bluuebunny/crossref_metadata_2025_split huggingface dataset:
Acute fat loss does not affect bone mass
Authors: Lagerquist Marie K. , Gustafsson Karin L. , Henning Petra , Farman Helen , Wu Jianyao , Sjögren Klara , Koskela Antti , Tuukkanen Juha , Ohlsson Claes , Wernstedt Asterholm Ingrid , Grahnemo Louise 
Published: July 2021

AbstractObesity has previously been thought to protect bone since high body weight and body mass index are associated with high bone mass. However, some more recent studies suggest that increased adiposity negatively impacts bone mass. Here, we aimed to test whether acute loss of adipose tissue, via adipocyte apoptosis, alters bone mass in age-related obese mice. Adipocyte apoptosis was induced in obese male FAT-ATTAC mice through AP20187 dimerizer-mediated activation of caspase 8 selectively in adipocytes. In a short-term experiment, dimerizer was administered to 5.5 month-old mice that were terminated 2 weeks later. At termination, the total fat mass weighed 58% less in dimerizer-treated mice compared with vehicle-treated controls, but bone mass did not differ. To allow for the detection of long-term effects, we used 9-month-old mice that were terminated six weeks after dimerizer administration. In this experiment, the total fat mass weighed less (− 68%) in the dimerizer-treated mice than in the controls, yet neither bone mass nor biomechanical properties differed between groups. Our findings show that adipose tissue loss, despite the reduced mechanical loading, does not affect bone in age-related obese mice. Future studies are needed to test whether adipose tissue loss is beneficial during more severe obesity.
Experimental demonstration of the novel “van-Hove integral method (vHI)” for measuring diffusive dynamics by elastic neutron scattering
Authors: Benedetto Antonio , Kearley Gordon J. 
Published: July 2021

AbstractQuasi-elastic neutron scattering (QENS)—based on the seminal work of Nobel Laureate Brockhouse—has been one of the major methods for studying pico-second to nano-second diffusive dynamics over the past 70 years. This is regarded as an “inelastic” method for dynamics. In contrast, we recently proposed a new neutron-scattering method for dynamics, which uses the elastic line of the scattering to access system dynamics directly in the time domain (Benedetto and Kearley in Sci Rep 9:11284, 2019). This new method has been denoted “vHI” that stands for “van Hove Integral”. The reason is that, under certain conditions, the measured elastic intensity corresponds to the running-time integral of the intermediate scattering function, $$I\left( {Q,t} \right)$$

I

Q
,
t

, up to a time that is inversely proportional to the energy band-width incident on the sample. As a result, $$I\left( {Q,t} \right)$$

I

Q
,
t

is accessed from the time derivative of the measured vHI profile. vHI has been supported by numerical and Monte-Carlo simulations, but has been difficult to validate experimentally due to the lack of a suitable instrument. Here we show that vHI works in practice, which we achieved by using a simple modification to the standard QENS backscattering spectrometer methodology. Basically, we varied the neutron-energy band-widths incident at the sample via a step-wise variation of the frequency of the monochromator Doppler-drive. This provides a measurement of the vHI profile at the detectors. The same instrument and sample were also used in standard QENS mode for comparison. The intermediate scattering functions, $$I\left( {Q,t} \right)$$

I

Q
,
t

, obtained by the two methods—vHI and QENS—are strikingly similar providing a direct experimental validation of the vHI method. Perhaps surprisingly, the counting statistics of the two methods are comparable even though the instrument used was expressly designed for QENS. This shows that the methodology modification adopted here can be used in practice to access vHI profiles at many of the backscattering spectrometers worldwide. We also show that partial integrations of the measured QENS spectrum cannot provide the vHI profile, which clarifies a common misconception. At the same time, we show a novel approach which does access $$I\left( {Q,t} \right)$$

I

Q
,
t

from QENS spectra.
Gaining insight into the assimilated diet of small bear populations by stable isotope analysis
Authors: Careddu Giulio , Ciucci Paolo , Mondovì Stella , Calizza Edoardo , Rossi Loreto , Costantini Maria Letizia 
Published: July 2021

