bluuebunny/crossref_metadata_2025_split huggingface dataset:
SLAM-MS: Mutation scanning of stem-loop amplicons with TaqMan probes by quantitative DNA melting analysis
Authors: Kondratova V. N. , Botezatu I. V. , Shelepov V. P. , Lichtenstein A. V. 
Published: March 2020

AbstractDNA Melting Analysis (DMA) with a TaqMan probe covering the mutation “hot spot” is a simple, sensitive, and “closed tube” method of mutation detection. However, DMA requires asymmetric PCR to produce single-stranded amplicons capable of interacting with TaqMan probes. This makes quantitative analysis impossible owing to low amplification efficiency. Moreover, bi-strand mutation detection necessitates two independent PCRs. The SLAM-MS (Stem-Loop AMplicon Mutation Scanning) assay, in which symmetric PCR is performed using primers with 5'-universal primer sequence (UPS), has been developed to detect KRAS mutations. Some of the resulting amplicons, sense and antisense, adopt single-stranded stem-loop conformation and become unable to renature, but able to hybridize with TaqMan probes. Hybrids of stem-loops and complementary TaqMan probes are suitable for melting analysis and simultaneous bi-strand mutation scanning. In addition, the areas under the melting peaks are determined by the PeakFit software, a non-linear iterative curve fitting program, to evaluate the wild-type/mutant allele ratio. Thus, the SLAM-MS assay permits quantification of both the number of copies of the target sequence and the percentage of mutant alleles. For mutant enrichment, the SLAM-MS assay uses TaqMan probes as PCR blocking agents allowing an ~10 times higher mutation detection sensitivity than High Resolution Melting (HRM) assay.
Parturitions, menopause and other physiological stressors are recorded in dental cementum microstructure
Authors: Cerrito Paola , Bailey Shara E. , Hu Bin , Bromage Timothy G. 
Published: March 2020

AbstractThe life history pattern of recent humans is uniquely derived in many of its aspects including an extended post-reproductive lifespan combined with short interbirth intervals. A number of theories have been proposed to explain the evolution of this unusual pattern. However most have been difficult to test due to the fragmentary nature of the hominin fossil record and the lack of methods capable of inferring such later life history events. In search of a method we tested the hypothesis that the physiologically impactful events of parturition and menopause are recorded in dental cementum microstructure. We performed histomorphological analyses of 47 teeth from 15 individuals with known life history events and were able to detect reproductive events and menopause in all females. Furthermore, we found that other stressful events such as systemic illnesses and incarceration are also detectable. Finally, through the development of a novel analytical method we were able to time all such events with high accuracy (R-squared = 0.92).
Assessing Autonomic Function from Electrodermal Activity and Heart Rate Variability During Cold-Pressor Test and Emotional Challenge
Authors: Ghiasi Shadi , Greco Alberto , Barbieri Riccardo , Scilingo Enzo Pasquale , Valenza Gaetano 
Published: March 2020

AbstractStandard functional assessment of autonomic nervous system (ANS) activity on cardiovascular control relies on spectral analysis of heart rate variability (HRV) series. However, difficulties in obtaining a reliable measure of sympathetic activity from HRV spectra limits the exploitation of sympatho-vagal metrics. On the other hand, measures of electrodermal activity (EDA) have been demonstrated to provide a reliable quantifier of sympathetic dynamics. In this study we propose novel indices of phasic autonomic regulation mechanisms by combining HRV and EDA correlates and thoroughly investigating their time-varying dynamics. HRV and EDA series were gathered from 26 healthy subjects during a cold-pressor test and emotional stimuli. Instantaneous linear and nonlinear (bispectral) estimates of vagal dynamics were obtained from HRV through inhomogeneous point-process models, and combined with a sensitive maker of sympathetic tone from EDA spectral power. A wavelet decomposition analysis was applied to estimate phasic components of the proposed sympatho-vagal indices. Results show significant statistical differences for the proposed indices between the cold-pressor elicitation and previous resting state. Furthermore, an accuracy of 73.08% was achieved for the automatic emotional valence recognition. The proposed nonlinear processing of phasic ANS markers brings novel insights on autonomic functioning that can be exploited in the field of affective computing and psychophysiology.
Iodine and bromine in fish consumed by indigenous peoples of the Russian Arctic
Authors: Sobolev Nikita , Aksenov Andrey , Sorokina Tatiana , Chashchin Valery , Ellingsen Dag G. , Nieboer Evert , Varakina Yulia , Plakhina Elena , Onuchina Alexandra , Thomassen Magny Skinlo , Thomassen Yngvar 
Published: March 2020

