bluuebunny/crossref_metadata_2025_split huggingface dataset:
Demographic stochasticity drives epidemiological patterns in wildlife with implications for diseases and population management
Authors: Lambert Sébastien , Ezanno Pauline , Garel Mathieu , Gilot-Fromont Emmanuelle 
Published: November 2018

AbstractInfectious diseases raise many concerns for wildlife and new insights must be gained to manage infected populations. Wild ungulates provide opportunities to gain such insights as they host many pathogens. Using modelling and data collected from an intensively monitored population of Pyrenean chamois, we investigated the role of stochastic processes in governing epidemiological patterns of pestivirus spread in both protected and hunted populations. We showed that demographic stochasticity led to three epidemiological outcomes: early infection fade-out, epidemic outbreaks with population collapse, either followed by virus extinction or by endemic situations. Without re-introduction, the virus faded out in >50% of replications within 4 years and did not persist >20 years. Test-and-cull of infected animals and vaccination had limited effects relative to the efforts devoted, especially in hunted populations in which only quota reduction somewhat improve population recovery. Success of these strategies also relied on the maintenance of a high level of surveillance of hunter-harvested animals. Our findings suggested that, while surveillance and maintenance of population levels at intermediate densities to avoid large epidemics are useful at any time, a ‘do nothing’ approach during epidemics could be the ‘least bad’ management strategy in populations of ungulates species facing pestivirus infection.
Marine mammal acoustic detections in the Greenland and Barents Sea, 2013 – 2014 seasons
Authors: De Vreese Steffen , van der Schaar Mike , Weissenberger Jürgen , Erbs Florence , Kosecka Monika , Solé Marta , André Michel 
Published: November 2018

AbstractWhile the Greenland and Barents Seas are known habitats for several cetacean and pinniped species there is a lack of long-term monitoring data in this rapidly changing environment. Moreover, little is known of the ambient soundscapes, and increasing off-shore anthropogenic activities can influence the ecosystem and marine life. Baseline acoustic data is needed to better assess current and future soundscape and ecosystem conditions. The analysis of a year of continuous data from three passive acoustic monitoring devices revealed species-dependent seasonal and spatial variation of a large variety of marine mammals in the Greenland and Barents Seas. Sampling rates were 39 and 78 kHz in the respective locations, and all systems were operational at a duty cycle of 2 min on, 30 min off. The research presents a description of cetacean and pinniped acoustic detections along with a variety of unknown low-frequency tonal sounds, and ambient sound level measurements that fall within the scope of the European Marine Strategy Framework (MSFD). The presented data shows the importance of monitoring Arctic underwater biodiversity for assessing the ecological changes under the scope of climate change.
A novel dry-bonding approach to reduce collagen degradation and optimize resin-dentin interfaces
Authors: Stape Thiago Henrique Scarabello , Seseogullari-Dirihan Roda , Tjäderhane Leo , Abuna Gabriel , Martins Luís Roberto Marcondes , Tezvergil-Mutluay Arzu 
Published: November 2018

AbstractIn dentistry, the wet-bonding approach relies on water to maintain demineralized collagen expanded for proper resin infiltration; nevertheless, hydrolytic instability of the resin-dentin interface is inevitable with current bonding techniques. Considering dimethyl sulfoxide’s (DMSO) ability to “biomodify” collagen and precipitate enzymes, the aim was to test whether the use of DMSO would permit adequate resin bonding to H3PO4-etched dehydrated dentin and assess its impact on collagen degradation by host-derived enzymes. Etched dentin surfaces from extracted sound human molars were randomly bonded in wet or dry conditions using aqueous or ethanolic DMSO solutions as pretreatments and bonding resins with or without DMSO. Bonded teeth were sectioned into resin-dentin slabs for confocal in situ zymography and beams for microtensile bond strength test. Demineralized powdered dentin was incubated in the tested DMSO -media and a hydroxyproline assay evaluated dissolution of collagen peptides. Zymography was performed on protein extracts obtained from dry and wet H3PO4-ecthed dentin powder treated with the DMSO- media. The correlative biochemical analysis demonstrated that reduction of water content during dentin hybridization by the innovative dry-bonding approaches with DMSO is effective to inactivate host-derived MMP-2 and MMP-9 and thus reduce collagen degradation while simultaneously optimizing resin-dentin bonding.
Deciphering the evolutionary signatures of pinnipeds using novel genome sequences: The first genomes of Phoca largha, Callorhinus ursinus, and Eumetopias jubatus
Authors: Park Jung Youn , Kim Kwondo , Sohn Hawsun , Kim Hyun Woo , An Yong-Rock , Kang Jung-Ha , Kim Eun-Mi , Kwak Woori , Lee Chul , Yoo DongAhn , Jung Jaehoon , Sung Samsun , Yoon Joon , Kim Heebal 
Published: November 2018

