bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of protein–protein complexes using replica exchange with repulsive scaling
Authors: Siebenmorgen Till , Engelhard Michael , Zacharias Martin 
Published: March 2020

AbstractThe realistic prediction of protein–protein complex structures is import to ultimately model the interaction of all proteins in a cell and for the design of new protein–protein interactions. In principle, molecular dynamics (MD) simulations allow one to follow the association process under realistic conditions including full partner flexibility and surrounding solvent. However, due to the many local binding energy minima at the surface of protein partners, MD simulations are frequently trapped for long times in transient association states. We have designed a replica‐exchange based scheme employing different levels of a repulsive biasing between partners in each replica simulation. The bias acts only on intermolecular interactions based on an increase in effective pairwise van der Waals radii (repulsive scaling (RS)‐REMD) without affecting interactions within each protein or with the solvent. For a set of five protein test cases (out of six) the RS‐REMD technique allowed the sampling of near‐native complex structures even when starting from the opposide site with respect to the native binding site for one partner. Using the same start structures and same computational demand regular MD simulations sampled near native complex structures only for one case. The method showed also improved results for the refinement of docked structures in the vicinity of the native binding geometry compared to regular MD refinement.
Double Diffusion Encoding for Probing Radiation‐Induced Microstructural Changes in a Tumor Model: A Proof‐of‐Concept Study With Comparison to the Apparent Diffusion Coefficient and Histology
Authors: Duchêne Gaëtan , Abarca‐Quinones Jorge , Feza‐Bingi Natacha , Leclercq Isabelle , Duprez Thierry , Peeters Frank 
Published: March 2020

BackgroundMicrostructure analyses are gaining interest in cancer MRI as an alternative to the conventional apparent diffusion coefficient (ADC), of which the determinants remain unclear.PurposeTo assess the sensitivity of parameters calculated from a double diffusion encoding (DDE) sequence to changes in a tumor's microstructure early after radiotherapy and to compare them with ADC and histology.Study TypeCohort study on experimental tumors.Animal ModelSixteen WAG/Rij rats grafted with one rhabdomyosarcoma fragment in each thigh. Thirty‐one were imaged at days 1 and 4, of which 17 tumors received a 20 Gy radiation dose after the first imagery.Field Strength/Sequence3T. Diffusion‐weighted imaging, DDE with flow compensated, and noncompensated measurements.Assessments1) To compare, after irradiation, DDE‐derived parameters (intracellular fraction, cell size, and cell density) to their histological counterparts (fraction of stained area, minimal Feret diameter, and nuclei count, respectively). 2) To compare percentage changes in DDE‐derived parameters and ADC. 3) To evaluate the evolution of DDE‐derived parameters describing perfusion.Statistical TestsWilcoxon rank sum test.Results1) Intracellular fraction, cell size, and cell density were respectively lower (−24%, P < 0.001), higher (+7.5%, P < 0.001) and lower (−38%, P < 0.001) in treated tumors as compared to controls. Fraction of stained area, minimal Feret diameter, and nuclei count were respectively lower (−20%, P < 0.001), higher (+28%, P < 0.001), and lower (−34%, P < 0.001) in treated tumors. 2) The magnitude of ADC's percentage change due to irradiation (16.4%) was superior to the one of cell size (8.4%, P < 0.01) but inferior to those of intracellular fraction (35.5%, P < 0.001) and cell density (42%, P < 0.001). 3) After treatment, the magnitude of the vascular fraction's decrease was higher than the increase of flow velocity (33.3%, vs. 13.3%, P < 0.001).Data ConclusionThe DDE sequence allows quantitatively monitoring the effects of radiotherapy on a tumor's microstructure, whereas ADC only reveals global changes.Evidence Level2.Technical EfficacyStage 4. J. Magn. Reson. Imaging 2020;52:941–951.
Pressure measurement and detection of small H2O amounts in high‐pressure H2O–CO2 fluid up to 141 MPa using Fermi diad splits and bandwidths of CO2
Authors: Hagiwara Yuuki , Torimoto Junji , Yamamoto Junji 
Published: March 2020

