Chan-Woo , Kim Yong-il , Aldalbahi Ali , Rahaman Mostafizur , Yoon Sam S.
Published: March 2020

With the ever-decreasing size of portable electronics to achieve greater versatility, the power density of electronic devices has increased substantially, to the point where efficient cooling has become a major concern for achieving stable device operation. Herein, we introduce a heat-dissipating film coated with carbon nanotubes (CNTs) entangled with silver nanowires (AgNWs), prepared by supersonic spraying. Low thermal resistance was obtained from the strong adhesion between the deposited nanomaterials and the substrate. The optimal hybrid film for achieving maximal cooling was identified by varying the number of spraying sweeps and the composition of the nanomaterials. The hybrid film, comprising both CNTs and AgNWs, afforded superior cooling owing to its improved thermal conductivity. Surface-texturing of the film also significantly impacted the convective-cooling performance. In addition, the superior heat-spreading capability of the hybrid film was demonstrated by comparing infrared images of the bare substrate, pure CNTs, and hybrid CNT/AgNW films. The wettability of these films was also studied to identify the wetting condition that would provide the maximum heat transfer. The hybrid CNT/AgNW film possessed the most hydrophilic surface, providing the most efficient spray-cooling scenario. The hydrophilic surface captured and held the sprayed droplets firmly throughout the process. Hence, these CNT/AgNW hybrid films represent a commercially viable solution for addressing hotspots in portable electronic devices.
All-polymer distributed Bragg reflector laser self-heals to original output power
Authors: Mandel Savannah
Published: March 2020

Doping certain polymers with rhodamine 6g allows a solid-state dye laser to recover its original output power after photodegradation.
Particle size in confined channels greatly affects pressure buildup
Authors: Mandel Savannah
Published: March 2020

Studies of particles moving through a confined channel show stiffness, adhesion and friction also play a role.
New advances in the catalysis of organic reactions by iron compounds
Authors: Khusnutdinov Ravil I. , Bayguzina Alfiya R.
Published: March 2020

The review summarizes and systematizes the literature data on a new promising application area of iron compounds, that is, catalysis of organic reactions. The considered reactions include halogenation, formation of C−C bonds with the participation of various substrates, new methods for the synthesis of ethers and aromatic and heteroaromatic carboxylic acid esters, N-alkylation of aliphatic and aromatic amines and amidation of olefins and cyclopropane-containing hydrocarbons. The advances in the synthesis of quinolines and unusual cyclization reactions catalyzed by iron complexes are described.

The bibliography includes 144 references.
Developing guidelines for the use of traps to capture koalas
Authors: Ashman Kita R. , Whisson Desley A.
Published: March 2020

Capture of wildlife is essential both for research and management, and minimising the amount of stress an animal experiences during capture is important. We examined the behavioural response of koalas to cage traps to improve protocols for trapping koalas. We used heat- and motion-sensing cameras to record the behaviour of koalas in traps, and the duration spent in traps. Behavioural responses were scored on a scale of 0 (no apparent response) to 3 (heightened response) from videos. We successfully trapped a koala in 19 of 21 attempts. For 12 occasions when traps were monitored with cameras, koalas spent 6.3–181.2min in traps and 8 of 12 koalas displayed heightened behavioural responses (score of ≥2). The frequency of response scores did not vary between males and females and was not influenced by trapped duration. We found that traps were effective for capturing koalas; however, to minimise overt behavioural responses by trapped koalas, trap-check intervals need to be as short as possible. We recommend the use of trap-trigger devices to alert personnel when a koala is trapped. The addition of such devices in trapping practices may reduce potential for adverse behavioural responses and improve the cost-efficacy of trapping.
New Perspectives on Photosystem II Reaction Centres
Authors: Hall Jeremy , Picorel Rafael , Cox Nicholas , Purchase Robin , Krausz Elmars
Published: March 2020

