bluuebunny/crossref_metadata_2025_split huggingface dataset:
Energy transfer of trapped electron turbulence in tokamak fusion plasmas
Authors: Qi Lei 
Published: March 2022

AbstractThe first principle gyrokinetic simulations of trapped electron turbulence in tokamak fusion plasmas demonstrate the energy transfers from the most linearly unstable modes at high $$k_\theta \rho _i\sim 1$$

k
θ

ρ
i

∼
1

to intermediate $$k_\theta$$

k
θ

via parametric decay process in a short period of linear-nonlinear transition phase. Dominant nonlinear wave-wave interactions occur near the mode rational surface $$m\simeq nq$$

m
≃
n
q

. In fully nonlinear turbulence, inverse energy cascade occurs between a cutoff wave number $$k_c$$

k
c

and $$k_\theta \rho _i\sim 1$$

k
θ

ρ
i

∼
1

with a power law scaling $$|\phi (k_\theta )|^2\propto k^{-3}$$

|
ϕ

(

k
θ

)

|

2

∝

k

-
3

, while modes with $$k<k_c$$

k
<

k
c

are suppressed. The numerical findings show fair agreement with both the weak turbulence theory and realistic experiments on Tore Supra tokamak.
A lensed fiber Bragg grating-based membrane-in-the-middle optomechanical cavity
Authors: Baraillon Joris , Taurel Boris , Labeye Pierre , Duraffourg Laurent 
Published: March 2022

AbstractOptomechanical systems benefit from the coupling between an optical field and mechanical vibrations. Fiber-based devices are well suited to easily exploit this interaction. We report an alternative approach of a silicon nitride membrane-in-the-middle of a high quality factor ($$10^6$$

10
6

–$$10^7$$

10
7

) Fabry–Perot, formed by a grating inscribed within a fiber core as an input mirror in front of a dielectric back mirror. The Pound–Drever–Hall technique used to stabilize the laser frequency on the optical resonance frequency allows us to reduce the low frequency noise down to $${4}\,{{\mathrm{kHz}}/\sqrt{\mathrm{Hz}}}$$

4

kHz
/

Hz

. We present a detailed methodology for the characterization of the optical and optomechanical properties of this stabilized system, using various membrane geometries, with corresponding resonance frequencies in the range of several hundred of $${\mathrm{kHz}}$$
kHz
. The excellent long-term stability is illustrated by continuous measurements of the thermomechanical noise spectrum over several days, with the laser source maintained at optical resonance. This major result makes this system an ideal candidate for optomechanical sensing.
Comparison of soft tissue simulations between two planning software programs for orthognathic surgery
Authors: Modabber Ali , Baron Tanja , Peters Florian , Kniha Kristian , Danesh Golamreza , Hölzle Frank , Ayoub Nassim , Möhlhenrich Stephan Christian 
Published: March 2022

AbstractThe aim of this study was to compare the soft tissue predicative abilities of two established programs depending on the surgical technique and amount of displacement. On the basis of 50 computed tomography images, 11 orthognathic operations with differences in displacement distances and technique (maxillary advancement, MxA; maxillary impaction, MxI; mandibular setback, MnS; mandibular advancement, MnA bimaxillary displacement, MxA/MnS) as well as corresponding soft tissue predictions were simulated using the programs Dolphin (D) and ProPlan (PP). For all the soft tissue predictions by the two programs, eight linear and two angular measurements were performed and compared. The simulation of maxillary impaction showed a similar soft tissue behaviour between the two programs. However, differences or divergent behaviours were observed for other procedures. In the middle third of the face these significant differences concerned in particular the nasolabial angle (Ns-Sn-Ls)(5 mm-MA, D: 119.9 ± 8.6° vs. PP: 129.5 ± 8.4°; 7 mm-MnS: D: 128.5 ± 8.2° vs. PP: 129.6 ± 8.1°; 10 mm-MnA D: 126.0 ± 8.0° vs. PP: 124.9 ± 8.4°; 5 mm-MxA/4 mm-MnS, D: 120.2 ± 8.7° vs. PP: 129.9 ± 8.3°; all p < 0.001) and in the lower third the mentolabial angle (Pog´-B´-Li) (5 mm-MA, D: 133.2 ± 11.4° vs. PP: 126.8 ± 11.6°; 7 mm-MnS: D: 133.1 ± 11.3° vs. PP: 124.6 ± 11.9°; 10 mm-MnA D: 133.3 ± 11.5° vs. PP: 146.3 ± 11.1°; bignathic 5 mm-MxA/4 mm-MnS, D: 133.1 ± 11.4° vs. PP: 122.7 ± 11.9°; all p < 0.001) and the distance of the inferior lip to the aesthetic Line (E-Line-Li) (5 mm-MA, D: 3.7 ± 2.3 mm vs. PP: 2.8 ± 2.5 mm; 7 mm-MnS: D: 5.1 ± 3.0 mm vs. PP: 3.3 ± 2.3 mm; 10 mm-MnA D: 2.5 ± 1.6 mm vs. PP: 3.9 ± 2.8 mm; bignathic 5 mm-MxA/4 mm-MnS, D: 4.8 ± 3.0 mm vs. PP: 2.9 ± 2.0 mm; all p < 0.001). The soft tissue predictions by the tested programs differed in simulation outcome, which led to the different, even divergent, results. However, the significant differences are often below a clinically relevant level. Consequently, soft tissue prediction must be viewed critically, and its actual benefit must be clarified.
DNA methylation in Friedreich ataxia silences expression of frataxin isoform E
Authors: Rodden Layne N. , Gilliam Kaitlyn M. , Lam Christina , Rojsajjakul Teerapat , Mesaros Clementina , Dionisi Chiara , Pook Mark , Pandolfo Massimo , Lynch David R. , Blair Ian A. , Bidichandani Sanjay I. 
Published: March 2022