AbstractDependence of residual pressures of fluid inclusions on their size and host mineral species provides valuable information related to the depth provenance and P–T–t path of the rocks. Although Raman‐based barometry is an effective method for ascertaining the internal pressure of H2O–CO2 fluid inclusions, few studies have elucidated Raman spectral features of CO2 in a system of high‐pressure H2O–CO2. New experiments using a high‐pressure optical cell in this binary system with compositions of 100, 75 ± 2, and 60 ± 2 mol% CO2 were conducted for this study to verify the availability of Raman CO2 barometers for use in assessing the temperature and pressure conditions of approximately 22°C and 17.3–141.4 MPa. Our results demonstrate that the existence of H2O does not affect the relation between Fermi diad splits (Δ, cm−1) and total pressure of pure CO2. These results suggest that the Δ–total pressure relation obtained from pure CO2 is also applicable to H2O–CO2 systems, even at high pressure. However, unlike Δ, because the peak positions of the Fermi diad in the system of H2O–CO2 shift to a higher wavenumber than those of pure CO2 at given pressure higher than 30 MPa, the peak positions are not very suitable for the pressure scale in an H2O–CO2 system. Additionally, we confirmed the availability of bandwidths of CO2 as an indicator of compositions that can identify the presence of very small amounts of H2O (at least 0.3 mol% H2O), even at room temperature.
Method for extracting Raman spectra characteristic variables of biological sample based on Hilbert–Huang transform
Authors: Zhao Xiaoyu , He Yan , Liu Zihao , Zhang Wei , Tong Liang 
Published: March 2020

AbstractBecause Raman peaks of the biological sample are superimposed on each other, the use of characteristic peak attribution is limited to some extent. In this study, we show that Hilbert–Huang transform (HHT) provides a Raman spectral feature extracting method, especially for biological samples. First, the empirical mode decomposition algorithm was used to decompose Raman spectra into intrinsic mode functions (IMFs). It is worth noticing that the IMF frequency is single or nearly single, so its further transformation (instantaneous amplitude, instantaneous angle, instantaneous angular frequency, Hilbert spectrum, and Hilbert marginal spectrum) from Hilbert processing is monotonous instead of the raw overlapping. Then, the Hilbert marginal spectrum was selected by one‐way analysis of variance and related with the rice type to establish a partial least squares regression (PLS) model with a 95.00% accuracy. This result is better than those based on characteristic variables screened by PLS, interval PLS, principal component analysis, independent component analysis, successive projections algorithm, haar, db, and coif (85.00%, 90.00%, 82.50%, 77.50%, 90.00%, 92.50%, 80.00%, and 85.00%). These results illustrate that HHT can accurately extract the characteristic variables from biological Raman spectra. The classification accuracy based on HHT is slightly lower than those based on bior 2.4, three‐layer decomposition (97.50%) and sym 5, five‐layer decomposition (97.50%). Significantly, no parameters need to be set such as the wavelet mother function and the decomposition layer in the HHT feature extraction process. This paper provides a HHT method for Raman spectral feature extraction, which is simple and effective.
Special dietary requirements: Restaurant sector responses across six tourist cities
Authors: Oktadiana Hera , Pearce Philip L. , Mohammadi Zohre 
Published: March 2020

AbstractThe key aims of the study were to document and analyze contemporary restaurant practices germane to meeting dietary requirements in significant tourist cities. Social practice theory informed the study. Detailed coding of menu information and TripAdvisor sources for 60 restaurants in six strategically selected tourist cities provided the bases for the work. The results identified locational differences; that overall religious and lifestyle requirements are moderately well presented, while health needs addressed less adequately. Social practice theory insights helped interpret the findings through issues of managerial caution, perceived competence, and image and identity management for both restaurants and customers.
High Interobserver Agreement in the Subjective Classification of 5‐Aminolevulinic Acid Fluorescence Levels in Newly Diagnosed Glioblastomas
Authors: Mischkulnig Mario , Kiesel Barbara , Borkovec Martin , Wadiura Lisa I. , Benner Dimitri , Hosmann Arthur , Hervey‐Jumper Shawn , Knosp Engelbert , Roessler Karl , Berger Mitchel S. , Widhalm Georg 
Published: March 2020

