bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiscale low-dimensional motor cortical state dynamics predict naturalistic reach-and-grasp behavior
Authors: Abbaspourazad Hamidreza , Choudhury Mahdi , Wong Yan T. , Pesaran Bijan , Shanechi Maryam M. 
Published: January 2021

AbstractMotor function depends on neural dynamics spanning multiple spatiotemporal scales of population activity, from spiking of neurons to larger-scale local field potentials (LFP). How multiple scales of low-dimensional population dynamics are related in control of movements remains unknown. Multiscale neural dynamics are especially important to study in naturalistic reach-and-grasp movements, which are relatively under-explored. We learn novel multiscale dynamical models for spike-LFP network activity in monkeys performing naturalistic reach-and-grasps. We show low-dimensional dynamics of spiking and LFP activity exhibited several principal modes, each with a unique decay-frequency characteristic. One principal mode dominantly predicted movements. Despite distinct principal modes existing at the two scales, this predictive mode was multiscale and shared between scales, and was shared across sessions and monkeys, yet did not simply replicate behavioral modes. Further, this multiscale mode’s decay-frequency explained behavior. We propose that multiscale, low-dimensional motor cortical state dynamics reflect the neural control of naturalistic reach-and-grasp behaviors.
Nonpolarizing oxygen-redox capacity without O-O dimerization in Na2Mn3O7
Authors: Tsuchimoto Akihisa , Shi Xiang-Mei , Kawai Kosuke , Mortemard de Boisse Benoit , Kikkawa Jun , Asakura Daisuke , Okubo Masashi , Yamada Atsuo 
Published: January 2021

AbstractReversibility of an electrode reaction is important for energy-efficient rechargeable batteries with a long battery life. Additional oxygen-redox reactions have become an intensive area of research to achieve a larger specific capacity of the positive electrode materials. However, most oxygen-redox electrodes exhibit a large voltage hysteresis >0.5 V upon charge/discharge, and hence possess unacceptably poor energy efficiency. The hysteresis is thought to originate from the formation of peroxide-like O22− dimers during the oxygen-redox reaction. Therefore, avoiding O-O dimer formation is an essential challenge to overcome. Here, we focus on Na2-xMn3O7, which we recently identified to exhibit a large reversible oxygen-redox capacity with an extremely small polarization of 0.04 V. Using spectroscopic and magnetic measurements, the existence of stable O−• was identified in Na2-xMn3O7. Computations reveal that O−• is thermodynamically favorable over the peroxide-like O22− dimer as a result of hole stabilization through a (σ + π) multiorbital Mn-O bond.
Ancient proteins provide evidence of dairy consumption in eastern Africa
Authors: Bleasdale Madeleine , Richter Kristine K. , Janzen Anneke , Brown Samantha , Scott Ashley , Zech Jana , Wilkin Shevan , Wang Ke , Schiffels Stephan , Desideri Jocelyne , Besse Marie , Reinold Jacques , Saad Mohamed , Babiker Hiba , Power Robert C. , Ndiema Emmanuel , Ogola Christine , Manthi Fredrick K. , Zahir Muhammad , Petraglia Michael , Trachsel Christian , Nanni Paolo , Grossmann Jonas , Hendy Jessica , Crowther Alison , Roberts Patrick , Goldstein Steven T. , Boivin Nicole 
Published: January 2021

AbstractConsuming the milk of other species is a unique adaptation ofHomo sapiens, with implications for health, birth spacing and evolution. Key questions nonetheless remain regarding the origins of dairying and its relationship to the genetically-determined ability to drink milk into adulthood through lactase persistence (LP). As a major centre of LP diversity, Africa is of significant interest to the evolution of dairying. Here we report proteomic evidence for milk consumption in ancient Africa. Using liquid chromatography tandem mass spectrometry (LC-MS/MS) we identify dairy proteins in human dental calculus from northeastern Africa, directly demonstrating milk consumption at least six millennia ago. Our findings indicate that pastoralist groups were drinking milk as soon as herding spread into eastern Africa, at a time when the genetic adaptation for milk digestion was absent or rare. Our study links LP status in specific ancient individuals with direct evidence for their consumption of dairy products.
IDH1 mutations induce organelle defects via dysregulated phospholipids
Authors: Lita Adrian , Pliss Artem , Kuzmin Andrey , Yamasaki Tomohiro , Zhang Lumin , Dowdy Tyrone , Burks Christina , de Val Natalia , Celiku Orieta , Ruiz-Rodado Victor , Nicoli Elena-Raluca , Kruhlak Michael , Andresson Thorkell , Das Sudipto , Yang Chunzhang , Schmitt Rebecca , Herold-Mende Christel , Gilbert Mark R. , Prasad Paras N. , Larion Mioara 
Published: January 2021

