bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking global fisheries discards
Authors: Gilman E. , Perez Roda A. , Huntington T. , Kennelly S. J. , Suuronen P. , Chaloupka M. , Medley P. A. H. 
Published: August 2020

AbstractDiscarding by fisheries is one of the most wasteful human marine activities, yet we have few estimates of its scale. Reliable estimates of global discards are essential for sustainable fisheries management. Using United Nations Food and Agriculture Organization databases on country-specific landings, we estimated the discard rate and magnitude for global marine and estuarine capture fisheries using fishery-specific discard rates derived from direct observations and global gear-specific discard rates estimated within a Bayesian modelling framework. An estimated 9.1 million tonnes are discarded annually (95% uncertainty interval: 7–16 M t)—or 10.8% of the global catch (95% UI: 10–12%). Encouragingly, this is about half of the annual global discard rate estimated in the late 1980s. Trawl fisheries, especially demersal otter trawls, warrant intensified efforts to reduce discards. Periodic benchmarks of global discards are needed to assess the performance of reduction efforts.
Elliptical metallic rings-shaped fractal metamaterial absorber in the visible regime
Authors: Bilal R. M. H. , Saeed M. A. , Choudhury P. K. , Baqir M. A. , Kamal W. , Ali M. M. , Rahim A. A. 
Published: August 2020

AbstractAchieving the broadband response of metamaterial absorbers has been quite challenging due to the inherent bandwidth limitations. Herein, the investigation was made of a unique kind of visible light metamaterial absorber comprising elliptical rings-shaped fractal metasurface using tungsten metal. It was found that the proposed absorber exhibits average absorption of over 90% in the visible wavelength span of 400–750 nm. The features of perfect absorption could be observed because of the localized surface plasmon resonance that causes impedance matching. Moreover, in the context of optoelectronic applications, the absorber yields absorbance up to ~ 70% even with the incidence obliquity in the range of 0°–60° for transverse electric polarization. The theory of multiple reflections was employed to further verify the performance of the absorber. The obtained theoretical results were found to be in close agreement with the simulation results. In order to optimize the results, the performance was analyzed in terms of the figure of merit and operating bandwidth. Significant amount of absorption in the entire visible span, wide-angle stability, and utilization of low-cost metal make the proposed absorber suitable in varieties of photonics applications, in particular photovoltaics, thermal emitters and sensors.
The metal binding site composition of the cation diffusion facilitator protein MamM cytoplasmic domain impacts its metal responsivity
Authors: Barber-Zucker Shiran , Shahar Anat , Kolusheva Sofiya , Zarivach Raz 
Published: August 2020

AbstractThe cation diffusion facilitator (CDF) is a conserved family of divalent d-block metal cation transporters that extrude these cations selectively from the cytoplasm. CDF proteins are composed of two domains: the transmembrane domain, through which the cations are transported, and a regulatory cytoplasmic C-terminal domain (CTD). It was recently shown that the CTD of the CDF protein MamM from magnetotactic bacteria has a role in metal selectivity, as binding of different metal cations exhibits distinctive affinities and conformations. It is yet unclear whether the composition of the CTD binding sites can impact metal selectivity and if we can manipulate the CTD to response to other non-native metals in CDF proteins. Here we performed a mutational study of the model protein MamM CTD, where we exchanged the native metal binding residues with different metal-binding amino acids. Using X-ray crystallography and Trp-fluorescence spectrometry, we studied the impact of these mutations on the CTD conformation in the presence of non-native metals. Our results reveal that the incorporation of such mutations alters the domain response to metals in vitro, as mutant forms of the CTD bind metals differently in terms of the composition of the binding sites and the CTD conformation. Therefore, the results demonstrate the direct influence of the CTD binding site composition on CDF proteins structure and hence, function, and constitute a first step for rational design of MamM for transporting different metals in vivo.
Symbiotic microalgal diversity within lichenicolous lichens and crustose hosts on Iberian Peninsula gypsum biocrusts
Authors: Moya Patricia , Molins Arantzazu , Chiva Salvador , Bastida Joaquín , Barreno Eva 
Published: August 2020