We apply the differential optical spectroscopy techniques of circular polarisation of luminescence (CPL) and magnetic CPL (MCPL) to the study of isolated reaction centres (RCs) of photosystem II (PS II). The data and subsequent analysis provide insights into aspects of the RC chromophore site energies, exciton couplings, and heterogeneities. CPL measurements are able to identify weak luminescence associated with the unbound chlorophyll-a (Chl-a) present in the sample. The overall sign and magnitude of the CPL observed relates well to the circular dichroism (CD) of the sample. Both CD and CPL are reasonably consistent with modelling of the RC exciton structure. The MCPL observed for the free Chl-a luminescence component in the RC samples is also easily understandable, but the MCPL seen near 680nm at 1.8K is anomalous, appearing to have a narrow, strongly negative component. A negative sign is inconsistent with MCPL of (exciton coupled) Qy states of either Chl-a or pheophytin-a (Pheo-a). We propose that this anomaly may arise as a result of the luminescence from a transient excited state species created following photo-induced charge separation within the RC. A comparison of CD spectra and modelling of RC preparations having a different number of pigments suggests that the non-conservative nature of the CD spectra observed is associated with the ‘special pair’ pigments PD1 and PD2.
A single concept to teach mood contrastin Spanish
Authors: Solá Simón Elena
Published: March 2020

Traditional methods for the teaching of the Spanish mood system are generally focused on the different morphosyntactic and semantic connections between the matrix and the embedded clause. This generally entails the provision of an extensive classification of subordinate clauses with the embedded verb in the subjunctive mood plus another classification with the exceptions which students need to learn/memorise in order to use them under controlled conditions. A preliminary study was carried out in which L2 learners were introduced to the subjunctive mood following a different approach (i.e. cognitive-operative). Based on the single binary opposition of declaration/non-declaration by Ruiz Campillo (2004), this approach provides a single operative value which can explain all the uses of the subjunctive without exception. The results were positive and showed that introducing Spanish mood contrast by means of this conceptual pair has the potential to improve learners’ ability to select between moods.
Unravelling the proteomic landscape of extracellular vesicles in prostate cancer by density‐based fractionation of urine
Authors: Dhondt Bert , Geeurickx Edward , Tulkens Joeri , Van Deun Jan , Vergauwen Glenn , Lippens Lien , Miinalainen Ilkka , Rappu Pekka , Heino Jyrki , Ost Piet , Lumen Nicolaas , De Wever Olivier , Hendrix An
Published: March 2020

Extracellular vesicles (EV) are increasingly being recognized as important vehicles of intercellular communication and promising diagnostic and prognostic biomarkers in cancer. Despite this enormous clinical potential, the plethora of methods to separate EV from biofluids, providing material of highly variable purity, and lacking knowledge regarding methodological repeatability pose a barrier to clinical translation. Urine is considered an ideal proximal fluid for the study of EV in urological cancers due to its direct contact with the urogenital system. We demonstrate that density‐based fractionation of urine by bottom‐up Optiprep density gradient centrifugation separates EV and soluble proteins with high specificity and repeatability. Mass spectrometry‐based proteomic analysis of urinary EV (uEV) in men with benign and malignant prostate disease allowed us to significantly expand the known human uEV proteome with high specificity and identifies a unique biological profile in prostate cancer not uncovered by the analysis of soluble proteins. In addition, profiling the proteome of EV separated from prostate tumour conditioned medium and matched uEV confirms the specificity of the identified uEV proteome for prostate cancer. Finally, a comparative proteomic analysis with uEV from patients with bladder and renal cancer provided additional evidence of the selective enrichment of protein signatures in uEV reflecting their respective cancer tissues of origin. In conclusion, this study identifies hundreds of previously undetected proteins in uEV of prostate cancer patients and provides a powerful toolbox to map uEV content and contaminants ultimately allowing biomarker discovery in urological cancers.
Inverted plasmonic lens design for nanometrology applications
Authors: Käseberg T , Siefke T , Kroker S , Bodermann B
Published: March 2020

