bluuebunny/crossref_metadata_2025_split huggingface dataset:
Late Holocene changes in vegetation and atmospheric circulation at Lake Uddelermeer (The Netherlands) reconstructed using lipid biomarkers and compound‐specific δD analysis
Authors: van den Bos V. , Engels S. , Bohncke S. J. P. , Cerli C. , Jansen B. , Kalbitz K. , Peterse F. , Renssen H. , Sachse D. 
Published: January 2018

ABSTRACTWe reconstructed middle to late Holocene changes in atmospheric circulation patterns and vegetation in north‐west Europe by applying novel geochemical techniques to the sediment record of Lake Uddelermeer (The Netherlands). A comparison of higher plant‐derived leaf wax n‐alkane distributions archived in the lake sediments with those in living plant material, combined with palynological analysis, indicates that the vegetation immediately surrounding the lake became more open at 3150 cal a BP, while the regional vegetation responded more gradually and ∼650 years later. Our record of the hydrogen isotopic composition of plant leaf waxes (δDwax) shows a deuterium enrichment starting from 3500 cal a BP, which we interpret as a change in atmospheric circulation. A similar δDwax record from nearby Meerfelder Maar (Germany) shows an opposite trend around this time, which could be explained by a change in sea‐level pressure resembling a negative North Atlantic Oscillation phase. This could account for depleted δD values of precipitation at Meerfelder Maar, while confounding factors related to the more maritime position of Uddelermeer cause the opposite shift there.
Three‐Dimensional Shear Wave Elastography for Differentiating Benign From Malignant Thyroid Nodules
Authors: Zhao Chong‐Ke , Chen Shi‐Gao , Alizad Azra , He Ya‐Ping , Wang Qiao , Wang Dan , Yue Wen‐Wen , Zhang Kun , Qu Shen , Wei Qing , Xu Hui‐Xiong 
Published: January 2018

ObjectivesTo prospectively evaluate the diagnostic performance of 3‐dimensional (3D) shear wave elastography (SWE) for assessing thyroid nodules.MethodsA total of 176 surgically or cytologically confirmed thyroid nodules (63 malignant and 113 benign) in 176 patients who had undergone conventional ultrasound (US), 2‐dimensional (2D) SWE, and 3D SWE examinations were included in this study. Quantitative elasticity values (mean elasticity, maximum elasticity, and standard deviation of elasticity of a large region of interest and mean elasticity of a 2‐mm region of interest) were measured on 2D and 3D SWE. Diagnostic performances of conventional US, 2D SWE, and 3D SWE were assessed. The role of 2D and 3D SWE in reducing unnecessary fine‐needle aspiration (FNA) for nodules with low suspicion was also evaluated.ResultsThe diagnostic performances in terms of the area under the receiver operating characteristic curve were 0.612 for conventional US, 0.836 for 2D SWE (P < .001 in comparison with conventional US), and 0.839 for 3D SWE (P < .001 in comparison with conventional US). The mean elasticity achieved the highest diagnostic performance in 2D SWE, whereas the standard deviation of elasticity achieved the highest performance in 3D SWE, although no significant difference was found between them (P > .05). Three‐dimensional SWE increased the specificity in comparison with 2D SWE (88.5% versus 82.3%; P = .039). For the 37 nodules with low suspicion on conventional US imaging, 2D SWE was able to avoid unnecessary FNA in 77.1% (27 of 35) of benign nodules, and 3D SWE further increased the number to 88.6% (31 of 35).ConclusionsThree‐dimensional SWE is a useful tool for predicting thyroid nodule malignancy and reducing unnecessary FNA procedures in thyroid nodules with low suspicion of malignancy.
The emerging role of Rab GTPases in the pathogenesis of Parkinson's disease
Authors: Gao Yujing , Wilson Gabrielle R. , Stephenson Sarah E. M. , Bozaoglu Kiymet , Farrer Matthew J. , Lockhart Paul J. 
Published: January 2018