AbstractInfiltrating gliomas are devastating and incurable tumors. Amongst all gliomas, those harboring a mutation in isocitrate dehydrogenase 1 mutation (IDH1mut) acquire a different tumor biology and clinical manifestation from those that are IDH1WT. Understanding the unique metabolic profile reprogrammed by IDH1 mutation has the potential to identify new molecular targets for glioma therapy. Herein, we uncover increased monounsaturated fatty acids (MUFA) and their phospholipids in endoplasmic reticulum (ER), generated by IDH1 mutation, that are responsible for Golgi and ER dilation. We demonstrate a direct link between the IDH1 mutation and this organelle morphology via D-2HG-induced stearyl-CoA desaturase (SCD) overexpression, the rate-limiting enzyme in MUFA biosynthesis. Inhibition of IDH1 mutation or SCD silencing restores ER and Golgi morphology, while D-2HG and oleic acid induces morphological defects in these organelles. Moreover, addition of oleic acid, which tilts the balance towards elevated levels of MUFA, produces IDH1mut-specific cellular apoptosis. Collectively, these results suggest that IDH1mut-induced SCD overexpression can rearrange the distribution of lipids in the organelles of glioma cells, providing new insight into the link between lipid metabolism and organelle morphology in these cells, with potential and unique therapeutic implications.
4D imaging reveals mechanisms of clay-carbon protection and release
Authors: Yang Judy Q. , Zhang Xinning , Bourg Ian C. , Stone Howard A. 
Published: January 2021

AbstractSoil absorbs about 20% of anthropogenic carbon emissions annually, and clay is one of the key carbon-capture materials. Although sorption to clay is widely assumed to strongly retard the microbial decomposition of soil organic matter, enhanced degradation of clay-associated organic carbon has been observed under certain conditions. The conditions in which clay influences microbial decomposition remain uncertain because the mechanisms of clay-organic carbon interactions are not fully understood. Here we reveal the spatiotemporal dynamics of carbon sorption and release within model clay aggregates and the role of enzymatic decomposition by directly imaging a transparent smectite clay on a microfluidic chip. We demonstrate that clay-carbon protection is due to the quasi-irreversible sorption of high molecular-weight sugars within clay aggregates and the exclusion of bacteria from these aggregates. We show that this physically-protected carbon can be enzymatically broken down into fragments that are released into solution. Further, we suggest improvements relevant to soil carbon models.
Uncovering de novo gene birth in yeast using deep transcriptomics
Authors: Blevins William R. , Ruiz-Orera Jorge , Messeguer Xavier , Blasco-Moreno Bernat , Villanueva-Cañas José Luis , Espinar Lorena , Díez Juana , Carey Lucas B. , Albà M. Mar 
Published: January 2021

AbstractDe novo gene origination has been recently established as an important mechanism for the formation of new genes. In organisms with a large genome, intergenic and intronic regions provide plenty of raw material for new transcriptional events to occur, but little is know about how de novo transcripts originate in more densely-packed genomes. Here, we identify 213 de novo originated transcripts in Saccharomyces cerevisiae using deep transcriptomics and genomic synteny information from multiple yeast species grown in two different conditions. We find that about half of the de novo transcripts are expressed from regions which already harbor other genes in the opposite orientation; these transcripts show similar expression changes in response to stress as their overlapping counterparts, and some appear to translate small proteins. Thus, a large fraction of de novo genes in yeast are likely to co-evolve with already existing genes.
Limitation by a shared mutualist promotes coexistence of multiple competing partners
Authors: Hammarlund Sarah P. , Gedeon Tomáš , Carlson Ross P. , Harcombe William R. 
Published: January 2021