AbstractApennine brown bears (Ursus arctos marsicanus) survive in an isolated and critically endangered population, and their food habits have been studied using traditional scat analysis. To complement current dietary knowledge, we applied Stable Isotope Analysis (SIA) to non-invasively collected bear hairs that had been individually recognized through multilocus genotyping. We analysed carbon (δ13C) and nitrogen (δ15N) stable isotopes of hair sections and bear key foods in a Bayesian mixing models framework to reconstruct the assimilated diet on a seasonal basis and to assess gender and management status effects. In total, we analysed 34 different seasonal bear key foods and 35 hair samples belonging to 27 different bears (16 females and 11 males) collected during a population survey in 2014. Most bears showed wide δ15N and δ13C ranges and individual differences in seasonal isotopic patterns. Vegetable matter (herbs, fleshy fruits and hard mast) represented the major component of the assimilated diet across the dietary seasons, whereas vegetable crops were rarely and C4 plants (i.e., corn) never consumed. We confirmed an overall low consumption of large mammals by Apennine bears consistently between sexes, with highest values in spring followed by early summer but null in the other seasons. We also confirmed that consumption of fleshy fruits peaked in late summer, when wild predominated over cultivated fleshy fruits, even though the latter tended to be consumed in higher proportion in autumn. Male bears had higher δ 15N values than females in spring and autumn. Our findings also hint at additional differences in the assimilated diet between sexes, with females likely consuming more herbs during spring, ants during early summer, and hard mast during fall compared to males. In addition, although effect sizes were small and credibility intervals overlapped considerably, management bears on average were 0.9‰ lower in δ 13C and 2.9‰ higher in δ 15N compared to non-management bears, with differences in isotopic values between the two bear categories peaking in autumn. While non-management bears consumed more herbs, wild fleshy fruits, and hard mast, management bears tended to consume higher proportions of cultivated fruits, ants, and large mammals, possibly including livestock. Although multi-year sampling and larger sample sizes are needed to support our findings, our application confirms that SIA can effectively integrate previous knowledge and be efficiently conducted using samples non-invasively collected during population surveys.
Integrative taxonomy and phylogeography of Telenomus remus (Scelionidae), with the first record of natural parasitism of Spodoptera spp. in Brazil
Authors: Wengrat Ana P. G. S. , Coelho Junior Aloisio , Parra Jose R. P. , Takahashi Tamara A. , Foerster Luis A. , Corrêa Alberto S. , Polaszek Andrew , Johnson Norman F. , Costa Valmir A. , Zucchi Roberto A. 
Published: July 2021

AbstractThe egg parasitoid Telenomus remus (Hymenoptera: Scelionidae) has been investigated for classical and applied biological control of noctuid pests, especially Spodoptera (Lepidoptera: Noctuidae) species. Although T. remus was introduced into Brazil over three decades ago for classical biological control of S. frugiperda, this wasp has not been recorded as established in corn or soybean crops. We used an integrative approach to identify T. remus, combining a taxonomic key based on the male genitalia with DNA barcoding, using a cytochrome c oxidase subunit I mitochondrial gene fragment. This is the first report of natural parasitism of T. remus on S. frugiperda and S. cosmioides eggs at two locations in Brazil. We also confirmed that the T. remus lineage in Brazil derives from a strain in Venezuela (originally from Papua New Guinea and introduced into the Americas, Africa, and Asia). The occurrence of T. remus parasitizing S. frugiperda and S. cosmioides eggs in field conditions, not associated with inundative releases, suggests that the species has managed to establish itself in the field in Brazil. This opens possibilities for future biological control programs, since T. remus shows good potential for mass rearing and egg parasitism of important agricultural pests such as Spodoptera species.
A myostatin-CCL20–CCR6 axis regulates Th17 cell recruitment to inflamed joints in experimental arthritis
Authors: Fennen Michelle , Weinhage Toni , Kracke Vanessa , Intemann Johanna , Varga Georg , Wehmeyer Corinna , Foell Dirk , Korb-Pap Adelheid , Pap Thomas , Dankbar Berno 
Published: July 2021

