bluuebunny/crossref_metadata_2025 huggingface dataset:
OxymaPure Coupling Reagents: Beyond Solid-Phase Peptide Synthesis
Authors: El-Faham Ayman , Albericio Fernando , Manne Srinivasa Rao , de la Torre Beatriz G.
Published: September 2020

OxymaPure [ethyl 2-cyano-2-(hydroxyimino)acetate] is an exceptional reagent with which to suppress racemization and enhance coupling efficiency during amide bond formation. The tremendous popularity of OxymaPure has led to the development of several Oxyma-based reagents. OxymaPure and its derived reagents are widely used in solid- and solution-phase peptide chemistry. This review summarizes the recent developments and applications of OxymaPure and Oxyma-based reagents in peptide chemistry, in particular in solution-phase chemistry. Moreover, the side reaction associated with OxymaPure is also discussed.

1 Introduction

2 Oxyma-Based Coupling Reagents

2.1 Aminium/Uronium Salts of OxymaPure

2.2 Phosphonium Salts of OxymaPure

2.3 Oxyma-Based Phosphates

2.4 Sulfonate Esters of OxymaPure

2.5 Benzoate Esters of OxymaPure

2.6 Carbonates of OxymaPure Derivatives

3 OxymaPure Derivatives

4 Other Oxime-Based Additives and Coupling Reagents

5 Side Reactions Using OxymaPure Derivatives

6 Conclusion

7 List of Abbreviations
Phosphorylation of Carboxylic Acids and Their Derivatives with P(O)–H Compounds Forming P(O)–C Bonds
Authors: Chen Tieqiao , Han Li-Biao , Tan Qihang , Liu Xue , Liu Long , Huang Tianzeng
Published: September 2020

Herein, we highlight advances in the phosphorylation of readily available carboxylic acids and their derivatives forming synthetically important P(O)–sp3C, P(O)–sp2C, and P(O)–spC bonds, with an emphasis on the results demonstrated since 2010. This review examines the challenges associated with the use of this strategy for the synthesis of organophosphorus compounds and details advances in the design of catalytic systems that suppress these problems thus resulting in notable progress. Mechanistic details are discussed where available.

1 Introduction

2 Formation of P(O)–sp3C Bonds

3 Formation of P(O)–sp2C Bonds

4 Formation of P(O)–spC Bonds

5 Outlook and Conclusion
Avaliação pós-operatória comparativa dos pacientes submetidos ao tratamento cirúrgico das luxações acromioclaviculares aguda versus crônica
Authors: Storti Thiago Medeiros , de Paula Leony Batista , Simionatto Carolina , Simionatto João Eduardo , Faria Rafael Salomon Silva , Paniago Alexandre Firmino
Published: September 2020

Objetivos Avaliar e comparar os resultados do tratamento cirúrgico das luxações acromioclaviculares (LACs) aguda e crônica, definindo o plano terapêutico mais eficaz.

Métodos Estudo retrospectivo realizado com 30 pacientes operados entre 2011 e 2018 para LAC tipos III e V, separados de acordo com a classificação temporal em subgrupo agudo (< 3 semanas; subgrupo I) e subgrupo crônico (> 3 semanas; subgrupo II). Todos os pacientes foram submetidos a avaliação pós-cirúrgica com protocolo padronizado composto por dados epidemiológicos, funcionais e radiográficos.

Resultados No subgrupo I, a pontuação na escala visual analógica (EVA) foi de 1,10, o escore de Constant-Murley foi de 92,3, e o escore da University of California at Los Angeles (UCLA) foi de 33,5. A distância coracoclavicular (CC) foi de 11,0 mm, e o aumento do espaço CC foi em média menor do que 8,9% em relação ao ombro contralateral. No subgrupo II, a EVA foi de 1,11, o escore de Constant-Murley foi de 94,2, e o da UCLA, 32,4. A distância CC foi de 13,8 mm, sendo o aumento do espaço CC de 22,9% em relação ao contralateral.

Conclusão Apesar de não ter havido diferença significativa entre os quesitos avaliados, houve uma tendência de o subgrupo agudo apresentar distância CC (p = 0,098) e percentual de aumento da distância CC (p = 0,095) menor do que o subgrupo crônico. Assim, é interessante que o tratamento cirúrgico seja realizado nas primeiras três semanas após o trauma, para tentar evitar essa tendência. Nos casos em que não for possível realizar o tratamento na fase aguda, a técnica de Weaver Dunn modificada apresenta bons resultados clínicos e funcionais.
O impacto das fraturas do quadril no SUS 2008 - 2017: O papel do ortopedista
Authors: Stolnicki Bernardo , Teixeira Bruno Casaes
Published: September 2020

Objective The present study intends to describe the profile of hospitalization and ambulatory rehabilitation of patients ≥ 50 years old due to hip fracture in the Brazilian Public Health System (SUS, in the Portuguese acronym).

Methods This is a cross-sectional study of patients hospitalized due to hip fracture in the SUS between 2008 and 2017. Data included 441,787 hip fracture-related hospitalizations from the hospitalization database of the department of informatics of the Brazilian Unified Health System (SIH/DATASUS, in the Portuguese acronym), and data of patients who underwent rehabilitation from the ambulatory database of the department of informatics of the Brazilian Unified Health System (SIA/DATASUS, in the Portuguese acronym.).