AbstractAlthough mutualisms are often studied as simple pairwise interactions, they typically involve complex networks of interacting species. How multiple mutualistic partners that provide the same service and compete for resources are maintained in mutualistic networks is an open question. We use a model bacterial community in which multiple ‘partner strains’ of Escherichia coli compete for a carbon source and exchange resources with a ‘shared mutualist’ strain of Salmonella enterica. In laboratory experiments, competing E. coli strains readily coexist in the presence of S. enterica, despite differences in their competitive abilities. We use ecological modeling to demonstrate that a shared mutualist can create temporary resource niche partitioning by limiting growth rates, even if yield is set by a resource external to a mutualism. This mechanism can extend to maintain multiple competing partner species. Our results improve our understanding of complex mutualistic communities and aid efforts to design stable microbial communities.
Tuning the electronic structure of Ag-Pd alloys to enhance performance for alkaline oxygen reduction
Authors: Zamora Zeledón José A. , Stevens Michaela Burke , Gunasooriya G. T. Kasun Kalhara , Gallo Alessandro , Landers Alan T. , Kreider Melissa E. , Hahn Christopher , Nørskov Jens K. , Jaramillo Thomas F. 
Published: January 2021

AbstractAlloying is a powerful tool that can improve the electrocatalytic performance and viability of diverse electrochemical renewable energy technologies. Herein, we enhance the activity of Pd-based electrocatalysts via Ag-Pd alloying while simultaneously lowering precious metal content in a broad-range compositional study focusing on highly comparable Ag-Pd thin films synthesized systematically via electron-beam physical vapor co-deposition. Cyclic voltammetry in 0.1 M KOH shows enhancements across a wide range of alloys; even slight alloying with Ag (e.g. Ag0.1Pd0.9) leads to intrinsic activity enhancements up to 5-fold at 0.9 V vs. RHE compared to pure Pd. Based on density functional theory and x-ray absorption, we hypothesize that these enhancements arise mainly from ligand effects that optimize adsorbate–metal binding energies with enhanced Ag-Pd hybridization. This work shows the versatility of coupled experimental-theoretical methods in designing materials with specific and tunable properties and aids the development of highly active electrocatalysts with decreased precious-metal content.
2D material programming for 3D shaping
Authors: Nojoomi Amirali , Jeon Junha , Yum Kyungsuk 
Published: January 2021

AbstractTwo-dimensional (2D) growth-induced 3D shaping enables shape-morphing materials for diverse applications. However, quantitative design of 2D growth for arbitrary 3D shapes remains challenging. Here we show a 2D material programming approach for 3D shaping, which prints hydrogel sheets encoded with spatially controlled in-plane growth (contraction) and transforms them to programmed 3D structures. We design 2D growth for target 3D shapes via conformal flattening. We introduce the concept of cone singularities to increase the accessible space of 3D shapes. For active shape selection, we encode shape-guiding modules in growth that direct shape morphing toward target shapes among isometric configurations. Our flexible 2D printing process enables the formation of multimaterial 3D structures. We demonstrate the ability to create 3D structures with a variety of morphologies, including automobiles, batoid fish, and real human face.
Who put the film in biofilm? The migration of a term from wastewater engineering to medicine and beyond
Authors: Flemming Hans-Curt , Baveye Philippe , Neu Thomas R. , Stoodley Paul , Szewzyk Ulrich , Wingender Jost , Wuertz Stefan 
Published: January 2021

AbstractSessile microorganisms were described as early as the seventeenth century. However, the term biofilm arose only in the 1960s in wastewater treatment research and was adopted later in marine fouling and in medical and dental microbiology. The sessile mode of microbial life was gradually recognized to be predominant on Earth, and the term biofilm became established for the growth of microorganisms in aggregates, frequently associated with interfaces, although many, if not the majority, of them not being continuous “films” in the strict sense. In this sessile form of life, microorganisms live in close proximity in a matrix of extracellular polymeric substances (EPS). They share emerging properties, clearly distinct from solitary free floating planktonic microbial cells. Common characteristics include the formation of synergistic microconsortia, using the EPS matrix as an external digestion system, the formation of gradients and high biodiversity over microscopically small distances, resource capture and retention, facilitated gene exchange as well as intercellular communication, and enhanced tolerance to antimicrobials. Thus, biofilms belong to the class of collective systems in biology, like forests, beehives, or coral reefs, although the term film addresses only one form of the various manifestations of microbial aggregates. The uncertainty of this term is discussed, and it is acknowledged that it will not likely be replaced soon, but it is recommended to understand these communities in the broader sense of microbial aggregates.
Effective routing design for remote entanglement generation on quantum networks
Authors: Li Changhao , Li Tianyi , Liu Yi-Xiang , Cappellaro Paola 
Published: January 2021

