Prospective motion correction with volumetric navigators (vNavs) reduces the bias and variance in brain morphometry induced by subject motion
Contributors: M. Dylan Tisdall, Martin Reuter, Abid Qureshi, Randy L. Buckner, Bruce Fischl, André J.W. van der Kouwe
... Recent work has demonstrated that subject motion produces systematic biases in the metrics computed by widely used morphometry software packages, even when the motion is too small to produce noticeable image artifacts. In the common situation where the control population exhibits different behaviors in the scanner when compared to the experimental population, these systematic measurement biases may produce significant confounds for between-group analyses, leading to erroneous conclusions about group differences. While previous work has shown that prospective motion correction can improve perceived image quality, here we demonstrate that, in healthy subjects performing a variety of directed motions, the use of the volumetric navigator (vNav) prospective motion correction system significantly reduces the motion-induced bias and variance in morphometry.
Contributors: Qianting Zhai, Meng He, Aimin Song, Kurt Deshayes, Vishva M. Dixit, Paul J. Carter
... Context-independent anti-hypusine antibodies that bind to the post-translational modification (PTM), hypusine, with minimal dependence on flanking amino acid sequences, were identified. The antibodies bind to both hypusine and deoxyhypusine or selectively to hypusine but not to deoxyhypusine. Phage display was used to further enhance the affinity of the antibodies. Affinity maturation of these anti-hypusine antibodies improved their performance in affinity capture of the only currently known hypusinated protein, eukaryotic translation initiation factor 5A. These anti-hypusine antibodies may have utility in the identification of novel hypusinated proteins. Crystal structures of the corresponding Fab fragments were determined in complex with hypusine- or deoxyhypusine-containing peptides. The hypusine or deoxyhypusine moiety was found to reside in a deep pocket formed between VH and VL domains of the Fab fragments. Interaction between the antibodies and hypusine includes an extensive hydrogen bond network. These are, to our knowledge, the first reported structures of context-independent anti-PTM antibodies in complex with the corresponding PTM.
Investigating the emerging role of comparative proteomics in the search for new biomarkers of metal contamination under varying abiotic conditions
Contributors: Céline Vellinger, Bénédicte Sohm, Marc Parant, Françoise Immel, Philippe Usseglio-Polatera
... This study aims at investigating the potential use of comparative proteomics as a multi-marker approach of metal contamination, taking into account the potential confounding effect of water temperature. The major objective was to identify combinations of proteins specifically responding to a given metal, even if included in a metal mixture. The diagnostic approach was performed via the comparative analysis of protein expression on spot mapping provided by adult males of Gammarus pulex (Amphipoda, Crustacea) respectively exposed to arsenate (As), cadmium (Cd) or a binary mixture of these metals (AsCd) at three realistic temperatures (5, 10 and 15°C). Proteomic expression analysis was performed by Differential in-Gel Electrophoresis (2D-DiGE), and completed by an adapted inferential statistical approach. Combinations of under/over-expressed protein spots discriminated the metal identity. However, none of these spots discriminated both the individual metal effect (As or Cd) and its effect in metal mixture (AsCd) whatever the tested temperature. Some limits of the two-dimensional analysis of protein spot maps in G. pulex have been highlighted: (i) the presence of contaminating peptides and/or abundant “déja-vu” proteins which can mask the responses of other proteins of interest or (ii) the presence of post-translational modifications. An optimization of the experimental design (especially during the sample preparation) has been described for future investigations.
Understanding environmental DNA detection probabilities: A case study using a stream-dwelling char Salvelinus fontinalis
Contributors: Taylor M. Wilcox, Kevin S. McKelvey, Michael K. Young, Adam J. Sepulveda, Bradley B. Shepard, Stephen F. Jane, Andrew R. Whiteley, Winsor H. Lowe, Michael K. Schwartz
... Environmental DNA sampling (eDNA) has emerged as a powerful tool for detecting aquatic animals. Previous research suggests that eDNA methods are substantially more sensitive than traditional sampling. However, the factors influencing eDNA detection and the resulting sampling costs are still not well understood. Here we use multiple experiments to derive independent estimates of eDNA production rates and downstream persistence from brook trout (Salvelinus fontinalis) in streams. We use these estimates to parameterize models comparing the false negative detection rates of eDNA sampling and traditional backpack electrofishing. We find that using the protocols in this study eDNA had reasonable detection probabilities at extremely low animal densities (e.g., probability of detection 0.18 at densities of one fish per stream kilometer) and very high detection probabilities at population-level densities (e.g., probability of detection >0.99 at densities of ≥3 fish per 100m). This is substantially more sensitive than traditional electrofishing for determining the presence of brook trout and may translate into important cost savings when animals are rare. Our findings are consistent with a growing body of literature showing that eDNA sampling is a powerful tool for the detection of aquatic species, particularly those that are rare and difficult to sample using traditional methods.
Contributors: Alexander O. Frolov, Marina N. Malysheva, Vyacheslav Yurchenko, Alexei Yu. Kostygov
... The trypanosomatid Phytomonas nordicus parasitizing the predatory bug Troilus luridus was described at the twilight of the morphotype-based systematics. Despite its monoxenous life cycle, this species was attributed to the dixenous genus Phytomonas due to the presence of long twisted promastigotes and development of flagellates in salivary glands. However, these characteristics were considered insufficient for proving the phytomonad nature of the species and therefore its description remained virtually unnoticed. Here, we performed molecular phylogenetic analyses using 18S ribosomal RNA (rRNA) gene and region containing internal trascribed spacers (ITS) 1 and 2 and convincingly demonstrated the affinity of P. nordicus to the genus Phytomonas. In addition, we investigated its development in the salivary glands. We argue that in many aspects the life cycle of monoxenous P. nordicus resembles that of its dixenous relatives represented by tomato-parasitizing Phytomonas serpens.