ABSTRACTThe identification of pathogenic mutations in Ras analog in brain 39B (RAB39B) and Ras analog in brain 32 (RAB32) that cause Parkinson's disease (PD) has highlighted the emerging role of protein trafficking in disease pathogenesis. Ras analog in brain (Rab) Guanosine triphosphatase (GTPase) function as master regulators of membrane trafficking, including vesicle formation, movement along cytoskeletal networks, and membrane fusion. Recent studies have linked Rab GTPases with α‐synuclein, Leucine‐rich repeat kinase 2, and Vacuolar protein sorting 35, 3 key proteins in PD pathogenesis. In this review, we discuss the various RAB GTPases associated with PD, current progress in the research, and potential future directions. Investigations into the function of RAB GTPases will likely provide significant insight into the etiology of PD and identify novel therapeutic targets for a currently incurable disease. © 2018 International Parkinson and Movement Disorder Society
Barriers and reinforcing factors to self‐management behaviour in rheumatoid arthritis patients: A qualitative study
Authors: Chaleshgar‐Kordasiabi M. , Enjezab B. , Akhlaghi M. , Sabzmakan I. 
Published: January 2018

AbstractObjectiveThe aim of the present study was to explore the view of rheumatoid arthritis (RA) patients about the barriers and reinforcing factors in practising self‐management behaviour (SMB).MethodsThis was a qualitative study based on directed content analysis of in‐depth semi‐structured interviews with 30 patients. The participants were selected using a purposeful sampling approach. The interviews continued until data saturation was reached. The study was conducted over 6 months in 2014–2015 at the Rheumatology Clinic of Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran.ResultsThree main themes and 14 subthemes were extracted. The main themes included behavioural barriers, environmental barriers and reinforcing factors. The subthemes included lack of awareness; poor physician–patient relationship; lack of motivation; negative attitude and willingness; lack of time; cost; housing conditions and in‐home equipment; negative social effects; social support; consequences of SMB; and comparing yourself with others.ConclusionBehavioural and environmental barriers, as well as social support and outcomes of SMB were the most important barriers and reinforcing factors of SMB. Therefore, considering these factors in patients may help in designing programmes that attempt to reduce barriers and increase reinforcing factors, which ultimately result in higher levels of SMB and quality of life among patients.
Neuralgic amyotrophy in children
Authors: Al‐Ghamdi Fouad , Ghosh Partha S. 
Published: January 2018

ABSTRACTIntroduction: Neuralgic amyotrophy (NA) is characterized by the clinical triad of pain, muscle weakness/atrophy, and sensory symptoms. Methods: We retrospectively identified children (≤18 years old) over the course of 15 years (2003–2017) at a single pediatric center. Results: We included 22 patients (8 females and 14 males, 6–18 years old); pain was the presenting manifestation in all of them. Clinical weakness involving the periscapular muscles was observed in 16 patients and scapular winging in 13 patients. Two patients had preceding viral infection. Electromyography was performed in 21 patients: sensory nerve abnormalities were detected in 5, and neurogenic changes were most commonly observed in the serratus anterior muscle. Treatment was mainly supportive, although 4 patients received immunotherapy. Persistent pain and residual motor deficits were observed in more than half of the patients at follow‐up. Discussion: NA is rare in children but clinicians should be aware of this entity to avoid delays in diagnosis. In our series, presentation was similar to that seen in adults. Muscle Nerve 57: 932–936, 2018
Apparent diffusion coefficients in prostate cancer: correlation with molecular markers Ki‐67, HIF‐1α and VEGF
Authors: Ma Teng , Yang Shaolin , Jing Haiyan , Cong Lin , Cao Zhixin , Liu Zhiling , Huang Zhaoqin 
Published: January 2018

