bluuebunny/crossref_metadata_2025 huggingface dataset:
Characteristics of Energetic Electrons Near Active Magnetotail Reconnection Sites: Tracers of a Complex Magnetic Topology and Evidence of Localized Acceleration
Authors: Turner Drew L. , Cohen Ian J. , Bingham Samuel T. , Stephens Grant K. , Sitnov Mikhail I. , Mauk Barry H. , Denton Richard E. , Leonard Trevor W. , Fennell Joseph F. , Blake J. Bernard , Torbert Roy B. , Burch James L.
Published: December 2020

We present detailed observations and reconstructed magnetic field topologies from a magnetic reconnection event observed directly by NASA's Magnetospheric Multiscale (MMS) mission. Comparing and contrasting energy and angular distributions of >50 keV electrons observed by three MMS spacecraft separated by only ∼18 km revealed a combination of chaotic motion and surprisingly coherent gyrophase bunching within a few thousand kilometers of the reconnection site. Such gyrophase‐bunched electrons have not been observed previously at these energies in relation to magnetic reconnection. Results indicate that the magnetic topology around the electron diffusion region was relatively stable over several seconds (i.e., more than a thousand electron gyro‐periods), and the observed gyrophase bunching may be the highest‐energy extent of coherent gyrophase structures observed at lower‐energies closer to the reconnection site. We hypothesize that the coherent gyrophase bunching was evidence of these energetic electrons being accelerated at the reconnection site and possibly also in the outflowing exhaust jets of the active reconnection. This case study exemplifies how energetic electrons can carry coherent signals of remote magnetic topologies and processes relevant to the physics of magnetic reconnection.
Soil Carbon Loss and Weak Fire Feedbacks During Pliocene C4 Grassland Expansion in Australia
Authors: Karp Allison T. , Andrae Jake W. , McInerney Francesca A. , Polissar Pratigya J. , Freeman Katherine H.
Published: December 2020

C4 grasslands proliferated later in Australia than they did on other continents (∼3.5 Ma vs. 10–5 Ma). It remains unclear whether this delay reflects differences in climate conditions or ecological feedbacks, such as fire, that promote C4 ecosystems. Here, we evaluated these factors using terrestrial biomarkers from marine sediments off western Australia. Fire‐derived polycyclic aromatic hydrocarbons (PAH) indicate fire ecology did not substantially change during or following C4 expansion. The presence of fire‐adapted C3 woody vegetation likely diminished the role of fire and delayed C4 expansion until it was prompted by climate drying between 3.5 and 3.0 Ma. At the same time, mass accumulation rates of weathered PAHs increased 100‐fold, which indicates a significant loss of soil carbon accompanied this ecosystem shift. The tight couplings between hydroclimate and carbon storage altered boundary conditions for Australian ecosystems, and similar abrupt behavior may shape environmental responses to climate change.
Probabilistic Projections of Multidimensional Flood Risks at a Convection‐Permitting Scale
Authors: Zhang B. , Wang S. , Wang Y.
Published: December 2020

Understanding future river flood risk is a prerequisite for developing climate change adaptation strategies and enhancing disaster resilience. Previous flood risk assessments can barely take into account future changes of fine‐scale hydroclimatic characteristics and hardly quantify multivariate interactions among flood variables, thereby resulting in an unreliable assessment of flood risk. In this study, for the first time, we develop probabilistic projections of multidimensional river flood risks at a convection‐permitting scale through the Weather Research and Forecasting (WRF) climate simulations with 4‐km horizontal grid spacing. Vine copula has been widely used to assess the multidimensional dependence structure of hydroclimate variables, but the commonly used frequentist approach may fail to identify the correct vine model and to obtain the uncertainty interval. Thus, a Bayesian vine copula approach is proposed to explicitly address the multidimensional dependence of flood characteristics (i.e., flood peak, volume, and duration) and underlying uncertainties. The proposed approach enables a robust assessment of return periods of future floods for Guadalupe and Mission river basins located in South Texas of the United States. Our findings reveal that the South Texas region is projected to experience more flood events with longer duration and greater discharge volume. The flood peak, however, will not necessarily increase even though precipitation extremes are expected to become more frequent. The projected flood return periods over the Guadalupe river basin do not show an obvious increase while the Mission river basin is projected to face a dramatic increase in flood risk with exposed to 100‐year and even severer floods nearly every 2 years, on average, when considering the combined effects of flood peak, volume, and duration.
Reply to Comment by Jakobi et al. (2020) on “Soil Texture Often Exerts a Stronger Influence Than Precipitation on Mesoscale Soil Moisture Patterns”
Authors: Dong J. , Ochsner T. E.
Published: December 2020

We appreciate the constructive comment by Jakobi et al. (2020), and we confirm the calculation mistakes which they discovered. In the corrected dataset, volumetric water content was more strongly correlated with sand content than with antecedent precipitation index (API) for 12 out of the 18 transect dates. For one of the dates when the API correlation was of larger magnitude than the sand content correlation, the API correlation was negative, which is physically illogical. The average correlation coefficient between volumetric water content and sand content was −0.48 across all transect dates. In contrast, the average correlation coefficient between the volumetric water content and API was only 0.25, approximately one‐half the magnitude of the sand content correlation. The spatial influence of precipitation on soil water content patterns is less stable and more complex compared to that of soil texture. We stand by the claim in our paper’s title, “Soil Texture Often Exerts a Stronger Influence Than Precipitation on Mesoscale Soil Moisture Patterns.”
Distinct genomic profiles of gestational choriocarcinoma, a unique cancer of pregnant tissues
Authors: Jung Seung-Hyun , Choi Youn Jin , Kim Min Sung , Park Hyeon-Chun , Han Mi-Ryung , Hur Soo Young , Lee Ah Won , Shin Ok Ran , Kim Jeana , Lee Sung Hak , Hong Dongwan , Song Sang Yong , Chung Yeun-Jun , Lee Sug Hyung
Published: December 2020