AbstractThis study analyses the interactions among crustose and lichenicolous lichens growing on gypsum biocrusts. The selected community was composed of Acarospora nodulosa, Acarospora placodiiformis, Diploschistes diacapsis, Rhizocarpon malenconianum and Diplotomma rivas-martinezii. These species represent an optimal system for investigating the strategies used to share phycobionts because Acarospora spp. are parasites of D. diacapsis during their first growth stages, while in mature stages, they can develop independently. R. malenconianum is an obligate lichenicolous lichen on D. diacapsis, and D. rivas-martinezii occurs physically close to D. diacapsis. Microalgal diversity was studied by Sanger sequencing and 454-pyrosequencing of the nrITS region, and the microalgae were characterized ultrastructurally. Mycobionts were studied by performing phylogenetic analyses. Mineralogical and macro- and micro-element patterns were analysed to evaluate their influence on the microalgal pool available in the substrate. The intrathalline coexistence of various microalgal lineages was confirmed in all mycobionts. D. diacapsis was confirmed as an algal donor, and the associated lichenicolous lichens acquired their phycobionts in two ways: maintenance of the hosts’ microalgae and algal switching. Fe and Sr were the most abundant microelements in the substrates but no significant relationship was found with the microalgal diversity. The range of associated phycobionts are influenced by thallus morphology.
A double-Flp-in method for stable overexpression of two genes
Authors: Jensen Ole , Ansari Salim , Gebauer Lukas , Müller Simon F. , Lowjaga Kira A. A. T. , Geyer Joachim , Tzvetkov Mladen V. , Brockmöller Jürgen 
Published: August 2020

AbstractOverexpression of single genes in mammalian cells is widely used to investigate protein function in basic and applied biosciences and in drug research. A better understanding of interactions of two proteins is an important next step in the advancement of our understanding of complex biological systems. However, simultaneous and robust overexpression of two or more genes is challenging. The Flp-In system integrates a vector into cell lines at a specific genomic locus, but has not been used for integration of more than one gene. Here we present a modification of the Flp-In system that enables the simultaneous targeted integration of two genes. We describe the modification and generation of the vectors required and give the complete protocol for transfection and validation of correct genomic integration and expression. We also provide results on the stability and reproducibility, and we functionally validated this approach with a pharmacologically relevant combination of a membrane transporter facilitating drug uptake and an enzyme mediating drug metabolism.
Glomerular galactose-deficient IgA1 expression analysis in pediatric patients with glomerular diseases
Authors: Ishiko Shinya , Horinouchi Tomoko , Fujimaru Rika , Shima Yuko , Kaito Hiroshi , Tanaka Ryojiro , Ishimori Shingo , Kondo Atsushi , Nagai Sadayuki , Aoto Yuya , Sakakibara Nana , Nagano China , Yamamura Tomohiko , Yoshimura Momoka , Nakanishi Koichi , Fujimura Junya , Kamiyoshi Naohiro , Nagase Hiroaki , Yoshikawa Norishige , Iijima Kazumoto , Nozu Kandai 
Published: August 2020

AbstractGalactose-deficient IgA1 (Gd-IgA1) is important in the pathogenesis of IgA nephropathy (IgAN). A Gd-IgA1-specific monoclonal antibody (KM55) has revealed glomerular Gd-IgA1 deposition solely in patients with IgAN and IgA vasculitis with nephritis (IgAV-N). However, this specificity is controversial and has not been demonstrated in pediatric patients. Here, we conducted double-immunofluorescence staining of IgA and Gd-IgA1 in 60 pediatric patients with various glomerular diseases. We divided patients into four groups: (1) patients with IgAN and IgAV-N (n = 23); (2) patients with immunocomplex-mediated glomerulonephritis accompanied by IgA deposition, including lupus nephritis, membranoproliferative glomerulonephritis, and membranous nephropathy (n = 14); (3) patients with other glomerular diseases involving IgA deposition, including idiopathic nephrotic syndrome (INS), oligomeganephronia, Alport syndrome, dense deposit disease, and crescentic glomerulonephritis (n = 11); and (4) patients with IgA-negative diseases including INS, membranoproliferative glomerulonephritis, membranous nephropathy, oligomeganephronia, Alport syndrome, C3 glomerulonephritis, poststreptococcal acute glomerulonephritis, and hemolytic uremic syndrome (n = 12). KM55 staining revealed Gd-IgA1-positive findings in 23/23 patients in Group 1 and 13/14 patients in Group 2, but not in patients in Groups 3 or 4. Therefore, KM55 may detect incidental IgA deposition in pediatric patients. Gd-IgA1 may be involved in the pathogenesis of these immune-related diseases; alternatively, KM55 may recognize IgA-related immunocomplexes in a non-specific manner.
Entropy formula of N-body system
Authors: Shim Jae Wan 
Published: August 2020