Prostate cancer (PCa) is the second most common cancer in men. The Gleason score (GS) and biomarkers play important roles in the diagnosis and treatment of patients with PCa. The purpose of this study was to investigate the relationship between the apparent diffusion coefficient (ADC) and the molecular markers Ki‐67, hypoxia‐inducible factor‐1α (HIF‐1α) and vascular endothelial growth factor (VEGF) in PCa. Thirty‐nine patients with 39 lesions, who had been diagnosed with PCa, were enrolled in this study. All patients underwent diffusion‐weighted magnetic resonance imaging (DW‐MRI) (b = 800 s/mm2). The expression of Ki‐67, HIF‐1α and VEGF was assessed by immunohistochemistry. Statistical analysis was applied to analyze the association between ADC and prostate‐specific antigen (PSA), GS and the expression of Ki‐67, HIF‐1α and VEGF. The group differences in ADC among different grades of Ki‐67, HIF‐1α and VEGF were also analyzed. The mean ± standard deviation of ADC was (0.76 ± 0.27) × 10−3 mm2/s. ADC correlated negatively with PSA and GS (p < 0.05). The Ki‐67 staining index (SI), HIF‐1α expression and VEGF expression in PCa were correlated inversely with ADC, controlling for age (r = –0.332, p < 0.05; r = −0.662, p < 0.0005; and r = −0.714, p < 0.0005, respectively). ADC showed a significant difference among different grades of Ki‐67 (F = 9.164, p = 0.005), HIF‐1α (F = 40.333, p < 0.0005) and VEGF (F = 22.048, p < 0.0005). In conclusion, ADC was correlated with PSA, GS, and Ki‐67, HIF‐1α and VEGF expression in patients with PCa. ADC may be used to evaluate tumor proliferation, hypoxia and angiogenesis in PCa.
Adjusting policy implementation frameworks for non‐pluralist conditions: A case study of Ukraine's single tax for small business
Authors: Fischer‐Smith Ruth 
Published: January 2018

SummaryTraditional frameworks for assessing policy implementation have been developed almost exclusively in the context of market‐based, pluralist democracies. This research explores policy processes in more diverse contexts, testing the applicability of existing implementation measurement models in the socio‐political context of a post‐Soviet country. Fieldwork conducted in Ukraine examines the factors affecting implementation of the Simplified Single Tax policy and considers the impact of formal and informal institutions on policy processes and small business conditions. Results include an expanded model for assessing policy implementation in non‐pluralist conditions, an original contribution to the fields of policy, small business, and development studies. The research further contributes to the literature concerning policy transfer, policy advocacy, and tax reform in developing nations. For theoreticians, this research may inform design considerations when conducting policy research outside of a pluralist democracy. For practitioners, it may inform efforts to mitigate implementation obstacles in diverse socio‐political contexts.
Lactose repressor hinge domain independently binds DNA
Authors: Xu Joseph S. , Hewitt Madeleine N. , Gulati Jaskeerat S. , Cruz Matthew A. , Zhan Hongli , Liu Shirley , Matthews Kathleen S. 
Published: January 2018

AbstractThe short 8–10 amino acid “hinge” sequence in lactose repressor (LacI), present in other LacI/GalR family members, links DNA and inducer‐binding domains. Structural studies of full‐length or truncated LacI‐operator DNA complexes demonstrate insertion of the dimeric helical “hinge” structure at the center of the operator sequence. This association bends the DNA ∼40° and aligns flanking semi‐symmetric DNA sites for optimal contact by the N‐terminal helix‐turn‐helix (HtH) sequences within each dimer. In contrast, the hinge region remains unfolded when bound to nonspecific DNA sequences. To determine ability of the hinge helix alone to mediate DNA binding, we examined (i) binding of LacI variants with deletion of residues 1–50 to remove the HtH DNA binding domain or residues 1–58 to remove both HtH and hinge domains and (ii) binding of a synthetic peptide corresponding to the hinge sequence with a Val52Cys substitution that allows reversible dimer formation via a disulfide linkage. Binding affinity for DNA is orders of magnitude lower in the absence of the helix‐turn‐helix domain with its highly positive charge. LacI missing residues 1–50 binds to DNA with ∼4‐fold greater affinity for operator than for nonspecific sequences with minimal impact of inducer presence; in contrast, LacI missing residues 1–58 exhibits no detectable affinity for DNA. In oxidized form, the dimeric hinge peptide alone binds to O1 and nonspecific DNA with similarly small difference in affinity; reduction to monomer diminished binding to both O1 and nonspecific targets. These results comport with recent reports regarding LacI hinge interaction with DNA sequences.
Crystal stuctures of MglB‐2 (TP0684), a topologically variant d‐glucose‐binding protein from Treponema pallidum, reveal a ligand‐induced conformational change
Authors: Brautigam Chad A. , Deka Ranjit K. , Liu Wei Z. , Norgard Michael V. 
Published: January 2018