Little is known about genomic alterations of gestational choriocarcinoma (GC), unique cancer that originates in pregnant tissues, and the progression mechanisms from the nonmalignant complete hydatidiform mole (CHM) to GC. Whole-exome sequencing (20 GCs) and/or single-nucleotide polymorphism microarray (29 GCs) were performed. We analyzed copy-neutral loss-of-heterozygosity (CN-LOH) in 29 GCs that exhibited androgenetic CN-LOHs (20 monospermic, 8 dispermic) and no CN-LOH (one with NLRP7 mutation). Most GCs (25/29) harboring recurrent copy number alterations (CNAs) and gains on 1q21.1-q44 were significantly associated with poor prognosis. We detected five driver mutations in the GCs, most of which were chromatin remodeling gene (ARID1A, SMARCD1, and EP300) mutations but not in common cancer genes such as TP53 and KRAS. One patient’s serial CHM/invasive mole/GC showed consistent CN-LOHs, but only the GC harbored CNAs, indicating that CN-LOH is an early pivotal event in HM-IM-GC development, and CNAs may be a late event that promotes CHM progression to GC. Our data indicate that GCs have unique profiles of CN-LOHs, mutations and CNAs that together differentiate GCs from non-GCs. Practically, CN-LOH and CNA profiles are useful for the molecular diagnosis of GC and the selection of GC patients with poor prognosis for more intensive treatments, respectively.
Adult mesenchymal stem cell ageing interplays with depressed mitochondrial Ndufs6
Authors: Zhang Yuelin , Guo Liyan , Han Shuo , Chen Ling , Li Cheng , Zhang Zhao , Hong Yimei , Zhang Xiaoxian , Zhou Xiaoya , Jiang Dan , Liang Xiaoting , Qiu Jianxiang , Zhang Jinqiu , Li Xin , Zhong Shilong , Liao Can , Yan Bin , Tse Hung-Fat , Lian Qizhou
Published: December 2020

Mesenchymal stem cell (MSC)-based therapy has emerged as a novel strategy to treat many degenerative diseases. Accumulating evidence shows that the function of MSCs declines with age, thus limiting their regenerative capacity. Nonetheless, the underlying mechanisms that control MSC ageing are not well understood. We show that compared with bone marrow-MSCs (BM-MSCs) isolated from young and aged samples, NADH dehydrogenase (ubiquinone) iron-sulfur protein 6 (Ndufs6) is depressed in aged MSCs. Similar to that of Ndufs6 knockout (Ndufs6−/−) mice, MSCs exhibited a reduced self-renewal and differentiation capacity with a tendency to senescence in the presence of an increased p53/p21 level. Downregulation of Ndufs6 by siRNA also accelerated progression of wild-type BM-MSCs to an aged state. In contrast, replenishment of Ndufs6 in Ndufs6−/−-BM-MSCs significantly rejuvenated senescent cells and restored their proliferative ability. Compared with BM-MSCs, Ndufs6−/−-BM-MSCs displayed increased intracellular and mitochondrial reactive oxygen species (ROS), and decreased mitochondrial membrane potential. Treatment of Ndufs6−/−-BM-MSCs with mitochondrial ROS inhibitor Mito-TEMPO notably reversed the cellular senescence and reduced the increased p53/p21 level. We provide direct evidence that impairment of mitochondrial Ndufs6 is a putative accelerator of adult stem cell ageing that is associated with excessive ROS accumulation and upregulation of p53/p21. It also indicates that manipulation of mitochondrial function is critical and can effectively protect adult stem cells against senescence.
In cis TP53 and RAD51C pathogenic variants may predispose to sebaceous gland carcinomas
Authors: Le Duc Diana , Hentschel Julia , Neuser Sonja , Stiller Mathias , Meier Carolin , Jäger Elisabeth , Abou Jamra Rami , Platzer Konrad , Monecke Astrid , Ziemer Mirjana , Markovic Aleksander , Bläker Hendrik , Lemke Johannes R.
Published: December 2020

Pathogenic variants inTP53have been classically thought to cause Li-Fraumeni syndrome (LFS), a cancer predisposition with high risks for various childhood- and adult-onset malignancies. However, increased genetic testing has lately revealed, that pathogenic variant carriers exhibit a broader range of phenotypes and that penetrance may be dependent both on variant type and modifiers. Using next generation sequencing and short tandem repeat analysis, we identified germline pathogenic variants inTP53andRAD51Clocated incison chromosome 17 in a 43-year-old male, who has developed a rare sebaceous gland carcinoma (SGC) but so far no tumors of the LFS spectrum. This course mirrors aTrp53-Rad51c-double-mutantcismouse-model, which similarly develops SGC, while the characteristicTrp53-associated tumor spectrum occurs with significantly lower frequency. Therefore, we propose that co-occurent pathogenic variants inRAD51CandTP53may predispose to SGC, reminiscent of Muir-Torre syndrome. Further, this report supports the diversity of clinical presentations associated with germlineTP53alterations, and thus, the proposed expansion of LFS to heritableTP53-related cancer syndrome.
Calculation of external climate costs for food highlights inadequate pricing of animal products
Authors: Pieper Maximilian , Michalke Amelie , Gaugler Tobias
Published: December 2020