Results Most of hip fracture-related hospitalizations (83.5%) happen to people ≥ 50 years old, with an average annual growth of 5.6% in hip fracture-related hospitalizations. The costs for the government have been growing in the same proportion and reached almost BRL 130 million in 2017, although with a 13.6% decrease in average cost per hospitalization. Besides the financial impact, hip fractures result in an in-hospital mortality rate around 5.0% in patients aged ≥ 50 years old. In addition, the percentage of patients that have undergone hip fracture-related rehabilitation increased from 2008 (14.0%) to 2012 (40.0%), and remained stable after that.

Conclusions The progressive increase in the incidence of hip fractures shows the financial and social impact, and the need for immediate actions to prevent this rising trend. Hip fractures are a risk for secondary fractures, the prevention is crucial, and the orthopedist plays a central role in this process.
Evaluation of Oxidative-Stress Pathway and Recovery of Sudden Sensorineural Hearing Loss
Authors: Elias Thaís Gomes Abrahão , Monsanto Rafael da Costa , do Amaral Jonatas Bussador , Oyama Lila Missae , Maza Paloma Korehisa , Penido Norma de Oliveira
Published: September 2020

Introduction Although the pathogenesis of sudden sensorineural hearing loss (SSNHL) has been discussed in the literature, many unclear points remain. Several authors have hypothesized that oxidative stress plays a role in the pathogenesis of noise-related hearing loss, as well as in drug- and aging-related hearing loss. Reactive oxygen species (ROS) may contribute to the pathogenesis of SSNHL in a similar way as in cases of ototoxicity, noise-induced hearing loss and presbyacusis.

Objective The aim of the present study was to find potential peripheral biomarkers to show the levels of oxidative stress in samples of peripheral blood collected from SSNHL patients with and withouth metabolic disease.

Methods In total, 80 consecutive patients with SSNHL were evaluated in the otolaryngology emergency room and outpatient clinic of a tertiary hospital between May 2017 and May 2019. All patients underwent detailed anamnesis, physical examination, audiometry, magnetic resonance imaging (MRI) of the inner ears, and blood tests for serum lipids and plasma activity of thiobarbituric acid reactive species (TBARS).

Results No significant effect of malondialdehyde (MDA) activity was observed regarding the hearing recovery of patients who developed SSNHL.

Conclusion We did not observe a significant correlation between the concentration of TBARs in the peripheral blood or the presence of arterial hypertension and the severity of the initial hearing loss or the prognosis of hearing recovery in patients with SSNHL. The concentration of TBARs in the peripheral blood may not adequately represent the abnormalities that occur in the intracoclear environment.
Cisto aracnóide após trauma na coluna torácica com compressão medular: Relato de caso
Authors: Zanon Igor de Barcellos , Kanas Michel , Joaquim Marcos Augusto Stávale , Martins Délio Eulálio , Wajchenberg Marcelo , Astur Nelson
Published: September 2020

Cistos aracnóides são raros, podem ocorrer em todos os níveis do saco dural, e sua origem pode ser congênita, traumática, iatrogênica ou inflamatória. Neste artigo, relatamos o caso de uma paciente com mielopatia torácica compressiva decorrente de um cisto aracnóide intradural incomum, de manifestação pós-traumática, assim como sua resolução, além de realizar revisão da literatura sobre o tema. A principal localização é na coluna torácica, seguida das colunas lombar, lombossacra e toracolombar. O cisto com origem traumática é causado por lesão da camada interna da dura-máter. Essas lesões produzem déficit neurológico por meio de efeito de massa sobre a medula espinhal. A existência de mielopatia compressiva associada é mais rara ainda. A ressecção ou drenagem dos cistos na vigência de mielopatia deve ser imediata, sendo o tratamento de escolha. Apesar de raros, podem ser uma complicação de fraturas da coluna vertebral que são muito comuns na prática de ortopedistas e neurocirurgiões, que devem estar preparados para essa situação incomum.
Avaliação da tenotomia ou tenodese bicipital na infiltração gordurosa do músculo bíceps
Authors: Simmer Filho Jair , Lara Paulo Henrique Schmidt , Leite Júnior Juarez , Belangero Paulo Santoro , Ejnisman Benno
Published: September 2020

Objetivo O objetivo do presente estudo foi determinar a existência de infiltração gordurosa (IG) na massa muscular do bíceps braquial após a tenotomia ou tenodese para tratamento de lesão no tendão da cabeça longa do bíceps e estabelecer uma relação entre a IG e alterações no comprimento das fibras musculares.

Métodos Análise clínica e de imagens de 2 grupos de pacientes (submetidos à tenodese do bíceps [16 indivíduos] ou tenotomia do bíceps [15 indivíduos]). Nos dois grupos, os achados foram comparados àqueles do lado contralateral de cada indivíduo (grupo controle). Todos os pacientes foram submetidos à tenodese ou tenotomia unilateral do bíceps, com acompanhamento pós-operatório > 1 ano. Exames de ressonância magnética (RM) foram realizados em ambos os braços de cada paciente de acordo com um protocolo específico. A força de flexão do cotovelo foi medida com dinamômetro manual e os resultados foram submetidos à análise estatística.

