bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving CRISPR/Cas9 mutagenesis efficiency by delaying the early development of zebrafish embryos
Authors: Terzioglu M. , Saralahti A. , Piippo H. , Rämet M. , Andressoo J.-O.
Published: December 2020

CRISPR/Cas9 driven mutagenesis in zygotes is a popular tool for introducing targeted mutations in model organisms. Compared to mouse, mutagenesis in zebrafish is relatively inefficient and results in somatic mosaicism most likely due to a short single-cell stage of about 40 min. Here we explored two options to improve CRISPR/Cas9 mutagenesis in zebrafish—extending the single-cell stage and defining conditions for carrying out mutagenesis in oocytes prior to in vitro fertilization. Previous work has shown that ovarian fluid from North American salmon species (coho and chinook salmon) prolong oocyte survival ex vivo so that they are viable for hours instead of dying within minutes if left untreated. We found that commonly farmed rainbow trout (Oncorhynchus mykiss) ovarian fluid (RTOF) has similar effect on zebrafish oocyte viability. In order to prolong single-cell stage, we incubated zebrafish zygotes in hydrogen sulfide (H2S) and RTOF but failed to see any effect. However, the reduction of temperature from standard 28 to 12 °C postponed the first cell division by about an hour. In addition, the reduction in temperature was associated with increased CRISPR/Cas9 mutagenesis rate. These results suggest that the easily applicable reduction in temperature facilitates CRISPR/Cas9 mutagenesis in zebrafish.
Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order
Authors: Gaba Sonam , Kumari Abha , Medema Marnix , Kaushik Rajeev
Published: December 2020

Halobacteria, a class of Euryarchaeota are extremely halophilic archaea that can adapt to a wide range of salt concentration generally from 10% NaCl to saturated salt concentration of 32% NaCl. It consists of the orders: Halobacteriales, Haloferaciales and Natriabales. Pan-genome analysis of class Halobacteria was done to explore the core (300) and variable components (Softcore: 998, Cloud:36531, Shell:11784). The core component revealed genes of replication, transcription, translation and repair, whereas the variable component had a major portion of environmental information processing. The pan-gene matrix was mapped onto the core-gene tree to find the ancestral (44.8%) and derived genes (55.1%) of the Last Common Ancestor of Halobacteria. A High percentage of derived genes along with presence of transformation and conjugation genes indicate the occurrence of horizontal gene transfer during the evolution of Halobacteria. A Core and pan-gene tree were also constructed to infer a phylogeny which implicated on the new super-order comprising of Natrialbales and Halobacteriales.
Preferred oriented cation configurations in high pressure phases IV and V of methylammonium lead iodide perovskite
Authors: Sukmas Wiwittawin , Sakulsupich Vichawan , Tsuppayakorn-aek Prutthipong , Pinsook Udomsilp , Pakornchote Teerachote , Klinkla Rakchat , Bovornratanaraks Thiti
Published: December 2020

A microscopic viewpoint of structure and dipolar configurations in hybrid organic–inorganic perovskites is crucial to understanding their stability and phase transitions. The necessity of incorporating dispersion interactions in the state-of-the-art density functional theory for the $$CH_3NH_3PbI_3$$

C

H
3

N

H
3

P
b

I
3

perovskite (MAPI) is demonstrated in this work. Some of the vdW methods were selected to evaluate the corresponding energetics properties of the cubic MAPI with various azimuthally rotated MA organic cation orientations. The highest energy barrier obtained from PBEsol reaches 18.6 meV/MA-ion, which is equivalent to 216 K, the temperature above which the MA cations randomly reorient. Energy profiles calculated by vdW incorporated functionals, on the other hand, exhibit various distinct patterns. The well-developed vdW-DF-cx functional was selected, thanks to its competence, to evaluate the total energies of different MA dipolar configurations in $$2\times 2\times 2$$

2
×
2
×
2

cubic supercell of MAPI under pressures. The centrosymmetric arrangement of the MA cations that provide zero total dipole moment configuration results in the lowest energy state profiles under pressure, while the non-centrosymmetric scheme displays a unique behaviour. Despite being overall unpolarised, the latter calculated with PBEsol leads to a rigid shift of energy from the profile obtained from the dispersive vdW-DF-cx functional. It is noteworthy that the energy profile responsible for the maximum polarised configuration nevertheless takes the second place in total energy under pressure.
Dynamics of grain boundary premelting
Authors: Torabi Rad M. , Boussinot G. , Apel M.
Published: December 2020

The mechanical strength of a polycrystalline material can be drastically weakened by a phenomenon known as grain boundary (GB) premelting that takes place, owing to the so-called disjoining potential, when the dry GB free energy $$\sigma _{gb}$$

σ

gb

exceeds twice the free energy of the solid–liquid interface $$\sigma _{sl}$$

σ

sl

. While previous studies of GB premelting are all limited to equilibrium conditions, we use a multi-phase field model to analyze premelting dynamics by simulating the steady-state growth of a liquid layer along a dry GB in an insulated channel and the evolution of a pre-melted polycrystalline microstructure. In both cases, our results reveal the crucial influence of the disjoining potential. A dry GB transforms into a pre-melted state for a grain-size-dependent temperature interval around $$T_m$$

