bluuebunny/crossref_metadata_2025_split huggingface dataset:
A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas)
Authors: Adolfi Mateus C. , Du Kang , Kneitz Susanne , Cabau Cédric , Zahm Margot , Klopp Christophe , Feron Romain , Paixão Rômulo V. , Varela Eduardo S. , de Almeida Fernanda L. , de Oliveira Marcos A. , Nóbrega Rafael H. , Lopez-Roques Céline , Iampietro Carole , Lluch Jérôme , Kloas Werner , Wuertz Sven , Schaefer Fabian , Stöck Matthias , Guiguen Yann , Schartl Manfred 
Published: November 2021

AbstractArapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGFβ signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes.
A novel parameter derived from post-processing procedure of dual energy CT for identification of gout
Authors: Xiang Chunlin , Zhang Hongyan , Wu Gang 
Published: November 2021

AbstractROI analysis is frequently used for obtaining acid content on rapid-kV-switching dual energy CT (DECT), providing inadequate accuracy. A new parameter derived from post-processing procedure, maximum lower limit with stain visible (MLLSV), was used by us to diagnose gout. 30 gout patients and 20 healthy volunteers were analyzed by using MLLSV. MLLSV was defined as the maximum lower limit of display window allowing only one stained site visible. Radiologists were asked to continuously increase the lower limit of display window of uric acid to decrease number of stained sites until the last stained site disappeared. MLLSV obtained by this way was compared between gout patients and volunteers. Receiver operating characteristic (ROC) curve was used to determine the performance. MLLSV of gout patients was significantly higher than that of volunteers (1373.3 ± 23.0 mg/cm3 vs. 1315.4 ± 20.7 mg/cm3, p = 0.000). The area under ROC curve of MLLSV was 0.993 in identifying gout. When using the optimal cutoff of 1342 mg/cm3, the sensitivity and specificity of MLLSV in identification of gout were 96.7% and 95% respectively. MLLSV derived from post-processing procedure of DECT is useful in discriminating gout patients from healthy people.
Gate induced quantum wires in GaAs/AlGaAs heterostructures by cleaved edge deposition
Authors: Alt L. , Reichl C. , Berl M. , Dietsche W. , Wegscheider W. 
Published: November 2021

AbstractElectric conductors with dimensions reduced to the nanometer scale are the prerequisite of the quantum devices upon which the future advanced electronics is expected to be based. In the past, the fabrication of one-dimensional (1D) wires has been a particular challenge because they have to be defect-free over their whole length, which can be several tens µm. Excellent 1D wires have been produced by cleaving semiconductors (GaAs, AlGaAs) in ultra high vacuum and overgrowing the pristine edge surface by molecular beam epitaxy (MBE)1,2. Unfortunately, this cleaved edge overgrowth (CEO) technique did not find wide-spread use because it requires a series of elaborate steps that are difficult to accomplish. In this Letter, we present a greatly simplified variation of this technique where the cleaving takes place in ambient air and the MBE overgrowth is replaced by a standard deposition process. Wires produced by this cleaved edge deposition (CED) technique have properties that are as least as good as the traditional CEO ones. Due to its simplicity, the CED technique offers a generally accessible way to produce 1D devices.
Propensity score-adjusted analysis on stent-assisted coiling versus coiling alone for ruptured intracranial aneurysms
Authors: Goertz Lukas , Liebig Thomas , Pennig Lenhard , Timmer Marco , Styczen Hanna , Grunz Jan-Peter , Lichtenstein Thorsten , Schlamann Marc , Kabbasch Christoph 
Published: November 2021