Resultados O período pós-operatório médio antes da realização da RM foi de 5 anos, e nenhum caso de IG foi observado no compartimento anterior de ambos os braços dos pacientes avaliados. Sete pacientes apresentaram deformidade moderada ou grave no braço operado. Não houve relação significativa entre deformidade do braço (p = 0,077), percentual de força de flexão (p = 0,07) ou dor à palpação do sulco bicipital (p = 0,103).

Conclusão Nenhum dos pacientes avaliados apresentou evidência de IG na massa muscular do compartimento anterior do braço após os procedimentos. Não foi possível estabelecer uma correlação entre a discrepância do comprimento do músculo bíceps, medido à RM, e a presença de IG no compartimento anterior do braço.
Correction: Romancing science for global solutions: on narratives and interpretative schemas of science diplomacy
Authors: Rungius Charlotte , Flink Tim
Published: September 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Thermodynamic aspects of creating effective high performance cryogenic helium units with dynamic-action machines (Review Article)
Authors: Lavrenchenko G. K. , Kravchenko M. B.
Published: September 2020

Different types of high performance cryogenic helium units with dynamic-action machines are proposed. The creation of a helium refrigerator with an energy-generating cryogenic stage (ECS), in which helium is compressed at a temperature of 85.8 K in a cold centrifugal compressor, is also considered. The optimization of the refrigerator with an ECS is performed at the same cooling capacity of 576 W, and a temperature level of about 4.5 K. The use of liquid nitrogen is not involved. It is shown that it is possible to develop an effective helium refrigerator based on dynamic-action machines, such as centrifugal compressors and centripetal turboexpanders.
Excitation of the collective states of qubits in a three-qubit system
Authors: Greenberg Ya. S. , Shtygashev A. A.
Published: September 2020

In the present paper, we have proposed the experimentally achievable method for the characterization of the collective states of qubits in a linear chain. We study a temporal dynamics of absorption of a single-photon pulse by three interacting qubits embedded in a one-dimensional open waveguide. Numerical simulations were performed for a Gaussian-shaped pulse with different frequency detunings and interaction parameters between qubits. The dynamic behavior of the excitation probability for each qubit is investigated. It was shown that the maximum probability amplitudes of excitation of qubits are reached when the frequency of external excitation coincides with the frequency of excitation of the corresponding eigenstate of the system. In this case, the magnitude of the probability amplitude of each qubit in the chain unambiguously correlates with the contribution of this qubit to the corresponding collective state of the system, and the decay of these amplitudes is determined by the resonance width arising from the interaction of the qubit with the photon field of the waveguide. Therefore, we show that the pulsed harmonic probe can be used for the characterization of the energies, widths, and the wave functions of the collective states in a one dimensional qubit chain.
Peculiarities of IV-characteristics and magnetization dynamics in the φ Josephson junction
Authors: Shukrinov Yu. M. , Rahmonov I. R. , Botha A. E.
Published: September 2020

The φ0 junction demonstrates a rich variety of dynamical states determined by parameters of the Josephson junction and the intermediate ferromagnetic layer. Here we find several peculiarities in the maximal amplitude of magnetic moment m^y, taken at each value of the bias current, which we correlate to the features of the IV-characteristics of the φ0 junction. We show that a kink behavior in the bias current (voltage) dependence of m^y along the IV-characteristics is related to the changes in the dynamical behavior of the magnetization precession in the ferromagnetic layer. We also demonstrate a transformation of the magnetization specific trajectories along the IV-curve, magnetization composite structures, and hysteretic behavior in the bias current dependence of m^y. Due to the correlations between features of m^y and the IV-characteristics, the presented results open a way for the experimental testing of the peculiar magnetization dynamics which characterize the φ0 junction.
In situ observations of jetting in the divergent rebound regime for high-velocity metallic microparticle impact
Authors: Sun Yuchen , Veysset David , Nelson Keith A. , Schuh Christopher A.
Published: September 2020

Metallic bonding of certain materials can be achieved via high-velocity impact, and this type of bonding is often linked to an intense extrusion of material from the impact site, known as jetting. We present in situ observations of hydrodynamic jetting and ejection of matter from high-velocity metallic microparticle impacts that still result in rebound of the particle. While the occurrence of jetting has been linked to permanent particle deposition in prior studies, the present findings reveal that any bonds that may form upon jetting can be rebroken by particle rebound in some circumstances. We further present asymmetric occurrences of jetting associated with localized delays in particle detachment followed by rotation during particle rebound, which may speak to transient bond formation at the jetting sites.
Emerging circularly polarized thermally activated delayed fluorescence materials and devices
Authors: Zhou Ling , Xie Guohua , Ni Fan , Yang Chuluo
Published: September 2020

Thermally activated delayed fluorescent (TADF) materials are capable of converting non-radiative triplets into radiative singlets in the presence of a tiny singlet-triplet splitting. Circularly polarized luminescent (CPL) materials with TADF properties have shown great potential in unity exciton utilization as well as high circularly polarized dissymmetry factors |gPL|. When employed in organic light-emitting devices (OLEDs), circularly polarized electroluminescence (CPEL) with high dissymmetry factors |gEL| is essential for reducing the optical loss and improving the quality of 3D, augment-reality, and virtual reality displays. This Perspective summarizes the recent advances in the cutting-edge research of CP-TADF-OLEDs and addresses the challenges in molecular and device engineering.
Recent developments in plasmon-assisted photocatalysis—A personal Perspective
Authors: Sivan Yonatan , Dubi Yonatan
Published: September 2020