Although the agricultural sector is globally a main emitter of greenhouse gases, thorough economic analysis of environmental and social externalities has not yet been conducted. Available research assessing agricultural external costs lacks a differentiation between farming systems and food categories. A method addressing this scientific gap is established in this paper and applied in the context of Germany. Using life-cycle assessment and meta-analytical approaches, we calculate the external climate costs of foodstuff. Results show that external greenhouse gas costs are highest for conventional and organic animal-based products (2.41€/kg product; 146% and 71% surcharge on producer price level), followed by conventional dairy products (0.24€/kg product; 91% surcharge) and lowest for organic plant-based products (0.02€/kg product; 6% surcharge). The large difference of relative external climate costs between food categories as well as the absolute external climate costs of the agricultural sector imply the urgency for policy measures that close the gap between current market prices and the true costs of food.
Li1.5La1.5MO6 (M = W6+, Te6+) as a new series of lithium-rich double perovskites for all-solid-state lithium-ion batteries
Authors: Amores Marco , El-Shinawi Hany , McClelland Innes , Yeandel Stephen R. , Baker Peter J. , Smith Ronald I. , Playford Helen Y. , Goddard Pooja , Corr Serena A. , Cussen Edmund J.
Published: December 2020

Solid-state batteries are a proposed route to safely achieving high energy densities, yet this architecture faces challenges arising from interfacial issues between the electrode and solid electrolyte. Here we develop a novel family of double perovskites, Li1.5La1.5MO6 (M = W6+, Te6+), where an uncommon lithium-ion distribution enables macroscopic ion diffusion and tailored design of the composition allows us to switch functionality to either a negative electrode or a solid electrolyte. Introduction of tungsten allows reversible lithium-ion intercalation below 1 V, enabling application as an anode (initial specific capacity >200 mAh g-1 with remarkably low volume change of ∼0.2%). By contrast, substitution of tungsten with tellurium induces redox stability, directing the functionality of the perovskite towards a solid-state electrolyte with electrochemical stability up to 5 V and a low activation energy barrier (<0.2 eV) for microscopic lithium-ion diffusion. Characterisation across multiple length- and time-scales allows interrogation of the structure-property relationships in these materials and preliminary examination of a solid-state cell employing both compositions suggests lattice-matching avenues show promise for all-solid-state batteries.
Overcoming gender inequality for climate resilient development
Authors: Andrijevic Marina , Crespo Cuaresma Jesus , Lissner Tabea , Thomas Adelle , Schleussner Carl-Friedrich
Published: December 2020

Gender inequalities are reflected in differential vulnerability, and exposure to the hazards posed by climate change and addressing them is key to increase the adaptive capacities of societies. We provide trajectories of the Gender Inequality Index (GII) alongside the Shared-Socioeconomic Pathways (SSPs), a scenario framework widely used in climate science. Here we find that rapid improvements in gender inequality are possible under a sustainable development scenario already in the near-term. The share of girls growing up in countries with the highest gender inequality could be reduced to about 24% in 2030 compared to about 70% today. Largely overcoming gender inequality as assessed in the GII would be within reach by mid-century. Under less optimistic scenarios, gender inequality may persist throughout the 21st century. Our results highlight the importance of incorporating gender in scenarios assessing future climate impacts and underscore the relevance of addressing gender inequalities in policies aiming to foster climate resilient development.
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity
Authors: Wylensek David , Hitch Thomas C. A. , Riedel Thomas , Afrizal Afrizal , Kumar Neeraj , Wortmann Esther , Liu Tianzhe , Devendran Saravanan , Lesker Till R. , Hernández Sara B. , Heine Viktoria , Buhl Eva M. , M. D’Agostino Paul , Cumbo Fabio , Fischöder Thomas , Wyschkon Marzena , Looft Torey , Parreira Valeria R. , Abt Birte , Doden Heidi L. , Ly Lindsey , Alves João M. P. , Reichlin Markus , Flisikowski Krzysztof , Suarez Laura Navarro , Neumann Anthony P. , Suen Garret , de Wouters Tomas , Rohn Sascha , Lagkouvardos Ilias , Allen-Vercoe Emma , Spröer Cathrin , Bunk Boyke , Taverne-Thiele Anja J. , Giesbers Marcel , Wells Jerry M. , Neuhaus Klaus , Schnieke Angelika , Cava Felipe , Segata Nicola , Elling Lothar , Strowig Till , Ridlon Jason M. , Gulder Tobias A. M. , Overmann Jörg , Clavel Thomas
Published: December 2020

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.
Uniform spatial pooling explains topographic organization and deviation from receptive-field scale invariance in primate V1
Authors: Chen Y. , Ko H. , Zemelman B. V. , Seidemann E. , Nauhaus I.
Published: December 2020