Planar plasmonic lenses have attracted a great deal of interest over the last few years for their super-resolution focusing capabilites. These highly compact structures with dimensions of only a few micrometres allow for the focusing of light to sub-wavelength-sized spots with focal lengths reaching into the far-field. This offers opportunities for new methods in nanometrology; for example, applications in microscopic Mueller matrix ellipsometry setups. However, the conventional plasmonic lens is challenging to fabricate. We present a new design for plasmonic lenses, which is called the inverted plasmonic lens, to accommodate the lithographic fabrication process. In this contribution, we used numerical simulations based on the finite element method in combination with particle swarm optimization to determine ideal parameter ranges and tolerances for the design of inverted plasmonic lenses for different wavelengths in the visible and near-infrared domain and focal lengths between 5 µm and 1 mm.
Kitchen capers—the question
Authors: Featonby David
Published: March 2020

A selection of challenging questions with experiments that can be performed in the kitchen, covering centre of mass, pressure and sound.
Spin momentum-dependent orbital motion
Authors: Yan Shaohui , Li Manman , Liang Yansheng , Cai Yanan , Yao Baoli
Published: March 2020

We present a theoretic analysis on (azimuthal) spin momentum-dependent orbital motion experienced by particles in a circularly-polarized annular focused field. Unlike vortex phase-relevant (azimuthal) orbital momentum flow whose direction is specified by the sign of topological charge, the direction of (azimuthal) spin momentum flow is determined by the product of the field’s polarization ellipticity and radial derivative of field intensity. For an annular focused field with a definite polarization ellipticity, the intensity’s radial derivative has opposite signs on two sides of the central ring (intensity maximum), causing the spin momentum flow to reverse its direction when crossing the central ring. When placed in such a spin momentum flow, a probe particle is expected to response to this flow configuration by changing the direction of orbital motion as it traversing from one side to the other. The reversal of the particle’s orbital motion is a clear sign that spin momentum flow can affect particles’ orbital motion alone even without orbital momentum flow. More interestingly, for dielectric particles the spin momentum-dependent orbital motion tends to be ‘negative’, i.e., in the opposite direction of the spin momentum flow. This arises mainly because of spin–orbit interaction during the scattering process. For the purpose of experimental observation, we suggest the introduction of an auxiliary radially-polarized illumination to adjust the particle’s radial equilibrium position, for the radial gradient force of the circularly-polarized annular focused field tends to constrain the particle at the ring of intensity maximum.
Bias variation detection in RF amplifiers using differential OBIST
Authors: Ballot M , Stander T
Published: March 2020

Oscillation-based built-in self-testing with differential power detection has been shown to be a promising method for detecting degradation in radio frequency (RF) amplifiers. We demonstrate the use of the method to detect supply voltage decrease and base current variation. The efficacy of the approach is verified using simulated results of a 2.4 GHz low-noise amplifier (LNA). It is shown that these variations can be detected by using only power detection.
Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
Authors: Xue Yaxin , Lanzén Anders , Jonassen Inge
Published: March 2020

Motivation

Technological advances in meta-transcriptomics have enabled a deeper understanding of the structure and function of microbial communities. ‘Total RNA’ meta-transcriptomics, sequencing of total reverse transcribed RNA, provides a unique opportunity to investigate both the structure and function of active microbial communities from all three domains of life simultaneously. A major step of this approach is the reconstruction of full-length taxonomic marker genes such as the small subunit ribosomal RNA. However, current tools for this purpose are mainly targeted towards analysis of amplicon and metagenomic data and thus lack the ability to handle the massive and complex datasets typically resulting from total RNA experiments.

Results

In this work, we introduce MetaRib, a new tool for reconstructing ribosomal gene sequences from total RNA meta-transcriptomic data. MetaRib is based on the popular rRNA assembly program EMIRGE, together with several improvements. We address the challenge posed by large complex datasets by integrating sub-assembly, dereplication and mapping in an iterative approach, with additional post-processing steps. We applied the method to both simulated and real-world datasets. Our results show that MetaRib can deal with larger datasets and recover more rRNA genes, which achieve around 60 times speedup and higher F1 score compared to EMIRGE in simulated datasets. In the real-world dataset, it shows similar trends but recovers more contigs compared with a previous analysis based on random sub-sampling, while enabling the comparison of individual contig abundances across samples for the first time.