It has been known for many years that metallic nanoparticles can catalyze various chemical reactions, both in the dark and under illumination, through different mechanisms. In the last decade or so, many claims of plasmon-assisted “hot” electron driven catalysis of bond-dissociation reactions have been put forward. These claims were challenged in a recent series of papers where both the underlying theory of “hot” electron generation and the use of specific experimental setups to discover them in chemical reactions were examined in detail. The conclusion that arose from these works is that as long as temperature gradients exist inside the system (as for typical experimental setups), a quantification of non-thermal effects is close to impossible. Instead, a standard thermal theory was shown to be capable of explaining the experimental findings quite accurately. Here, we review the central lines of thought that led to these conclusions from a personal point of view. We lay out the key aspects of the theory and point to the specific caveats one must be aware of in performing photo-catalysis experiments. Finally, we provide some future directions of study.
Selective Identification of Phenylalanine Using Cucurbit[7,8]uril-Based Fluorescent Probes
Authors: Li Xiao-Xia , Xu Wei-Tao , Deng Xin-Yu , Tian Li-Fei , Huang Ying , Tao Zhu
Published: September 2020

The interactions of two host–guest inclusion complexes comprised of cucurbit[7]uril (Q[7]) and cucurbit[8]uril (Q[8]) with a derivative of toluidine blue O (TB) have been investigated using 1H NMR and fluorescence spectroscopy. The experimental results revealed that the Q[7] host interacts with a TB molecule to form a 1:1 inclusion complex and the Q[8] host interacts with two TB guest molecules to form a 1:2 inclusion complex. The inclusion of the TB guest molecule within the Q[7] host gave rise to significant fluorescence enhancement, whereas the inclusion of the TB guest molecule within the Q[8] host resulted in significant fluorescence quenching. Further recognition experiments involving a series of l-α-amino acids revealed that the TB@Q[7] inclusion fluorescence probe exhibits high selectivity for the recognition of phenylalanine via significant fluorescence quenching in an aqueous solution, whereas the TB@Q[8] inclusion fluorescence probe also exhibited high selectivity for phenylalanine recognition via fluorescence enhancement in an aqueous solution.
Characterisation of Sardinian germplasm of the perennial pasture grass Phalaris aquatica
Authors: Culvenor Richard A. , Kemp Stuart , Reed Kevin F. M.
Published: September 2020

Germplasm of the perennial pasture grass Phalaris aquatica L., from Sardinia, Italy, is a potentially valuable source for grass breeders owing to climatic similarities to regions where P. aquatica is used, a relatively high incidence of acidic soils, and exposure to prolonged grazing pressure. At field sites in south-eastern Australia, Sardinian accessions were compared as spaced plants and drill-rows with accessions from southern Europe and north-western Africa and with commercial cultivars. They were also evaluated in grazed swards at three sites over 4 years under conditions that challenge persistence, including heavy grazing pressure, acid soils and drought. Morphologically, the accessions were comparatively dense, fine and short, with similarities to southern European accessions and cultivars of the cv. Australian type. However, they were earlier heading and more summer-dormant, particularly those from southern Sardinia. In drill-rows, Sardinian accessions were later heading and less productive in winter than accessions from Morocco. In swards, Sardinian accessions had lower seedling vigour and winter growth potential than modern winter-active cultivars. However, they were dense and persistent under high grazing pressure, and some accessions survived better than all cultivars on an acid, low-fertility soil. Developing cultivars that are superior to the cv. Australian type with acceptable seed production and alkaloid levels presents a challenge to breeders. However Sardinian germplasm offers a range of maturity times combined with higher levels of summer dormancy and a grazing-tolerant morphology, attributes that may expand the area of adaptation of the species into the hotter and more drought-prone margin.
The proline-rich domain promotes Tau liquid–liquid phase separation in cells
Authors: Zhang Xuemei , Vigers Michael , McCarty James , Rauch Jennifer N. , Fredrickson Glenn H. , Wilson Maxwell Z. , Shea Joan-Emma , Han Songi , Kosik Kenneth S.
Published: September 2020

Tau protein in vitro can undergo liquid–liquid phase separation (LLPS); however, observations of this phase transition in living cells are limited. To investigate protein state transitions in living cells, we attached Cry2 to Tau and studied the contribution of each domain that drives the Tau cluster in living cells. Surprisingly, the proline-rich domain (PRD), not the microtubule binding domain (MTBD), drives LLPS and does so under the control of its phosphorylation state. Readily observable, PRD-derived cytoplasmic condensates underwent fusion and fluorescence recovery after photobleaching consistent with the PRD LLPS in vitro. Simulations demonstrated that the charge properties of the PRD predicted phase separation. Tau PRD formed heterotypic condensates with EB1, a regulator of plus-end microtubule dynamic instability. The specific domain properties of the MTBD and PRD serve distinct but mutually complementary roles that use LLPS in a cellular context to implement emergent functionalities that scale their relationship from binding α-beta tubulin heterodimers to the larger proportions of microtubules.
Spatial and temporal control of targeting Polo-like kinase during meiotic prophase
Authors: Brandt James N. , Hussey Katarzyna A. , Kim Yumi
Published: September 2020