AbstractThe interactions of fibroblast-like synoviocyte (FLS)-derived pro-inflammatory cytokines/chemokines and immune cells support the recruitment and activation of inflammatory cells in RA. Here, we show for the first time that the classical myokine myostatin (GDF-8) is involved in the recruitment of Th17 cells to inflammatory sites thereby regulating joint inflammation in a mouse model of TNFalpha-mediated chronic arthritis. Mechanistically, myostatin-deficiency leads to decreased levels of the chemokine CCL20 which is associated with less infiltration of Th17 cells into the inflamed joints. In vitro, myostatin alone or in combination with IL-17A enhances the secretion of CCL20 by FLS whereas myostatin-deficiency reduces CCL20 secretion, associated with an altered transmigration of Th17 cells. Thus, the communication between activated FLS and Th17 cells through myostatin and IL-17A may likely contribute to a vicious cycle of inflammation, accounting for the persistence of joint inflammation in chronic arthritis. Blockade of the CCL20–CCR6 axis by inhibition of myostatin may, therefore, be a promising treatment option for chronic inflammatory diseases such as arthritis.
A hybrid CNN-LSTM model for pre-miRNA classification
Authors: Tasdelen Abdulkadir , Sen Baha 
Published: July 2021

AbstractmiRNAs (or microRNAs) are small, endogenous, and noncoding RNAs construct of about 22 nucleotides. Cumulative evidence from biological experiments shows that miRNAs play a fundamental and important role in various biological processes. Therefore, the classification of miRNA is a critical problem in computational biology. Due to the short length of mature miRNAs, many researchers are working on precursor miRNAs (pre-miRNAs) with longer sequences and more structural features. Pre-miRNAs can be divided into two groups as mirtrons and canonical miRNAs in terms of biogenesis differences. Compared to mirtrons, canonical miRNAs are more conserved and easier to be identified. Many existing pre-miRNA classification methods rely on manual feature extraction. Moreover, these methods focus on either sequential structure or spatial structure of pre-miRNAs. To overcome the limitations of previous models, we propose a nucleotide-level hybrid deep learning method based on a CNN and LSTM network together. The prediction resulted in 0.943 (%95 CI ± 0.014) accuracy, 0.935 (%95 CI ± 0.016) sensitivity, 0.948 (%95 CI ± 0.029) specificity, 0.925 (%95 CI ± 0.016) F1 Score and 0.880 (%95 CI ± 0.028) Matthews Correlation Coefficient. When compared to the closest results, our proposed method revealed the best results for Acc., F1 Score, MCC. These were 2.51%, 1.00%, and 2.43% higher than the closest ones, respectively. The mean of sensitivity ranked first like Linear Discriminant Analysis. The results indicate that the hybrid CNN and LSTM networks can be employed to achieve better performance for pre-miRNA classification. In future work, we study on investigation of new classification models that deliver better performance in terms of all the evaluation criteria.
Engineering of the genome editing protein Cas9 to slide along DNA
Authors: Banerjee Trishit , Takahashi Hiroto , Subekti Dwiky Rendra Graha , Kamagata Kiyoto 
Published: July 2021

AbstractThe genome editing protein Cas9 faces engineering challenges in improving off–target DNA cleavage and low editing efficiency. In this study, we aimed to engineer Cas9 to be able to slide along DNA, which might facilitate genome editing and reduce off-target cleavage. We used two approaches to achieve this: reducing the sliding friction along DNA by removing the interactions of Cas9 residues with DNA and facilitating sliding by introducing the sliding-promoting tail of Nhp6A. Seven engineered mutants of Cas9 were prepared, and their performance was tested using single-molecule fluorescence microscopy. Comparison of the mutations enabled the identification of key residues of Cas9 to enhance the sliding along DNA in the presence and absence of single guide RNA (sgRNA). The attachment of the tail to Cas9 mutants enhanced sliding along DNA, particularly in the presence of sgRNA. Together, using the proposed approaches, the sliding ability of Cas9 was improved up to eightfold in the presence of sgRNA. A sliding model of Cas9 and its engineering action are discussed herein.
The electronic origins of the “rare earth” texture effect in magnesium alloys
Authors: Mahjoub Reza , Stanford Nikki 
Published: July 2021

