bluuebunny/crossref_metadata_2025_split huggingface dataset:
Baltic Sea Hypoxia Takes Many Shapes and Sizes
Authors: Carstensen Jacob , Conley Daniel J. 
Published: November 2019

AbstractThe Baltic Sea is naturally prone to hypoxia, but the frequency and extent have increased multifold over the last century. Hypoxia manifests itself as perennial in the open central part, seasonal at the entrance area, and episodic at many coastal sites, and the expression of hypoxia is largely driven by differences in bottom water residence times and stratification patterns. Enhanced nutrient inputs from land and atmosphere are the main drivers of expanding hypoxia in the Baltic Sea although deoxygenation has also been exacerbated by increasing temperature over the past 3–4 decades. Hypoxia severely influences ecosystem functions such as fish production through reduced trophic efficiency and harmful cyanobacteria blooms sustained by phosphorus release from sediments. Nutrient inputs from land have created the largest man‐made hypoxic area in the world and the only viable long‐term solution to mitigation is to continue efforts to reduce nutrient loading.
Acetylome analysis of lysine acetylation in the plant pathogenic bacterium Brenneria nigrifluens
Authors: Li Yong , Xue Han , Bian Dan‐ran , Xu Guantang , Piao Chungen 
Published: November 2019

AbstractProtein lysine acetylation, a dynamic and reversible posttranslational modification, plays a crucial role in several cellular processes, including cell cycle regulation, metabolism, enzymatic activities, and protein interactions. Brenneria nigrifluens is a pathogen of walnut trees with shallow bark canker and can cause serious disease in walnut trees. Until now, a little has been known about the roles of lysine acetylation in plant pathogenic bacteria. In the present study, the lysine acetylome of B. nigrifluens was determined by high‐resolution LC‐MS/MS analysis. In total, we identified 1,866 lysine acetylation sites distributed in 737 acetylated proteins. Bioinformatics results indicated that acetylated proteins participate in many different biological functions in B. nigrifluens. Four conserved motifs, namely, LKac, Kac*F, I*Kac, and L*Kac, were identified in this bacterium. Protein interaction network analysis indicated that all kinds of interactions are modulated by protein lysine acetylation. Overall, 12 acetylated proteins were related to the virulence of B. nigrifluens.
Isolation of time‐dependent DNA damage induced by energetic carbon ions and their fragments using fluorescent nuclear track detectors
Authors: McFadden Conor H. , Rahmanian Shirin , Flint David B. , Bright Scott J. , Yoon David S. , O’Brien Daniel J. , Asaithamby Aroumougame , Abdollahi Amir , Greilich Steffen , Sawakuchi Gabriel O. 
Published: November 2019

PurposeHigh energetic carbon (C‐) ion beams undergo nuclear interactions with tissue, producing secondary nuclear fragments. Thus, at depth, C‐ion beams are composed of a mixture of different particles with different linear energy transfer (LET) values. We developed a technique to enable isolation of DNA damage response (DDR) in mixed radiation fields using beam line microscopy coupled with fluorescence nuclear track detectors (FNTDs).MethodsWe imaged live cells on a coverslip made of FNTDs right after C‐ion, proton or photon irradiation using an in‐house built confocal microscope placed in the beam path. We used the FNTD to link track traversals with DNA damage and separated DNA damage induced by primary particles from fragments.ResultsWe were able to spatially link physical parameters of radiation tracks to DDR in live cells to investigate spatiotemporal DDR in multi‐ion radiation fields in real time, which was previously not possible. We demonstrated that the response of lesions produced by the high‐LET primary particles associates most strongly with cell death in a multi‐LET radiation field, and that this association is not seen when analyzing radiation induced foci in aggregate without primary/fragment classification.ConclusionsWe report a new method that uses confocal microscopy in combination with FNTDs to provide submicrometer spatial‐resolution measurements of radiation tracks in live cells. Our method facilitates expansion of the radiation‐induced DDR research because it can be used in any particle beam line including particle therapy beam lines.CategoryBiological Physics and Response Prediction.
A novel segmentation framework dedicated to the follow‐up of fat infiltration in individual muscles of patients with neuromuscular disorders
Authors: Ogier Augustin C. , Heskamp Linda , Michel Constance P. , Fouré Alexandre , Bellemare Marc‐Emmanuel , Le Troter Arnaud , Heerschap Arend , Bendahan David 
Published: November 2019