T
m

, such that a critical overheating of the dry GBs over $$T_m$$

T
m

should be exceeded for the classical melting process to take place, the liquid layer to achieve a macroscopic width, and the disjoining potential to vanish. Our simulations suggest a steady-state velocity for this transformation proportional to $$\sigma _{gb} -2 \sigma _{sl}$$

σ

gb

-
2

σ

sl

. Concerning the poly-crystalline evolution, we find unusual grain morphologies and dynamics, deriving from the existence of a pre-melted polycrystalline equilibrium that we evidence. We are then able to identify the regime in which, due to the separation of the involved length scales, the dynamics corresponds to the same curvature-driven dynamics as for dry GBs, but with enhanced mobility.
Marine protected areas do not prevent marine heatwave-induced fish community structure changes in a temperate transition zone
Authors: Freedman R. M. , Brown J. A. , Caldow C. , Caselle J. E.
Published: December 2020

Acute climate events like marine heatwaves have the potential to temporarily or permanently alter community structure with effects on biodiversity and ecosystem services. We aimed to quantify the magnitude and consistency of climate driven community shifts inside and outside Marine Protected Areas before and after a marine heatwave using a kelp forest fish community dataset in southern California, USA. Abundance, biomass, diversity and recruitment of warm-water affinity species during the marine heatwave were significantly greater compared with prior years yet cool-water affinity species did not show commensurate declines. Fish communities inside MPAs were not buffered from these community shifts. This result is likely because the particular species most responsible for the community response to environmental drivers, were not fisheries targets. Resource managers working to preserve biodiversity in a changing climate will need to consider additional management tools and strategies in combination with protected areas to mitigate the effect of warming on marine communities.
Metabolic reprogramming of osteoclasts represents a therapeutic target during the treatment of osteoporosis
Authors: Taubmann Jule , Krishnacoumar Brenda , Böhm Christina , Faas Maria , Müller Dorothea I. H. , Adam Susanne , Stoll Cornelia , Böttcher Martin , Mougiakakos Dimitrios , Sonnewald Uwe , Hofmann Jörg , Schett Georg , Krönke Gerhard , Scholtysek Carina
Published: December 2020

Osteoclasts are specialised bone resorbing cells that control both physiological and pathological bone turnover. Functional changes in the differentiation and activity of osteoclasts are accompanied by active metabolic reprogramming. However, the biological significance and the in vivo relevance of these events has remained unclear. Here we show that bone resorption of differentiated osteoclasts heavily relies on increased aerobic glycolysis and glycolysis-derived lactate production. While pharmacological inhibition of glycolysis did not affect osteoclast differentiation or viability, it efficiently blocked bone resorption in vitro and in vivo and consequently ameliorated ovariectomy-induced bone loss. Our experiments thus highlight the therapeutic potential of interfering with osteoclast-intrinsic metabolic pathways as possible strategy for the treatment of diseases characterized by accelerated bone loss.
SHROOM3, the gene associated with chronic kidney disease, affects the podocyte structure
Authors: Matsuura Ryo , Hiraishi Atsuko , Holzman Lawrence B. , Hanayama Hiroki , Harano Koji , Nakamura Eiichi , Hamasaki Yoshifumi , Doi Kent , Nangaku Masaomi , Noiri Eisei
Published: December 2020

Chronic kidney disease is a public health burden and it remains unknown which genetic loci are associated with kidney function in the Japanese population, our genome-wide association study using the Biobank Japan dataset (excluding secondary kidney diseases, such as diabetes mellitus) clearly revealed that almost half of the top 50 single nucleotide polymorphisms associated with estimated glomerular filtration rate are located in the SHROOM3 gene, suggesting that SHROOM3 will be responsible for kidney function. Thus, to confirm this finding, supportive functional analyses were performed on Shroom3 in mice using fullerene-based siRNA delivery, which demonstrated that Shroom3 knockdown led to albuminuria and podocyte foot process effacement. The in vitro experiment shows that knockdown of Shroom3 caused defective formation of lamellipodia in podocyte, which would lead to the disruption of slit diaphragm. These results from the GWAS, in vivo and in vitro experiment were consistent with recent studies reporting that albuminuria leads to impairment of kidney function.
Characterizing the type 2 diabetes mellitus epidemic in Jordan up to 2050
Authors: Awad Susanne F. , Huangfu Peijue , Dargham Soha R. , Ajlouni Kamel , Batieha Anwar , Khader Yousef S. , Critchley Julia A. , Abu-Raddad Laith J.
Published: December 2020

We aimed to characterize the type 2 diabetes mellitus (T2DM) epidemic and the role of key risk factors in Jordan between 1990–2050, and to forecast the T2DM-related costs. A recently-developed population-level T2DM mathematical model was adapted and applied to Jordan. The model was fitted to six population-based survey data collected between 1990 and 2017. T2DM prevalence was 14.0% in 1990, and projected to be 16.0% in 2020, and 20.6% in 2050. The total predicted number of T2DM cases were 218,326 (12,313 were new cases) in 1990, 702,326 (36,941 were new cases) in 2020, and 1.9 million (79,419 were new cases) in 2050. Out of Jordan’s total health expenditure, 19.0% in 1990, 21.1% in 2020, and 25.2% in 2050 was forecasted to be spent on T2DM. The proportion of T2DM incident cases attributed to obesity was 55.6% in 1990, 59.5% in 2020, and 62.6% in 2050. Meanwhile, the combined contribution of smoking and physical inactivity hovered around 5% between 1990 and 2050. Jordan’s T2DM epidemic is predicted to grow sizably in the next three decades, driven by population ageing and high and increasing obesity levels. The national strategy to prevent T2DM needs to be strengthened by focusing it on preventive interventions targeting T2DM and key risk factors.
Distinct roles for the hypoxia-inducible transcription factors HIF-1α and HIF-2α in human osteoclast formation and function
Authors: Knowles Helen J.
Published: December 2020