AbstractWe prove a proposition that the entropy of the system composed of finite N molecules of ideal gas is the q-entropy or Havrda–Charvát–Tsallis entropy, which is also known as Tsallis entropy, with the entropic index $$q=\frac{D(N-1)-4}{D(N-1)-2}$$

q
=

D
(
N
-
1
)
-
4

D
(
N
-
1
)
-
2

in D-dimensional space. The indispensable infinity assumption used by Boltzmann and others in their derivation of entropy formulae is not involved in our derivation, therefore our derived formula is exact. The analogy of the N-body system brings us to obtain the entropic index of a combined system $$q_C$$

q
C

formed from subsystems having different entropic indexes $$q_A$$

q
A

and $$q_B$$

q
B

as $$\frac{1}{1-q_C}=\frac{1}{1-q_A}+\frac{1}{1-q_B}+\frac{D+2}{2}$$

1

1
-

q
C

=

1

1
-

q
A

+

1

1
-

q
B

+

D
+
2

2

. It is possible to use the number N for the physical measure of deviation from Boltzmann entropy.
Silencing Srsf6 does not modulate incomplete splicing of the huntingtin gene in Huntington’s disease models
Authors: Mason Michael A. , Gomez-Paredes Casandra , Sathasivam Kirupa , Neueder Andreas , Papadopoulou Aikaterini-Smaragdi , Bates Gillian P. 
Published: August 2020

AbstractWe have previously shown that the incomplete splicing of exon 1 to exon 2 of theHTTgene results in the production of a small polyadenylated transcript (Httexon1) that encodes the highly pathogenic exon 1 HTT protein. There is evidence to suggest that the splicing factor SRSF6 is involved in the mechanism that underlies this aberrant splicing event. Therefore, we set out to test this hypothesis, by manipulating SRSF6 levels in Huntington’s disease models in which an expanded CAG repeat had been knocked in to the endogenousHttgene. We began by generating mice that were knocked out forSrsf6, and demonstrated that reduction of SRSF6 to 50% of wild type levels had no effect on incomplete splicing in zQ175 knockin mice. We found that nullizygosity forSrsf6was embryonic lethal, and therefore, to decrease SRSF6 levels further, we established mouse embryonic fibroblasts (MEFs) from wild type, zQ175, and zQ175::Srsf6+/−mice and transfected them with anSrsf6siRNA. The incomplete splicing ofHttwas recapitulated in the MEFs and we demonstrated that ablation of SRSF6 did not modulate the levels of theHttexon1transcript. We conclude that SRSF6 is not required for the incomplete splicing ofHTTin Huntington’s disease.
Topological transitions in superconductor nanomembranes under a strong transport current
Authors: Rezaev R. O. , Smirnova E. I. , Schmidt O. G. , Fomin V. M. 
Published: August 2020