Receptive field (RF) size and preferred spatial frequency (SF) vary greatly across the primary visual cortex (V1), increasing in a scale invariant fashion with eccentricity. Recent studies reveal that preferred SF also forms a fine-scale periodic map. A fundamental open question is how local variability in preferred SF is tied to the overall spatial RF. Here, we use two-photon imaging to simultaneously measure maps of RF size, phase selectivity, SF bandwidth, and orientation bandwidth—all of which were found to be topographically organized and correlate with preferred SF. Each of these newly characterized inter-map relationships strongly deviate from scale invariance, yet reveal a common motif—they are all accounted for by a model with uniform spatial pooling from scale invariant inputs. Our results and model provide novel and quantitative understanding of the output from V1 to downstream circuits.
The default network of the human brain is associated with perceived social isolation
Authors: Spreng R. Nathan , Dimas Emile , Mwilambwe-Tshilobo Laetitia , Dagher Alain , Koellinger Philipp , Nave Gideon , Ong Anthony , Kernbach Julius M. , Wiecki Thomas V. , Ge Tian , Li Yue , Holmes Avram J. , Yeo B. T. Thomas , Turner Gary R. , Dunbar Robin I. M. , Bzdok Danilo
Published: December 2020

Humans survive and thrive through social exchange. Yet, social dependency also comes at a cost. Perceived social isolation, or loneliness, affects physical and mental health, cognitive performance, overall life expectancy, and increases vulnerability to Alzheimer’s disease-related dementias. Despite severe consequences on behavior and health, the neural basis of loneliness remains elusive. Using the UK Biobank population imaging-genetics cohort (n = ~40,000, aged 40–69 years when recruited, mean age = 54.9), we test for signatures of loneliness in grey matter morphology, intrinsic functional coupling, and fiber tract microstructure. The loneliness-linked neurobiological profiles converge on a collection of brain regions known as the ‘default network’. This higher associative network shows more consistent loneliness associations in grey matter volume than other cortical brain networks. Lonely individuals display stronger functional communication in the default network, and greater microstructural integrity of its fornix pathway. The findings fit with the possibility that the up-regulation of these neural circuits supports mentalizing, reminiscence and imagination to fill the social void.
In situ differentiation of iridophore crystallotypes underlies zebrafish stripe patterning
Authors: Gur Dvir , Bain Emily J. , Johnson Kory R. , Aman Andy J. , Pasolli H. Amalia , Flynn Jessica D. , Allen Michael C. , Deheyn Dimitri D. , Lee Jennifer C. , Lippincott-Schwartz Jennifer , Parichy David M.
Published: December 2020

Skin color patterns are ubiquitous in nature, impact social behavior, predator avoidance, and protection from ultraviolet irradiation. A leading model system for vertebrate skin patterning is the zebrafish; its alternating blue stripes and yellow interstripes depend on light-reflecting cells called iridophores. It was suggested that the zebrafish’s color pattern arises from a single type of iridophore migrating differentially to stripes and interstripes. However, here we find that iridophores do not migrate between stripes and interstripes but instead differentiate and proliferate in-place, based on their micro-environment. RNA-sequencing analysis further reveals that stripe and interstripe iridophores have different transcriptomic states, while cryogenic-scanning-electron-microscopy and micro-X-ray diffraction identify different crystal-arrays architectures, indicating that stripe and interstripe iridophores are different cell types. Based on these results, we present an alternative model of skin patterning in zebrafish in which distinct iridophore crystallotypes containing specialized, physiologically responsive, organelles arise in stripe and interstripe by in-situ differentiation.
Use of cyclic peptides to induce crystallization: case study with prolyl hydroxylase domain 2
Authors: Chowdhury Rasheduzzaman , Abboud Martine I. , McAllister Tom E. , Banerji Biswadip , Bhushan Bhaskar , Sorensen John L. , Kawamura Akane , Schofield Christopher J.
Published: December 2020

Crystallization is the bottleneck in macromolecular crystallography; even when a protein crystallises, crystal packing often influences ligand-binding and protein–protein interaction interfaces, which are the key points of interest for functional and drug discovery studies. The human hypoxia-inducible factor prolyl hydroxylase 2 (PHD2) readily crystallises as a homotrimer, but with a sterically blocked active site. We explored strategies aimed at altering PHD2 crystal packing by protein modification and molecules that bind at its active site and elsewhere. Following the observation that, despite weak inhibition/binding in solution, succinamic acid derivatives readily enable PHD2 crystallization, we explored methods to induce crystallization without active site binding. Cyclic peptides obtained via mRNA display bind PHD2 tightly away from the active site. They efficiently enable PHD2 crystallization in different forms, both with/without substrates, apparently by promoting oligomerization involving binding to the C-terminal region. Although our work involves a specific case study, together with those of others, the results suggest that mRNA display-derived cyclic peptides may be useful in challenging protein crystallization cases.
MiR-125b-2 knockout increases high-fat diet-induced fat accumulation and insulin resistance
Authors: Wei Li-Min , Sun Rui-Ping , Dong Tao , Liu Jie , Chen Ting , Zeng Bin , Wu Jia-Han , Luo Jun-yi , Sun Jia-Jie , Xi Qian-Yun , Zhang Yong-Liang
Published: December 2020

