bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy and precision of small saccades
Authors: Poletti Martina , Intoy Janis , Rucci Michele 
Published: September 2020

AbstractDespite recent advances on the mechanisms and purposes of fine oculomotor behavior, a rigorous assessment of the precision and accuracy of the smallest saccades is still lacking. Yet knowledge of how effectively these movements shift gaze is necessary for understanding their functions and is helpful in further elucidating their motor underpinnings. Using a combination of high-resolution eye-tracking and gaze-contingent control, here we examined the accuracy and precision of saccades aimed toward targets ranging from $$7^\prime$$

7
′

to $$80^\prime$$

80
′

eccentricity. We show that even small saccades of just 14–$$20^\prime$$

20
′

are very effective in centering the stimulus on the retina. Furthermore, we show that for a target at any given eccentricity, the probability of eliciting a saccade depends on its efficacy in reducing the foveal offset. The pattern of results reported here is consistent with current knowledge on the motor mechanisms of microsaccade production.
Rhizodegradation of PAHs differentially altered by C3 and C4 plants
Authors: Sivaram Anithadevi Kenday , Subashchandrabose Suresh Ramraj , Logeshwaran Panneerselvan , Lockington Robin , Naidu Ravi , Megharaj Mallavarapu 
Published: September 2020

AbstractPyrosequencing of 16S ribosomal RNA (rRNA) was employed to characterize bacterial communities colonizing the rhizosphere of plants with C3 and C4 photosynthetic pathways grown in soil contaminated with polycyclic aromatic hydrocarbons (PAHs) after 60 and 120 days. The results of this study exhibited a clear difference in bacterial diversity between the rhizosphere and non-rhizosphere samples and between the rhizospheres of the C3 and C4 plants after 120 days. In both C3 and C4 rhizospheres, an incremental change in PAHs degrading bacterial genera was observed in the 120th day samples compared to the 60th day ones. Among the PAHs degrading bacterial genera,Pseudomonasshowed good resistance to PAHs in the 120th day rhizosphere of both C3 and C4 plants. Conversely, the genusSphingomonasshowed sensitivity to PAHs in the 120th day rhizosphere soils of C3 plants only. Also, a significant increase in the PAHs degrading genera was observed at 120th day in the C4 rhizosphere in comparison to the C3 rhizosphere, which was reflected in a reduced PAHs concentration measured in the soil remediated with C4 plants rather than C3 plants. These results suggest that the rhizoremediation of PAHs was primarily governed by the plant photosystems, which led to differences in root secretions that caused the variation in bacterial diversity seen in the rhizospheres. This study is the first report to demonstrate the greater effectiveness of C4 plants in enhancing the PAHs degrading bacterial community than C3 plants.
Metabolomic biomarkers in midtrimester maternal plasma can accurately predict the development of preeclampsia
Authors: Lee Seung Mi , Kang Yujin , Lee Eun Mi , Jung Young Mi , Hong Subeen , Park Soo Jin , Park Chan-Wook , Norwitz Errol R. , Lee Do Yup , Park Joong Shin 
Published: September 2020

AbstractEarly identification of patients at risk of developing preeclampsia (PE) would allow providers to tailor their prenatal management and adopt preventive strategies, such as low-dose aspirin. Nevertheless, no mid-trimester biomarkers have as yet been proven useful for prediction of PE. This study investigates the ability of metabolomic biomarkers in mid-trimester maternal plasma to predict PE. A case–control study was conducted including 33 pregnant women with mid-trimester maternal plasma (gestational age [GA], 16–24 weeks) who subsequently developed PE and 66 GA-matched controls with normal outcomes (mid-trimester cohort). Plasma samples were comprehensively profiled for primary metabolic and lipidomic signatures based on gas chromatography time-of-flight mass spectrometry (GC-TOF MS) and liquid chromatography Orbitrap mass spectrometry (LC-Orbitrap MS). A potential biomarker panel was computed based on binary logistic regression and evaluated using receiver operating characteristic (ROC) analysis. To evaluate whether this panel can be also used in late pregnancy, a retrospective cohort study was conducted using plasma collected from women who delivered in the late preterm period because of PE (n = 13) or other causes (n = 21) (at-delivery cohort). Metabolomic biomarkers were compared according to the indication for delivery. Performance of the metabolomic panel to identify patients with PE was compared also to a commonly used standard, the plasma soluble fms-like tyrosine kinase-1/placental growth factor (sFlt-1/PlGF) ratio. In the mid-trimester cohort, a total of 329 metabolites were identified and semi-quantified in maternal plasma using GC-TOF MS and LC-Orbitrap-MS. Binary logistic regression analysis proposed a mid-trimester biomarker panel for the prediction of PE with five metabolites (SM C28:1, SM C30:1, LysoPC C19:0, LysoPE C20:0, propane-1,3-diol). This metabolomic model predicted PE better than PlGF (AUC [95% CI]: 0.868 [0.844–0.891] vs 0.604 [0.485–0.723]) and sFlt-1/PlGF ratio. Analysis of plasma from the at-delivery cohort confirmed the ability of this biomarker panel to distinguish PE from non-PE, with comparable discrimination power to that of the sFlt-1/PlGF ratio. In conclusion, an integrative metabolomic biomarker panel in mid-trimester maternal plasma can accurately predict the development of PE and showed good discriminatory power in patients with PE at delivery.
Thermal melanism explains macroevolutionary variation of dorsal pigmentation in Eurasian vipers
Authors: Martínez-Freiría Fernando , Toyama Ken S. , Freitas Inês , Kaliontzopoulou Antigoni 
Published: September 2020