Contributors: Aleksander Karolczuk, Krzysztof Kluger, Tadeusz Łagoda
... The paper presents the algorithm for calculating the fatigue life taking into account the variability of coefficients occurring in the multiaxial fatigue criterion depending on the number of cycles to failure. The algorithm has been analysed under uniaxial cyclic loads and a combination of bending and torsion for four structural materials. Significant increase of convergence of calculated and experimental fatigue life using the new algorithm as compared to the classical approach for five selected multiaxial fatigue criteria based on a critical plane has been demonstrated.
A novel approach for removing ECG interferences from surface EMG signals using a combined ANFIS and wavelet
Contributors: Sara Abbaspour, Ali Fallah, Maria Lindén, Hamid Gholamhosseini
... In recent years, the removal of electrocardiogram (ECG) interferences from electromyogram (EMG) signals has been given large consideration. Where the quality of EMG signal is of interest, it is important to remove ECG interferences from EMG signals. In this paper, an efficient method based on a combination of adaptive neuro-fuzzy inference system (ANFIS) and wavelet transform is proposed to effectively eliminate ECG interferences from surface EMG signals. The proposed approach is compared with other common methods such as high-pass filter, artificial neural network, adaptive noise canceller, wavelet transform, subtraction method and ANFIS. It is found that the performance of the proposed ANFIS–wavelet method is superior to the other methods with the signal to noise ratio and relative error of 14.97dB and 0.02 respectively and a significantly higher correlation coefficient (p<0.05).
Where do the Neotropical Empidini lineages (Diptera: Empididae: Empidinae) fit in a worldwide context?
Contributors: Mirian Watts, Isaac S. Winkler, Christophe Daugeron, Claudio J.B. de Carvalho, Steven P. Turner, Brian M. Wiegmann
... The tribe Empidini (Diptera: Empididae: Empidinae) is a diverse group with fourteen genera, seven of which are exclusive to the Neotropical region: Bolrhamphomyia Rafael, Chilerhamphomyia Rafael, Hystrichonotus Collin, Lamprempis Wheeler and Melander, Macrostomus Wiedemann, Opeatocerata Melander and Porphyrochroa Melander. Although Empidini itself is likely paraphyletic, many presumably monophyletic genera and species groups are recognized. Here, we apply DNA sequences from multiple genes to infer the phylogeny of Empidini, focusing on placing the Neotropical lineages within the entire tribe and identifying monophyletic groups. We included 98 Empidini taxa along with 18 outgrous terminals, spanning the diversity within the group. The results from the analyses performed are largely similar, with major groupings of genera in common. Specifically, the analyses recovered a monophyletic Hilarini and a paraphyletic Empidini. Most species from Chile and Argentina (Andean region) are found to belong to an early branching lineage within Empidinae, and are not monophyletic with other Empidini. A large portion of the remaining Neotropical Empidini (not Andean) comprises a single clade that includes four endemic genera and a number of Neotropical Empis Linneaus species. Macrostomus and Porphyrochroa each recovered as monophyletic and sister to one another, although generic placement of a few taxa remains uncertain due to conflicting morphological features. Lamprempis+Opeatocerata are also found to be sister-taxa in most analyses. Several large genera were found to be polyphyletic or paraphyletic including Empis and Rhamphomyia Meigen. We evaluate our findings and discuss them in light of current Empidinae taxonomy.
A preliminary model of iron fertilisation by baleen whales and Antarctic krill in the Southern Ocean: Sensitivity of primary productivity estimates to parameter uncertainty
Contributors: Lavenia Ratnarajah, Jessica Melbourne-Thomas, Martin P. Marzloff, Delphine Lannuzel, Klaus M. Meiners, Fanny Chever, Stephen Nicol, Andrew R. Bowie
... Large marine animals may play a crucial role in storing and recycling bioavailable iron in surface waters by consuming iron-rich prey and subsequent defecation of iron that is excess to their requirements. This biological recycling of iron could enhance primary productivity in iron-limited waters. However, quantifying the effects of marine animals on ocean primary productivity remains challenging because of a limited understanding of the key biogeochemical processes involved. In this paper, we develop a preliminary model that explores these uncertainties and examines the potential effects of historical populations of blue, fin and humpback whales, and the biomass of Antarctic krill required to support the whale populations, on primary productivity in the Southern Ocean.
Contributors: Boqiang Lin, Xuan Xie
... In a joint U.S.–China statement on climate change, the Chinese government declared to peak CO2 emissions around 2030. This demonstrates the government's determination to deal with carbon emission and climate change. Although the food industry is not a carbon emission-intensive industry, its large scale makes the emission reduction in the industry very important. Based on the input–output structural decomposition method, this paper calculates the CO2 emissions of China's food industry from 1991 to 2012, and decomposes the change in CO2 emissions of the industry during 1992–1997, 1997–2002, 2002–2007 and 2007–2010 into four main effects: emission factor, energy structure, energy intensity, and total output (including four sub-effects: intermediate use, domestic final demand, import substitution and export extension). The results show that changes in CO2 emissions in the food industry mainly depends on total output effect and energy intensity effect. Energy intensity effect is the most important factor reducing CO2 emissions, as it reduced cumulative 213 million tons (Mt) CO2 emissions of the industry. Among total output effect, the effects of intermediate use and domestic final demand are the two biggest contributors to carbon emissions. Finally, we provide some policy advices for constraining and reducing CO2 emissions of China's food industry. The advices include increasing R&D investment and the substitution of energy with other input factors to decrease energy intensity, increasing the added value of the food industry, optimizing the energy structure with more clean and low-carbon energy, and maintaining the prices of raw materials of the food industry (i.e. agricultural products) with taxes or subsidies.