Polo-like kinases (PLKs) play widely conserved roles in orchestrating meiotic chromosome dynamics. However, how PLKs are targeted to distinct subcellular localizations during meiotic progression remains poorly understood. Here, we demonstrate that the cyclin-dependent kinase CDK-1 primes the recruitment of PLK-2 to the synaptonemal complex (SC) through phosphorylation of SYP-1 in C. elegans. SYP-1 phosphorylation by CDK-1 occurs just before meiotic onset. However, PLK-2 docking to the SC is prevented by the nucleoplasmic HAL-2/3 complex until crossover designation, which constrains PLK-2 to special chromosomal regions known as pairing centers to ensure proper homologue pairing and synapsis. PLK-2 is targeted to crossover sites primed by CDK-1 and spreads along the SC by reinforcing SYP-1 phosphorylation on one side of each crossover only when threshold levels of crossovers are generated. Thus, the integration of chromosome-autonomous signaling and a nucleus-wide crossover-counting mechanism partitions holocentric chromosomes relative to the crossover site, which ultimately defines the pattern of chromosome segregation during meiosis I.
Improvement of quality and stability of MAPbI3 films grown by post annealing under high pressure argon atmosphere
Authors: Jiang Junjie , Tang Wenchao , Yang Xingming , Sun Xiaofan , Yang Jincheng , Cai H L , Zhang F M , Wu X S
Published: September 2020

Organic-inorganic hybrid perovskite MAPbI3 films with large grain size and excellent photoelectric properties are obtained by annealing the precursors at Ar atmosphere with pressure up to 10 MPa. In comparing to the film annealing at Ar with 0.1 MPa, 4 times lager grains are observed with the film annealing at the Ar atmosphere with the pressure of 6 MPa. The structural stability in respect to temperature is confirmed by the temperature dependence of x-ray diffraction. The band gap of MAPbI3 films may be adjusted by varying the annealing pressure. There is one order of magnitude in intensity of photoluminescence (PL) due to annealing at the Ar atmosphere with high pressure, even the intensity of PL increases with increasing the temperature up to 35 °C. Post annealing with high atmosphere pressure may be a new method in fabricating high performance MAPbI3 films.
Variance reduction for effective energies of random lattices in the Thomas–Fermi–von Weizsäcker model
Authors: Fischer Julian , Kniely Michael
Published: September 2020

In the computation of the material properties of random alloys, the method of ‘special quasirandom structures’ attempts to approximate the properties of the alloy on a finite volume with higher accuracy by replicating certain statistics of the random atomic lattice in the finite volume as accurately as possible. In the present work, we provide a rigorous justification for a variant of this method in the framework of the Thomas–Fermi–von Weizsäcker (TFW) model. Our approach is based on a recent analysis of a related variance reduction method in stochastic homogenization of linear elliptic PDEs and the locality properties of the TFW model. Concerning the latter, we extend an exponential locality result by Nazar and Ortner to include point charges, a result that may be of independent interest.
GEANT4 simulation of a range verification method using delayed γ spectroscopy of a 92Mo marker
Authors: Kasanda E , Burbadge C , Bildstein V , Turko J , Spyrou A , Höhr C , Mücher D
Published: September 2020

In this work, we propose a novel technique for in-vivo proton therapy range verification. This technique makes use of a molybdenum hadron tumour marker, implanted at a short distance from the clinical treatment volume. Signals emitted from the marker during treatment can provide a direct measurement of the proton beam energy at the marker’s position. Fusion-evaporation reactions between the proton beam and marker nucleus result in the emission of delayed characteristic γ rays, which are detected off-beam for an improved signal-to-noise ratio. In order to determine the viability of this technique and to establish an experimental setup for future work, the Monte Carlo package GEANT4 was used in combination with ROOT to simulate a treatment scenario with the new method outlined in this work. These simulations show that the intensity of delayed γ rays produced from competing reactions yields a precise measurement of the range of the proton beam relative to the marker, with sub-millimetre uncertainty.
Scattering proton CT
Authors: Krah N , Quiñones C T , Létang J M , Rit S
Published: September 2020

Proton computed tomography (CT) is an imaging modality investigated mainly in the context of proton therapy as a complement to x-ray CT. It uses protons with high enough energy to fully traverse the imaged object. Common prototype systems measure each proton’s position and direction upstream and downstream of the object as well as the energy loss which can be converted into the water equivalent thickness. A reconstruction algorithm then produces a map of the relative stopping power in the object. As an alternative to energy-loss proton CT, it has been proposed to reconstruct a map of the object’s scattering power based on the protons’ angular dispersion which can be estimated from the measured directions. As in energy-loss proton CT, reconstruction should best be performed considering the non-linear shape of proton trajectories due to multiple Coulomb scattering (MCS), but no algorithm to achieve this is so far available in the literature.

In this work, we propose a filtered backprojection algorithm with distance-driven binning to account for the protons’ most likely path. Furthermore, we present a systematic study of scattering proton CT in terms of inherent noise and spatial resolution and study the artefacts which arise from the physics of MCS. Our analysis is partly based on analytical models and partly on Monte Carlo simulations.