AbstractColouration may endorse thermoregulatory and antipredatory functions in snakes. Thethermal melanism hypothesispredicts that dark-coloured individuals are ecologically favoured in cool climates. However, the loss of aposematic and cryptic colourations may imply high predation for melanistic snakes. Here, we used the monophyletic group of Eurasian vipers (subfamily Viperinae) to test whether an increase in the extent of dark area inside the characteristic zigzag dorsal pattern is associated to colder environments. We measured two colouration traits in zigzag-patterned individuals (number of dorsal marks and weighted pigmentation index) and used a phylogenetic comparative approach to explore macroevolutionary patterns of dorsal pigmentation and test whether its extent is associated to ecogeographic characteristics of lineages’ ranges. Phylogenetically-naïve and phylogenetically-informed analyses yielded a significant association between the degree of pigmentation of the zigzag pattern and environmental variables such as solar radiation, elevation and latitude. The degree of pigmentation of the zigzag pattern is highlighted as an adaptive trait that matches range attributes mirroring cold environments irrespective of the phylogeny. These results constitute the first large-scale evidence supporting the thermal melanism hypothesis in snakes, opening new avenues of inquiry for the mechanisms that shape the evolution of colour phenotypes.
CO oxidation and organic dyes degradation over graphene–Cu and graphene–CuNi catalysts obtained by solution combustion synthesis
Authors: Khort Alexander , Romanovski Valentin , Leybo Denis , Moskovskikh Dmitry 
Published: September 2020

AbstractGraphene and its analogs in combination with metal nanopowders are among the most promising catalysts for various industry valuable processes. The newly obtained solution combustion synthesized graphene–Cu and graphene–CuNi nanocomposites were examined in heterogeneous catalysis of thermal activated CO oxidation and photoactivated degradation of acid telon blue and direct blue dyes. The nanocomposites are characterized by a closely connected solution combustion synthesized graphene-metal structure with a number of graphene layers from 1 to 3 and fine metal grains sizes of 31 nm (Cu) and 14 nm (CuNi). The experimental data showed the obtained graphene-metal nanocomposites are among the most effective catalysts for CO oxidation with a temperature of 100% conversion of 150 °C and 200 °C for Cu and CuNi containing catalysts, respectively. At the same time, both nanopowders were found inactive for dyes degradation.
Identification of PIEZO1 as a potential prognostic marker in gliomas
Authors: Zhou Wenjianlong , Liu Xiangxiang , van Wijnbergen Jan Willem Maurits , Yuan Linhao , Liu Yuan , Zhang Chuanbao , Jia Wang 
Published: September 2020