AbstractThe pinnipeds, which comprise seals, sea lions, and walruses, are a remarkable group of marine animals with unique adaptations to semi-aquatic life. However, their genomes are poorly characterized. In this study, we sequenced and characterized the genomes of three pinnipeds (Phoca largha, Callorhinus ursinus, and Eumetopias jubatus), focusing on site-wise sequence changes. We detected rapidly evolving genes in pinniped lineages and substitutions unique to pinnipeds associated with amphibious sound perception. Phenotypic convergence-related sequence convergences are not common in marine mammals. For example, FASN, KCNA5, and IL17RA contain substitutions specific to pinnipeds, yet are potential candidates of phenotypic convergence (blubber, response to hypoxia, and immunity to pathogens) in all marine mammals. The outcomes of this study will provide insight into targets for future studies of convergent evolution or gene function.
Reading ability and phoneme categorization
Authors: O’Brien Gabrielle E. , McCloy Daniel R. , Kubota Emily C. , Yeatman Jason D. 
Published: November 2018

AbstractDyslexia is associated with abnormal performance on many auditory psychophysics tasks, particularly those involving the categorization of speech sounds. However, it is debated whether those apparent auditory deficits arise from (a) reduced sensitivity to particular acoustic cues, (b) the difficulty of experimental tasks, or (c) unmodeled lapses of attention. Here we investigate the relationship between phoneme categorization and reading ability, with special attention to the nature of the cue encoding the phoneme contrast (static versus dynamic), differences in task paradigm difficulty, and methodological details of psychometric model fitting. We find a robust relationship between reading ability and categorization performance, show that task difficulty cannot fully explain that relationship, and provide evidence that the deficit is not restricted to dynamic cue contrasts, contrary to prior reports. Finally, we demonstrate that improved modeling of behavioral responses suggests that performance does differ between children with dyslexia and typical readers, but that the difference may be smaller than previously reported.
SEPROGADIC – serum protein-based gastric cancer prediction model for prognosis and selection of proper adjuvant therapy
Authors: Ahn Hee-Sung , Sohn Tae Sung , Kim Mi Jeong , Cho Byoung Kyu , Kim Su Mi , Kim Seung Tae , Yi Eugene C. , Lee Cheolju 
Published: November 2018

AbstractGastric cancer (GC) patients usually receive surgical treatment. Postoperative therapeutic options such as anticancer adjuvant therapies (AT) based on prognostic prediction models would provide patient-specific treatment to decrease postsurgical morbidity and mortality rates. Relevant prognostic factors in resected GC patient’s serum may improve therapeutic measures in a non-invasive manner. In order to develop a GC prognostic model, we designed a retrospective study. In this study, serum samples were collected from 227 patients at a 4-week recovery period after D2 lymph node dissection, and 103 cancer-related serum proteins were analyzed by multiple reaction monitoring mass spectrometry. Using the quantitative values of the serum proteins, we developed SEPROGADIC (SErum PROtein-based GAstric cancer preDICtor) prognostic model consisting of 6 to 14 serum proteins depending on detailed purposes of the model, prognosis prediction and proper AT selection. SEPROGADIC could clearly classify patients with good or bad prognosis at each TNM stage (1b, 2, 3 and 4) and identify a patient subgroup who would benefit from CCRT (combined chemoradiation therapy) rather than CTX (chemotherapy), or vice versa. Our study demonstrated that serum proteins could serve as prognostic factors along with clinical stage information in patients with resected gastric cancer, thus allowing patient-tailored postsurgical treatment.
Role of flow of information in the speedup of quantum evolution
Authors: Wang J. , Wu Y. N. , Xie Z. Y. 
Published: November 2018