AbstractAlthough magnesium alloys are lightweight, recyclable and relatively cheap, they suffer from poor ductility. This can be improved by the addition of rare earth (RE) elements, and this is now a well-established criterion for wrought alloy design. It is notable that this behavior is largely restricted to the lanthanides, but no hypothesis is yet available to explain why other elements do not have the same effect. To answer this question, ab initio simulations of crystallographically complex boundaries have been undertaken to examine the electronic origin of the RE effect. While the electronic structure provided strong bonding between the RE elements and their Mg surroundings, local disruption in atomic arrangement at the grain boundaries was found to modify this effect. This work shows quantifiable changes in electronic structure of solutes resulting from grain boundary crystallography, and is suggested to be a contributing factor to the RE texture effect.
Shifts in ecological strategy spectra of typical forest vegetation types across four climatic zones
Authors: Han Xin , Huang Jihong , Zang Runguo 
Published: July 2021

AbstractEcological strategy spectrum is the relative proportion of species in different categories of ecological strategies in a biotic community. Here, we explored ecological strategy spectra in typical forest vegetation types across four climatic zones in China. We classified ecological strategy categories by using the “StrateFy” ordination method based on three leaf functional traits. Results showed that the predominant ecological strategies of species in the tropical rainforest were CS-selected, and the predominant categories in the evergreen-deciduous broadleaved mixed forest and warm-temperate coniferous-broadleaved mixed forest were CSR and S/CSR categories respectively, whereas those in the cold-temperate coniferous forest were the S-selected ones. Ecological strategy richness of forest vegetation decreased significantly with the increase of latitude. The categories of ecological strategies with more component S increased while those with more component C decreased with the change of typical forest vegetation types from tropical rainforest through evergreen-deciduous broadleaved mixed forest and warm-temperate coniferous-broadleaved mixed forest to cool-temperate coniferous forest. Our findings highlight the usefulness of Grime’s C-S-R scheme for predicting the responses of vegetation to environmental changes, and the results are helpful in further elucidating species coexistence and community assembly in varied climatic and geographic settings.
Cryo-electron tomography provides topological insights into mutant huntingtin exon 1 and polyQ aggregates
Authors: Galaz-Montoya Jesús G. , Shahmoradian Sarah H. , Shen Koning , Frydman Judith , Chiu Wah 
Published: July 2021

AbstractHuntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentous mHTT inclusions in the brain (hallmarks of HD implicated in neurotoxicity) remain elusive. Using cryo-electron tomography and subtomogram averaging, here we show that mHTT exon 1 and polyQ-only aggregates in vitro are structurally heterogenous and filamentous, similar to prior observations with other methods. Yet, we find filaments in both types of aggregates under ~2 nm in width, thinner than previously reported, and regions forming large sheets. In addition, our data show a prevalent subpopulation of filaments exhibiting a lumpy slab morphology in both aggregates, supportive of the polyQ core model. This provides a basis for future cryoET studies of various aggregated mHTT and polyQ constructs to improve their structure-based modeling as well as their identification in cells without fusion tags.
A reference-grade genome identifies salt-tolerance genes from the salt-secreting mangrove species Avicennia marina
Authors: Natarajan Purushothaman , Murugesan Ashok Kumar , Govindan Ganesan , Gopalakrishnan Ayyaru , Kumar Ravichandiran , Duraisamy Purushothaman , Balaji Raju , Tanuja  , Shyamli Puhan Sushree , Parida Ajay K. , Parani Madasamy 
Published: July 2021