Our results show that the proposed algorithm performs well in reconstructing relative scattering power maps, i.e. scattering power relative to that of water. Spatial resolution is improved by almost a factor of three compared to straight line projection and is comparable to energy-loss proton CT. Image noise, on the other hand, is inherently much higher. For example, in a water cylinder of 20 cm diameter, representative of a human head, noise in the central image pixel is about 40 times higher in scattering proton CT than in energy-loss proton CT. Relative scattering power in dense regions such as bone inserts is systematically underestimated by a few percent, depending on beam energy and phantom geometry.
Interfacial viscoelasticity and jamming of colloidal particles at fluid–fluid interfaces: a review
Authors: Ji Xiaoliang , Wang Xiaolu , Zhang Yongjian , Zang Duyang
Published: September 2020

Colloidal particles can be adsorbed at fluid–fluid interfaces, a phenomenon frequently observed in particle-stabilized foams, Pickering emulsions, and bijels. Particles adsorbed at interfaces exhibit unique physical and chemical behaviors, which affect the mechanical properties of the interface. Therefore, interfacial colloidal particles are of interest in terms of both fundamental and applied research. In this paper, we review studies on the adsorption of colloidal particles at fluid–fluid interfaces, from both thermodynamic and mechanical points of view, and discuss the differences as compared with surfactants and polymers. The unique particle interactions induced by the interfaces as well as the particle dynamics including lateral diffusion and contact line relaxation will be presented. We focus on the rearrangement of the particles and the resultant interfacial viscoelasticity. Particular emphasis will be given to the effects of particle shape, size, and surface hydrophobicity on the interfacial particle assembly and the mechanical properties of the obtained particle layer. We will also summarize recent advances in interfacial jamming behavior caused by adsorption of particles at interfaces. The buckling and cracking behavior of particle layers will be discussed from a mechanical perspective. Finally, we suggest several potential directions for future research in this area.
Resilience to climate shocks in the tropics
Authors: Hirons Mark , Beauchamp Emilie , Whitfield Stephen , Conway Declan , Asare Rebecca , Malhi Yadvinder
Published: September 2020

This focus collection on resilience to climate shocks in the tropics draws together 16 papers that predominantly examine the impacts of, and responses to, the 2015/2016 El Niño-Southern Oscillation event, in a range of contexts. This introductory synthesis contextualises the collection of papers by reviewing important concepts and highlighting some important insights that emerge from the collection. The papers in this collection collectively highlight: the value of longitudinal and interdisciplinary research in understanding both the roots of, and responses to, resilience challenges; the critical interaction between climatic and land-use changes; and the ways in which governance arrangements underpin societal decision-making across a range of scales and contexts to shape resilience.
Machine learning for aquatic plastic litter detection, classification and quantification (APLASTIC-Q)
Authors: Wolf Mattis , van den Berg Katelijn , Garaba Shungudzemwoyo P , Gnann Nina , Sattler Klaus , Stahl Frederic , Zielinski Oliver
Published: September 2020

Large quantities of mismanaged plastic waste are polluting and threatening the health of the blue planet. As such, vast amounts of this plastic waste found in the oceans originates from land. It finds its way to the open ocean through rivers, waterways and estuarine systems. Here we present a novel machine learning algorithm based on convolutional neural networks (CNNs) that is capable of detecting and quantifying floating and washed ashore plastic litter. The aquatic plastic litter detection, classification and quantification system (APLASTIC-Q) was developed and trained using very high geo-spatial resolution imagery (∼5 pixels cm−1 = 0.002 m pixel−1) captured from aerial surveys in Cambodia. APLASTIC-Q was made up of two machine learning components (i) plastic litter detector (PLD-CNN) and (ii) plastic litter quantifier (PLQ-CNN). PLD-CNN managed to categorize targets as water, sand, vegetation and plastic litter with an 83% accuracy. It also provided a qualitative count of litter as low or high based on a thresholding approach. PLQ-CNN further distinguished and enumerated the litter items in each of the classes defined as water bottles, Styrofoam, canisters, cartons, bowls, shoes, polystyrene packaging, cups, textile, carry bags small or large. The types and amounts of plastic litter provide benchmark information that is urgently needed for decision-making by policymakers, citizens and other public and private stakeholders. Quasi-quantification was based on automated counts of items present in the imagery with caveats of underlying object in case of aggregated litter. Our scientific evidence-based machine learning algorithm has the prospects of complementing net trawl surveys, field campaigns and clean-up activities for improved quantification of plastic litter. APLASTIC-Q is a smart algorithm that is easy to adapt for fast and automated detection as well as quantification of floating or washed ashore plastic litter from aerial, high-altitude pseudo satellites and space missions.
Generating directed networks with prescribed Laplacian spectra
Authors: Nicoletti Sara , Carletti Timoteo , Fanelli Duccio , Battistelli Giorgio , Chisci Luigi
Published: September 2020

Complex real-world phenomena are often modeled as dynamical systems on networks. In many cases of interest, the spectrum of the underlying graph Laplacian sets the system stability and ultimately shapes the matter or information flow. This motivates devising suitable strategies, with rigorous mathematical foundation, to generate Laplacians that possess prescribed spectra. In this paper, we show that a weighted Laplacian can be constructed so as to exactly realize a desired complex spectrum. The method configures as a non trivial generalization of existing recipes which assume the spectra to be real. Applications of the proposed technique to (i) a network of Stuart–Landau oscillators and (ii) to the Kuramoto model are discussed. Synchronization can be enforced by assuming a properly engineered, signed and weighted, adjacency matrix to rule the pattern of pairing interactions.
Detecting symmetries with neural networks
Authors: Krippendorf Sven , Syvaeri Marc
Published: September 2020