AbstractQuantum evolution can be accelerated in a non-Markovian environment. Previous results show that the formation of a system-environment bound state governs the quantum speedup. Although a stronger bound state in the system-environment spectrum may seem like it should cause greater speed of evolution, this seemingly intuitive thinking may not always be correct. We illustrate this by investigating a classical-driven qubit interacting with a photonic crystal waveguide in the presence of a mirror, resulting in non-Markovian dynamics for the system. Within the considered model, we show the influence of the mirror and the classical field on the evolution speed of the system. In particular, we find that the formation of a bound state is not the essential reason for the acceleration of evolution. The quantum speedup is attributed to the flow of information, regardless of the direction in which the information flows. Our conclusion can also be used in other non-Markovian environments.
Clinical performance of an analytically validated assay in comparison to microarray technology to assess PITX2 DNA-methylation in breast cancer
Authors: Schricker Gabriele , Napieralski Rudolf , Noske Aurelia , Piednoir Elodie , Manner Olivia , Schüren Elisabeth , Lauber Jürgen , Perkins Jonathan , Magdolen Viktor , Schmitt Manfred , Ulm Kurt , Weichert Wilko , Kiechle Marion , Martens John W. M. , Wilhelm Olaf G. 
Published: November 2018

AbstractSignificant evidence has accumulated that DNA-methylation of the paired-like homeodomain transcription factor 2 (PITX2) gene can serve as a prognostic and predictive biomarker in breast cancer. PITX2 DNA-methylation data have been obtained so far from microarray and polymerase chain reaction (PCR)-based research tests. The availability of an analytically validated in vitro methylation-specific real-time PCR assay format (therascreen PITX2 RGQ PCR assay) intended for the determination of the percent methylation ratio (PMR) in the (PITX2) promoter 2 prompted us to investigate whether the clinical performance of these different assay systems generate comparable clinical outcome data. Mathematically converted microarray data of a previous breast cancer study (n = 204) into PMR values leads to a PITX2 cut-off value at PMR 14.73. Recalculation of the data to experimentally equivalent PMRs with the PCR PITX2 assay leads to a cut-off value at PMR 12 with the highest statistical significance. This cut-off predicts outcome of high-risk breast cancer patients to adjuvant anthracycline-based chemotherapy (n = 204; Hazard Ratio 2.48; p < 0.001) comparable to microarray generated results (n = 204; Hazard ratio 2.32; p < 0.0001). The therascreen PITX2 RGQ PCR assay is an analytically validated test with high reliability and robustness and predicts outcome of high-risk breast cancer patients to anthracycline-based chemotherapy.
Safe and efficient novel approach for non-invasive gene electrotransfer to skin
Authors: Pasquet Lise , Chabot Sophie , Bellard Elisabeth , Markelc Bostjan , Rols Marie-Pierre , Reynes Jean-Paul , Tiraby Gérard , Couillaud Franck , Teissie Justin , Golzio Muriel 
Published: November 2018

AbstractGene transfer into cells or tissue by application of electric pulses (i.e. gene electrotransfer (GET)) is a non-viral gene delivery method that is becoming increasingly attractive for clinical applications. In order to make GET progress to wide clinical usage its efficacy needs to be improved and the safety of the method has to be confirmed. Therefore, the aim of our study was to increase GET efficacy in skin, by optimizing electric pulse parameters and the design of electrodes. We evaluated the safety of our novel approach by assaying the thermal stress effect of GET conditions and the biodistribution of a cytokine expressing plasmid. Transfection efficacy of different pulse parameters was determined using two reporter genes encoding for the green fluorescent protein (GFP) and the tdTomato fluorescent protein, respectively. GET was performed using non-invasive contact electrodes immediately after intradermal injection of plasmid DNA into mouse skin. Fluorescence imaging of transfected skin showed that a sophistication in the pulse parameters could be selected to get greater transfection efficacy in comparison to the standard ones. Delivery of electric pulses only mildly induced expression of the heat shock protein Hsp70 in a luminescent reporting transgenic mouse model, demonstrating that there were no drastic stress effects. The plasmid was not detected in other organs and was found only at the site of treatment for a limited period of time. In conclusion, we set up a novel approach for GET combining new electric field parameters with high voltage short pulses and medium voltage long pulses using contact electrodes, to obtain a high expression of both fluorescent reporter and therapeutic genes while showing full safety in living animals.
Hyperactivated stallion spermatozoa fail to exhibit a rheotaxis-like behaviour, unlike other species
Authors: Romero-Aguirregomezcorta Jon , Sugrue Emer , Martínez-Fresneda Lucía , Newport David , Fair Sean 
Published: November 2018