AbstractEpigenetic silencing in Friedreich ataxia (FRDA), induced by an expanded GAA triplet-repeat in intron 1 of theFXNgene, results in deficiency of the mitochondrial protein, frataxin. A lesser known extramitochondrial isoform of frataxin detected in erythrocytes, frataxin-E, is encoded via an alternate transcript (FXN-E) originating in intron 1 that lacks a mitochondrial targeting sequence. We show thatFXN-Eis deficient in FRDA, including in patient-derived cell lines, iPS-derived proprioceptive neurons, and tissues from a humanized mouse model. In a series of FRDA patients, deficiency of frataxin-E protein correlated with the length of the expanded GAA triplet-repeat, and with repeat-induced DNA hypermethylation that occurs in close proximity to the intronic origin ofFXN-E. CRISPR-induced epimodification to mimic DNA hypermethylation seen in FRDA reproducedFXN-Etranscriptional deficiency. Deficiency of frataxin E is a consequence of FRDA-specific epigenetic silencing, and therapeutic strategies may need to address this deficiency.
Despite its sequence identity with canonical H4, Drosophila H4r product is enriched at specific chromatin regions
Authors: Ábrahám Andrea , Villányi Zoltán , Zsindely Nóra , Nagy Gábor , Szabó Áron , Bodai László , Henn László , Boros Imre M. 
Published: March 2022

AbstractHistone variants are different from their canonical counterparts in structure and are encoded by solitary genes with unique regulation to fulfill tissue or differentiation specific functions. A single H4 variant gene (His4r or H4r) that is located outside of the histone cluster and gives rise to a polyA tailed messenger RNA via replication-independent expression is preserved in Drosophila strains despite that its protein product is identical with canonical H4. In order to reveal information on the possible role of this alternative H4 we epitope tagged endogenous H4r and studied its spatial and temporal expression, and revealed its genome-wide localization to chromatin at the nucleosomal level. RNA and immunohistochemistry analysis of H4r expressed under its cognate regulation indicate expression of the gene throughout zygotic and larval development and presence of the protein product is evident already in the pronuclei of fertilized eggs. In the developing nervous system a slight disequibrium in H4r distribution is observable, cholinergic neurons are the most abundant among H4r-expressing cells. ChIP-seq experiments revealed H4r association with regulatory regions of genes involved in cellular stress response. The data presented here indicate that H4r has a variant histone function.
In vitro plant tissue culture as the fifth generation of bioenergy
Authors: Norouzi Omid , Hesami Mohsen , Pepe Marco , Dutta Animesh , Jones Andrew Maxwell P. 
Published: March 2022