Availability and implementation

The source code of MetaRib is freely available at https://github.com/yxxue/MetaRib.

Contact

yaxin.xue@uib.no or Inge.Jonassen@uib.no

Supplementary information

Supplementary data are available at Bioinformatics online.
Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm
Authors: Firtina Can , Kim Jeremie S , Alser Mohammed , Senol Cali Damla , Cicek A Ercument , Alkan Can , Mutlu Onur
Published: March 2020

Motivation

Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to construct an assembly (i.e. the subject’s genome), which is further used in downstream genome analysis. Unfortunately, third-generation sequencing technologies have high sequencing error rates and a large proportion of base pairs in these long reads is incorrectly identified. These errors propagate to the assembly and affect the accuracy of genome analysis. Assembly polishing algorithms minimize such error propagation by polishing or fixing errors in the assembly by using information from alignments between reads and the assembly (i.e. read-to-assembly alignment information). However, current assembly polishing algorithms can only polish an assembly using reads from either a certain sequencing technology or a small assembly. Such technology-dependency and assembly-size dependency require researchers to (i) run multiple polishing algorithms and (ii) use small chunks of a large genome to use all available readsets and polish large genomes, respectively.

Results

We introduce Apollo, a universal assembly polishing algorithm that scales well to polish an assembly of any size (i.e. both large and small genomes) using reads from all sequencing technologies (i.e. second- and third-generation). Our goal is to provide a single algorithm that uses read sets from all available sequencing technologies to improve the accuracy of assembly polishing and that can polish large genomes. Apollo (i) models an assembly as a profile hidden Markov model (pHMM), (ii) uses read-to-assembly alignment to train the pHMM with the Forward–Backward algorithm and (iii) decodes the trained model with the Viterbi algorithm to produce a polished assembly. Our experiments with real readsets demonstrate that Apollo is the only algorithm that (i) uses reads from any sequencing technology within a single run and (ii) scales well to polish large assemblies without splitting the assembly into multiple parts.

Availability and implementation

Source code is available at https://github.com/CMU-SAFARI/Apollo.

Supplementary information

Supplementary data are available at Bioinformatics online.
Fit for measure? Evaluation in community development
Authors: Ardle Oonagh Mc , Murray Una
Published: March 2020

Community development is a process where people concerned with social and environmental justice act together as engaged and active citizens1 to change their collective circumstances. A concern to deliver change through these processes raises the questions: How do we know if our work is effective? What do we mean by and how do we assess outcomes? What ‘evidence’ will help us articulate and improve how we do our work? Over the past decades, there has been a growing trend globally towards evaluation to understand and improve practice. Nevertheless, there is a lack of clarity about, and application of, appropriate frameworks for community development evaluation (Motherway, 2006; CDF, 2010; Whelan et al., 2019). Drawing on current practice, this paper explores challenges, principles and methods for evaluation in community development. We argue that ‘measurement’ requires a clear understanding and agreement of community development purpose and processes, including recognition of community as within and beyond place. Drawing on international evaluation criteria and models, we conclude that community development work could learn from these, as long as communities are in central decision-making roles. We offer suggestions for principles to inform evaluation efforts in community development, suggesting that good community development processes and associated outcomes represent in themselves a theory of change.
Twitter promotion predicts citation rates of cardiovascular articles: a preliminary analysis from the ESC Journals Randomized Study
Authors: Ladeiras-Lopes Ricardo , Clarke Sarah , Vidal-Perez Rafael , Alexander Michael , Lüscher Thomas F
Published: March 2020

Aims

The association between the dissemination of scientific articles on Twitter and online visibility (including Altmetric score) is still controversial and the impact on citation rates has never been addressed for cardiovascular medicine journals.

