bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractHumans 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

AbstractSkin 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

AbstractCrystallization 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

AbstractObese 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

AbstractDue 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

AbstractHere 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

AbstractSummarized 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

AbstractThe 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

AbstractDrying 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

AbstractThe 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

AbstractPhotocatalytic 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

AbstractAnopheles 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

AbstractMicroalgae 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

AbstractThe 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

AbstractIn 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.