PurposeTo propose a novel segmentation framework that is dedicated to the follow‐up of fat infiltration in individual muscles of patients with neuromuscular disorders.MethodsWe designed a semi‐automatic segmentation pipeline of individual leg muscles in MR images based on automatic propagation through nonlinear registrations of initial delineation in a minimal number of MR slices. This approach has been validated for the segmentation of individual muscles from MRI data sets, acquired over a 10‐month period, from thighs and legs in 10 patients with muscular dystrophy. The robustness of the framework was evaluated using conventional metrics related to muscle volume and clinical metrics related to fat infiltration.ResultsHigh accuracy of the semi‐automatic segmentation (mean Dice similarity coefficient higher than 0.89) was reported. The provided method has excellent reliability regarding the reproducibility of the fat fraction estimation, with an average intraclass correlation coefficient score of 0.99. Furthermore, the present segmentation framework was determined to be more reliable than the intra‐expert performance, which had an average intraclass correlation coefficient of 0.93.ConclusionThe proposed framework of segmentation can successfully provide an effective and reliable tool for accurate follow‐up of any MRI biomarkers in neuromuscular disorders. This method could assist the quantitative assessment of muscular changes occurring in such diseases.
Functional outcomes and safety of GreenLight photovaporization of the prostate in the high‐risk patient with lower urinary tract symptoms due to benign prostatic enlargement
Authors: Barco‐Castillo Catalina , Plata Mauricio , Zuluaga Laura , Santander Jessica , Trujillo Carlos Gustavo , Caicedo Juan Ignacio , Serrano Adolfo , Fernández Nicolás , Azuero Julián 
Published: November 2019

AbstractAimsPhotovaporization of the prostate (PVP) with GreenLight Laser is a surgical treatment for lower urinary tract symptoms. It is considered safe in elderly patients with comorbidities, however, the evidence is inconclusive. The objective of this study is to evaluate the efficacy and safety outcomes of PVP according to the American Society of Anesthesiologists Physical Status (ASAPS).MethodsA cohort of 675 patients who underwent PVP between 2012 and 2018 was evaluated. Patients were classified according to their ASAPS as low (I and II) and high risk (III and IV). Surgical characteristics and improvement of symptoms and Quality of Life (QoL) were evaluated.ResultsThe median age of high‐risk group was higher than low‐risk group. The high‐risk group had more history of anticoagulation, antiaggregation, urinary catheterization, urinary retention and urethral stricture. Longer times of hospitalization (23.7 [interquartile range {IQR} = 18.9‐41.35] vs 21.8 hours [IQR = 18.7‐26.6], P = .008) and catheterization (19.55 [IQR = 15.6‐35.57] vs 17.67 hours [IQR = 14.76‐22.5], P = .004) were found in the high‐risk group. Conversion and bleeding control were not different between groups. In the follow‐up, improvement of International Prostate Symptoms Score (IPSS) and QoL was significant in all patients when compared before and after surgery scores (P < .001). There were no difference between groups for QoL, however, IPSS was lower for the low‐risk group (8 [IQR = 4‐14.5] vs 5 [2‐12], P = .001).ConclusionPVP with GreenLight Laser is a safe and efficient procedure for all patients despite their comorbidities, with comparable middle‐term outcomes which makes it a standard treatment for the entire aging population, improving their QoL.
The association of patients' daily summarized self‐rated “real‐time” pain scores with physical recovery after major surgery – A repeated measurement design
Authors: Wikström Lotta , Nilsson Mats , Eriksson Kerstin 
Published: November 2019