AbstractThe journey of spermatozoa through the female genital tract is facilitated by rheotaxis, or the cell’s preference to swim against a flow, as well as thigmotaxis, the wall tracking behaviour, which guides them to the site of fertilisation. The aim of this study was to characterise the rheotactic and thigmotactic response of stallion sperm within a microfluidic channel. Stallion sperm rheotaxis was assessed within the microfluidic channel with regard to: (i) A range of flow velocities, (ii) Varying media viscosity and (iii) Sperm hyperactivation. Sperm distribution across the microfluidic channel was also studied and compared to human and ram sperm. Stallion sperm progressed furthest at a velocity range of 10–30 µm/s, with an optimum velocity of 20 µm/s. A flow viscosity of 2.5cP or greater reduced sperm rheotaxis (P < 0.05). Stallion sperm that were hyperactivated were unable to exhibit rheotaxis within the microfluidic channel, whereas, both hyperactivated human and ram sperm did exhibit positive rheotaxis under the same conditions. The number of sperm swimming near the microfluidic channel walls was higher than in the microfluidic channel centre (P < 0.05). This is the first study to illustrate that stallion sperm are rheotactically responsive and increasing viscosity reduces this response. We also demonstrated that sperm are predominantly inclined to swim along a surface and uniquely, hyperactivated stallion sperm are non-progressive and do not exhibit a rheotactic response unlike other species.
Tracing whale myoglobin evolution by resurrecting ancient proteins
Authors: Isogai Yasuhiro , Imamura Hiroshi , Nakae Setsu , Sumi Tomonari , Takahashi Ken-ichi , Nakagawa Taro , Tsuneshige Antonio , Shirai Tsuyoshi 
Published: November 2018

AbstractExtant cetaceans, such as sperm whale, acquired the great ability to dive into the ocean depths during the evolution from their terrestrial ancestor that lived about 50 million years ago. Myoglobin (Mb) is highly concentrated in the myocytes of diving animals, in comparison with those of land animals, and is thought to play a crucial role in their adaptation as the molecular aqualung. Here, we resurrected ancestral whale Mbs, which are from the common ancestor between toothed and baleen whales (Basilosaurus), and from a further common quadrupedal ancestor between whale and hippopotamus (Pakicetus). The experimental and theoretical analyses demonstrated that whale Mb adopted two distinguished strategies to increase the protein concentration in vivo along the evolutionary history of deep sea adaptation; gaining precipitant tolerance in the early phase of the evolution, and increase of folding stability in the late phase.
Amyloid β toxic conformer has dynamic localization in the human inferior parietal cortex in absence of amyloid plaques
Authors: Kageyama Yusuke , Saito Atsushi , Pletnikova Olga , Rudow Gay L. , Irie Yumi , An Yang , Murakami Kazuma , Irie Kazuhiro , Resnick Susan M. , Fowler David R. , Martin Lee J. , Troncoso Juan C. 
Published: November 2018

AbstractAmyloid β (Aβ) plays a critical role in the pathogenesis of Alzheimer’s disease. Nevertheless, its distribution and clearance before Aβ plaque formation needs to be elucidated. Using an optimized immunofluorescent staining method, we examined the distribution of Aβ in the post-mortem parietal cortex of 35 subjects, 30 to 65 years of age, APOE ε3/ε3, without AD lesions. We used 11A1, an antibody against an Aβ conformer which forms neurotoxic oligomers. 11A1 immunoreactivity (IR) was present in cortical neurons, pericapillary spaces, astrocytes and the extracellular compartment at 30 years of age. The percentage of neurons with 11A1 IR did not change with age, but the number and percentage of astrocytes with 11A1 IR gradually increased. Notably, the percentage of pericapillary spaces labeled with 11A1 IR declined significantly in the 5th decade of the life, at the same time that 11A1 IR increased in the extracellular space. Our findings indicate that the Aβ toxic conformer is normally present in various cell types and brain parenchyma, and appears to be constitutively produced, degraded, and cleared from the inferior parietal cortex. The decrease in pericapillary Aβ and the concomitant increase of extracellular Aβ may reflect an age-associated impairment in Aβ clearance from the brain.
Rapid and selective recovery of palladium from platinum group metals and base metals using a thioamide-modified calix[4]arene extractant in environmentally friendly hydrocarbon fluids
Authors: Yamada Manabu , Rajiv Gandhi Muniyappan , Shibayama Atsushi 
Published: November 2018