AbstractFish muscle may constitute one of the main sources of iodine (I) for the indigenous peoples of the Russian Arctic, although limited information is available about its content in commonly consumed fish species. In the current study, bromine (Br), I, the essential elements (copper, selenium and zinc) and other non-essential elements — specifically mercury, arsenic (As), cadmium, lead and nickel — have been quantified in 10 fish species consumed by people living in the Nenets and Chukotka Regions. Fish muscle was analysed by ICP-MS after nitric acid or tetramethylammonium hydroxide digestion. Certified reference materials were employed and concentrations are reported as geometric means (GMs). Atlantic cod (6.32 mg/kg) and navaga (0.934 mg/kg) contained substantially higher amounts of I than all other fish species, while broad whitefish had the lowest (0.033 mg/kg). By comparison, navaga contained more Br (14.5 mg/kg) than the other fish species, ranging 7.45 mg/kg in Atlantic cod to 2.39 mg/kg in northern pike. A significant inter-fish association between As and I in freshwater and marine fish was observed, suggesting common sources and perhaps parallel absorption patterns. Only Atlantic cod and, to lesser extent, navaga constituted significant dietary sources of I.
Stability of copper acetate at high P-T and the role of organic acids and CO2 in metallic mineralization
Authors: Ni Zhiyong , Chen Yanjing , Zheng Haifei , Li Nuo , Li Heping 
Published: March 2020

AbstractMany metal deposits were formed by carbonic fluids (rich in CO2) as indicated by fluid inclusions in minerals, but the precise role of CO2 in metal mineralization remains unclear. The main components in fluid inclusions, i.e. H2O and CO2, correspond to the decomposed products of organic acids, which lead us to consider that in the mineralization process the organic acids transport and then discharge metals when they are stable and unstable, respectively. Here we show that the thermal stability of copper acetate solution at 15–350 °C (0.1–830 MPa) provides insight as to the role of organic acids in metal transport. Results show that the copper acetate solution is stable at high P-T conditions under low geothermal gradient of <19 °C/km, with an isochore of P = 1.89 T + 128.58, verifying the possibility of copper transportation as acetate solution. Increasing geothermal gradient leads to thermal dissociation of copper acetate in the way of 4Cu(CH3 COO)2 + 2H2O = 4Cu + 2CO2 + 7CH3COOH. The experimental results and inferences in this contribution agree well with the frequently observed fluid inclusions and wall-rock alterations of carbonate, sericite and quartz in hydrothermal deposits, and provide a new dimension in the understanding of the role of CO2 during mineralization.
First principles study of oxygen vacancy activation energy barrier in zirconia-based resistive memory
Authors: Hur Ji-Hyun 
Published: March 2020

AbstractUnlike experimental measurements that appeared to be quite large activation barriers, oxygen vacancies in zirconia-based resistive random access memory (ReRAM) are believed to migrate with a fairly low energy barrier, and this discrepancy has not been noticed nor seriously questioned up to date. In this paper, we work on this problem by means of first-principles calculations categorizing all the possible migration pathways by crystallographic directions. From the results, it is found that the low activation energy of oxygen vacancy that is expected from the switching characteristic of the device is originated from +2q charged oxygen vacancies in a nanometer-sized filament migrating into a particular crystallographic direction of monoclinic zirconia.
Neural magnetic field dependent fMRI toward direct functional connectivity measurements: A phantom study
Authors: Ito Yosuke , Ueno Masahito , Kobayashi Tetsuo 
Published: March 2020