AbstractDeveloping and applying a novel and sustainable energy crop is essential to reach an efficient and economically feasible technology for bioenergy production. In this study, plant tissue culture, also referred to as in vitro culture, is introduced as one of the most promising and environmentally friendly methods for the sustainable supply of biofuels. The current study investigates the potential of in vitro -grown industrial hemp calli obtained from leaf, root, and stem explants as a new generation of energy crop. For this purpose, the in vitro grown explants were first fully characterized in terms of elemental and chemical composition. Secondly, HTL experiments were designed by Design Expert 11 with a particular focus on biocrude. Finally, the chemical components, functional groups, and petroleum-like hydrocarbons present in the biocrude were identified by PY-GCMS. A 22.61 wt.% biocrude was produced for the sample grown through callogenesis of the leaf (CL). The obtained biocrude for CL consisted of 19.55% acids, 0.42% N compounds, 15.44% ketones, 16.03% aldehydes, 2.21% furans, 20.01% aromatics, 5.2% alcohols, and 19.88% hydrocarbons. To the best of the authors’ knowledge, this is the first report that in vitro -grown biomass is hydrothermally liquefied toward biocrude production; the current work paves the way for integrating plant tissue culture and thermochemical processes for the generation of biofuels and value-added chemicals.
On the durability of surgical masks after simulated handling and wear
Authors: Varanges Vincent , Caglar Baris , Lebaupin Yann , Batt Till , He Weidong , Wang Jing , Rossi René M. , Richner Gilles , Delaloye Jean-Romain , Michaud Véronique 
Published: March 2022

AbstractAfter the spread of COVID-19, surgical masks became highly recommended to the public. They tend to be handled and used multiple times, which may impact their performance. To evaluate this risk, surgical masks of Type IIR were submitted to four simulated treatments: folding, ageing with artificial saliva or sweat and washing cycles. The air permeability, mechanical integrity, electrostatic potential, and filtration efficiency (FE) of the masks were measured to quantify possible degradation. Overall, air permeability and mechanical integrity were not affected, except after washing, which slightly degraded the filtering layers. Electrostatic potential and FE showed a strong correlation, highlighting the role of electrostatic charges on small particle filtration. A slight decrease in FE for 100 nm particles was found, from 74.4% for the reference masks to 70.6% for the mask treated in saliva for 8 h. A strong effect was observed for washed masks, resulting in FE of 46.9% (± 9.5%), comparable to that of a control group with no electrostatic charges. A dry store and reuse strategy could thus be envisaged for the public if safety in terms of viral and bacterial charge is ensured, whereas washing strongly impacts FE and is not recommended.
Children transition from simple associations to explicitly reasoned social learning strategies between age four and eight
Authors: Blakey Kirsten H. , Renner Elizabeth , Atkinson Mark , Rafetseder Eva , Caldwell Christine A. 
Published: March 2022

AbstractTo differentiate the use of simple associations from use of explicitly reasoned selective social learning, we can look for age-related changes in children’s behaviour that might signify a switch from one social learning strategy to the other. We presented 4- to 8-year-old children visiting a zoo in Scotland (N = 109) with a task in which the perceptual access of two informants was determined by the differing opacity of two screens of similar visual appearance during a hiding event. Initially success could be achieved by forming an association or inferring a rule based on salient visual (but causally irrelevant) cues. However, following a switch in the scenario, success required explicit reasoning about informants’ potential to provide valuable information based on their perceptual access. Following the switch, older children were more likely to select a knowledgeable informant. This suggests that some younger children who succeeded in the pre-switch trials had inferred rules or formed associations based on superficial, yet salient, visual cues, whereas older children made the link between perceptual access and the potential to inform. This late development and apparent cognitive challenge are consistent with proposals that such capacities are linked to the distinctiveness of human cumulative culture.
LCZ696 ameliorates doxorubicin-induced cardiomyocyte toxicity in rats
Authors: Miyoshi Toru , Nakamura Kazufumi , Amioka Naofumi , Hatipoglu Omer F. , Yonezawa Tomoko , Saito Yukihiro , Yoshida Masashi , Akagi Satoshi , Ito Hiroshi 
Published: March 2022