Background and ObjectivesFluorescence‐guided resection of glioblastomas (GBM) using 5‐aminolevulinic acid (5‐ALA) improves intraoperative tumor visualization and is thus widely used nowadays. During resection, different fluorescence levels can usually be distinguished within the same tumor. Recently, we demonstrated that strong, vague, and no fluorescence correspond to distinct histopathological characteristics in newly diagnosed GBM. However, the qualitative fluorescence classification by the neurosurgeon is subjective and currently no comprehensive data on interobserver variability is available. The aim of this study was thus to investigate the interobserver variability in the classification of 5‐ALA fluorescence levels in newly diagnosed GBM.Study Design/Materials and MethodsA questionnaire investigating the interobserver variability in 5‐ALA fluorescence quantification was performed at a nation‐wide neurosurgical oncology meeting. The participants involved in the neurosurgical/neurooncological field were asked to categorize 30 cases of 5‐ALA fluorescence images derived from GBM resection on a lecture hall screen according to the widely used three‐tier fluorescence classification scheme (negative, vague, or strong fluorescence). Additionally, participants were asked for information on their medical background such as specialty, level of training, and experience with 5‐ALA fluorescence‐guided procedures. Interobserver agreement was defined as the calculated mean κ values for each observer.ResultsA total of 36 questionnaires were included in the final analysis. The mean average κ value in fluorescence classification within the entire cohort was 0.71 ± 0.12 and 29 (81%) participants had a substantial or almost perfect interobserver agreement (κ values 0.6–1.0). Interobserver agreement was significantly higher in neurosurgeons (mean κ: 0.83) as compared with non‐neurosurgeons involved in the neurooncological field (mean κ: 0.52; P < 0.001). Furthermore, interobserver agreement was significantly higher in participants who had experience with at least 25 5‐ALA fluorescence‐guided surgeries (mean κ: 0.87) compared with less experienced colleagues (mean κ: 0.82; P = 0.039).ConclusionOur study found a high interobserver agreement in the qualitative classification of different 5‐ALA fluorescence levels in newly diagnosed GBM. Interobserver agreement increases significantly in more experienced participants and therefore a high level of experience is crucial for reliable intraoperative fluorescence classification. Lasers Surg. Med. © 2020 The Authors. Lasers in Surgery and Medicine published by Wiley Periodicals, Inc.
Oscillatory solutions of fourth order advanced trinomial differential equations
Authors: Dzurina Jozef , Baculikova Blanka , Jadlovska Irena 
Published: March 2020

AbstractThe paper deals with the oscillatory behavior of the fourth‐order linear three‐terms advanced differential equation of the form
Assuming that all solutions of the auxiliary third‐order differential equation
are nonoscillatory, two types of easily verifiable oscillation criteria for the studied equation are established. The obtained results are illustrated by two examples.
Avian uterine fluid proteome: Exosomes and biological processes potentially involved in sperm survival
Authors: Riou Cindy , Brionne Aurélien , Cordeiro Luiz , Harichaux Grégoire , Gargaros Audrey , Labas Valérie , Gautron Joël , Gérard Nadine 
Published: March 2020

AbstractUterine fluid is an aqueous milieu to which sperm are exposed during their storage and ascent. In this study, a bottom‐up proteomic strategy and bioinformatic analysis of hen uterine fluid was performed to improve the understanding of this fluid and its potential role in sperm survival mechanisms. The proteomic data were submitted to ProteomeXchange. Among the 913 proteins identified, 160 are known to be secreted and 640 are referenced in exosomes databases. We isolated exosomes from the avian uterine fluid, analyzed them using electron microscopy, and targeted several exosomes markers (ANXA1/2/4/5, VCP, HSP90A, HSPA8, PARK7, and MDH1) using immunoblotting. Electron microscopy and immunohistochemistry were also used to analyze uterovaginal junctions for the exosomal proteins ANXA4, VCP, and PARK7. Exosomes were observed both at the surface epithelium and inside sperm storage tubules. Our data were compared with two previously published studies on proteomic of hen uterine fluid, and with one study describing the proteomic content of rooster seminal plasma and sperm. In conclusion, we demonstrated for the first time that avian uterine fluid contains exosomes. These may play a key role in preserving sperm functions within the female genital tract. Their presence in the sperm storage tubules may represent an important mechanism regarding interaction between the female genital tract and sperm.
Effect of Dietary Inorganic Copper on Growth Performance and Some Hematological Indices of Siberian Sturgeon Acipenser baerii Juveniles
Authors: Moazenzadeh Kadusa , Rajabi Islami Houman , Zamini Abasali , Soltani Mehdi 
Published: March 2020