AbstractRecently, the main issue in neuroscience has been the imaging of the functional connectivity in the brain. No modality that can measure functional connectivity directly, however, has been developed yet. Here, we show the novel MRI sequence, called the partial spinlock sequence toward direct measurements of functional connectivity. This study investigates a probable measurement of phase differences directly associated with functional connectivity. By employing partial spinlock imaging, the neural magnetic field might influence the magnetic resonance signals. Using simulation and phantom studies to model the neural magnetic fields, we showed that magnetic resonance signals vary depending on the phase of an externally applied oscillating magnetic field with non-right flip angles. These results suggest that the partial spinlock sequence is a promising modality for functional connectivity measurements.
Resveratrol and its Related Polyphenols Contribute to the Maintenance of Genome Stability
Authors: Matsuno Yusuke , Atsumi Yuko , Alauddin Md. , Rana Md. Masud , Fujimori Haruka , Hyodo Mai , Shimizu Atsuhiro , Ikuta Tomoki , Tani Hiroko , Torigoe Hidetaka , Nakatsu Yoshimichi , Tsuzuki Teruhisa , Komai Michio , Shirakawa Hitoshi , Yoshioka Ken-ichi 
Published: March 2020

AbstractGenomic destabilisation is associated with the induction of mutations, including those in cancer-driver genes, and subsequent clonal evolution of cells with abrogated defence systems. Such mutations are not induced when genome stability is maintained; however, the mechanisms involved in genome stability maintenance remain elusive. Here, resveratrol (and related polyphenols) is shown to enhance genome stability in mouse embryonic fibroblasts, ultimately protecting the cells against the induction of mutations in the ARF/p53 pathway. Replication stress-associated DNA double-strand breaks (DSBs) that accumulated with genomic destabilisation were effectively reduced by resveratrol treatment. In addition, resveratrol transiently stabilised the expression of histone H2AX, which is involved in DSB repair. Similar effects on the maintenance of genome stability were observed for related polyphenols. Accordingly, we propose that polyphenol consumption can contribute to the suppression of cancers that develop with genomic instability, as well as lifespan extension.
Near-future ocean warming and acidification alter foraging behaviour, locomotion, and metabolic rate in a keystone marine mollusc
Authors: Horwitz Rael , Norin Tommy , Watson Sue-Ann , Pistevos Jennifer C. A. , Beldade Ricardo , Hacquart Simon , Gattuso Jean-Pierre , Rodolfo-Metalpa Riccardo , Vidal-Dupiol Jeremie , Killen Shaun S. , Mills Suzanne C. 
Published: March 2020

AbstractEnvironmentally-induced changes in fitness are mediated by direct effects on physiology and behaviour, which are tightly linked. We investigated how predicted ocean warming (OW) and acidification (OA) affect key ecological behaviours (locomotion speed and foraging success) and metabolic rate of a keystone marine mollusc, the sea hareStylocheilus striatus, a specialist grazer of the toxic cyanobacteriumLyngbya majuscula. We acclimated sea hares to OW and/or OA across three developmental stages (metamorphic, juvenile, and adult) or as adults only, and compare these to sea hares maintained under current-day conditions. Generally, locomotion speed and time to locate food were reduced ~1.5- to 2-fold when the stressors (OW or OA) were experienced in isolation, but reduced ~3-fold when combined. Decision-making was also severely altered, with correct foraging choice nearly 40% lower under combined stressors. Metabolic rate appeared to acclimate to the stressors in isolation, but was significantly elevated under combined stressors. Overall, sea hares that developed under OW and/or OA exhibited a less severe impact, indicating beneficial phenotypic plasticity. Reduced foraging success coupled with increased metabolic demands may impact fitness in this species and highlight potentially large ecological consequences under unabated OW and OA, namely in regulating toxic cyanobacteria blooms on coral reefs.
Accuracy of Two Point-of-Care Tests for Rapid Diagnosis of Bovine Tuberculosis at Animal Level using Non-Invasive Specimens
Authors: Kelley Holden V. , Waibel Sarah M. , Sidiki Sabeen , Tomatis-Souverbielle Cristina , Scordo Julia M. , Hunt W. Garret , Barr N. , Smith R. , Silwani Sayeed N. , Averill James J. , Baer Susan , Hengesbach Janet , Yildiz Vedat O. , Pan Xueliang , Gebreyes Wondwossen A. , Balada-Llasat Joan-Miquel , Wang Shu-Hua , Torrelles Jordi B. 
Published: March 2020