Bone homeostasis is maintained by a balance between osteoblast-mediated bone formation and osteoclast-driven bone resorption. Hypoxia modulates this relationship partially via direct and indirect effects of the hypoxia-inducible factor-1 alpha (HIF-1α) transcription factor on osteoclast formation and bone resorption. Little data is available on the role(s) of the HIF-2α isoform of HIF in osteoclast biology. Here we describe induction of HIF-1α and HIF-2α during the differentiation of human CD14+ monocytes into osteoclasts. Knockdown ofHIF-1αdid not affect osteoclast differentiation but prevented the increase in bone resorption that occurs under hypoxic conditions.HIF-2αknockdown did not affect bone resorption but moderately inhibited osteoclast formation. Growth of osteoclasts in 3D gels reversed the effect ofHIF-2αknockdown;HIF-2αsiRNA increasing osteoclast formation in 3D. Glycolysis is the main HIF-regulated pathway that drives bone resorption.HIFknockdown only affected glucose uptake and bone resorption in hypoxic conditions. Inhibition of glycolysis with 2-deoxy-d-glucose (2-DG) reduced osteoclast formation and activity under both basal and hypoxic conditions, emphasising the importance of glycolytic metabolism in osteoclast biology. In summary, HIF-1α and HIF-2α play different but overlapping roles in osteoclast biology, highlighting the importance of the HIF pathway as a potential therapeutic target in osteolytic disease.
The change of conditions does not affect Ros87 downhill folding mechanism
Authors: Grazioso Rinaldo , García-Viñuales Sara , D’Abrosca Gianluca , Baglivo Ilaria , Pedone Paolo Vincenzo , Milardi Danilo , Fattorusso Roberto , Isernia Carla , Russo Luigi , Malgieri Gaetano
Published: December 2020

Downhill folding has been defined as a unique thermodynamic process involving a conformations ensemble that progressively loses structure with the decrease of protein stability. Downhill folders are estimated to be rather rare in nature as they miss an energetically substantial folding barrier that can protect against aggregation and proteolysis. We have previously demonstrated that the prokaryotic zinc finger protein Ros87 shows a bipartite folding/unfolding process in which a metal binding intermediate converts to the native structure through a delicate barrier-less downhill transition. Significant variation in folding scenarios can be detected within protein families with high sequence identity and very similar folds and for the same sequence by varying conditions. For this reason, we here show, by means of DSC, CD and NMR, that also in different pH and ionic strength conditions Ros87 retains its partly downhill folding scenario demonstrating that, at least in metallo-proteins, the downhill mechanism can be found under a much wider range of conditions and coupled to other different transitions. We also show that mutations of Ros87 zinc coordination sphere produces a different folding scenario demonstrating that the organization of the metal ion core is determinant in the folding process of this family of proteins.
Unconventional magnetization textures and domain-wall pinning in Sm–Co magnets
Authors: Pierobon Leonardo , Kovács András , Schäublin Robin E. , Gerstl Stephan S. A. , Caron Jan , Wyss Urs V. , Dunin-Borkowski Rafal E. , Löffler Jörg F. , Charilaou Michalis
Published: December 2020

Some of the best-performing high-temperature magnets are Sm–Co-based alloys with a microstructure that comprises an $$\hbox {Sm}_2\hbox {Co}_{17}$$

Sm
2

Co
17

matrix and magnetically hard $$\hbox {SmCo}_5$$

SmCo
5

cell walls. This generates a dense domain-wall-pinning network that endows the material with remarkable magnetic hardness. A precise understanding of the coupling between magnetism and microstructure is essential for enhancing the performance of Sm–Co magnets, but experiments and theory have not yet converged to a unified model. Here, transmission electron microscopy, atom probe tomography, and nanometer-resolution off-axis electron holography have been combined with micromagnetic simulations to reveal that the magnetization state in Sm–Co magnets results from curling instabilities and domain-wall pinning effects at the intersections of phases with different magnetic hardness. Additionally, this study has found that topologically non-trivial magnetic domains separated by a complex network of domain walls play a key role in the magnetic state by acting as nucleation sites for magnetization reversal. These findings reveal previously hidden aspects of magnetism in Sm–Co magnets and, by identifying weak points in the microstructure, provide guidelines for improving these high-performance magnetic materials.
Chemical composition of Polish propolis and its antiproliferative effect in combination with Bacopa monnieri on glioblastoma cell lines
Authors: Moskwa Justyna , Naliwajko Sylwia K. , Markiewicz-Żukowska Renata , Gromkowska-Kępka Krystyna J. , Nowakowski Patryk , Strawa Jakub W. , Borawska Maria H. , Tomczyk Michał , Socha Katarzyna
Published: December 2020