AbstractAimTo determine the associations of patients' documented self‐rated pain with self‐rated early postoperative physical recovery.DesignObservational with repeated measures.MethodsGeneral and orthopaedic inpatients (N = 479) were during the period 2012–2015 screened for pain. Individual daily median pain scores at rest and during activity were based on 4–9 self‐ratings on postoperative days 1 and 2, using the Numeric Rating Scale. Nine items reflecting physical recovery from the “Postoperative Recovery Profile” were used in a questionnaire.ResultsAssociations between median pain scores on postoperative day 1 and physical recovery (fatigue, sleeping difficulties, bladder function, mobilization, muscle weakness and personal hygiene) the same day were found. Additionally, associations were found between median pain scores on day 1 and physical recovery (fatigue, sleeping difficulties, mobilization and muscle weakness) on day 2.
A homoisoflavonoid and a fatty acid in common purslane (Portulaca oleracea L.) synergistically inhibit growth of Spodoptera litura larvae
Authors: Wang Zhenzhen , Yang Renyue , Li Ping , Yang Zhongyan , Ling Ruimei , Shen Tunkai , Peng Weiyao , Yang Quan , Yan Jian 
Published: November 2019

AbstractBACKGROUNDPortulaca oleracea L., common purslane, is an insecticidal plant that has been documented as a ‘Chinese indigenous pesticide’, and it is seldom visited by insects in the field. However, identification of anti‐insect compounds and mechanisms of action are still unclear.RESULTSInterplanting purslane with Chinese cabbage demonstrated that purslane may contain secondary compounds that S. litura avoids eating. Four compounds were isolated from P. oleracea by directed anti‐insect activity, and their chemical structures were identified by NMR spectra as (9Z,11E,15Z)‐13‐hydroxyoctadeca‐9,11,15‐trienoic acid (1), portulacanone A (2), portulacanone D (3), and a new natural product 2,4′‐dihydroxy‐3′,5′‐dimethoxychalcone (4). A combination of compound 1 and 2 possessed stronger activity than other combinations (compounds 1 + 3; 1 + 4; 2 + 3; 2 + 4; 3 + 4). Both active compounds were detected in all samples from 23 regions in China, and concentrations in samples collected from 17 regions were generally above 500 μg/kg. Concentrations of compounds 1 and 2 fluctuated greatly from April to November, and reached maximum concentrations of 45 951.44 μg/kg for compound 1 and 3739.09 μg/kg for compound 2 in November. The combination of these compounds (1 + 2) caused mid‐gut structural deformation and tissue decay as determined by mid‐gut histopathology of S. litura.CONCLUSIONIn general, these active compounds coexisting contributed to partly protect purslane from insects. This research also provides new insights into the use of purslane as important ingredient of botanical pesticide alternatives to traditional chemical pesticides. © 2019 Society of Chemical Industry
Development of analytical method of melamine in placenta from pregnant women by isotope‐dilution liquid chromatography/tandem mass spectrometry
Authors: Wu Chia‐Fang , Cheng Ching‐Mei , Hsu Yu‐Ming , Li Sih‐Shyan , Huang Chung‐Yi , Chen Yung‐Hung , Kuo Fu‐Chen , Wu Ming‐Tsang 
Published: November 2019

RationaleMelamine is ubiquitously present in our daily life. It has a known effect on the kidneys, but it may also adversely affect the reproduction system. We have developed an analytical method for measuring melamine levels in maternal placenta and correlated these levels with melamine concentrations in urine, a necessary step in finding out if melamine might cross the placenta and enter the circulation of the fetus.MethodsWe used liquid–liquid extraction, clean up by solid‐phase extraction (SPE), and isotope‐dilution liquid chromatography/tandem mass spectrometry (LC/MS/MS) to measure melamine in placenta specimens. The results of this method were assessed for linearity, limits of quantitation (LOQs), and intra‐ and inter‐assay precision as well as accuracy, matrix effect, and recovery rate.ResultsCalibration curves indicated good linearity (r >0.995) over concentrations ranging from 5 to 500 ng/mL in placenta specimens, intra‐ and inter‐assay precision from 0.89% to 27.07%, and accuracy from 92.4% to123.5%. Recovery ranged from 63.9 to 83.9%, and the LOQ was 5 ng/mL in placenta (0.2 g). Placental melamine levels ranged from 7.87 to19.64 ng/mL, all detectable (n = 8). Pregnant women with higher levels of urinary melamine had higher placenta melamine levels than those with non‐detectable urinary melamine, though the results were not significantly different (p = 0.149, n = 4 in each group).ConclusionsThe results of this study suggest that pregnant women were exposed to low doses of melamine in their daily lives as measured in urine samples and placenta specimens. It is unclear whether placenta melamine concentrations can better represent long‐term exposure than urine or whether melamine in the uterus can enter the fetus via this route.
Untargeted characterisation of dissolved organic matter contributions to rivers from anthropogenic point sources using direct‐infusion and high‐performance liquid chromatography/Orbitrap mass spectrometry
Authors: Pemberton Jonathan A. , Lloyd Charlotte E.M. , Arthur Christopher J. , Johnes Penny J. , Dickinson Michael , Charlton Adrian J. , Evershed Richard P. 
Published: November 2019