Identifying symmetries in data sets is generally difficult, but knowledge about them is crucial for efficient data handling. Here we present a method how neural networks can be used to identify symmetries. We make extensive use of the structure in the embedding layer of the neural network which allows us to identify whether a symmetry is present and to identify orbits of the symmetry in the input. To determine which continuous or discrete symmetry group is present we analyse the invariant orbits in the input. We present examples based on rotation groups SO(n) and the unitary group SU(2). Further we find that this method is useful for the classification of complete intersection Calabi-Yau manifolds where it is crucial to identify discrete symmetries on the input space. For this example we present a novel data representation in terms of graphs.
A curvature-free 𝐿𝑜𝑔(2𝑘-1) theorem
Authors: Balacheff Florent , Merlin Louis
Published: September 2020

This paper presents a curvature-free version of the

Log
(
2
k
−
1
)

\text {Log}(2k-1)

Theorem of Anderson, Canary, Culler, and Shalen [J. Differential Geometry 44 (1996), pp. 738–782]. It generalizes a result by Hou [J. Differential Geometry 57 (2001), no. 1, pp. 173–193] and its proof is rather straightforward once we know the work by Lim [Trans. Amer. Math. Soc. 360 (2008), no. 10, pp. 5089–5100] on volume entropy for graphs. As a byproduct we obtain a curvature-free version of the Collar Lemma in all dimensions.
DNA content contributes to nuclear size control inXenopus laevis
Authors: Heijo Hiroko , Shimogama Sora , Nakano Shuichi , Miyata Anna , Iwao Yasuhiro , Hara Yuki
Published: September 2020

Physical properties of DNA, including quantity and chromatin structure within the nucleus, contribute to nuclear expansion dynamics and final nuclear size in Xenopus egg extracts and embryos.
ELSA 2018 Cohort: Protective Behavioral Strategies as Mediators of the Relationship between Risk Factors and Alcohol Outcomes in Argentinean College Freshmen
Authors: Pilatti Angelina , Bravo Adrian J , Michelini Yanina , Pautassi Ricardo Marcos
Published: September 2020

Aims

The present study examined which types of alcohol protective behavioral strategies ([PBSs], Manner of Drinking [MOD] strategies, Serious Harm Reduction [SHR] or Limiting/Stopping Drinking strategies [LSD]) mediate the effects of a comprehensive number of distal antecedents on alcohol drinking quantity and alcohol-related negative consequences.

Methods

A sample of 762 last-month college freshman drinkers from Argentina (Mean age = 19.60 ± 3.80) completed a survey that assessed alcohol outcomes (drinking quantity during a typical week and alcohol-related negative consequences), frequency of use of PBS and a set of distal antecedents (i.e. age at drinking onset, drinking motives, college alcohol beliefs and impulsivity-like traits).

Results

MOD significantly mediated the effects of college alcohol beliefs (higher beliefs were associated with lower MOD use) and coping motives (higher coping motives were associated with lower MOD use) on alcohol outcomes. SHR significantly mediated the effects of sex (women reported more frequent SHR use) and enhancement motives (higher motivation was associated with lower SHR use) on alcohol-related negative consequences.

Conclusion

Our findings partially support a mediational role of PBS in the association between risk factors and alcohol outcomes, and offer valuable information for the design of interventions to reduce alcohol use in South-American college students. More studies examining PBS as mediators of distal antecedents are needed to fully understand the peculiarities of these associations in different cultures.
PhyloWGA: chromosome-aware phylogenetic interrogation of whole genome alignments
Authors: Adams Richard H , Castoe Todd A , DeGiorgio Michael
Published: September 2020

Here, we present PhyloWGA, an open source R package for conducting phylogenetic analysis and investigation of whole genome data.

Availabilityand implementation

Available at Github (https://github.com/radamsRHA/PhyloWGA).

Supplementary information

Supplementary data are available at Bioinformatics online.
Genetic source completeness of HIV-1 circulating recombinant forms (CRFs) predicted by multi-label learning
Authors: Tang Runbin , Yu Zuguo , Ma Yuanlin , Wu Yaoqun , Phoebe Chen Yi-Ping , Wong Limsoon , Li Jinyan
Published: September 2020

Motivation

Infection with strains of different subtypes and the subsequent crossover reading between the two strands of genomic RNAs by host cells’ reverse transcriptase are the main causes of the vast HIV-1 sequence diversity. Such inter-subtype genomic recombinants can become circulating recombinant forms (CRFs) after widespread transmissions in a population. Complete prediction of all the subtype sources of a CRF strain is a complicated machine learning problem. It is also difficult to understand whether a strain is an emerging new subtype and if so, how to accurately identify the new components of the genetic source.

Results

We introduce a multi-label learning algorithm for the complete prediction of multiple sources of a CRF sequence as well as the prediction of its chronological number. The prediction is strengthened by a voting of various multi-label learning methods to avoid biased decisions. In our steps, frequency and position features of the sequences are both extracted to capture signature patterns of pure subtypes and CRFs. The method was applied to 7185 HIV-1 sequences, comprising 5530 pure subtype sequences and 1655 CRF sequences. Results have demonstrated that the method can achieve very high accuracy (reaching 99%) in the prediction of the complete set of labels of HIV-1 recombinant forms. A few wrong predictions are actually incomplete predictions, very close to the complete set of genuine labels.