AbstractIn multiple solid tumours, including gliomas, the mechanical properties change as the disease progresses. If and how mechanical cues regulate tumour cell proliferation is currently not fully studied. PIEZO1 has recently been identified as a crucial mechanosensitive cation channel in multiple solid tumours. However, we didn’t find any clinical data describing the association between PIEZO1 expression and glioma. To investigate the role of PIEZO1 in gliomas, we analysed PIEZO1 gene expression at the transcriptome level, genomic profiles and the association of PIEZO1 with clinical practice. In total, 1633 glioma samples with transcriptome data, including data from the Chinese Glioma Genome Atlas RNAseq, the Cancer Genome Atlas RNAseq and GSE16011 databases, were included in this study. Clinical information and genomic profiles including somatic mutations were also obtained. We found that PIEZO1 expression was highly correlated with malignant clinical and molecular subtypes of glioma. Gene ontology analysis showed that expression of PIEZO1 was correlated with tumour microenvironment-related genes that encode proteins involved in extracellular matrix (ECM) organization, angiogenesis and cell migration. Additionally, PIEZO1 was shown to be involved in tumour progression by serving as the central checkpoint of multiple ECM remodelling-related signalling pathways to modulate tumour cell proliferation and the tumour microenvironment in turn. Finally, high PIEZO1 expression was correlated with reduced survival time and acted as a robust biomarker for poor prognosis in gliomas. Taken together, the results indicated that high PIEZO1 expression is closely associated with highly malignant gliomas. Importantly, PIEZO1 serves as a key factor involved in sensing mechanical properties in the tumour and can regulate both tumour cells and their microenvironment to promote glioma progression, and it is also a potential therapeutic target for the treatment of gliomas.
DJ-1 (Park7) affects the gut microbiome, metabolites and the development of innate lymphoid cells (ILCs)
Authors: Singh Yogesh , Trautwein Christoph , Dhariwal Achal , Salker Madhuri S. , Alauddin Md , Zizmare Laimdota , Pelzl Lisann , Feger Martina , Admard Jakob , Casadei Nicolas , Föller Michael , Pachauri Vivek , Park David S. , Mak Tak W. , Frick Julia-Stefanie , Wallwiener Diethelm , Brucker Sara Y. , Lang Florian , Riess Olaf 
Published: September 2020

AbstractThe proper communication between gut and brain is pivotal for the maintenance of health and, dysregulation of the gut-brain axis can lead to several clinical disorders. In Parkinson’s disease (PD) 85% of all patients experienced constipation many years before showing any signs of motor phenotypes. For differential diagnosis and preventive treatment, there is an urgent need for the identification of biomarkers indicating early disease stages long before the disease phenotype manifests. DJ-1 is a chaperone protein involved in the protection against PD and genetic mutations in this protein have been shown to cause familial PD. However, how the deficiency of DJ-1 influences the risk of PD remains incompletely understood. In the present study, we provide evidence that DJ-1 is implicated in shaping the gut microbiome including; their metabolite production, inflammation and innate immune cells (ILCs) development. We revealed that deficiency of DJ-1 leads to a significant increase in two specific genera/species, namelyAlistipesandRikenella. In DJ-1 knock-out (DJ-1-/-) mice the production of fecal calprotectin and MCP-1 inflammatory proteins were elevated. Fecal and serum metabolic profile showed that malonate which influences the immune system was significantly more abundant in DJ-1−/−mice. DJ-1 appeared also to be involved in ILCs development. Further, inflammatory genes related to PD were augmented in the midbrain of DJ-1−/−mice. Our data suggest that metabolites and inflammation produced in the gut could be used as biomarkers for PD detection. Perhaps, these metabolites and inflammatory mediators could be involved in triggering inflammation resulting in PD pathology.
Compound specific isotope analysis of lipid residues provides the earliest direct evidence of dairy product processing in South Asia
Authors: Chakraborty Kalyan Sekhar , Slater Greg F. , Miller Heather M.-L. , Shirvalkar Prabodh , Rawat Yadubirsingh 
Published: September 2020

AbstractThe early evidence of domesticated animals and human–animal interaction in South Asia can be traced back to the seventh millennium BCE; however, our understanding of their use is incomplete and limited to the analysis of animal bones from archaeological sites. By the third millennium BCE with the emergence of the Indus Civilization, cattle and water-buffalo became the primary domesticates and outnumbered any other animals at the majority of the Indus settlements. Based on the analysis of skeletal remains and ethnographic data, a number of studies have suggested that cattle and water-buffalo were utilized for their meat, dairy, hides, and other labor-oriented jobs. While some of these claims are backed by empirical data, others are primarily discussed as hypotheses, for example, the exploitation of dairy. In this paper, by analyzing the absorbed lipid residues from fifty-nine ceramic sherds recovered from an agro-pastoral settlement that was occupied during the peak of the Indus period around mid- to late third millennium BCE, we provide the earliest direct evidence of dairy product processing, particularly from cattle and possibly from some water-buffalo. By providing direct evidence of animal product processing, we identify the use of primary domesticated animals and other resources in the diet during the Indus Civilization.
Efficient microbial colony growth dynamics quantification with ColTapp, an automated image analysis application
Authors: Bär Julian , Boumasmoud Mathilde , Kouyos Roger D. , Zinkernagel Annelies S. , Vulin Clément 
Published: September 2020