Propolis and Bacopa monnieri (L.) Wettst. (Brahmi) are natural products that contain many active substances and possess anticancer properties. The aim of this study was to investigate the chemical composition of Polish propolis extract (PPE) by gas chromatography-mass spectrometry (GC–MS), B. monnieri extracts (BcH, BcS) by high performance liquid chromatography with diode array detector and mass spectrometry coupled with electrospray ionization (LC–ESI–MS) and finally determine its anti-proliferative potential combined with BcH and BcS in glioblastoma cell lines (T98G, LN-18, U87MG). The antiproliferative activity of PPE, BcH, BcS and their combination (PPE + BcH) was determined by a cytotoxicity test, and DNA binding was determined by [3H]-thymidine incorporation. Flavonoids and phenylpropenoids were the main components of PPE. BcH and BcS samples were also successfully analyzed. Their main constituents were saponins such as bacoside A3, bacopaside II, X and bacopasaponin C and its isomer. The inhibitory effects on the viability and proliferation of the tested glioma cells observed after incubation with the combination of PPE and BcH were significantly stronger than the effects of these two extracts separately. These findings suggest that propolis in combination with B. monnieri shows promising anticancer activity for the treatment of glioblastoma. However, further studies are still required.
BRCAness as a prognostic indicator in patients with early breast cancer
Authors: Liu Lei , Matsunaga Yuki , Tsurutani Junji , Akashi-Tanaka Sadako , Masuda Hiroko , Ide Yoshimi , Hashimoto Rikako , Inuzuka Mayuko , Watanabe Chie , Taruno Kanae , Sawada Terumasa , Okuyama Hiromi , Ata Arisa , Kuwayama Takashi , Nakayama Sayuka , Tonouchi Yumi , Nakamura Seigo
Published: December 2020

BRCAness is defined as a phenotypic copy of germline BRCA mutations, which describes presence of homologous recombination defects in sporadic cancers. We detected BRCAness by multiplex ligation-dependent probe amplification (MLPA) and explored whether BRCAness can be used as a predictor of prognosis. BRCAness status was classified for total 121 breast cancer patients. Forty-eight patients (39.7%) were identified as BRCAness positive. Tumors of BRCAness were more likely to be hormone receptors negative (95.8% vs. 50.7%, P < 0.001), nuclear grade III (76.1% vs. 48.4%, P = 0.001) and triple-negative breast cancer subtype (91.6% vs. 42.5%, P < 0.001). Five-year disease free survival (DFS) (54.0% vs. 88.0%, P < 0.001) and overall survival (OS) (76.3% vs. 93.1%, P = 0.002) were significantly lower in BRCAness patients. In neoadjuvant chemotherapy subgroup analysis, clinical response rate for taxane-based regimen was significantly lower in BRCAness patients (58.3% vs. 77.8%, P = 0.041). Cox regression multivariate analysis showed that BRCAness was the independent prognostic factor for DFS (HR 2.962, 95%CI 1.184–7.412, P = 0.020), but not for OS (HR 2.681, 95%CI 0.618–11.630, P = 0.188). BRCAness is associated with specific characteristics and may suggest resistance to taxane-based chemotherapy. BRCAness can be used as a negative prognostic indicator for breast cancer.
Effect of foliar and soil application of plant growth promoting bacteria on growth, physiology, yield and seed quality of maize under Mediterranean conditions
Authors: Efthimiadou Aspasia , Katsenios Nikolaos , Chanioti Sofia , Giannoglou Marianna , Djordjevic Nikola , Katsaros George
Published: December 2020

The use of plant growth promoting bacteria (PGPB) as biostimulants favors the increase of crop productivity and the improvement of yield quality. The main objective of the present study was to investigate the effect of the PGPB biostimulants (Azotobacter chroococcum, Bacillus subtilis, Bacillus megatherium and their mixes) and the application method (foliar and soil) on the growth, the physiology, the yield and the quality of maize. The obtained results showed that A. chroococcum treatment increased the chlorophyll content up to 6.1%, the photosynthetic rate up to 18.4% and the transpiration rate up to 34.3%. The highest maize yields were performed by the treatments B. megatherium (244.67 g) and the mix of A. chroococcum and B. subtilis (1:1) (243.67 g) when applied on the soil. The Soil application of the PGPB resulted in increased yield of maize from 5.5 to 13.4% compared to control treatment. Concerning quality characteristics, B. subtilis treatment increased total solids content in harvested maize seeds by 92%, as well as crude fiber content by 46% compared to control. The results confirmed that the use of PGPB could contribute as a new cultivation practice for sustainable growth, productivity and quality of grain crops.
Acute invariant NKT cell activation triggers an immune response that drives prominent changes in iron homeostasis
Authors: Huang Hua , Zuzarte-Luis Vanessa , Fragoso Gabriela , Calvé Annie , Hoang Tuan Anh , Oliero Manon , Chabot-Roy Geneviève , Mullins-Dansereau Victor , Lesage Sylvie , Santos Manuela M.
Published: December 2020