Availability and implementation

https://github.com/Runbin-tang/The-source-of-HIV-CRFs-prediction.

Supplementary information

Supplementary data are available at Bioinformatics online.
Hippocampal and Parahippocampal Gray Matter Structural Integrity Assessed by Multimodal Imaging Is Associated with Episodic Memory in Old Age
Authors: Köhncke Ylva , Düzel Sandra , Sander Myriam C , Lindenberger Ulman , Kühn Simone , Brandmaier Andreas M
Published: September 2020

Maintained structural integrity of hippocampal and cortical gray matter may explain why some older adults show rather preserved episodic memory. However, viable measurement models for estimating individual differences in gray matter structural integrity are lacking; instead, findings rely on fallible single indicators of integrity. Here, we introduce multitrait–multimethod methodology to capture individual differences in gray matter integrity, based on multimodal structural imaging in a large sample of 1522 healthy adults aged 60–88 years from the Berlin Aging Study II, including 333 participants who underwent magnetic resonance imaging. Structural integrity factors expressed the common variance of voxel-based morphometry, mean diffusivity, and magnetization transfer ratio for each of four regions of interest: hippocampus, parahippocampal gyrus, prefrontal cortex, and precuneus. Except for precuneus, the integrity factors correlated with episodic memory. Associations with hippocampal and parahippocampal integrity persisted after controlling for age, sex, and education. Our results support the proposition that episodic memory ability in old age benefits from maintained structural integrity of hippocampus and parahippocampal gyrus. Exploratory follow-up analyses on sex differences showed that this effect is restricted to men. Multimodal factors of structural brain integrity might help to improve our biological understanding of human memory aging.
Genotypic Resistance of Pyrazinamide but Not Minimum Inhibitory Concentration Is Associated With Longer Time to Sputum Culture Conversion in Patients With Multidrug-resistant Tuberculosis
Authors: Kuhlin Johanna , Davies Forsman Lina , Mansjö Mikael , Jonsson Nordvall Michaela , Wijkander Maria , Wagrell Charlotta , Jonsson Jerker , Groenheit Ramona , Werngren Jim , Schön Thomas , Bruchfeld Judith
Published: September 2020

Background

Pyrazinamide (PZA) resistance in multidrug-resistant tuberculosis (MDR-TB) is common; yet, it is not clear how it affects interim and treatment outcomes. Although rarely performed, phenotypic drug susceptibility testing (pDST) is used to define PZA resistance, but genotypic DST (gDST) and minimum inhibitory concentration (MIC) could be beneficial. We aimed to assess the impact of PZA gDST and MIC on time to sputum culture conversion (SCC) and treatment outcome in patients with MDR-TB.

Methods

Clinical, microbiological, and treatment data were collected in this cohort study for all patients diagnosed with MDR-TB in Sweden from 1992–2014. MIC, pDST, and whole-genome sequencing of the pncA, rpsA, and panD genes were used to define PZA resistance. A Cox regression model was used for statistical analyses.

Results

Of 157 patients with MDR-TB, 56.1% (n = 88) had PZA-resistant strains and 49.7% (n = 78) were treated with PZA. In crude and adjusted analysis (hazard ratio [HR], 0.49; 95% conficence interval [CI], .29-.82; P = .007), PZA gDST resistance was associated with a 29-day longer time to SCC. A 2-fold decrease in dilutions of PZA MIC for PZA-susceptible strains showed no association with SCC in crude or adjusted analyses (HR, 0.98; 95% CI, .73–1.31; P = .89). MIC and gDST for PZA were not associated with treatment outcome.

Conclusions

In patients with MDR-TB, gDST PZA resistance was associated with a longer time to SCC. Rapid PZA gDST is important to identify patients who may benefit from PZA treatment.
#Crohn’s: Historical Cohort of Twitter Activity
Authors: Facanali Marcio Roberto , Bortolozzo Graciolli Facanali Carolina , Queiroz Natália Sousa Freitas , Sobrado Carlos Walter , Nahas Sérgio Carlos , Safatle-Ribeiro Adriana Vaz
Published: September 2020

Background

Analysis of the Twitter activity on #Crohn’s, identifying individuals with interest in Crohn’s disease on Twitter.

Methods

A historic cohort study was conducted about Twitter activity evaluation of #Crohn’s analyzed over a period of 9 years. For the Twitter analysis, a health-care social media analytics tool, Symplur Signals, was adopted.

Results

From 2011 until 2019, 627,000 tweets of #Crohn’s were detected, with 276,380 retweets by 109,937 users; of these users, 32.4% were patient advocates and 12.6% were doctors. There was a pattern of annual peak activity of the #Crohn’s, mainly in May and December, and less activity, usually in July. Of all tweets, 52.5% were categorized as positive and 47.5% as negative.

Conclusions

Social media, especially Twitter, represents an important information tool, but it is still underutilized by gastroenterologists. This study suggests a significant interference of international awareness campaigns about inflammatory bowel disease in the activity of #Crohn’s on Twitter, denoting an increase in debating this topic on the platform. Discussions on the subject by health professionals are still below expectations regarding the importance of the theme.