AbstractBovine tuberculosis (BTB) testing in cattle requires a significant investment of time, equipment, and labor. Novel, rapid, cheaper and accurate methods are needed. The Alere Determine TB lipoarabinomannan antigen (LAM-test) is a World Health Organization-endorsed point-of-care urine test designed to detect active TB disease in humans. The Lionex Animal TB Rapid Test (Lionex-test) is a novel animal specific TB diagnostic blood test. An animal level analysis was performed using urine (n = 141) and milk (n = 63) samples from depopulated BTB-suspected cattle to test the accuracy of the LAM-test when compared to results of positive TB detection by any routine BTB tests (BOVIGAM, necropsy, histology, culture, PCR) that are regularly performed by the United States Department of Agriculture (USDA). The agreement between the urine LAM-test and USDA standard tests were poor at varying testing time points. The same milk samples did not elicit statistically significant agreement with the Lionex-test, although positive trends were present. Hence, we cannot recommend the LAM-test as a valid BTB diagnostic test in cattle using either urine or milk. The Lionex-test’s production of positive trends using milk samples suggests larger sample sizes may validate the Lionex-test in accurately diagnosing BTB in cattle using milk samples, potentially providing a quick and reliable field test for BTB.
Organomineral Fertilizer as Source of P and K for Sugarcane
Authors: Crusciol Carlos Alexandre Costa , Campos Murilo de , Martello Jorge Martinelli , Alves Cleiton José , Nascimento Carlos Antonio Costa , Pereira Júlio Cesar dos Reis , Cantarella Heitor 
Published: March 2020

AbstractSugarcane (Saccharum spp) crop has high social, economic and environmental importance for several regions throughout the world. However, the increasing demand for efficiency and optimization of agricultural resources generates uncertainties regarding high mineral fertilizer consumption. Thereby, organomineral fertilizers are to reduce the conventional sources consumption. Thus, this study was carried out to evaluate the agronomic and economic sugarcane performancies and the residual effect of P and K under mineral and organomineral fertilization. Growth and technological parameters, leaf and soil nutrients concentration in surface and subsurface layers were analyzed from sugarcane planting (plant cane) until the first ratoon. Agronomic and economic sugarcane efficiency were evaluated. At the first ratoon, resin-extractable P provided by mineral and organomineral fertilizers were, respectively, 15 and 11 mg kg−1 in the 0.0–0.2 m, and 28 and 31 mg kg−1 in 0.2–0.4 m layer. However, exchangeable K in the 0.0–0.2 m layer was 1.88 and 1.58 mmolc kg−1 for mineral and organomineral fertilizers, respectively. The yield gains over the control reached with mineral and organomineral fertilizers were, respectively, 10.99 and 17 Mg ha−1 at the lowest fertilizer rate; and 29.25 and 61.3 Mg ha−1 at the highest fertilizer rate. Agronomic and economic organomineral fertilizer efficiencies are more pronounced in plant cane. Summing two harvests, the organomineral is 7% more profitable than mineral fertilizer.
Viruses with different genome types adopt a similar strategy to pack nucleic acids based on positively charged protein domains
Authors: Requião Rodrigo D. , Carneiro Rodolfo L. , Moreira Mariana Hoyer , Ribeiro-Alves Marcelo , Rossetto Silvana , Palhano Fernando L. , Domitrovic Tatiana 
Published: March 2020

AbstractCapsid proteins often present a positively charged arginine-rich sequence at their terminal regions, which has a fundamental role in genome packaging and particle stability for some icosahedral viruses. These sequences show little to no conservation and are structurally dynamic such that they cannot be easily detected by common sequence or structure comparisons. As a result, the occurrence and distribution of positively charged domains across the viral universe are unknown. Based on the net charge calculation of discrete protein segments, we identified proteins containing amino acid stretches with a notably high net charge (Q > + 17), which are enriched in icosahedral viruses with a distinctive bias towards arginine over lysine. We used viral particle structural data to calculate the total electrostatic charge derived from the most positively charged protein segment of capsid proteins and correlated these values with genome charges arising from the phosphates of each nucleotide. We obtained a positive correlation (r = 0.91, p-value <0001) for a group of 17 viral families, corresponding to 40% of all families with icosahedral structures described to date. These data indicated that unrelated viruses with diverse genome types adopt a common underlying mechanism for capsid assembly based on R-arms.
Increase in environmental temperature affects exploratory behaviour, anxiety and social preference in Danio rerio
Authors: Angiulli E. , Pagliara V.  , Cioni C. , Frabetti F. , Pizzetti F. , Alleva E. , Toni M. 
Published: March 2020