Methods and Results

The ESC Journals Study randomized 696 papers published in the ESC Journals family (March 2018–May 2019) for promotion on Twitter or to a control arm (with no active tweeting from ESC channels) and aimed to assess if Twitter promotion was associated with an increase in citation rate (primary endpoint) and Altmetric score. This is a preliminary analysis of 536 articles (77% of total) published until December 2018 (therefore, papers published at least 6 months before collecting citation and Altmetrics data). In the analysis of the primary endpoint, Twitter promotion of articles was associated with a 1.43 (95% confidence interval 1.29–1.58) higher rate of citations, and this effect was independent of the type of article. Both Altmetric score and number of users tweeting were positively associated with the number of citations in both arms, with evidence of a stronger association (interaction) in the Twitter arm.

Conclusion

Therefore, a social media strategy of Twitter promotion for cardiovascular medicine papers seems to be associated with increased online visibility and higher number of citations. The final analysis will include 696 papers and 2-year scientific citation rate and is estimated to be concluded in March 2021.
Bacillus subtilis RZ001 improves intestinal integrity and alleviates colitis by inhibiting the Notch signalling pathway and activating ATOH-1
Authors: Li Yanru , Zhang Tengxun , Guo Congcong , Geng Meng , Gai Sailun , Qi Wei , Li Zhongyuan , Song Yajian , Luo Xuegang , Zhang Tongcun , Wang Nan
Published: March 2020

Intestinal mucosal barriers help the body resist many intestinal inflammatory diseases, such as inflammatory bowel disease (IBD). In this study, we identified a novel bacterium promoting the repair of intestinal mucosa and investigated the potential mechanisms underlying its activity. Culture supernatant of Bacillus subtilis RZ001 upregulated the expression of mucin 2 (MUC2) and tight junction (TJ) proteins in HT-29 cells in vitro. Oral administration of B. subtilis RZ001 may have significantly reduced symptoms such as the dextran sulfate sodium (DSS)-induced decrease in body weight, shortening of colon length and overproduction of proinflammatory factors. The number of goblet cells and levels of MUC2 and TJ proteins were significantly increased in adult mice fed with B. subtilis RZ001. B. subtilis RZ001 cells upregulated the levels of MUC2 in the intestinal organoids. Furthermore, culture supernatant of B. subtilis RZ001 could suppress the Notch signalling pathway and activate the expression of atonal homolog 1 (Atoh1). The transcription factor Atoh1 is required for intestinal secretory cell differentiation and activates transcription of MUC2 via binding to E-boxes on the MUC2 promoter. Taken together, B. subtilis strain RZ001 has the potential for treating IBD. The present study is helpful to elucidate the mechanisms of B. subtilis action.
Impact of Low Muscle Mass and Low Muscle Strength According to EWGSOP2 and EWGSOP1 in Community-Dwelling Older People
Authors: Costanzo Luisa , De Vincentis Antonio , Di Iorio Angelo , Bandinelli Stefania , Ferrucci Luigi , Antonelli Incalzi Raffaele , Pedone Claudio
Published: March 2020

Background

A universal definition of sarcopenia is still lacking. Since the European criteria have been recently revised, we aimed at studying prevalence of low muscle strength (LMS) and low muscle mass (LMM), as defined according to the European Working Group of Sarcopenia in Older People (EWGSOP) 2 and 1 definitions, and their individual contribution toward mortality and incident mobility disability in a cohort of community-dwelling older people.

Methods

Longitudinal analysis of 535 participants of the InCHIANTI study. LMS and LMM were defined according to the criteria indicated in the EWGSOP2 and 1. Cox and log-binomial regressions were used to examine association with mortality and 3-year mobility disability (inability to walk 400 m).

Results

We observed a lower prevalence of the combination LMM/LMS according to EWGSOP2 compared to EWGSOP1 (3.2% vs 6.2%). Using the new criteria, all sarcopenia components were associated with mortality, although the hazard ratio [HR] for the group LMM/LMS was no longer significant after adjustment for confounders (LMM: HR 2.69, 95% confidence interval [CI] 1.04–6.94; LMS: HR 3.18, 95% CI 1.44–7.01; LMM/LMS: HR 2.95, 95% CI 0.86–10.16). Using EWGSOP1, LMS alone was independently associated with mortality (HR 4.43, 95% CI 1.85–10.57). None of the sarcopenia components conferred a higher risk of mobility disability.