RationaleAnthropogenic organic inputs to freshwaters can exert detrimental effects on aquatic ecosystems, raising growing concern for both environmental conservation and water security. Current regulation by the EU water framework directive (European Union, 2000/60/EC) relates to organic pollution by monitoring selected micropollutants; however, aquatic ecosystem responses require a comprehensive understanding of dissolved organic matter (DOM) composition. The introduction of high‐resolution mass spectrometry (HRMS) is set to greatly increase our understanding of the composition of DOM of both natural and anthropogenic origin derived from diffuse and point sources.MethodsDOM was extracted from riverine and treated sewage effluent using solid‐phase extraction (SPE) and analysed using dissolved organic carbon analysis, direct‐infusion high‐resolution mass spectrometry (DI‐HRMS) and high‐performance liquid chromatography (HPLC)/HRMS. The data obtained were analysed using univariate and multivariate statistics to demonstrate differences in background DOM, anthropogenic inputs and in‐river mixing. Compound identifications were achieved based on MS2 spectra searched against on‐line databases.ResultsDI‐HRMS spectra showed the highly complex nature of all DOM SPE extracts. Classification and visualisation of extracts containing many thousands of individual compounds were achieved using principal component analysis (PCA) and hierarchical cluster analysis. Kruskal‐Wallis analyses highlighted significant discriminating ions originating from the sewage treatment works for more in‐depth investigation by HPLC/HRMS. The generation of MS2 spectra in HPLC/HRMS provided the basis for identification of anthropogenic compounds including; pharmaceuticals, illicit drugs, metabolites and oligomers, although many thousands of compounds remain unidentified.ConclusionsThis new approach enables comprehensive analysis of DOM in extracts without any preconceived ideas of the compounds which may be present. This approach has the potential to be used as a high throughput, qualitative, screening method to determine if the composition of point sources differs from that of the receiving water bodies, providing a new approach to the identification of hitherto unrecognised organic contribution to water bodies.
Identification and distribution of mycosporine‐like amino acids in Brazilian cyanobacteria using ultrahigh‐performance liquid chromatography with diode array detection coupled to quadrupole time‐of‐flight mass spectrometry
Authors: Geraldes Vanessa , Jacinavicius Fernanda Rios , Genuário Diego Bonaldo , Pinto Ernani 
Published: November 2019

RationaleMycosporine‐like amino acids (MAAs) are UV‐absorbing compounds produced by fungi, algae, lichens, and cyanobacteria when exposed to UV radiation. These compounds have photoprotective and antioxidant functions and have been widely studied for possible use in sunscreens and anti‐aging products. This study aims to identify MAA‐producing cyanobacteria with potential application in cosmetics.MethodsA method for the identification of MAAs was developed using ultrahigh‐performance liquid chromatography with diode array detection coupled to quadrupole time‐of‐flight mass spectrometry (UHPLC‐DAD/QTOFMS). Chromatographic separation was carried out using a Synergi 4 μ Hydro‐RP 80A column (150 × 2,0 mm) at 30°C with 0.1% formic acid aqueous solution + 2 mM ammonium formate and acetonitrile/water (8:2) + 0.1% formic acid as a mobile phase.ResultsOut of the 69 cyanobacteria studied, 26 strains (37%) synthesized MAAs. Nine different MAAs were identified using UHPLC‐DAD/QTOFMS. Iminomycosporines were the major group detected (7 in 9 MAAs). In terms of abundance, the most representative genera for MAA production were heterocyte‐forming groups. Oscilatoria sp. CMMA 1600, of homocyte type, produced the greatest diversity of MAAs.ConclusionsThe UHPLC‐DAD/QTOFMS method is a powerful tool for identification and screening of MAAs in cyanobacterial strains as well as in other organisms such as dinoflagellates, macroalgae, and microalgae. The different cyanobacterial genera isolated from diverse Brazilian biomes and environments are prolific sources of MAAs.
Development of a photoinduced fragmentation ion trap for infrared multiple photon dissociation spectroscopy
Authors: Penna Tatiana C. , Cervi Gustavo , Rodrigues‐Oliveira André F. , Yamada Bruno D. , Lima Rafael Z.C. , Menegon Jair J. , Bastos Erick L. , Correra Thiago C. 
Published: November 2019