AbstractPopulations of genetically identical bacteria are phenotypically heterogeneous, giving rise to population functionalities that would not be possible in homogeneous populations. For instance, a proportion of non-dividing bacteria could persist through antibiotic challenges and secure population survival. This heterogeneity can be studied in complex environmental or clinical samples by spreading the bacteria on agar plates and monitoring time to growth resumption in order to infer their metabolic state distribution. We present ColTapp, the Colony Time-lapse application for bacterial colony growth quantification. Its intuitive graphical user interface allows users to analyze time-lapse images of agar plates to monitor size, color and morphology of colonies. Additionally, images at isolated timepoints can be used to estimate lag time. Using ColTapp, we analyze a dataset of Staphylococcus aureus time-lapse images including populations with heterogeneous lag time. Colonies on dense plates reach saturation early, leading to overestimation of lag time from isolated images. We show that this bias can be corrected by taking into account the area available to each colony on the plate. We envision that in clinical settings, improved analysis of colony growth dynamics may help treatment decisions oriented towards personalized antibiotic therapies.
Influence of the surface viscous stress on the pinch-off of free surfaces loaded with nearly-inviscid surfactants
Authors: Ponce-Torres A. , Rubio M. , Herrada M. A. , Eggers J. , Montanero J. M. 
Published: September 2020

AbstractWe analyze the breakup of a pendant water droplet loaded with SDS. The free surface minimum radius measured in the experiments is compared with that obtained from a numerical solution of the Navier–Stokes equations for different values of the shear and dilatational surface viscosities. This comparison shows the small but measurable effect of the surface viscous stresses for sufficiently small spatiotemporal distances from the breakup point, and allows to establish upper bounds for the values of the shear and dilatational viscosities. We study numerically the distribution of Marangoni and viscous stresses over the free surface as a function of the time to the pinching, and describe how surface viscous stresses grow in the pinching region as the free surface approaches its breakup. When Marangoni and surface viscous stresses are taken into account, the surfactant is not swept away from the thread neck in the time interval analyzed. Surface viscous stresses eventually balance the driving capillary pressure in in the pinching region for small enough values of the time to pinching. Based on this result, we propose a scaling law to account for the effect of the surface viscosities on the last stage of temporal evolution of the neck radius.
Mutational analysis of Escherichia coli GreA protein reveals new functional activity independent of antipause and lethal when overexpressed
Authors: Fernández-Coll Llorenç , Potrykus Katarzyna , Cashel Michael , Balsalobre Carlos 
Published: September 2020

AbstractThere is a growing appreciation for the diverse regulatory consequences of the family of proteins that bind to the secondary channel of E. coli RNA polymerase (RNAP), such as GreA, GreB or DksA. Similar binding sites could suggest a competition between them. GreA is characterised to rescue stalled RNAP complexes due to its antipause activity, but also it is involved in transcription fidelity and proofreading. Here, overexpression of GreA is noted to be lethal independent of its antipause activity. A library of random GreA variants has been used to isolate lethality suppressors to assess important residues for GreA functionality and its interaction with the RNA polymerase. Some mutant defects are inferred to be associated with altered binding competition with DksA, while other variants seem to have antipause activity defects that cannot reverse a GreA-sensitive pause site in a fliC::lacZ reporter system. Surprisingly, apparent binding and cleavage defects are found scattered throughout both the coiled-coil and globular domains. Thus, the coiled-coil of GreA is not just a measuring stick ensuring placement of acidic residues precisely at the catalytic centre but also seems to have binding functions. These lethality suppressor mutants may provide valuable tools for future structural and functional studies.
Turning date palm waste into carbon nanodots and nano zerovalent iron composites for excellent removal of methylthioninium chloride from water
Authors: Ahmad Munir , Akanji Mutair A. , Usman Adel R. A. , Al-Farraj Abdullah S. F. , Tsang Yiu Fai , Al-Wabel Mohammad I. 
Published: September 2020