AbstractStent-assisted coiling (SAC) for ruptured intracranial aneurysms (RIAs) remains controversial due to an inherent risk of potential thromboembolic and hemorrhagic complications. We compared SAC and coiling alone for the management of RIAs using propensity score-adjustment. Sixty-four patients treated by SAC and 220 by stand-alone coiling were retrospectively reviewed and compared using inverse probability of treatment weighting (IPTW) with propensity scores. Functional outcome, procedure-related and overall complications and angiographic results were analyzed. Aneurysms treated by SAC had a larger diameter, a wider neck and were more frequently located at the posterior circulation. SAC had a higher risk for thromboembolic complications (17.2% vs. 7.7%, p = 0.025), however, this difference did not persist in the IPTW analysis (OR 1.2, 95% CI 0.7–2.3, adjusted p = 0.458). In the adjusted analysis, rates of procedural cerebral infarction (p = 0.188), ventriculostomy-related hemorrhage (p = 0.584), in-hospital mortality (p = 0.786) and 6-month favorable functional outcome (p = 0.471) were not significantly different between the two groups. SAC yielded a higher complete occlusion (80.0% vs. 67.2%, OR 3.2, 95% CI 1.9–5.4, p < 0.001) and a lower recanalization rate (17.5% vs. 26.1%, OR 0.3, 95% CI 0.2–0.6, p < 0.001) than stand-alone coiling at 6-month follow-up. In conclusion, SAC of large and wide-necked RIAs provided higher aneurysm occlusion and similar clinical outcome, when compared to stand-alone coiling.
Land use influences stream bacterial communities in lowland tropical watersheds
Authors: Chavarria Karina A. , Saltonstall Kristin , Vinda Jorge , Batista Jorge , Lindmark Megan , Stallard Robert F. , Hall Jefferson S. 
Published: November 2021

AbstractLand use is known to affect water quality yet the impact it has on aquatic microbial communities in tropical systems is poorly understood. We used 16S metabarcoding to assess the impact of land use on bacterial communities in the water column of four streams in central Panama. Each stream was influenced by a common Neotropical land use: mature forest, secondary forest, silvopasture and traditional cattle pasture. Bacterial community diversity and composition were significantly influenced by nearby land uses. Streams bordered by forests had higher phylogenetic diversity (Faith’s PD) and similar community structure (based on weighted UniFrac distance), whereas the stream surrounded by traditional cattle pasture had lower diversity and unique bacterial communities. The silvopasture stream showed strong seasonal shifts, with communities similar to forested catchments during the wet seasons and cattle pasture during dry seasons. We demonstrate that natural forest regrowth and targeted management, such as maintaining and restoring riparian corridors, benefit stream-water microbiomes in tropical landscapes and can provide a rapid and efficient approach to balancing agricultural activities and water quality protection.
Improved production of the non-native cofactor F420 in Escherichia coli
Authors: Shah Mihir V. , Nazem-Bokaee Hadi , Antoney James , Kang Suk Woo , Jackson Colin J. , Scott Colin 
Published: November 2021

AbstractThe deazaflavin cofactor F420 is a low-potential, two-electron redox cofactor produced by some Archaea and Eubacteria that is involved in methanogenesis and methanotrophy, antibiotic biosynthesis, and xenobiotic metabolism. However, it is not produced by bacterial strains commonly used for industrial biocatalysis or recombinant protein production, such as Escherichia coli, limiting our ability to exploit it as an enzymatic cofactor and produce it in high yield. Here we have utilized a genome-scale metabolic model of E. coli and constraint-based metabolic modelling of cofactor F420 biosynthesis to optimize F420 production in E. coli. This analysis identified phospho-enol pyruvate (PEP) as a limiting precursor for F420 biosynthesis, explaining carbon source-dependent differences in productivity. PEP availability was improved by using gluconeogenic carbon sources and overexpression of PEP synthase. By improving PEP availability, we were able to achieve a ~ 40-fold increase in the space–time yield of F420 compared with the widely used recombinant Mycobacterium smegmatis expression system. This study establishes E. coli as an industrial F420-production system and will allow the recombinant in vivo use of F420-dependent enzymes for biocatalysis and protein engineering applications.
Prandtl number dependence of stellar convection: Flow statistics and convective energy transport
Authors: Käpylä P. J. 
Published: November 2021