Conclusions

The EWGSOP2 algorithm leads to a reduction in the estimated prevalence of sarcopenia defined as combination of LMM/LMS. The finding that, independent of the adopted criteria, people with LMS and normal mass have a higher mortality risk compared to robust individuals, confirms that evaluation of muscle strength has a central role for prognosis evaluation.
CNS glycosylphosphatidylinositol deficiency results in delayed white matter development, ataxia and premature death in a novel mouse model
Authors: Lukacs Marshall , Blizzard Lauren E , Stottmann Rolf W
Published: March 2020

The glycosylphosphatidylinositol (GPI) anchor is a post-translational modification added to approximately 150 different proteins to facilitate proper membrane anchoring and trafficking to lipid rafts. Biosynthesis and remodeling of the GPI anchor requires the activity of over 20 distinct genes. Defects in the biosynthesis of GPI anchors in humans lead to inherited glycosylphosphatidylinositol deficiency (IGD). IGD patients display a wide range of phenotypes though the central nervous system (CNS) appears to be the most commonly affected tissue. A full understanding of the etiology of these phenotypes has been hampered by the lack of animal models due to embryonic lethality of GPI biosynthesis gene null mutants. Here we model IGD by genetically ablating GPI production in the CNS with a conditional mouse allele of phosphatidylinositol glycan anchor biosynthesis, class A (Piga) and Nestin-Cre. We find that the mutants do not have structural brain defects but do not survive past weaning. The mutants show progressive decline with severe ataxia consistent with defects in cerebellar development. We show that the mutants have reduced myelination and defective Purkinje cell development. Surprisingly, we found that Piga was expressed in a fairly restricted pattern in the early postnatal brain consistent with the defects we observed in our model. Thus, we have generated a novel mouse model of the neurological defects of IGD which demonstrates a critical role for GPI biosynthesis in cerebellar and white matter development.
Transition Without Transformation: The Legacy of Sudan’s Comprehensive Peace Agreement
Authors: Carolan Gene
Published: March 2020

In recent years, the transitional justice framework has expanded to include a broader notion of transformative justice, which strives for socio-political reform in addition to legal accountability. Over the course of two civil wars, Sudan has grappled with various attempts at transition and transformation with mixed results. Though the 2005 Comprehensive Peace Agreement brought an end to decades of North–South conflict, South Sudan’s subsequent descent into civil war has been characterised by a flawed transition and a lack of any immediate transformative potential.

This paper analyses the Comprehensive Peace Agreement’s transitional mechanisms. In doing so, it explores how certain mechanisms frame the ‘meta-conflict’ about what the conflict is about, and how this can cut off a range of conflict resolution opportunities. It concludes by considering the legacy of the Comprehensive Peace Agreement in contemporary Sudan and South Sudan, and how it might inform the prospective transitions in both countries.
Generalized Cesàro Operators: Geometry of Spectra and Quasi-Nilpotency
Authors: Limani Adem , Malman Bartosz
Published: March 2020

For the class of Hardy spaces and standard weighted Bergman spaces of the unit disk, we prove that the spectrum of a generalized Cesàro operator $T_g$ is unchanged if the symbol $g$ is perturbed to $g+h$ by an analytic function $h$ inducing a quasi-nilpotent operator $T_h$, that is, spectrum of $T_h$ equals $\{0\}$. We also show that any $T_g$ operator that can be approximated in the operator norm by an operator $T_h$ with bounded symbol $h$ is quasi-nilpotent. In the converse direction, we establish an equivalent condition for the function $g \in \textbf{BMOA}$ to be in the $\textbf{BMOA}$ norm closure of $H^{\infty }$. This condition turns out to be equivalent to quasi-nilpotency of the operator $T_g$ on the Hardy spaces. This raises the question whether similar statement is true in the context of Bergman spaces and the Bloch space. Furthermore, we provide some general geometric properties of the spectrum of $T_{g}$ operators.