AbstractNovel carbon nanodots (nCD-DBC) and nano zero-valent iron composites (nZVI-DBC) were synthesized using date palm waste-derived biochar (DBC). The synthesized materials were analyzed for chemical and structural composition by using FTIR, SEM, XRD, and TGA, and evaluated for their methylthioninium chloride dye (MB) removal efficiency from contaminated aqueous solutions. pH 7.0 was found optimum for the highest MB removal in sorption batch studies. Kinetics sorption of MB onto the sorbents was best described by pseudo-second-order (R2 = 0.93–0.99) and Elovich models (R2 = 0.86–0.97) implying that sorption was being controlled by chemisorption. Langmuir model predicted maximum sorption capacities for nCD-DBC, nZVI-DBC, and DBC were 1558.66, 1182.90, and 851.67 mg g−1, respectively, which correlated with the results of kinetics sorption. Likewise, nCD-DBC yielded the highest partition coefficient (7067 mL g−1), followed by nZVI-DBC (1460 mL g−1), and DBC (930 mL g−1). Post-sorption XRD, FTIR, and SEM analyses depicted the binding of MB onto the sorbents. It was suggested that electrostatic interactions, π–π electron donor-accepter interactions, degradation, and diffusion were responsible for MB removal by the synthesized materials. Therefore, the nCD-DBC, nZVI-DBC, and DBC can potentially be used for scavenging MB dye from contaminated aqueous solutions.
Comparative clinical outcomes of dronedarone and sotalol in Asian patients with atrial fibrillation: a nationwide cohort study
Authors: Lee So-Ryoung , Choi Eue-Keun , Kim Ji-Hyun , Kim Jung-Ae , Kwon Tae-Yeon , Lee Young Eun , Oh Seil 
Published: September 2020

AbstractWe aimed to evaluate the effectiveness and safety of dronedarone versus sotalol in real-world practice in Asian patients with atrial fibrillation (AF). Using the Korean nationwide claims database from August 2013 to December 2016, we identified patients with AF recently prescribed dronedarone or sotalol and analyzed the hospitalization risk and all-cause death until December 2017. Overall, 3119 and 1575 patients treated with dronedarone and sotalol, respectively, were included. After propensity score weighting, no significant differences were observed between the treatment groups. Dronedarone use was associated with a lower risk of all-cause hospitalization than sotalol use (hazard ratio [HR], 0.79; 95% confidence interval [CI], 0.70–0.88). The dronedarone group demonstrated a significantly lower risk of cardiovascular (CV) hospitalization than the sotalol group (HR 0.62, 95% CI 0.53–0.72); however, no significant difference was observed in non-CV hospitalization. No difference in the risk of all-cause death was observed between groups. The dronedarone group was significantly less likely to receive nonpharmacological treatment for AF than the sotalol group (HR 0.63, 95% CI 0.51–0.77). In a large-scale population of Asian patients with AF, dronedarone was associated with a lower risk of CV hospitalization and a lower need for nonpharmacological treatment for AF than sotalol.
Base-resolution methylomes of gliomas bearing histone H3.3 mutations reveal a G34 mutant-specific signature shared with bone tumors
Authors: Sangatsuda Yuhei , Miura Fumihito , Araki Hiromitsu , Mizoguchi Masahiro , Hata Nobuhiro , Kuga Daisuke , Hatae Ryusuke , Akagi Yojiro , Amemiya Takeo , Fujioka Yutaka , Arai Yasuhito , Yoshida Akihiko , Shibata Tatsuhiro , Yoshimoto Koji , Iihara Koji , Ito Takashi 
Published: September 2020

AbstractTwo recurrent mutations, K27M and G34R/V, in H3F3A, encoding non-canonical histone H3.3, are reported in pediatric and young adult gliomas, whereas G34W mutation is prevalent in bone tumors. In contrast to K27M mutation, it remains elusive how G34 mutations affect the epigenome. Here we performed whole-genome bisulfite sequencing of four G34R-mutated gliomas and the G34V-mutated glioma cell line KNS-42 for comparison with gliomas harboring K27M and no mutations in H3F3A and with G34W-mutated bone tumors. G34R-mutated gliomas exhibited lower global methylation levels, similar CpG island (CGI) methylation levels, and compromised hypermethylation of telomere-proximal CGIs, compared to the other two glioma subgroups. Hypermethylated regions specific to G34R-mutated gliomas were enriched for CGIs, including those of OLIG1, OLIG2, and canonical histone genes in the HIST1 cluster. They were notably hypermethylated in osteosarcomas with, but not without, G34W mutation. Independent component analysis revealed that G34 mutation-specific components shared a significant similarity between glioma and osteosarcoma, suggesting that G34 mutations exert characteristic methylomic effects regardless of the tumor tissue-of-origin. CRISPR/Cas9-mediated disruption of G34V-allele in KNS-42 cells led to demethylation of a subset of CGIs hypermethylated in G34R-mutated gliomas. These findings will provide a basis for elucidating epigenomic roles of G34 oncohistone in tumorigenesis.