AbstractPreviously, we determined the crystal structure of apo‐TpMglB‐2, a d‐glucose‐binding component of a putative ABC transporter from the syphilis spirochete Treponema pallidum. The protein had an unusual topology for this class of proteins, raising the question of whether the d‐glucose‐binding mode would be different in TpMglB‐2. Here, we present the crystal structures of a variant of TpMglB‐2 with and without d‐glucose bound. The structures demonstrate that, despite its aberrant topology, the protein undergoes conformational changes and binds d‐glucose similarly to other Mgl‐type proteins, likely facilitating d‐glucose uptake in T. pallidum.
Vibrational entropy estimation can improve binding affinity prediction for non‐obligatory protein complexes
Authors: Škrbić Tatjana , Zamuner Stefano , Hong Rolando , Seno Flavio , Laio Alessandro , Trovato Antonio 
Published: January 2018

AbstractPredicting the binding affinity between protein monomers is of paramount importance for the understanding of thermodynamical and structural factors that guide the formation of a complex. Several numerical techniques have been developed for the calculation of binding affinities with different levels of accuracy. Approaches such as thermodynamic integration and Molecular Mechanics/Poisson‐Boltzmann Surface Area (MM/PBSA) methodologies which account for well defined physical interactions offer good accuracy but are computationally demanding. Methods based on the statistical analysis of experimental structures are much cheaper but good performances have only been obtained throughout consensus energy functions based on many different molecular descriptors. In this study we investigate the importance of the contribution to the binding free energy of the entropic term due to the fluctuations around the equilibrium structures. This term, which we estimated employing an elastic network model, is usually neglected in most statistical approaches. Our method crucially relies on a novel calibration procedure of the elastic network force constant. The residue mobility profile is fitted to the one obtained through a short all‐atom molecular dynamics simulation on a subset of residues only. Our results show how the proper consideration of vibrational entropic contributions can improve the quality of the prediction on a set of non‐obligatory protein complexes whose binding affinity is known.
Evidence for activation of nitenpyram by a mitochondrial cytochrome P450 in Drosophila melanogaster
Authors: Harrop Thomas WR , Denecke Shane , Yang Ying Ting , Chan Janice , Daborn Phillip J , Perry Trent , Batterham Philip 
Published: January 2018

AbstractBACKGROUNDNitenpyram is a member of the economically important neonicotinoid class of insecticides. The in vivo metabolism of nitenpyram is not well characterised, but cytochrome P450 activity is the major mechanism of resistance to neonicotinoids identified in insect pests, and P450s metabolise other neonicotinoids including imidacloprid.RESULTSHere, we used the GAL4‐UAS targeted expression system to direct RNA interference (RNAi) against the cytochrome P450 redox partners to interrupt P450 functions in specific tissues in Drosophila melanogaster. RNAi of the mitochondrial redox partner defective in the avoidance of repellents (dare) in the digestive tissues reduced nitenpyram mortality, suggesting an activation step in the metabolism of nitenpyram carried out by a mitochondrial P450. RNAi of the mitochondrial cytochrome P450 Cyp12a5, which is expressed in the digestive tissues, resulted in the same phenotype, and transgenic overexpression of Cyp12a5 increased nitenpyram sensitivity.CONCLUSIONThese results suggest that in vivo metabolism of nitenpyram by the mitochondrial P450 CYP12A5 results in the formation of a product with higher toxicity than the parent compound. © 2018 Society of Chemical Industry
Robot‐guided stereoelectroencephalography without a computed tomography scan for referencing: Analysis of accuracy
Authors: Spyrantis Andrea , Cattani Adriano , Strzelczyk Adam , Rosenow Felix , Seifert Volker , Freiman Thomas M. 
Published: January 2018

AbstractObjectiveRecent studies with robot‐guided stereotaxy use computed tomography (CT) scans for referencing. We will provide evidence that using preoperative MRI datasets referenced with a laser scan of the patient's face is sufficient for sEEG implantation.MethodsIn total, 40 sEEG electrodes were implanted in five patients by the robotic surgical assistant (ROSA). The postoperative CT scan for identifying electrode positions was fused with the preoperative MRI‐based planning data. The accuracy was determined by the target point error (TPE) and the entry point error (EPE), applying the Euclidean distance.ResultsThe mean TPE amounted to 2.96 mm, the mean EPE to 2.53 mm. The accuracy was improved in 1.5 T MRI: the mean TPE amounted to 1.72 mm, the EPE to 0.97 mm. No complications, haemorrhages, infections, etc., were observed.ConclusionsRobot‐guided sEEG based on 3 T MRI reduces radiation exposure for the patient and can still be performed safely.
How do instream flow increase and gravel augmentation impact biological communities in large rivers: A case study on the Upper Rhine River
Authors: Staentzel C. , Arnaud F. , Combroux I. , Schmitt L. , Trémolières M. , Grac C. , Piégay H. , Barillier A. , Chardon V. , Beisel J.‐N. 
Published: January 2018