Iron homeostasis is an essential biological process that ensures the tissue distribution of iron for various cellular processes. As the major producer of hepcidin, the liver is central to the regulation of iron metabolism. The liver is also home to many immune cells, which upon activation may greatly impact iron metabolism. Here, we focus on the role of invariant natural killer T (iNKT) cells, a subset of T lymphocytes that, in mice, is most abundant in the liver. Activation of iNKT cells with the prototypical glycosphingolipid antigen, α-galactosylceramide, resulted in immune cell proliferation and biphasic changes in iron metabolism. This involved an early phase characterized by hypoferremia, hepcidin induction and ferroportin suppression, and a second phase associated with strong suppression of hepcidin despite elevated levels of circulating and tissue iron. We further show that these changes in iron metabolism are fully dependent on iNKT cell activation. Finally, we demonstrate that the biphasic regulation of hepcidin is independent of NK and Kupffer cells, and is initially driven by the STAT3 inflammatory pathway, whereas the second phase is regulated by repression of the BMP/SMAD signaling pathway. These findings indicate that iNKT activation and the resulting cell proliferation influence iron homeostasis.
An investigation of reconstituted terlipressin infusion stability for use in hepatorenal syndrome
Authors: Bui Thi Ngoc Nhieu , Sandar Su , Luna Giuseppe , Beaman Jasmine , Sunderland Bruce , Czarniak Petra
Published: December 2020

Hepatorenal syndrome (HRS) is a fatal complication of renal dysfunction associated with ascites, liver failure and advanced cirrhosis. Although the best option for long-term survival is liver transplantation, in the critical acute phase, vasoconstrictors are considered first-line supportive agents. Terlipressin is the most widely used vasoconstrictor globally but owing to its short elimination half-life, it is usually administered six hourly by slow intravenous bolus injection. This requires patients to remain in hospital, increasing hospital bed costs and affecting their quality of life. An alternative option for administration of terlipressin is as a continuous infusion using an elastomeric infusor device in the patient’s home. However, stability data on terlipressin in elastomeric infusor devices is lacking. This research aimed to evaluate the stability of terlipressin reconstituted in infusor devices for up to 7 days at 2–8 °C and subsequently at 22.5 °C for 24 h, to mimic home storage and administration temperatures. We report that terlipressin was physically and chemically stable under these conditions; all reconstituted infusor concentrations retained above 90% of the original concentration over the test conditions. No colour change or precipitation in the solutions were evident.
Asymmetric practices of reading and writing shape visuospatial attention and discrimination
Authors: Mendonça Rita , Garrido Margarida V. , Semin Gün R.
Published: December 2020

Movement is generally conceived of as unfolding laterally in the writing direction that one is socialized into. In ‘Western’ languages, this is a left-to-right bias contributing to an imbalance in how attention is distributed across space. We propose that the rightward attentional bias exercises an additional unidirectional influence on discrimination performance thus shaping the congruency effect typically observed in Posner-inspired cueing tasks. In two studies, we test whether faces averted laterally serve as attention orienting cues and generate differences in both target discrimination latencies and gaze movements across left and right hemifields. Results systematically show that right-facing faces (i.e. aligned with the script direction) give rise to an advantage for cue-target pairs pertaining to the right (versus left) side of space. We report an asymmetry between congruent conditions in the form of right-sided facilitation for: (a) response time in discrimination decisions (experiment 1–2) and (b) eye-gaze movements, namely earlier onset to first fixation in the respective region of interest (experiment 2). Left and front facing cues generated virtually equal exploration patterns, confirming that the latter did not prime any directionality. These findings demonstrate that visuospatial attention and consequent discrimination are highly dependent on the asymmetric practices of reading and writing.
Low cost, high performance ultrafiltration membranes from glass fiber-PTFE–graphene composites
Authors: Khan Umar , Biccai Sonia , Boland Conor S. , Coleman Jonathan N.
Published: December 2020

The development of low-cost ultrafiltration membranes with relatively high flow rate and selectivity is an important goal which could improve access to clean water in the developing world. Here we demonstrate a method to infuse mixtures of graphene nanosheets and Teflon nanoparticles into ultra-cheap glass fibre membranes. Annealing the resultant composites leads to coalescence of the Teflon, resulting in very stable membranes with significantly enhanced mechanical properties. In filtration tests, while adding ~ 10 wt% graphene/Teflon to the glass fibre membrane decreased the flow rate by × 100, the selectivity improved by × 103 compared to the neat glass fibre membrane. This combination of selectively and flow rate was significantly better than any commercial membrane tested under similar circumstances. We found these membranes could remove > 99.99% of 25–250 nm diameter SiC nanoparticles dispersed in ethanol, transmitting only particles with diameters < 40 nm, performance which is superior to commercial alumina membranes. Field trials on dirty canal water showed these composite membranes to remove aluminium to a level × 10 below the EU limit for drinking water and reduce iron and bacteria contents to below detectable levels.
UV induced resistive switching in hybrid polymer metal oxide memristors
Authors: Stathopoulos Spyros , Tzouvadaki Ioulia , Prodromakis Themis
Published: December 2020