Obese individuals are more susceptible to comorbidities than individuals of healthy weight, including cardiovascular disease and metabolic disorders. MicroRNAs are a class of small and noncoding RNAs that are implicated in the regulation of chronic human diseases. We previously reported that miR-125b plays a critical role in adipogenesis in vitro. However, the involvement of miR-125b-2 in fat metabolism in vivo remains unknown. In the present study, miR-125b-2 knockout mice were generated using CRISPR/CAS9 technology, resulting in mice with a 7 bp deletion in the seed sequence of miR-125b-2. MiR-125b-2 knockout increased the weight of liver tissue, epididymal white fat and inguinal white fat. MiR-125b-2 knockout also increased adipocyte volume in HFD-induced obese mice, while there were no significant differences in body weight and feed intake versus mice fed a normal diet. Additionally, qRT-PCR and western blot analysis revealed that the expression of the miR-125b-2 target gene SCD-1 and fat synthesis-associated genes, such as PPARγ and C/EBPα, were significantly up-regulated in miR-125b-2KO mice (P < 0.05). Moreover, miR-125b-2KO altered HFD-induced changes in glucose tolerance and insulin resistance. In conclusion, we show that miR-125b-2 is a novel potential target for regulating fat accumulation, and also a candidate target to develop novel treatment strategies for obesity and diabetes.
Impact of outdoor nature-related activities on gut microbiota, fecal serotonin, and perceived stress in preschool children: the Play&Grow randomized controlled trial
Authors: Sobko Tanja , Liang Suisha , Cheng Will H. G. , Tun Hein M.
Published: December 2020

Due to rapid urbanization, children today have fewer opportunities to interact with nature and this may result in a greater risk for developing stress and depression. Outdoor nature-related activities can enhance general well-being. However, the underlying mechanisms are not fully delineated. Here we recruited 54 preschool children to participate in a 10-week structured nature-related “Play&Grow” program. Following the intervention, children were assessed for connectedness to nature and perceived stress levels using validated questionnaires. Moreover, fecal serotonin level and gut microbiota profiles were measured by ELISA and 16S rDNA amplicon sequencing, respectively. Children were significantly more connected to nature after the intervention. Their gut microbiota altered, especially by modulating the abundance of Roseburia and the fecal-serotonin level. Moreover, we also observed a reduction in the overall perceived stress, particularly in the frequency of anger among these children. This study is the first to demonstrate the impact of nature-related activities on gut microbiota, fecal serotonin and psychosocial behaviour of preschool children. However, further mechanistic studies are needed to confirm the functional role of gut microbiota in the association between connectedness to nature and improved psychosocial behavior.
Arabidopsis antibody resources for functional studies in plants
Authors: Oh Jaesung , Wilson Michael , Hill Kristine , Leftley Nicola , Hodgman Charlie , Bennett Malcolm J. , Swarup Ranjan
Published: December 2020

Here we report creation of a unique and a very valuable resource for Plant Scientific community worldwide. In this era of post-genomics and modelling of multi-cellular systems using an integrative systems biology approach, better understanding of protein localization at sub-cellular, cellular and tissue levels is likely to result in better understanding of their function and role in cell and tissue dynamics, protein–protein interactions and protein regulatory networks. We have raised 94 antibodies against key Arabidopsis root proteins, using either small peptides or recombinant proteins. The success rate with the peptide antibodies was very low. We show that affinity purification of antibodies massively improved the detection rate. Of 70 protein antibodies, 38 (55%) antibodies could detect a signal with high confidence and 22 of these antibodies are of immunocytochemistry grade. The targets include key proteins involved in hormone synthesis, transport and perception, membrane trafficking related proteins and several sub cellular marker proteins. These antibodies are available from the Nottingham Arabidopsis Stock Centre.
Collective dynamics of stock market efficiency
Authors: Alves Luiz G. A. , Sigaki Higor Y. D. , Perc Matjaž , Ribeiro Haroldo V.
Published: December 2020

Summarized by the efficient market hypothesis, the idea that stock prices fully reflect all available information is always confronted with the behavior of real-world markets. While there is plenty of evidence indicating and quantifying the efficiency of stock markets, most studies assume this efficiency to be constant over time so that its dynamical and collective aspects remain poorly understood. Here we define the time-varying efficiency of stock markets by calculating the permutation entropy within sliding time-windows of log-returns of stock market indices. We show that major world stock markets can be hierarchically classified into several groups that display similar long-term efficiency profiles. However, we also show that efficiency ranks and clusters of markets with similar trends are only stable for a few months at a time. We thus propose a network representation of stock markets that aggregates their short-term efficiency patterns into a global and coherent picture. We find this financial network to be strongly entangled while also having a modular structure that consists of two distinct groups of stock markets. Our results suggest that stock market efficiency is a collective phenomenon that can drive its operation at a high level of informational efficiency, but also places the entire system under risk of failure.
Biodegradable carboxymethyl cellulose based material for sustainable packaging application
Authors: Yaradoddi Jayachandra S. , Banapurmath Nagaraj R. , Ganachari Sharanabasava V. , Soudagar Manzoore Elahi M. , Mubarak N. M. , Hallad Shankar , Hugar Shoba , Fayaz H.
Published: December 2020