AbstractThe topological defects, vortices in bulk superconductors (SCs) and phase slips in low-dimensional SCs are known to lead to the occurrence of a finite resistance. We report on a topological transition between the both types of topological defects under a strong transport current in an open SC nanotube with a submicron-scale inhomogeneity of the normal-to-the-surface component of the applied magnetic field. When the magnetic field is orthogonal to the axis of the nanotube, which carries the transport current in the azimuthal direction, the phase-slip regime is characterized by the vortex/antivortex lifetime ∼ 10−14 s versus the vortex lifetime ∼ 10−11 s for vortex chains in the half-tubes, and the induced voltage shows a pulse as a function of the magnetic field. The topological transition between the vortex-chain and phase-slip regimes determines the magnetic-field–voltage and current–voltage characteristics of curved SC nanomembranes to pursue high-performance applications in advanced electronics and quantum computing.
Antibacterial activity of Mn(i) and Re(i) tricarbonyl complexes conjugated to a bile acid carrier molecule
Authors: Betts Jono W , Roth Patrick , Pattrick Calum A , Southam Hannah M , La Ragione Roberto M , Poole Robert K , Schatzschneider Ulrich 
Published: August 2020

Abstract
A bifunctional cholic acid–bis(2-pyridylmethyl)amine (bpa) ligand featuring an amide linker was coordinated to a manganese(i) or rhenium(i) tricarbonyl moiety to give [M(bpacholamide)(CO)3] with M = Mn, Re in good yield and very high purity. Strong antibacterial activity was observed against four strains of methicillin-susceptible (MSSA) and methicillin-resistant (MRSA) Staphylococcus aureus, with minimum inhibitory concentrations (MICs) in the range of 2–3.5 μM. No difference in response was observed for the MSSA vs. MRSA strains. Activity was also independent of the nature of the metal center, as the Mn and Re complexes showed essentially identical MIC values. In contrast to some other metal carbonyl complexes, the activity seems to be unrelated to the release of carbon monoxide, as photoactivation of the Mn complex reduced the potency by a factor of 2–8. Both metal complexes were non-toxic in Galleria mellonella larvae at concentrations of up to 100× the MIC value. In vivo testing in Galleria larvae infected with MRSA/MSSA demonstrated a significant increase in overall survival rates from 46% in the control to 88% in the group treated with the metal complexes. ICP-MS analysis showed that the Mn and Re cholamide complexes are efficiently internalized by E. coli cells and do not interfere with membrane integrity, as evident from a lack of release of intracellular ATP. An increased sensitivity was observed in acrB, acrD, and mdt mutants that are defective in multidrug exporters, indicating that the compounds have an intracellular mechanism of action. Furthermore, E. coli mntP mutants defective in the gene encoding an Mn exporter were more sensitive than the wildtype, while inactivation of the regulator that controls expression of the Mn uptake proteins MntP and MntH slightly increased sensitivity to the compound. Single knockout mutants defective in genes linked to bile salt and oxidative stress response (dinF, yiaH, sodA, katE, and soxS) did not show increased sensitivity relative to the wild type. Overall, neither the cholic acid moiety nor the metal-carbonyl fragment alone appear to be responsible for the biological activity observed and thus the search for the primary intracellular target continues.
Identification, cloning, expression and functional interrogation of the biosynthetic pathway of the polychlorinated triphenyls ambigol A–C fromFischerella ambigua108b
Authors: Duell Elke R. , Milzarek Tobias M. , El Omari Mustafa , Linares-Otoya Luis J. , Schäberle Till F. , König Gabrielle M. , Gulder Tobias A. M. 
Published: August 2020

The biosynthetic pathway to the ambigols A–C from Fischerella ambigua 108b has been identified, cloned, heterologously expressed and functionally studied, including in-depth analysis of the biaryl coupling biochemistryin vivoandin vitro.
miR-4454 up-regulated by HPV16 E6/E7 promotes invasion and migration by targeting ABHD2/NUDT21 in cervical cancer
Authors: Wang Hui , Hu Hui , Luo Zhenzhao , Liu Shuiyi , Wu Wangze , Zhu Man , Wang Jing , Liu Yingle , Lu Zhongxin 
Published: August 2020