There is an increasing interest for alternative ways to program memristive devices to arbitrary resistive levels. Among them, light-controlled programming approach, where optical input is used to improve or to promote the resistive switching, has drawn particular attention. Here, we present a straight-forward method to induce resistive switching to a memristive device, introducing a new version of a metal-oxide memristive architecture coupled with a UV-sensitive hybrid top electrode obtained through direct surface treatment with PEDOT:PSS of an established resistive random access memory platform. UV-illumination ultimately results to resistive switching, without involving any additional stimulation, and a relation between the switching magnitude and the applied wavelength is depicted. Overall, the system and method presented showcase a promising proof-of-concept for granting an exclusively light-triggered resistive switching to memristive devices irrespectively of the structure and materials comprising their main core, and, in perspective can be considered for functional integrations optical-induced sensing.
Increased expression of fibroblast growth factor 23 is the signature of a deteriorated Ca/P balance in ageing laying hens
Authors: Gloux A. , Le Roy N. , Même N. , Piketty M. L. , Prié D. , Benzoni G. , Gautron J. , Nys Y. , Narcy A. , Duclos M. J.
Published: December 2020

The present study concerned the effect of ageing in laying hens, from 23 to 90 weeks of age, on the regulation of Ca metabolism related to the requirement for eggshell mineralization. Samples were collected from parathyroid gland (PG), liver, jejunum, medullary bone (MB) and kidney for a quantitative study of candidate gene expression. Although parathyroid hormone (PTH) gene expression in the PG did not vary with age, a stronger challenge to Ca homeostasis was suggested in aged hens. Indeed gene expression of Ca transporters , Vitamin D Receptor (VDR) in the jejunum, and that of transient receptor potential channel subfamily V member 5 (TRPV5) in the kidney decreased. This could exacerbate bone resorption and impair bone accretion, as attested by a higher expression of the Carbonic Anhydrase 2 (CA2) gene and a lower expression of collagen type I alpha 1 chain (COL1A1) in the MB. The increased expression of Fibroblast Growth Factor 23 (FGF23) in the MB likely contributed to the decreased plasma levels of 1.25(OH)2D3 and the altered expression of target genes under its regulation. Our data highlights the molecular mechanisms underlying the osteoporotic syndrome previously documented in aged laying hens, thus providing new perspectives for future interventions.
Blurring of ancient wall paintings caused by binder decay in the pigment layer
Authors: Zheng Lizhen , Wang Zhuorui , Shen Shukun , Xia Yin , Li Yuhu , Hu Daodao
Published: December 2020

In this paper, the effect of binder decay rather than a change in the pigments on the blurring of ancient wall paintings was researched. The simulated wall paintings were prepared by brushing an aqueous solution containing gelatine and ochre grains on the surface of cylindrical compressed soil samples. Then, the dried samples were calcined at 650 °C for 2 h to obtain the simulated wall paintings with the degraded binder gelatine. Next, the calcined samples were brushed with a certain amount of acetone solution containing an ionic liquid ([BMIm]PF6) to obtain the corresponding repaired samples. Based on the results from various characterization methods (UV–vis, FTIR, XRD, XPS, SEM, TG), the following conclusions were drawn. The degradation of the binder caused by calcination increases the surface roughness of the painting layer, resulting in enhanced scattering. In this case, because scattering decrease the light absorption by the pigments, even if unchanged pigment exists in the painting layer, its colour can become blurred. The filling of the ionic liquid into the pores caused by gelatine decay in the painting layer can decrease the scattering, and the blurred colour can be restored to some extent. As typical examples, this principle was successfully applied to restore the blurred colour of an ancient Chinese wall painting (Tang Dynasty) and a pottery (Eastern Han Dynasty).
Comprehensive studies on the properties of apple juice treated by non-thermal atmospheric plasma in a flow-through system
Authors: Dzimitrowicz Anna , Bielawska-Pohl Aleksandra , Pohl Pawel , Cyganowski Piotr , Motyka-Pomagruk Agata , Klis Tymoteusz , Policht Malgorzata , Klimczak Aleksandra , Jamroz Piotr
Published: December 2020

We present an optimized non-thermal atmospheric plasma (NTAP)-based reaction-discharge system that was applied for a continuous-flow treatment of apple juice (AJ). To optimize this system for a high-throughput production of AJ with ameliorated properties, the effect of several parameters was studied using design of experiments approach followed by the response surface methodology. Additionally, nutritional, physicochemical, microbiological and cytotoxic properties of resulting AJ were assessed. It was established that NTAP treatment of AJ led to rise in concentration of Ca, Fe, K, Mg, Na and Sr by 8–10% as well as Al, B, Ba, Cu, Mn and Zn by 11–15%. Additionally, the increased total phenolic content by ~ 11% in addition to the prolonged by up to 12 days shelf life of the product were observed. Moreover, it was found that the NTAP-treatment of AJ did not change the structure of organic compounds present in AJ, in addition to its °Brix value, color and ferric ion reducing antioxidant power. Furthermore, AJ subjected to NTAP did not show any cytotoxic activity towards non-malignant human intestinal epithelial cells but exhibited induced cell cytotoxicity in human colorectal adenocarcinoma cells. Our study provided arguments for future introduction of these types of preparations to the global market.
Understanding the mesoscopic scaling patterns within cities
Authors: Dong Lei , Huang Zhou , Zhang Jiang , Liu Yu
Published: December 2020