AbstractQuantum network is a promising platform for many ground-breaking applications that lie beyond the capability of its classical counterparts. Efficient entanglement generation on quantum networks with relatively limited resources such as quantum memories is essential to fully realize the network’s capabilities, the solution to which calls for delicate network design and is currently at the primitive stage. In this study we propose an effective routing scheme to enable automatic responses for multiple requests of entanglement generation between source-terminal stations on a quantum lattice network with finite edge capacities. Multiple connection paths are exploited for each connection request while entanglement fidelity is ensured for each path by performing entanglement purification. The routing scheme is highly modularized with a flexible nature, embedding quantum operations within the algorithmic workflow, whose performance is evaluated from multiple perspectives. In particular, three algorithms are proposed and compared for the scheduling of capacity allocation on the edges of quantum network. Embodying the ideas of proportional share and progressive filling that have been well-studied in classical routing problems, we design another scheduling algorithm, the propagatory update method, which in certain aspects overrides the two algorithms based on classical heuristics in scheduling performances. The general solution scheme paves the road for effective design of efficient routing and flow control protocols on applicational quantum networks.
Potential discharge, attenuation and exposure risk of SARS-CoV-2 in natural water bodies receiving treated wastewater
Authors: Kumar Manish , Alamin Md. , Kuroda Keisuke , Dhangar Kiran , Hata Akihiko , Yamaguchi Hiromichi , Honda Ryo 
Published: January 2021

AbstractRecently reported detection of SARS-CoV-2 in wastewater around the world has led to emerging concerns on potential risk in water bodies receiving treated wastewater effluent. This review aims to provide an up-to-date state of key knowledge on the impact of SARS-CoV-2 in natural water bodies receiving treated wastewater. In this review, SARS-CoV-2 concentrations in wastewater, expected removal in WWTPs, and possible dilution and decay in water bodies are reviewed based on past studies on SARS-CoV-2 and related enveloped viruses. We suggest a quantitative microbial risk assessment (QMRA) framework to estimate the potential risk of SARS-CoV-2 in natural water bodies through various water activities. Dose–response model of SARS-CoV and Poisson’s distribution is employed to estimate possible viral ingestion and the annual chance of infection through several water activities in natural water bodies. Finally, future perspectives and research needs have been addressed to overcome the limitations and uncertainty in the risk assessment of SARS-CoV-2 in natural water bodies.
Macroeconomic changes and educational inequalities in traffic fatalities in the Baltic countries and Finland in 2000–2015: a register-based study
Authors: Stickley Andrew , Baburin Aleksei , Jasilionis Domantas , Krumins Juris , Martikainen Pekka , Kondo Naoki , Leinsalu Mall 
Published: January 2021

AbstractThis study examined trends and inequalities in road traffic accident (RTA) mortality in the Baltic countries (Estonia, Latvia, Lithuania) and Finland in relation to large-scale macroeconomic changes in the 2000s. Educational inequalities in RTA mortality in 2000–2003, 2004–2007, 2008–2011 and 2012–2015 among 30–74 year olds were examined using census-linked longitudinal mortality data and by estimating the relative and slope index of inequality. Overall RTA mortality decreased substantially between 2000–2003 and 2012–2015. From 2004–2007 to 2008–2011, the RTA mortality decline accelerated but was larger in the Baltic countries. Among men the RTA mortality decline was mostly driven by a larger fall among the high and middle educated. Among women, the changes in RTA mortality by educational level had no clear pattern. From 2000–2003 to 2012–2015 relative educational inequalities in RTA mortality increased among men, although more in the Baltic countries. Among women the pattern was mixed across countries. Absolute inequalities fell in all countries among both sexes. Educational inequalities in male RTA mortality may be growing because of increasingly less access to safer cars and a more hazardous driving culture among the lower educated.
Fluorescent thermal shift-based method for detection of NF-κB binding to double-stranded DNA
Authors: Leitner Peter D. , Vietor Ilja , Huber Lukas A. , Valovka Taras 
Published: January 2021