AbstractDoxorubicin (DOX)-based chemotherapy induces cardiotoxicity, which is considered the main bottleneck for its clinical application. In this study, we investigated the potential benefit of LCZ696, an angiotensin receptor–neprilysin inhibitor against DOX-induced cardiotoxicity in rats and H9c2 cells and determined whether the mechanism underlying any such effects involves its antioxidant activity. Male Sprague–Dawley rats were randomly separated into four groups, each consisting of 15 rats (DOX (1.5 mg/kg/day intraperitoneally for 10 days followed by non-treatment for 8 days); DOX + valsartan (31 mg/kg/day by gavage from day 1 to day 18); DOX + LCZ696 (68 mg/kg/day by gavage from day 1 to day 18); and control (saline intraperitoneally for 10 days). DOX-induced elevation of cardiac troponin T levels on day 18 was significantly reduced by LCZ696, but not valsartan. The DOX-induced increase in myocardial reactive oxygen species (ROS) levels determined using dihydroethidium was significantly ameliorated by LCZ696, but not valsartan, and was accompanied by the suppression of DOX-induced increase in p47phox. LCZ696 recovered the DOX-induced decrease in phosphorylation of adenosine monophosphate-activated protein kinase and increased the ratio of Bax and Bcl-2. In H9c2 cardiomyocytes, LCZ696 reduced DOX-induced mitochondrial ROS generation and improved cell viability more than valsartan. Our findings indicated that LCZ696 ameliorated DOX-induced cardiotoxicity in rat hearts in vivo and in vitro, possibly by mediating a decrease in oxidative stress.
Saffron extract and crocin exert anti-inflammatory and anti-oxidative effects in a repetitive mild traumatic brain injury mouse model
Authors: Salem Marwa , Shaheen Mariam , Tabbara Abeer , Borjac Jamilah 
Published: March 2022

AbstractSaffron Crocus sativus L. (C. sativus) is a flower from the iridaceous family. Crocin, saffron’s major constituent, and saffron have anti-oxidative and anti-inflammatory activities. In this work, the neuroprotective effects of saffron and crocin are being investigated in a repetitive mild traumatic brain injury (rmTBI) mouse model. A weight drop model setup was employed to induce mild brain injury in male albino BABL/c mice weighing 30–40 g. Saffron (50 mg/kg) and crocin (30 mg/kg) were administrated intraperitoneally 30 min before mTBI induction. Behavioral tests were conducted to assess behavioral deficits including the modified neurological severity score (NSS), Morris water maze (MWM), pole climb test, rotarod test, and adhesive test. The levels of TNF alpha (TNF-α), interferon-gamma (IFN-γ), myeloperoxidase activity (MPO), malonaldehyde (MDA), and reduced glutathione (GSH) were measured. Histological analysis of different brain parts was performed. Both saffron and crocin demonstrated marked improved neurological, cognitive, motor, and sensorimotor functions. Besides, both compounds significantly reduced the oxidative stress and inflammatory processes. No abnormal histological features were observed in any of the injured groups. Saffron extract and crocin provide a neuroprotective effect in a mouse model of rmTBI by decreasing oxidative stress, inflammatory responses, and behavioral deficits.
Long-term nutritional trends in the Finnish population estimated from a large laboratory database from 1987 to 2020
Authors: Tuuminen Tamara , Sorsa Mikko , Tornudd Martin , Lähteenmäki Pertti Lauri , Poussa Tuija , Suonsivu Pyry , Pitkänen Eeva Marja , Antila Erkki , Jaakkola Kaarlo 
Published: March 2022

AbstractThe assessments of malnutrition in adults with MUST or NRS-2002 criteria do not give a detailed insight into the sufficiency of micronutrients. Sufficiency assessment of essential micronutrients on the individual level can be achieved only with laboratory measurements. The aim of this study was to estimate long-term trends in micronutrient sufficiency in the Finnish population with regards to gender and sex covariates. We retrieved from the clinical laboratory database (n = 67,236) all results on whole blood Magnesium, (B-Mg), Manganese (B-Mn), Zinc (B-Zn), Selenium (B-Se) and Copper from erythrocytes (E-Cu) and fasting serum β-carotenes (fS-BKarot), vitamin A (fS-A-vit), coenzyme Q10 (Ubiquinone, fS-Q10) and serum vitamin D (S-D-25) from the database of clinical laboratory Mineraalilaboratorio Mila Oy from the years 1987–2020. A weak positive linear trend is seen for B-Mg, B-Zn and ln(fS-Q10) both for children and adults, but a moderate linear positive trend was observed for ln(S-D-25) based on correlation between calendar year and ln(S-D-25), R = 0.44 and 0.41, p < 0.001 for adults and children, respectively. Laboratory database is helpful to monitor the nutritional public policy to prevent hidden malnutrition in the society.
Enhancing multiple scales of seafloor biodiversity with mussel restoration
Authors: Sea Mallory A. , Hillman Jenny R. , Thrush Simon F. 
Published: March 2022