AbstractActions are being developed to address the adverse consequences of engineering works on large European rivers by developing and implementing restoration activities in order to enhance the functionality and biodiversity of fluvial hydrosystems. However, as has frequently been mentioned in the scientific literature, quantitative and qualitative evaluation of the project benefits, if any, and their sustainability are hindered by the difficulty in assessing the responses of aquatic and riparian communities to the methods employed. A case study was conducted on a by‐passed section of the Upper Rhine River (France and Germany) to investigate the effects of instream flow increase and gravel augmentation on selected aquatic and riparian communities (macroinvertebrates, macrophytes, and riparian plants). This paper presents the results of a 6‐year interdisciplinary, before‐after control‐impact design monitoring study. The complexity of the study lies in carrying out a separate assessment of the cumulative effects on a site‐based, project‐specific basis. The results showed that (a) the instream flow increase resulted in greater richness of macrophyte species in the newly created backwaters, (b) the artificial gravel bar favoured the recruitment of pioneer species, including invasive species, although gravel redistribution by floods prevented their development, and (c) gravel augmentation tended to promote the taxonomic richness of macroinvertebrate communities with the appearance of species adapted to the new substrate areas. These findings should help to fill the knowledge gaps in large‐scale restoration and contribute key responses to the most frequently arising issues in this area, especially those concerning the efficiency and sustainability of river restoration projects.
Influence of tributaries on the longitudinal patterns of benthic invertebrate communities
Authors: Jones N.E. , Schmidt B.J. 
Published: January 2018

AbstractThere has been little effort to understand how tributaries influence mainstem rivers at large scales beyond the immediate influence of the tributary and downstream of the mixing zone. Such knowledge is needed to create breaks in stream networks that can aid in the classification of stream valley segments and conservation studies that rely on the delineation of zones. We use benthic invertebrate assemblages to infer longitudinal gradients and discontinuities and relate these patterns to confluence symmetry ratio (CSR; the size ratio of the tributary basin to the mainstem basin upstream of the confluence). In addition, we briefly explore reach and catchment‐scale environmental influences. We found evidence for both gradual and abrupt longitudinal changes in benthic invertebrate communities. There was not a smooth continuous gradient but a sawtooth pattern with an overarching trend. Two major discontinuities were found: one associated with a large CSR = 0.74 and reach scale factors including predominance of sand and an abundance of benthic organic matter that provided a unique habitat; and a second associated with a large CSR = 0.64 and a transition from coarse textured morainal deposits to glaciolacustrine deposits. There were synchronous additions of some benthic invertebrates (e.g., Eukiefferiella brehmi, Antocha, Hydropsyche morosa, and Oligochaeta) showing an affinity for downstream reaches, whereas others showed an affinity for headwater reaches (e.g., Simulium tuberosum, Baetis tricaudatus, and Micropsectra). Benthic invertebrate communities were driven by a combination of confluence symmetry ratio, landscape, and reach scale factors that can confound interpretation.
Line percolation
Authors: Balister Paul , Bollobás Béla , Lee Jonathan , Narayanan Bhargav 
Published: January 2018

AbstractWe study a new geometric bootstrap percolation model, line percolation, on the d‐dimensional integer grid . In line percolation with infection parameter r, infection spreads from a subset of initially infected lattice points as follows: if there exists an axis‐parallel line L with r or more infected lattice points on it, then every lattice point of on L gets infected, and we repeat this until the infection can no longer spread. The elements of the set A are usually chosen independently, with some density p, and the main question is to determine , the density at which percolation (infection of the entire grid) becomes likely. In this paper, we determine up to a multiplicative factor of and up to a multiplicative constant as for every fixed . We also determine the size of the minimal percolating sets in all dimensions and for all values of the infection parameter.