The main goal of the present work was to develop a value-added product of biodegradable material for sustainable packaging. The use of agriculture waste-derived carboxymethyl cellulose (CMC) mainly is to reduce the cost involved in the development of the film, at present commercially available CMS is costly. The main focus of the research is to translate the agricultural waste-derived CMC to useful biodegradable polymer suitable for packaging material. During this process CMC was extracted from the agricultural waste mainly sugar cane bagasse and the blends were prepared using CMC (waste derived), gelatin, agar and varied concentrations of glycerol; 1.5% (sample A), 2% (sample B), and 2.5% (sample C) was added. Thus, the film derived from the sample C (gelatin + CMC + agar) with 2.0% glycerol as a plasticizer exhibited excellent properties than other samples A and B. The physiochemical properties of each developed biodegradable plastics (sample A, B, C) were characterized using Fourier Transform Infra-Red (FTIR) spectroscopy and Differential Scanning Calorimetry (DSC), Thermogravimetric analysis (TGA). The swelling test, solubility in different solvents, oil permeability coefficient, water permeability (WP), mechanical strength of the produced material was claimed to be a good material for packaging and meanwhile its biodegradability (soil burial method) indicated their environmental compatibility nature and commercial properties. The reflected work is a novel approach, and which is vital in the conversion of organic waste to value-added product development. There is also another way to utilize commercial CMC in preparation of polymeric blends for the packaging material, which can save considerable time involved in the recovery of CMC from sugarcane bagasse.
Influences of drying temperature and storage conditions for preserving the quality of maize postharvest on laboratory and field scales
Authors: Coradi Paulo Carteri , Maldaner Vanessa , Lutz Éverton , da Silva Daí Paulo Vinícius , Teodoro Paulo Eduardo
Published: December 2020

Drying and storage methods are fundamental for maintaining the grain quality until processing. Therefore, the aim of this study was to evaluate the associations of the drying temperature with storage systems and conditions as a strategy for preserving the quality of maize grain postharvest on laboratory and field scales. An increase in temperature accelerated the reduction in grain moisture, but increased the deterioration. The wetting during the storage period reduced the grain quality. Hermetic and aerated storage systems maintained the chemical quality of the grains. The control with healthy and whole corn dried at 80 °C and stored in silos with natural aeration provided a satisfactory quality, equivalent to those of controlled drying and storage under airtight conditions and at low temperatures. Different conditions of drying and storage of corn on the laboratory and field scales were evaluated, which provides an appropriate management of these operations to maintain the grain quality.
Possible proteomic biomarkers for the detection of pancreatic cancer in oral fluids
Authors: Deutsch O. , Haviv Y. , Krief G. , Keshet N. , Westreich R. , Stemmer S. M. , Zaks B. , Navat S. P. , Yanko R. , Lahav O. , Aframian D. J. , Palmon A.
Published: December 2020

The 80% mortality rate of pancreatic-cancer (PC) makes early diagnosis a challenge. Oral fluids (OF) may be considered the ultimate body fluid for non-invasive examinations. We have developed techniques to improve visualization of minor OF proteins thereby overcoming major barriers to using OF as a diagnostic fluid. The aim of this study was to establish a short discriminative panel of OF biomarkers for the detection of PC. Unstimulated OF were collected from PC patients and controls (n = 30). High-abundance-proteins were depleted and the remaining proteins were analyzed by two-dimensional-gel-electrophoresis and quantitative dimethylation-liquid-chromatography-tandem mass-spectrometry. Label-free quantitative-mass-spectrometry analysis (qMS) was performed on 20 individual samples (n = 20). More than 100 biomarker candidates were identified in OF samples, and 21 had a highly differential expression profile. qMS analysis yielded a ROC-plot AUC value of 0.91 with 90.0% sensitivity and specificity for a combination of five biomarker candidates. We found a combination of five biomarkers for PC. Most of these proteins are known to be related to PC or other gastric cancers, but have never been detected in OF. This study demonstrates the importance of novel OF depletion methodologies for increased protein visibility and highlights the clinical applicability of OF as a diagnostic fluid.
Anatase TiO2 deposited at low temperature by pulsing an electron cyclotron wave resonance plasma source
Authors: Dey B. , Bulou S. , Gaulain T. , Ravisy W. , Richard-Plouet M. , Goullet A. , Granier A. , Choquet P.
Published: December 2020

Photocatalytic surfaces have the potentiality to respond to many of nowadays societal concerns such as clean H2 generation, CO2 conversion, organic pollutant removal or virus inactivation. Despite its numerous superior properties, the wide development of TiO2 photocatalytic surfaces suffers from important drawbacks. Hence, the high temperature usually required (> 450 °C) for the synthesis of anatase TiO2 is still a challenge to outreach. In this article, we report the development and optimisation of an ECWR-PECVD process enabling the deposition of anatase TiO2 thin films at low substrate temperature. Scanning of experimental parameters such as RF power and deposition time was achieved in order to maximise photocatalytic activity. The careful selection of the deposition parameters (RF power, deposition time and plasma gas composition) enabled the synthesis of coatings exhibiting photocatalytic activity comparable to industrial references such as P25 Degussa and Pilkington Activ at a substrate temperature below 200 °C. In addition, to further decrease the substrate temperature, the interest of pulsing the plasma RF source was investigated. Using a duty cycle of 50%, it is thus possible to synthesise photocatalytic anatase TiO2 thin films at a substrate temperature below 115 °C with a deposition rate around 10 nm/min.
Mating-regulated atrial proteases control reinsemination rates in Anopheles gambiae females
Authors: Bascuñán Priscila , Gabrieli Paolo , Mameli Enzo , Catteruccia Flaminia
Published: December 2020