RationaleMethods for isomer discrimination by mass spectroscopy are of increasing interest. Here we describe the development of a three‐dimensional ion trap for infrared multiple photon dissociation (IRMPD) spectroscopy that enables the acquisition of the infrared spectrum of selected ions in the gas phase. This system is suitable for the study of a myriad of chemical systems, including isomer mixtures.MethodsA modified three‐dimensional ion trap was coupled to a CO2 laser and an optical parametric oscillator/optical parametric amplifier (OPO/OPA) system operating in the range 2300 to 4000 cm−1. Density functional theory vibrational frequency calculations were carried out to support spectral assignments.ResultsDetailed descriptions of the interface between the laser and the mass spectrometer, the hardware to control the laser systems, the automated system for IRMPD spectrum acquisition and data management are presented. The optimization of the crystal position of the OPO/OPA system to maximize the spectroscopic response under low‐power laser radiation is also discussed.ConclusionsOPO/OPA and CO2 laser‐assisted dissociation of gas‐phase ions was successfully achieved. The system was validated by acquiring the IRMPD spectra of model species and comparing with literature data. Two isomeric alkaloids of high economic importance were characterized to demonstrate the potential of this technique, which is now available as an open IRMPD spectroscopy facility in Brazil.
Development of a novel intelligent laparoscope system for semi‐automatic minimally invasive surgery
Authors: Sun Yanwen , Pan Bo , Fu Yili , Cao Fayi 
Published: November 2019

AbstractBackgroundIntelligent surgical robot has great significance to alleviate the fatigue of surgeons. In the minimally invasive surgery robot system, adding intelligent control method to the laparoscope control has great realizability and significance.MethodsDepth independent image Jacobian matrix was modified to make it suitable for laparoscope trocar constraint. We propose a method for intelligent and autonomous adjustment of surgeon's surgical field of view, enabling it to track and predict the motion trajectory of surgical instruments.ResultsThe result of experiment shows that the proposed method could realize tracking the surgical instruments and adjusting the surgical field of view autonomously. In case of occlusion, motion trajectory of surgical instruments can be predicted.ConclusionThe intelligent laparoscope system could improve the intelligent level of surgical robot system. Given providing “a third hand” for the surgeon, the proposed system is a highly improvement for semi‐autonomous surgical robot system.
A novel hybrid 3D endoscope zooming and repositioning system: Design and feasibility study
Authors: De Pauw Tim , Kalmar Alain , Van De Putte Dirk , Mabilde Cyriel , Blanckaert Bart , Maene Lieven , Lievens Mauranne , Van Haver Anne‐Sophie , Bauwens Kevin , Van Nieuwenhove Yves , Dewaele Frank 
Published: November 2019

AbstractBackgroundManipulation of the endoscope during minimally invasive surgery is a major source of inconvenience and discomfort. This report elucidates the architecture of a novel one‐hand controlled endoscope positioning device and presents a practicability evaluation.Methods and materialsSetup time and total surgery time, number and duration of the manipulations, side effects of three‐dimensional (3D) imaging, and ergonomic complaints were assessed by three surgeons during cadaveric and in vivo porcine trials.ResultsSetup was accomplished in an average (SD) of 230 (120) seconds. The manipulation time was 3.87 (1.77) seconds for angular movements and 0.83 (0.24) seconds for zooming, with an average (SD) of 30.5 (16.3) manipulations per procedure. No side effects of 3D imaging or ergonomic complaints were reported.ConclusionsThe integration of an active zoom into a passive endoscope holder delivers a convenient synergy between a human and a machine‐controlled holding device. It is shown to be safe, simple, and intuitive to use and allows unrestrained autonomic control of the endoscope by the surgeon.