AbstractThe nuclear factor kappa B (NF-κB) family of dimeric transcription factors regulates a wide range of genes by binding to their specific DNA regulatory sequences. NF-κB is an important therapeutic target linked to a number of cancers as well as autoimmune and inflammatory diseases. Therefore, effective high-throughput methods for the detection of NF-κB DNA binding are essential for studying its transcriptional activity and for inhibitory drug screening. We describe here a novel fluorescence-based assay for quantitative detection of κB consensus double-stranded (ds) DNA binding by measuring the thermal stability of the NF-κB proteins. Specifically, DNA binding proficient NF-κB probes, consisting of the N-terminal p65/RelA (aa 1–306) and p50 (aa 1–367) regions, were designed using bioinformatic analysis of protein hydrophobicity, folding and sequence similarities. By measuring the SYPRO Orange fluorescence during thermal denaturation of the probes, we detected and quantified a shift in the melting temperatures (ΔTm) of p65/RelA and p50 produced by the dsDNA binding. The increase in Tm was proportional to the concentration of dsDNA with apparent dissociation constants (KD) of 2.228 × 10–6 M and 0.794 × 10–6 M, respectively. The use of withaferin A (WFA), dimethyl fumarate (DMF) and p-xyleneselenocyanate (p-XSC)verified the suitability of this assay for measuring dose-dependent antagonistic effects on DNA binding. In addition, the assay can be used to analyse the direct binding of inhibitors and their effects on structural stability of the protein probe. This may facilitate the identification and rational design of new drug candidates interfering with NF-κB functions.
Impact of Newtonian heating and Fourier and Fick’s laws on a magnetohydrodynamic dusty Casson nanofluid flow with variable heat source/sink over a stretching cylinder
Authors: Ramzan Muhammad , Shaheen Naila , Chung Jae Dong , Kadry Seifedine , Chu Yu-Ming , Howari Fares 
Published: January 2021

AbstractThe present investigation aims to deliberate the magnetohydrodynamic (MHD) dusty Casson nanofluid with variable heat source/sink and modified Fourier’s and Fick’s laws over a stretching cylinder. The novelty of the flow model is enhanced with additional effects of the Newtonian heating, activation energy, and an exothermic chemical reaction. In an exothermic chemical reaction, the energy of the reactants is higher than the end products. The solution to the formulated problem is attained numerically by employing the MATLAB software function bvp4c. The behavior of flow parameters versus involved profiles is discussed graphically at length. For large values of momentum dust particles, the velocity field for the fluid flow declines, whereas an opposite trend is perceived for the dust phase. An escalation is noticed for the Newtonian heating in the temperature profile for both the fluid and dust-particle phase. A comparison is also added with an already published work to check the validity of the envisioned problem.
Low-dose Drosera rotundifolia induces gene expression changes in 16HBE human bronchial epithelial cells
Authors: Arruda-Silva Fabio , Bellavite Paolo , Marzotto Marta 
Published: January 2021

AbstractDrosera rotundifoliahas been traditionally used for the treatment of respiratory diseases in phytotherapy and homeopathy. The mechanisms of action recognized so far are linked to the known effects of specific components, such as flavonoids, but are not completely understood. In this study, the biological functions ofD. rotundifoliawere explored in vitro following the treatment of bronchial epithelial cells, which are the potential targets of the pharmacological effects of the herbal medicine. To do so, the whole plant ethanolic extract was 1000-fold diluted in water (D. rotundifolia3×) and added to a 16HBE human cell line culture for 3 h or 6 h. The effects on gene expression of the treatments and corresponding controls were then investigated by RNA sequencing. The differentially expressed genes were validated through RT-qPCR, and the enriched biological functions involved in the effects of treatment were investigated.D. rotundifolia3× did not impair cell viability and was shown to be a stimulant of cell functions by regulating the expression of dozens of genes after 3 h, and the effects were amplified after 6 h of treatment. The main differentially expressed genes encoded ligands of epithelial growth factor receptor, proteins involved in xenobiotic detoxification and cytokines, suggesting thatD. rotundifolia3× could stimulate self-repair systems, which are impaired in airway diseases. Furthermore,D. rotundifolia3× acts on a complex and multifaceted set of genes and may potentially affect different layers of the bronchial mucosa.