AbstractWater scarcity and salinity are major challenges facing agriculture today, which can be addressed by engineering plants to grow in the boundless seawater. Understanding the mangrove plants at the molecular level will be necessary for developing such highly salt-tolerant agricultural crops. With this objective, we sequenced the genome of a salt-secreting and extraordinarily salt-tolerant mangrove species,Avicennia marina, that grows optimally in 75% seawater and tolerates >250% seawater. Our reference-grade ~457 Mb genome contains 31 scaffolds corresponding to its chromosomes. We identified 31,477 protein-coding genes and a salinome consisting of 3246 salinity-responsive genes and homologs of 614 experimentally validated salinity tolerance genes. The salinome provides a strong foundation to understand the molecular mechanisms of salinity tolerance in plants and breeding crops suitable for seawater farming.
βA3/A1-crystallin regulates apical polarity and EGFR endocytosis in retinal pigmented epithelial cells
Authors: Shang Peng , Stepicheva Nadezda , Teel Kenneth , McCauley Austin , Fitting Christopher Scott , Hose Stacey , Grebe Rhonda , Yazdankhah Meysam , Ghosh Sayan , Liu Haitao , Strizhakova Anastasia , Weiss Joseph , Bhutto Imran A. , Lutty Gerard A. , Jayagopal Ashwath , Qian Jiang , Sahel José-Alain , Samuel Zigler J. , Handa James T. , Sergeev Yuri , Rajala Raju V. S. , Watkins Simon , Sinha Debasish 
Published: July 2021

AbstractThe retinal pigmented epithelium (RPE) is a monolayer of multifunctional cells located at the back of the eye. High membrane turnover and polarization, including formation of actin-based apical microvilli, are essential for RPE function and retinal health. Herein, we demonstrate an important role for βA3/A1-crystallin in RPE. βA3/A1-crystallin deficiency leads to clathrin-mediated epidermal growth factor receptor (EGFR) endocytosis abnormalities and actin network disruption at the apical side that result in RPE polarity disruption and degeneration. We found that βA3/A1-crystallin binds to phosphatidylinositol transfer protein (PITPβ) and that βA3/A1-crystallin deficiency diminishes phosphatidylinositol 4,5-biphosphate (PI(4,5)P2), thus probably decreasing ezrin phosphorylation, EGFR activation, internalization, and degradation. We propose that βA3/A1-crystallin acquired its RPE function before evolving as a structural element in the lens, and that in the RPE, it modulates the PI(4,5)P2 pool through PITPβ/PLC signaling axis, coordinates EGFR activation, regulates ezrin phosphorylation and ultimately the cell polarity.
Integrating circular economy in urban Amazon
Authors: Paes Michel Xocaira , Campos-Silva João Vitor , de Oliveira José Antonio Puppim 
Published: July 2021

AbstractThe Amazon hosts a large biological and cultural diversity with a deeply established knowledge of natural resource management. Nevertheless, many parts of the Amazon are increasingly urban, lacking basic urban services, such as waste management. In this context, the design of new development pathways based on the principles of the circular economy is a promising alternative to align biodiversity conservation and urban changes. Here, based on an analysis of Carauari municipality in the western Brazilian Amazon, we discuss how the principles of the circular economy can be integrated in the Amazonian urban development frontline using the existing co-management organizations.
Silk granular hydrogels self-reinforced with regenerated silk fibroin fibers
Authors: Wyss Céline Samira , Karami Peyman , Demongeot Adrien , Bourban Pierre-Etienne , Pioletti Dominique P. 
Published: July 2021

The swelling of microgels is used to concentrate the surrounding solution and regenerate silk fibroin in situ. The obtained materials are self-reinforced composite granular hydrogels with high stability, strength and toughness.
Recent advancements in the exploitation of the gut microbiome in the diagnosis and treatment of colorectal cancer
Authors: Stott Katie J. , Phillips Bethan , Parry Lee , May Stephanie 
Published: July 2021

Abstract
Over the last few decades it has been established that the complex interaction between the host and the multitude of organisms that compose the intestinal microbiota plays an important role in human metabolic health and disease. Whilst there is no defined consensus on the composition of a healthy microbiome due to confounding factors such as ethnicity, geographical locations, age and sex, there are undoubtably populations of microbes that are consistently dysregulated in gut diseases including colorectal cancer (CRC). In this review, we discuss the most recent advances in the application of the gut microbiota, not just bacteria, and derived microbial compounds in the diagnosis of CRC and the potential to exploit microbes as novel agents in the management and treatment of CRC. We highlight examples of the microbiota, and their derivatives, that have the potential to become standalone diagnostic tools or be used in combination with current screening techniques to improve sensitivity and specificity for earlier CRC diagnoses and provide a perspective on their potential as biotherapeutics with translatability to clinical trials.