Abstract
This research work was conducted to evaluate the effect of dietary copper (Cu) levels on growth performance, feed utilization, and some hematological parameters of juvenile Siberian Sturgeon Acipenser baerii. Five semipurified diets containing 0, 3, 6, 12, and 24 mg Cu/kg in the form of copper sulfate pentahydrate (CuSO4·5H2O) were formulated to provide the actual dietary copper values of 1.8, 5.7, 10.1, 15.9, and 28.3 mg Cu/kg diet, respectively. The obtained results exhibited a significant improvement in the final weight, protein efficiency ratio, daily growth coefficient, and hepatosomatic index with increasing dietary copper levels up to 10.1 mg/kg diet, while the feed conversion ratio significantly decreased. Also, erythrocyte count, hemoglobin, and hematocrit values increased with increasing levels of dietary copper, but no steady trend was observed in mean corpuscular hemoglobin changes. Furthermore, the neutrophils were significantly increased with enhancing the copper level in the fish diet, while the lymphocytes declined. Findings of the current research illustrate that an appropriate dietary copper level is required for improvement of growth performance, oxygen transfer capability, and white blood cell proliferation. Based on the broken-line regression analysis of leukocyte count and monocyte percentage, the optimum dietary copper supplementation was estimated to be 10.63 and 10.36 mg Cu/kg diet, respectively.
Action needed for the EU Common Agricultural Policy to address sustainability challenges
Authors: Pe'er Guy , Bonn Aletta , Bruelheide Helge , Dieker Petra , Eisenhauer Nico , Feindt Peter H. , Hagedorn Gregor , Hansjürgens Bernd , Herzon Irina , Lomba Ângela , Marquard Elisabeth , Moreira Francisco , Nitsch Heike , Oppermann Rainer , Perino Andrea , Röder Norbert , Schleyer Christian , Schindler Stefan , Wolf Christine , Zinngrebe Yves , Lakner Sebastian 
Published: March 2020

Abstract

Making agriculture sustainable is a global challenge. In the European Union (EU), the Common Agricultural Policy (CAP) is failing with respect to biodiversity, climate, soil, land degradation as well as socio‐economic challenges.

The European Commission's proposal for a CAP post‐2020 provides a scope for enhanced sustainability. However, it also allows Member States to choose low‐ambition implementation pathways. It therefore remains essential to address citizens' demands for sustainable agriculture and rectify systemic weaknesses in the CAP, using the full breadth of available scientific evidence and knowledge.

Concerned about current attempts to dilute the environmental ambition of the future CAP, and the lack of concrete proposals for improving the CAP in the draft of the European Green Deal, we call on the European Parliament, Council and Commission to adopt 10 urgent action points for delivering sustainable food production, biodiversity conservation and climate mitigation.

Knowledge is available to help moving towards evidence‐based, sustainable European agriculture that can benefit people, nature and their joint futures.

The statements made in this article have the broad support of the scientific community, as expressed by above 3,600 signatories to the preprint version of this manuscript. The list can be found here (https://doi.org/10.5281/zenodo.3685632).

A free Plain Language Summary can be found within the Supporting Information of this article.
Pediatric hematology and oncology fellow education in sexual and reproductive health: A survey of fellowship program directors in the United States
Authors: Frederick Natasha N. , Fine Elizabeth , Michaud Alexis , Recklitis Christopher J. , Bober Sharon L. 
Published: March 2020

AbstractPurposePediatric oncology clinicians identify a need for increased sexual and reproductive health (SRH) education with adolescent and young adult (AYA) cancer patients. By surveying pediatric oncology fellowship directors, this study clarifies the state of current fellowship education about SRH for the AYA patient.MethodsA survey was sent to all pediatric oncology fellowship program directors (PDs) in the United States consisting of 13 questions pertaining to three primary SRH domains: sexual health, fertility, and safe sex practices. Descriptive statistics and χ2 were used in data analyses.ResultsSixty‐three PDs responded to the survey (91% response rate). Of these, 88% reported having formal instruction regarding fertility, 41% reported curriculum regarding contraception and 30% reported some education regarding sexual health. The curriculum “being too full” was identified as a barrier to education on fertility (29%), sexual health (40%), and safe sex practices (38%). Not being a required or expected part of the program was more likely to be endorsed as a barrier for sexual health (26%) and safe sex practices (30%) compared with fertility (8%) (P < 0.005). Lack of experts to teach was a more frequently endorsed barrier to education on sexual health (47%) compared with either fertility (23%) or safe sex practices (25%) (P < 0.005).ConclusionsThis study identifies important gaps in oncology fellow education about SRH. Future research must explore optimal education strategies that are feasible and acceptable by PDs and fellow learners, and effective in optimizing AYA SRH care.
Plot extraction from aerial imagery: A precision agriculture approach
Authors: Bruce Robert W. , Rajcan Istvan , Sulik John 
Published: March 2020