Understanding quantitative relationships between urban elements is crucial for a wide range of applications. The observation at the macroscopic level demonstrates that the aggregated urban quantities (e.g., gross domestic product) scale systematically with population sizes across cities, also known as urban scaling laws. However, at the mesoscopic level, we lack an understanding of whether the simple scaling relationship holds within cities, which is a fundamental question regarding the spatial origin of scaling in urban systems. Here, by analyzing four extensive datasets covering millions of mobile phone users and urban facilities, we investigate the scaling phenomena within cities. We find that the mesoscopic infrastructure volume and socioeconomic activity scale sub- and super-linearly with the active population, respectively. For a same scaling phenomenon, however, the exponents vary in cities of similar population sizes. To explain these empirical observations, we propose a conceptual framework by considering the heterogeneous distributions of population and facilities, and the spatial interactions between them. Analytical and numerical results suggest that, despite the large number of complexities that influence urban activities, the simple interaction rules can effectively explain the observed regularity and heterogeneity in scaling behaviors within cities.
Mucin-2 knockout is a model of intercellular junction defects, mitochondrial damage and ATP depletion in the intestinal epithelium
Authors: Borisova Mariya A. , Achasova Kseniya M. , Morozova Ksenia N. , Andreyeva Evgeniya N. , Litvinova Ekaterina A. , Ogienko Anna A. , Morozova Maryana V. , Berkaeva Mariya B. , Kiseleva Elena , Kozhevnikova Elena N.
Published: December 2020

The disruption of the protective intestinal barrier—the ‘leaky gut’—is a common complication of the inflammatory bowel disease. There is limited data on the mechanisms of the intestinal barrier disruption upon low-grade inflammation characteristic of patients with inflammatory bowel disease in clinical remission. Thus, animal models that recapitulate the complexity of chronic intestinal inflammation in vivo are of particular interest. In this study, we used Mucin-2 (Muc2) knockout mice predisposed to colitis to study intestinal barrier upon chronic inflammation. We used 4-kDa FITC-Dextran assay and transmission electron microscopy to demonstrate the increased intestinal permeability and morphological defects in intercellular junctions in Muc2 knockout mice. Confocal microscopy revealed the disruption of the apical F-actin cytoskeleton and delocalization of tight junction protein Claudin-3 from the membrane. We further demonstrate mitochondrial damage, impaired oxygen consumption and the reduction of the intestinal ATP content in Muc2 knockout mice. Finally, we show that chemically induced mitochondrial uncoupling in the wild type mice mimics the intestinal barrier disruption in vivo and causes partial loss of F-actin and membrane localization of Claudin-3. We propose that mitochondrial damage and metabolic shifts during chronic inflammation contribute to the leaky gut syndrome in Muc2 knockout animal model of colitis.
Movements and behaviour of blue whales satellite tagged in an Australian upwelling system
Authors: Mӧller Luciana M. , Attard Catherine R. M. , Bilgmann Kerstin , Andrews-Goff Virginia , Jonsen Ian , Paton David , Double Michael C.
Published: December 2020

Knowledge about the movement ecology of endangered species is needed to identify biologically important areas and the spatio-temporal scale of potential human impacts on species. Blue whales (Balaenoptera musculus) are endangered due to twentieth century whaling and currently threatened by human activities. In Australia, they feed in the Great Southern Australian Coastal Upwelling System (GSACUS) during the austral summer. We investigate their movements, occupancy, behaviour, and environmental drivers to inform conservation management. Thirteen whales were satellite tagged, biopsy sampled and photo-identified in 2015. All were genetically confirmed to be of the pygmy subspecies (B. m. brevicauda). In the GSACUS, whales spent most of their time over the continental shelf and likely foraging in association with several seascape variables (sea surface temperature variability, depth, wind speed, sea surface height anomaly, and chlorophylla). When whales left the region, they migrated west and then north along the Australian coast until they reached West Timor and Indonesia, where their movements indicated breeding or foraging behaviour. These results highlight the importance of the GSACUS as a foraging ground for pygmy blue whales inhabiting the eastern Indian Ocean and indicate the whales’ migratory route to proposed breeding grounds off Indonesia. Information about the spatio-temporal scale of potential human impacts can now be used to protect this little-known subspecies of blue whale.
ALK variants, PD-L1 expression, and their association with outcomes in ALK-positive NSCLC patients
Authors: Chang Gee-Chen , Yang Tsung-Ying , Chen Kun-Chieh , Hsu Kuo-Hsuan , Huang Yen-Hsiang , Su Kang-Yi , Yu Sung-Liang , Tseng Jeng-Sen
Published: December 2020

It remains unclear how programmed death-ligand 1 (PD-L1) expression interacts with anaplastic lymphoma kinase (ALK) mutation, its variants, and the outcome of treatment. One hundred and twenty four out of 1255 patients (9.9%) were deemed ALK-positive by the Ventana IHC assay. PD-L1 status and ALK variants were available in 100 and 59 patients, respectively. PD-L1 positive (TPS ≥ 1%) and strong positive (TPS ≥ 50%) rate was 50% and 16%, respectively. A total of 64 variant types were detected in 59 patients. V1 (32.8%) and V3a/b (28.1%) were the most common variants. There was no significant association between ALK variants and the PD-L1 expression. The presence of V3a/b subtype independently predicted a worse overall survival in patients receiving ALK inhibitor(s) (aHR 5.10 [95% CI 1.22–21.25], P = 0.025) and platinum plus pemetrexed (aHR 9.62 [95% CI 1.90–48.80], P = 0.006). While incorporating ALK variants and PD-L1 expression together, patients with non-V3a/b/positive PD-L1 showed a trend towards longer OS. In conclusion, ALK-positive NSCLC patients possess a high PD-L1 expression rate. Although there was no significant association between PD-L1 expression and ALK variants, the outcome of ALK-positive patients could be sorted by these two biomarkers.
Non-invasive measurement of leaf water content and pressure–volume curves using terahertz radiation
Authors: Li Ran , Lu Yaojie , Peters Jennifer M. R. , Choat Brendan , Lee Andrew J.
Published: December 2020