AbstractA novel macrocyclic calix[4]arene extractant having a long alkyl chain thioamide, 25,26,27,28-tetrakis(N-n-octylthiocarbamoyl)methoxy-5,11,17,23-tetra-tert-butylcalix[4]arene (1), was synthesized from 25,26,27,28-tetrakis(N-n-octylcarbamoyl)methoxy-5,11,17,23-tetra-tert-butylcalix[4]arene (2) using Lawesson’s reagent. Extractant1was characterized using1H NMR,13C NMR, FT-IR spectroscopy, and elemental analysis. The Pd(II) extraction abilities of1and2were studied in high-boiling-point and environmentally friendly hydrocarbon diluents. Pd(II) extraction experiments were conducted using single-metal Pd(II) solutions, simulated mixed palladium group metal (PGM) solutions, and acid-leached automotive catalyst residue solutions. Different experimental conditions, including the shaking time, HCl/HNO3concentration, Pd(II) concentration, extractant concentration, and the organic/aqueous phase ratio, were studied systematically. Extractant1showed very selective (> 99.9%) Pd(II) extraction from the mixed PGM/base metal solutions and the acid-leached automotive catalyst residue solution. Conversely, the Pd(II) extraction ability of extractant2was found to be negligible. Extractant1showed very fast extraction kinetics and a high extraction capacity as compared to those of the commercial extractant di-n-octyl sulfide. Effective stripping of Pd(II) from1was performed using HCI, HNO3, NH3, and HCl-thiourea solutions. Furthermore,1was successfully recycled over five extraction/stripping cycles. The Pd(II) extraction mechanism of1was studied using FT-IR spectroscopy. Extractant1exhibited very selective Pd(II) extraction and high acid stability, demonstrating its industrial applicability for the extraction of Pd(II) from leached automotive catalyst liquors containing PGMs and base metals.
Rapid detection of colistin resistance in Acinetobacter baumannii using MALDI-TOF-based lipidomics on intact bacteria
Authors: Dortet Laurent , Potron Anais , Bonnin Rémy A. , Plesiat Patrick , Naas Thierry , Filloux Alain , Larrouy-Maumus Gerald 
Published: November 2018

AbstractWith the dissemination of extremely drug resistant bacteria, colistin is now considered as the last-resort therapy for the treatment of infection caused by Gram-negative bacilli (including carbapenemase producers). Unfortunately, the increase use of colistin has resulted in the emergence of resistance as well. In A. baumannii, colistin resistance is mostly caused by the addition of phosphoethanolamine to the lipid A through the action of a phosphoethanolamine transferase chromosomally-encoded by the pmrC gene, which is regulated by the two-component system PmrA/PmrB. In A. baumannii clinical isolate the main resistance mechanism to colistin involves mutations in pmrA, pmrB or pmrC genes leading to the overexpression of pmrC. Although, rapid detection of resistance is one of the key issues to improve the treatment of infected patient, detection of colistin resistance in A. baumannii still relies on MIC determination through microdilution, which is time-consuming (16–24 h). Here, we evaluated the performance of a recently described MALDI-TOF-based assay, the MALDIxin test, which allows the rapid detection of colistin resistance-related modifications to lipid A (i.e phosphoethanolamine addition). This test accurately detected all colistin-resistant A. baumannii isolates in less than 15 minutes, directly on intact bacteria with a very limited sample preparation prior MALDI-TOF analysis.
Wide-range tuning of interfacial exchange coupling between ferromagnetic Au/Co and ferrimagnetic Tb/Fe(Co) multilayers
Authors: Frąckowiak Łukasz , Kuświk Piotr , Urbaniak Maciej , Chaves-O’Flynn Gabriel David , Stobiecki Feliks 
Published: November 2018

AbstractThe ability to perform wide-range tuning of the magnetic field required to switch the magnetization of ferromagnetic layers with perpendicular magnetic anisotropy is of great importance for many applications. We show that, for (Au/Co)2(3) multilayers, this field can be changed from minus several kOe to plus several kOe because of changes to the coupling with a ferrimagnetic multilayer [either (Tb/Fe)6 or (Tb/Co)6] across a Au spacer (either homogeneous 1 nm thick or wedge-shaped). The adjustable parameters are the ratio of sublayer thicknesses of the ferrimagnet and the sequence of layers around the Au spacer. The change of the sequence from Co/Au/Co to Tb/Au/Co is accompanied by both the reduction of the interaction energy and the change of the magnetic field sign necessary to switch the magnetization of ferromagnetic multilayers. For a 1 nm thick Au spacer this fields change from positive (negative) to negative (positive) if the ferrimagnet is dominated by the transition metal (rare earth) as a result of its composition. The characteristic oscillatory behavior of RKKY-like coupling is demonstrated using a system with a wedge-shaped Au spacer.