Anopheles gambiae mosquitoes are the most important vectors of human malaria. The reproductive success of these mosquitoes relies on a single copulation event after which the majority of females become permanently refractory to further mating. This refractory behavior is at least partially mediated by the male-synthetized steroid hormone 20-hydroxyecdysone (20E), which is packaged together with other seminal secretions into a gelatinous mating plug and transferred to the female atrium during mating. In this study, we show that two 20E-regulated chymotrypsin-like serine proteases specifically expressed in the reproductive tract of An. gambiae females play an important role in modulating the female susceptibility to mating. Silencing these proteases by RNA interference impairs correct plug processing and slows down the release of the steroid hormone 20E from the mating plug. In turn, depleting one of these proteases, the Mating Regulated Atrial Protease 1 (MatRAP1), reduces female refractoriness to further copulation, so that a significant proportion of females mate again. Microscopy analysis reveals that MatRAP1 is localized on a previously undetected peritrophic matrix-like structure surrounding the mating plug. These data provide novel insight into the molecular mechanisms shaping the post-mating biology of these important malaria vectors.
Chlamydomonas reinhardtii LHCSR1 and LHCSR3 proteins involved in photoprotective non-photochemical quenching have different quenching efficiency and different carotenoid affinity
Authors: Perozeni Federico , Beghini Giorgia , Cazzaniga Stefano , Ballottari Matteo
Published: December 2020

Microalgae are unicellular photosynthetic organisms considered as potential alternative sources for biomass, biofuels or high value products. However, their limited biomass productivity represents a bottleneck that needs to be overcome to meet the applicative potential of these organisms. One of the domestication targets for improving their productivity is the proper balance between photoprotection and light conversion for carbon fixation. In the model organism for green algae, Chlamydomonas reinhardtii, a photoprotective mechanism inducing thermal dissipation of absorbed light energy, called Non-photochemical quenching (NPQ), is activated even at relatively low irradiances, resulting in reduced photosynthetic efficiency. Two pigment binding proteins, LHCSR1 and LHCSR3, were previously reported as the main actors during NPQ induction in C. reinhardtii. While previous work characterized in detail the functional properties of LHCSR3, few information is available for the LHCSR1 subunit. Here, we investigated in vitro the functional properties of LHCSR1 and LHCSR3 subunits: despite high sequence identity, the latter resulted as a stronger quencher compared to the former, explaining its predominant role observed in vivo. Pigment analysis, deconvolution of absorption spectra and structural models of LHCSR1 and LHCR3 suggest that different quenching efficiency is related to a different occupancy of L2 carotenoid binding site.
Data preprocessing workflow for exhaled breath analysis by GC/MS using open sources
Authors: Sola Martínez Rosa Alba , Pastor Hernández José María , Lozano Terol Gema , Gallego-Jara Julia , García-Marcos Luis , Cánovas Díaz Manuel , de Diego Puente Teresa
Published: December 2020

The noninvasive diagnosis and monitoring of high prevalence diseases such as cardiovascular diseases, cancers and chronic respiratory diseases are currently priority objectives in the area of health. In this regard, the analysis of volatile organic compounds (VOCs) has been identified as a potential noninvasive tool for the diagnosis and surveillance of several diseases. Despite the advantages of this strategy, it is not yet a routine clinical tool. The lack of reproducible protocols for each step of the biomarker discovery phase is an obstacle of the current state. Specifically, this issue is present at the data preprocessing step. Thus, an open source workflow for preprocessing the data obtained by the analysis of exhaled breath samples using gas chromatography coupled with single quadrupole mass spectrometry (GC/MS) is presented in this paper. This workflow is based on the connection of two approaches to transform raw data into a useful matrix for statistical analysis. Moreover, this workflow includes matching compounds from breath samples with a spectral library. Three free packages (xcms, cliqueMS and eRah) written in the language R are used for this purpose. Furthermore, this paper presents a suitable protocol for exhaled breath sample collection from infants under 2 years of age for GC/MS.
Unequal contribution of two paralogous CENH3 variants in cowpea centromere function
Authors: Ishii Takayoshi , Juranić Martina , Maheshwari Shamoni , Bustamante Fernanda de Oliveira , Vogt Maximilian , Salinas-Gamboa Rigel , Dreissig Steven , Gursanscky Nial , How Tracy , Demidov Dmitri , Fuchs Joerg , Schubert Veit , Spriggs Andrew , Vielle-Calzada Jean-Philippe , Comai Luca , Koltunow Anna M. G. , Houben Andreas
Published: December 2020

In most diploids the centromere-specific histone H3 (CENH3), the assembly site of active centromeres, is encoded by a single copy gene. Persistance of two CENH3 paralogs in diploids species raises the possibility of subfunctionalization. Here we analysed both CENH3 genes of the  diploid dryland crop cowpea. Phylogenetic analysis suggests that gene duplication of CENH3 occurred independently during the speciation ofVigna unguiculata. Both functionalCENH3variants are transcribed, and the corresponding proteins are intermingled in subdomains of different types of centromere sequences in a tissue-specific manner together with the kinetochore protein CENPC. CENH3.2 is removed from the generative cell of mature pollen, while CENH3.1 persists. CRISPR/Cas9-based inactivation ofCENH3.1resulted in delayed vegetative growth and sterility, indicating that this variant is needed for plant development and reproduction. By contrast,CENH3.2knockout individuals did not show obvious defects during vegetative and reproductive development. Hence, CENH3.2 of cowpea is likely at an early stage of pseudogenization and less likely undergoing subfunctionalization.
Detection of locus-specific N6-methyladenosine modification based on Ag+-assisted ligation and supersandwich signal amplification
Authors: Wang Yanxia , Zheng Ji , Duan Chengjie , Jiao Jin , Gong Youjing , Shi Hai , Xiang Yang
Published: December 2020