AbstractThe aim of this work is to investigate the effect of a temperature increase on the behaviour of adult zebrafish (Danio rerio) maintained for 21 days at 34 °C (treatment) and 26 °C (control). The temperatures chosen are within the vital range of zebrafish and correspond to temperatures that this species encounters in the natural environment. Previous results showed that the same treatment affects the brain proteome and the behaviour of adult zebrafish by producing alterations in the proteins involved in neurotransmitter release and synaptic function and impairing fish exploratory behaviour. In this study, we have investigated the performance of treated and control zebrafish during environmental exploration by using four behavioural tests (novel tank diving, light and dark preference, social preference and mirror biting) that are paradigms for assessing the state of anxiety, boldness, social preference and aggressive behaviour, respectively. The results showed that heat treatment reduces anxiety and increases the boldness of zebrafish, which spent more time in potentially dangerous areas of the tank such as the top and the uncovered bright area and at a distance from the social group, thus decreasing protection for the zebrafish. These data suggest that the increase in ambient temperature may compromise zebrafish survival rate in the natural environment.
From thoughtless awareness to effortful cognition: alpha - theta cross-frequency dynamics in experienced meditators during meditation, rest and arithmetic
Authors: Rodriguez-Larios Julio , Faber Pascal , Achermann Peter , Tei Shisei , Alaerts Kaat 
Published: March 2020

AbstractNeural activity is known to oscillate within discrete frequency bands and the synchronization between these rhythms is hypothesized to underlie information integration in the brain. Since strict synchronization is only possible for harmonic frequencies, a recent theory proposes that the interaction between different brain rhythms is facilitated by transient harmonic frequency arrangements. In this line, it has been recently shown that the transient occurrence of 2:1 harmonic cross-frequency relationships between alpha and theta rhythms (i.e. falpha ≈ 12 Hz; ftheta ≈ 6 Hz) is enhanced during effortful cognition. In this study, we tested whether achieving a state of ‘mental emptiness’ during meditation is accompanied by a relative decrease in the occurrence of 2:1 harmonic cross-frequency relationships between alpha and theta rhythms. Continuous EEG recordings (19 electrodes) were obtained from 43 highly experienced meditators during meditation practice, rest and an arithmetic task. We show that the occurrence of transient alpha:theta 2:1 harmonic relationships increased linearly from a meditative to an active cognitive processing state (i.e. meditation < rest < arithmetic task). It is argued that transient EEG cross-frequency arrangements that prevent alpha:theta cross-frequency coupling could facilitate the experience of ‘mental emptiness’ by avoiding the interaction between the memory and executive components of cognition.
Horizontal and Vertical Distance Perception in Altered Gravity
Authors: Clément Gilles , Bukley Angie , Loureiro Nuno , Lindblad Louise , Sousa Duarte , Zandvilet André 
Published: March 2020

AbstractThe perception of the horizontal and vertical distances of a visual target to an observer was investigated in parabolic flight during alternating short periods of normal gravity (1 g). microgravity (0 g), and hypergravity (1.8 g). The methods used for obtaining absolute judgments of egocentric distance included verbal reports and visually directed motion toward a memorized visual target by pulling on a rope with the arms (blind pulling). The results showed that, for all gravity levels, the verbal reports of distance judgments were accurate for targets located between 0.6 and 6.0 m. During blind pulling, subjects underestimated horizontal distances as distances increased, and this underestimation decreased in 0 g. Vertical distances for up targets were overestimated and vertical distances for down targets were underestimated in both 1 g and 1.8 g. This vertical asymmetry was absent in 0 g. The results of the present study confirm that blind pulling and verbal reports are independently influenced by gravity. The changes in distance judgments during blind pulling in 0 g compared to 1 g support the view that, during an action-based task, subjects base their perception of distance on the estimated motor effort of navigating to the perceived object.