In this paper we describe a non-invasive method of measuring leaf water content using THz radiation and combine this with psychrometry for determination of leaf pressure–volume relationships. In contrast to prior investigations using THz radiation to measure plant water status, the reported method exploits the differential absorption characteristic of THz radiation at multiple frequencies within plant leaves to determine absolute water content in real-time. By combining the THz system with a psychrometer, pressure–volume curves were generated in a completely automated fashion for the determination of leaf tissue water relations parameters including water potential at turgor loss, osmotic potential at full turgor and the relative water content at the turgor loss point. This novel methodology provides for repeated, non-destructive measurement of leaf water content and greatly increased efficiency in generation of leaf PV curves by reducing user handling time.
Layer-wise relevance propagation of InteractionNet explains protein–ligand interactions at the atom level
Authors: Cho Hyeoncheol , Lee Eok Kyun , Choi Insung S.
Published: December 2020

Development of deep-learning models for intermolecular noncovalent (NC) interactions between proteins and ligands has great potential in the chemical and pharmaceutical tasks, including structure–activity relationship and drug design. It still remains an open question how to convert the three-dimensional, structural information of a protein–ligand complex into a graph representation in the graph neural networks (GNNs). It is also difficult to know whether a trained GNN model learns the NC interactions properly. Herein, we propose a GNN architecture that learns two distinct graphs—one for the intramolecular covalent bonds in a protein and a ligand, and the other for the intermolecular NC interactions between the protein and the ligand—separately by the corresponding covalent and NC convolutional layers. The graph separation has some advantages, such as independent evaluation on the contribution of each convolutional step to the prediction of dissociation constants, and facile analysis of graph-building strategies for the NC interactions. In addition to its prediction performance that is comparable to that of a state-of-the art model, the analysis with an explainability strategy of layer-wise relevance propagation shows that our model successfully predicts the important characteristics of the NC interactions, especially in the aspect of hydrogen bonding, in the chemical interpretation of protein–ligand binding.
The effect of the papillary renal cell carcinoma subtype on oncological outcomes
Authors: Pan Honghong , Ye Liefu , Zhu Qingguo , Yang Zesong , Hu Minxiong
Published: December 2020

The study aimed to compare the clinicopathological features and prognosis between type I and type II papillary renal cell carcinoma (PRCC) and to investigate whether the subtypes of PRCC would affect oncological outcomes. A total of 102 patients with PRCC were recruited, of which 42 were type I PRCC and 60 type II. The clinicopathological features and oncologic outcomes of the patients were evaluated. The type II cases had a higher WHO/ISUP grading (P < 0.001), T (P = 0.003), N (P = 0.010) stage and stage grouping (P = 0.011) than the type I. During a median follow-up period of 61.4 months, 1-year cancer specific survival (CSS) of the type I was 100%, 5-year CSS was 95.2%, the 1-year CSS of the type II was 96.2%, and 5-year CSS was 75.7%. The univariate analysis showed that subtype, symptoms, TNM, stage grouping, WHO/ISUP grading and surgical methods appeared to affect prognosis of the patients with PRCC. However, multivariate analysis revealed that only stage grouping was the independent risk factor. After the stage grouping factor was adjusted for the analysis, there were no statistically significant differences in CSS (P = 0.214) and PFS (P = 0.190) between the localized type I and type II PRCC groups. Compared with type I PRCC, type II had higher pathological T, N stage and WHO/ISUP grading. However, it was the Stage grouping that made a great difference to oncological outcomes, rather than the subtype of PRCC.
Early evidence of a shift in juvenile fish communities in response to conditions in nursery areas
Authors: Matić-Skoko Sanja , Vrdoljak Dario , Uvanović Hana , Pavičić Mišo , Tutman Pero , Bojanić Varezić Dubravka
Published: December 2020

A multivariate analysis of juvenile fish community data, sampled at two nursery sites at an interval of 17 years (2000—early, and 2017—late), was conducted to elucidate the trends of change in littoral juvenile fish communities along the eastern Adriatic coast. Fishing, trophic and taxonomic composition to the community data were analysed for possible causality. The ichthyofaunal composition differed significantly for Site, Period and all interactions. According to the mMDS ordination plot, four groups of communities were defined, with clear cyclicity. No patterns were found in species composition between sites in the early period, while the observed community changes were governed by the same pattern at both sites in the late period. The species that contributed most to the observed changes were non-commercial, small, benthic resident fishes, such as gobiids and blennids, or those associated with canopy alga for shelter and feeding. The analysis correctly allocated samples based on community information to Sites and Periods. The data obtained provided an invaluable opportunity to test for the generality of potential patterns of change in littoral fish communities, suggesting that significantly modified juvenile fish communities may be the result of constant human embankment and marine infrastructure construction along the coast in recent decades, rather than climate change or fishing pressure, as generally considered.