Emerging evidence reveals that the epitranscriptomic mark N6-methyladenosine (m6A) plays vital roles in organisms, including gene regulation and disease progression.
A multi-location peak parking approach for calculation of second dimensional retention indices for improved volatile compound identification with cryogen-free comprehensive heart-cut two-dimensional gas chromatography
Authors: Janta Pannipa , Pinyo Duangkamol , Yodta Yamonporn , Vasasiri Porames , Weidenbach Meinolf , Pursch Matthias , Yang Xiuhan (Grace) , Kulsing Chadin
Published: December 2020

Comprehensive heart-cut multidimensional gas chromatography (CH/C MDGC) without a cryogenic trapping device was developed with an approach for calculation of first and second dimensional retention indices (1I and 2I).
Identification and characterization of in vitro, in vivo, and reactive metabolites of tandutinib using liquid chromatography ion trap mass spectrometry
Authors: Al-Shakliah Nasser S. , Attwa Mohamed W. , AlRabiah Haitham , Kadi Adnan A.
Published: December 2020

Ten metabolites and five cyano adducts of TND were characterized using LC-ITMS. All metabolic and bioactivation reactions occurred at the N-piperidine and piperazine groups, which were predicted to be responsible for the TND toxicity and instability.
Regioselective C(sp3)–H fluorination of ketones: from methyl to the monofluoromethyl group
Authors: Wu Qiu-Zi , Mao Yang-Jie , Zhou Kun , Hao Hong-Yan , Chen Lei , Wang Shuang , Xu Zhen-Yuan , Lou Shao-Jie , Xu Dan-Qian
Published: December 2020

A novel strategy was developed for the modular synthesis of CH2F-containing ketones through palladium catalysed β-selective methyl C(sp3)–H fluorination.
Controlling the length of self-assembled microtubes through mechanical stress-induced scission
Authors: Kabir Arif Md. Rashedul , Sada Kazuki , Kakugo Akira
Published: December 2020

The length of a self-assembled, micro-scale tubular structure is tightly regulated through scission under tensile and compressive stress.
A first exploration of isostructurality in transition metal nitroprussides: X-ray analysis, magnetic properties and DFT calculations
Authors: Pérez Hiram , Di Santo Alejandro , Piro Oscar E. , Echeverría Gustavo A. , Cano A. , González M. , Rodríguez-Hernández J. , Ben Altabef A. , Frontera Antonio , Gil Diego M.
Published: December 2020

Transition metal M(ii) (M = Mn, Fe, Cu, Zn, Cd) nitroprussides with 1-methyl-imidazole were prepared and characterized by spectroscopic techniques, thermal analysis, and powder (Fe complex) and single-crystal XRD.
Activation of C–H bonds by a nonheme iron(iv)–oxo complex: mechanistic evidence through a coupled EDXAS/UV-Vis multivariate analysis
Authors: Tavani Francesco , Capocasa Giorgio , Martini Andrea , Sessa Francesco , Di Stefano Stefano , Lanzalunga Osvaldo , D'Angelo Paola
Published: December 2020

The understanding of reactive processes involving organic substrates is crucial to chemical knowledge and requires multidisciplinary efforts for its advancement.
Infrared spectroscopy from electrostatic embedding QM/MM: local normal mode analysis of infrared spectra of arabidopsis thaliana plant cryptochrome
Authors: Huix-Rotllant Miquel , Schwinn Karno , Ferré Nicolas
Published: December 2020

Combined QM/MM Hessians and local normal mode analysis are powerful tools to simulate and interpret complex IR spectra of biological macromolecules.
Jan Peter Toennies: an ebullient serendipitous adventurer
Authors: Friedrich Bretislav , Herschbach Dudley
Published: December 2020

A celebration of the 90th birthday of Professor Jan Peter Toennies.
Controllable coordination of a phosphotungstic acid-modified carbon matrix for anchoring Pt species with different sizes: from single atoms and subnanoclusters to nanoparticles
Authors: Li Jiazhe , Yan Zhiyuan , Bao Lingxiang , Sun Chenghui , Pang Siping
Published: December 2020

Pt species with different sizes were uniformly dispersed on phosphotungstic acid-modified carbon, and Pt SAs0.5/PTA-C exhibited outstanding catalytic performance.
Highly efficient Ru/CeO2 catalysts for formaldehyde oxidation at low temperature and the mechanistic study
Authors: Qin Xiaoxiao , Chen Xueyan , Chen Min , Zhang Jianghao , He Hong , Zhang Changbin
Published: December 2020

Ru species have a high redox capacity on a CeO2 support, and the metallic Ru species could be easily oxidized back to RuOx species.
Ionothermal synthesis of octahedral lanthanoid coordination networks exhibiting slow magnetization relaxation and efficient photoluminescence
Authors: Yang Ting-Hai , Wang Shu-Fan , Lin Chen-Lan , Wang Xin , Zhu Binglong , Wu Dayu
Published: December 2020

An ionothermal reaction of lanthanoid salts with tetraethyl-p-xylenediphosphonate (tepxdp) in ionic liquids, such as choline chloride and malonic acid, resulted in the formation of three novel lanthanoid–organic coordination networks with the formula [Ln(H2pxdp)1.5]n.
Construction of Bi2MoO6/CdS heterostructures with enhanced visible light photocatalytic activity for fuel denitrification
Authors: Hu Weineng , Jiang Mengmeng , Liang Ruowen , Huang Renkun , Xia Yuzhou , Liang Zhiyu , Yan Guiyang
Published: December 2020

A newly designed and successfully prepared step-scheme Bi2MoO6/CdS heterojunction photocatalyst shows enhanced fuel denitrification activity and stability.