AbstractThe plant phenotyping community is adopting technological innovations in order to record phenotypic attributes more quickly and objectively. Low altitude aerial imaging is an appealing option for increasing throughput but there are still challenges in the image processing pipeline. One such challenge involves the assignment of a spatial reference to each plot entry in an experimental layout. Image‐based approaches are increasingly popular since plot boundaries are often, but not always, clearly visible in low altitude imagery. In addition, workflows that make geometric assumptions about plot layout also show promise. We outline an alternative approach to generate plot boundaries to overlay with aerial imagery. The proposed method involves high‐accuracy georeferencing (i.e., within a few cm) of imagery and planter activity, after which georeferencing of all plot entries is complete and only requires a few simple steps to convert logged spatial positions to polygons using open source geographic information systems (GIS) software. Compared with other approaches, the proposed method provides imagery that is precisely aligned over time and always aligns with plot boundaries, which are fixed and do not vary from image to image.
Implantable LENUS pro pump for treprostinil infusion in three pediatric patients
Authors: Álvarez‐Fuente Maria , Garrido‐Lestache Elvira , Rivero Natalia , Centella Tomasa , Lamas Maria J. , Pérez‐Caballero Cesar , Vázquez Jose L. , Del Cerro Maria J. 
Published: March 2020

AbstractBackgroundProstanoid treatment in patients with severe pulmonary arterial hypertension (PAH) has been proven safe and effective. Subcutaneous administration of treprostinil has side effects, which limits their use and acceptance. An implantable pump for continuous intravenous treprostinil infusion has been recently approved. We describe our experience with the implantable pump in three pediatric patients.Description of CasesThe LENUS pro pump was implanted in three adolescents with severe PAH, who were treated with tadalafil, ambrisentan, and subcutaneous treprostinil. The indication of the Lenus pro pump implantation was the local side effects of subcutaneous treprostinil (pain, inflammation, and local infection) that were not well tolerated and that severely decreased their quality of life. The pump was surgically implanted under general anesthesia.One patient, in functional class IV, suffered postoperative hemodynamic instability and small pneumothorax,  requiring an increase in treprostinil dose up to 85 ng/kg/min and a decrease 9 days after the pump implantation. The second patient who was discharged 4 days after surgery with treprostinil at 60 ng/kg/min reported improvement in his quality of life, but the dose requirement increased up to 92 ng/kg/min. After a 21‐month follow‐up, this patient received a lung transplant. The third patient presented a hematoma at the pump site with no other complications and had a follow‐up of 9 months with an improvement in her quality of life.CommentsImplantable pumps for continuous parenteral prostanoid infusion in pediatric patients are an alternative to external pumps, especially when familiar psychological or psychomotor issues hinder the use of external pumps.
Study of Initial Pressure Rise in Multi Grain Solid Propellant Rocket Motor
Authors: Ropia Balesh , Shekhar Himanshu K. , Thakur Dinesh G. 
Published: March 2020

AbstractIn the present research, an experimental and numerical investigation has been performed to study initial pressure rise in multi grain solid rocket motor. A cluster of seven uninhibited tubular grains of double base propellant is analysed to get near neutral pressure in rocket motor. It is experimentally observed that in some static firings initial pressure rise in first 100 ms is higher than the predicted value of ∼7.5 MPa. The average pressure in the rocket motor is ∼7 MPa and total burning time of these grains is ∼2 s. ANSYS software is used for numerical analysis to investigate the effects of various % openings of nozzle end (NE) metal grid on pressure rise in the rocket motor with and without peripheral opening. The analysed results are compared with experiments. It is found that, as the %opening of NE metal grid increases, the initial pressure in the rocket motor decreases. The peripheral opening is also important to reduce pressure rise in rocket motor. This study helps in reducing the initial pressure rise in the combustion chamber which is essential for safe working of the rocket motor.