Abstract
The abnormal expression of HPV16 E6/E7 activates oncogenes and/or inactivates tumor suppressor genes, resulting in the selective growth and malignant transformation of cancer cells. miR-4454 was selected by sequencing due to its abnormal high expression in HPV16 E6/E7 positive CaSki cell compared with HPV16 E6/E7 negative C33A cell. Overexpression of miR-4454 enhances cervical cancer cell invasion and migration. ABHD2 and NUDT21 are identified as a target gene of miR-4454.The effects of ABHD2 and NUDT21 on migration and invasion of CaSki and C33A cells were determined. The dual luciferase and RT-qPCR assays confirmed that miR-4454 might regulate its targets ABHD2 and NUDT21 to promote the proliferation, invasion and migration, whereas, inhibit the apoptosis in CaSki and C33A cells.
Navarro-Frenk-White dark matter profile and the dark halos around disk systems
Authors: Dehghani R. , Salucci P. , Ghaffarnejad H. 
Published: August 2020

Context. The Λ cold dark matter (ΛCDM) scenario is able to describe the Universe at large scales, but clearly shows some serious difficulties at small scales. The core-cusp question is one of these difficulties: the inner dark matter (DM) density profiles of spiral galaxies generally appear to be cored, without the r−1 profile that is predicted by N-body simulations in the above scenario.
Aims. It is well known that in a more physical context, the baryons in the galaxy might backreact and erase the original cusp through supernova explosions. Before the efficiency and the presence of this effect is investigated, it is important to determine how wide and frequent the discrepancy between observed and N-body-predicted profiles is and what its features are.
Methods. We used more than 3200 quite extended rotation curves (RCs) of good quality and high resolution of disk systems that included normal and dwarf spirals as well as low surface brightness galaxies. The curves cover all magnitude ranges. All these RCs were condensed into 26 coadded RCs, each of them built with individual RCs of galaxies of similar luminosity and morphology. We performed mass models of these 26 RCs using the Navarro-Frenk-White (NFW) profile for the contribution of the DM halo to the circular velocity and the exponential Freeman disk for the contribution of the stellar disk.
Results. The fits are generally poor in all the 26 cases: in several cases, we find χred2 > 2. Moreover, the best-fitting values of three parameters of the model (c, MD, and Mvir) combined with those of their 1σ uncertainty clearly contradict well-known expectations of the ΛCDM scenario. We also tested the scaling relations that exist in spirals with the outcome of the current mass modeling: the modeling does not account for these scaling relations.
Conclusions. The results of testing the NFW profile in disk systems indicate that this DM halo density law cannot account for the kinematics of the whole family of disk galaxies. It is therefore mandatory for the success of the ΛCDM scenario in any disk galaxy of any luminosity or maximum rotational velocity to transform initial cusps into the observed cores.
Investigating gravitational collapse of a pebble cloud to form transneptunian binaries
Authors: Robinson J. E. , Fraser W. C. , Fitzsimmons A. , Lacerda P. 
Published: August 2020

Context. A large fraction of transneptunian objects are found in binary pairs, ~30% in the cold classical population between ahel ~ 39 and ~48 AU. Observationally, these binaries generally have components of similar size and colour. Previous work has shown that gravitational collapse of a pebble cloud is an efficient mechanism for producing such systems. Since the bi-lobate nature of 2014 MU69 (Arrokoth) was discovered, interest in gravitational collapse as a pathway for forming contact binaries has also grown.
Aims. We investigate the formation of binary systems through gravitational collapse by considering a wider range of binary masses than previous studies. We analysed in detail the properties of the bound systems that are formed and compared them to observations.
Methods. We performed N-body simulations of gravitational collapse of a pebble cloud using the REBOUND package, with an integrator designed for rotating reference frames and robust collision detection. We conducted a deep search for gravitationally bound particles at the end of the gravitational collapse phase and tested their stability. For all systems produced, not just for the most massive binaries, we investigated the population characteristics of their mass and orbital parameters.
Results. We found that gravitational collapse is an efficient producer of bound planetesimal systems. On average, about 1.5 bound systems were produced per cloud in the mass range studied here. In addition to large equal-sized binaries, we found that gravitational collapse produces massive bodies with small satellites and low-mass binaries with a high mass ratio. Our results disfavour the collapse of high-mass clouds, in line with reported upper mass limits of clouds formed by the streaming instability. Gravitational collapse can create binary systems analogous to Arrokoth, and collisions in a collapsing cloud should be gentle enough to preserve a bi-lobed structure.