AbstractRestoration projects are underway internationally in response to global declines in shellfish beds. As diverse biological assemblages underpin a variety of ecosystem services, understanding broader changes in biodiversity associated with mussel restoration becomes increasingly valuable to scientists and restoration practitioners. Studies generally show bivalve beds increase species richness and abundance, but results are scale-dependent and conditional on the mobility of specific communities observed. We examined biodiversity at multiple scales to determine how communities with varying levels of mobility are influenced by subtidal mussel restoration. Significant changes in assemblage structure were observed in both mobile fish and epifaunal communities, with enhanced species richness and total abundance of associated individuals. In contrast, we observed site-dependent effects of bivalve restoration on macrofaunal community structure and composition, with sheltered, harbour mussel bed communities numerically dominated by detritivores accustomed to organically enriched, muddy sediments. Sediment organic matter significantly increased within mussel beds, and distance-based linear models showed that sediment organic matter was an important predictor of macrofaunal assemblage structure on mussel beds, highlighting the significance of benthic-pelagic coupling and biodeposition to soft-sediment communities. This study contributes novel methods and ecological insights on the role of species mobility and site selection in structuring restoration outcomes, better informing future mussel restoration efforts aimed at emphasising functionally-driven ecosystem services.
Megapixel camera arrays enable high-resolution animal tracking in multiwell plates
Authors: Barlow Ida L. , Feriani Luigi , Minga Eleni , McDermott-Rouse Adam , O’Brien Thomas James , Liu Ziwei , Hofbauer Maximilian , Stowers John R. , Andersen Erik C. , Ding Siyu Serena , Brown André E. X. 
Published: March 2022

AbstractTracking small laboratory animals such as flies, fish, and worms is used for phenotyping in neuroscience, genetics, disease modelling, and drug discovery. An imaging system with sufficient throughput and spatiotemporal resolution would be capable of imaging a large number of animals, estimating their pose, and quantifying detailed behavioural differences at a scale where hundreds of treatments could be tested simultaneously. Here we report an array of six 12-megapixel cameras that record all the wells of a 96-well plate with sufficient resolution to estimate the pose of C. elegans worms and to extract high-dimensional phenotypic fingerprints. We use the system to study behavioural variability across wild isolates, the sensitisation of worms to repeated blue light stimulation, the phenotypes of worm disease models, and worms’ behavioural responses to drug treatment. Because the system is compatible with standard multiwell plates, it makes computational ethological approaches accessible in existing high-throughput pipelines.
Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics uncovered across a river catchment using environmental DNA
Authors: Blackman Rosetta C. , Ho Hsi-Cheng , Walser Jean-Claude , Altermatt Florian 
Published: March 2022

AbstractAccurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2riverine network over seasons using environmental DNA. We found contrasting biodiversity patterns between major taxonomic groups. Local richness showed statistically significant, season-dependent increases and decreases towards downstream location within the catchment for fish and bacteria, respectively. Meanwhile, invertebrate richness remained spatially unchanged but varied across seasons. The structure of local food webs, such as link density and nestedness, also varied across space and time. However, these patterns did not necessarily mirror those observed for biodiversity and functional feeding characteristics. Our results suggest that biodiversity patterns and food-web dynamics are not directly scalable to each other even at the same spatial and temporal scales. In order to conserve species diversity as well as the functional trophic integrity of communities, patterns of biodiversity and food-web characteristics must thus be jointly studied.
A multi-encoder variational autoencoder controls multiple transformational features in single-cell image analysis
Authors: Ternes Luke , Dane Mark , Gross Sean , Labrie Marilyne , Mills Gordon , Gray Joe , Heiser Laura , Chang Young Hwan 
Published: March 2022

AbstractImage-based cell phenotyping relies on quantitative measurements as encoded representations of cells; however, defining suitable representations that capture complex imaging features is challenged by the lack of robust methods to segment cells, identify subcellular compartments, and extract relevant features. Variational autoencoder (VAE) approaches produce encouraging results by mapping an image to a representative descriptor, and outperform classical hand-crafted features for morphology, intensity, and texture at differentiating data. Although VAEs show promising results for capturing morphological and organizational features in tissue, single cell image analyses based on VAEs often fail to identify biologically informative features due to uninformative technical variation. Here we propose a multi-encoder VAE (ME-VAE) in single cell image analysis using transformed images as a self-supervised signal to extract transform-invariant biologically meaningful features, including emergent features not obvious from prior knowledge. We show that the proposed architecture improves analysis by making distinct cell populations more separable compared to traditional and recent extensions of VAE architectures and intensity measurements by enhancing phenotypic differences between cells and by improving correlations to other analytic modalities. Better feature extraction and image analysis methods enabled by the ME-VAE will advance our understanding of complex cell biology and enable discoveries previously hidden behind image complexity ultimately improving medical outcomes and drug discovery.