Context. The ratio of kinematic viscosity to thermal diffusivity, the Prandtl number, is much smaller than unity in stellar convection zones.
Aims. The main goal of this work is to study the statistics of convective flows and energy transport as functions of the Prandtl number.
Methods. Three-dimensional numerical simulations of compressible non-rotating hydrodynamic convection in Cartesian geometry are used. The convection zone (CZ) is embedded between two stably stratified layers. The dominant contribution to the diffusion of entropy fluctuations comes in most cases from a subgrid-scale diffusivity whereas the mean radiative energy flux is mediated by a diffusive flux employing Kramers opacity law. Here, we study the statistics and transport properties of up- and downflows separately.
Results. The volume-averaged rms velocity increases with decreasing Prandtl number. At the same time, the filling factor of downflows decreases and leads to, on average, stronger downflows at lower Prandtl numbers. This results in a strong dependence of convective overshooting on the Prandtl number. Velocity power spectra do not show marked changes as a function of Prandtl number except near the base of the convective layer where the dominance of vertical flows is more pronounced. At the highest Reynolds numbers, the velocity power spectra are more compatible with the Bolgiano-Obukhov k−11/5 than the Kolmogorov-Obukhov k−5/3 scaling. The horizontally averaged convected energy flux (F̅conv), which is the sum of the enthalpy (F̅enth) and kinetic energy fluxes (F̅kin), is independent of the Prandtl number within the CZ. However, the absolute values of F̅enth and F̅kin increase monotonically with decreasing Prandtl number. Furthermore, F̅enth and F̅kin have opposite signs for downflows and their sum F̅↓conv diminishes with Prandtl number. Thus, the upflows (downflows) are the dominant contribution to the convected flux at low (high) Prandtl numbers. These results are similar to those from Rayleigh-Benárd convection in the low Prandtl number regime where convection is vigorously turbulent but inefficient at transporting energy.
Conclusions. The current results indicate a strong dependence of convective overshooting and energy flux on the Prandtl number. Numerical simulations of astrophysical convection often use a Prandtl number of unity because it is numerically convenient. The current results suggest that this can lead to misleading results and that the astrophysically relevant low Prandtl number regime is qualitatively different from the parameter regimes explored in typical contemporary simulations.
Kepler-223 resonance holds information about turbulence during the gas-disk phase
Authors: Hühn L.-A. , Pichierri G. , Bitsch B. , Batygin K. 
Published: November 2021

Context. Planet formation remains an open field of research, and many fundamental physical processes regarding planetary formation in protoplanetary disks are still imperfectly understood. It remains to be investigated how different conditions in these protoplanetary disks affect the emergence of different types of observed systems. An elusive phenomenon is the turbulence in these disks. Observations are available of planetary systems and of some protoplanetary disks, which can serve as a starting point for these investigations. The detected systems reveal different architectures of planets. One particularly interesting case to consider is the Kepler-223 system, which contains a rare configuration of four planets in a resonance chain. This implies a certain migration history.
Aims. We aim to use the orbital configuration of the Kepler-223 planets to constrain the parameters of the protoplanetary disk that allow the formation of a chain of mean-motion resonances that resembles the resonances of Kepler-223. We primarily investigate the disk viscosity and surface density.
Methods. We used the swift_symba N-body integrator with additional dissipative forces to mimic planet-disk interactions.
Results. We constrained the surface densities and viscosities that allow the formation of a resonant chain like that of Kepler-223. We find that surface densities of up to a few minimum mass solar nebula surface densities and disk viscosity parameters α of a few × 10−3 up to × 10−2 are most successful at reproducing the architecture of this particular planetary system. We describe the connection of these two quantities with each other, considering the success of reproducing the chain. We find that higher disk surface densities in turn require lower viscosities to build the chain.
Conclusions. Our results show that well-characterized observed planetary systems hold information about their formation conditions in the protoplanetary disks and that it is possible to extract this information, namely the initial disk surface density and viscosity. This helps to constrain planet formation.
Raloxifene in the Treatment of Osteoporosis in Postmenopausal Women
with End-Stage Renal Disease: A Systematic Review and
Meta-Analysis
Authors: Ma Hao-Yang , Chen Shuang , Lu Ling-Ling , Gong Wei , Zhang Ai-Hua 
Published: November 2021

AbstractAs a selective estrogen receptor modulator (SERM), raloxifene is used in healthy
postmenopausal women to prevent bone loss and reduce fractures. However, the
benefit of raloxifene is uncertain in the treatment of osteoporosis among
patients with end-stage renal disease (ESRD) or those who require maintenance
dialysis. We assessed the safety and efficacy of raloxifene in this particular
population. Studies were selected from PubMed, Springer, CNKI (Chinese National
Knowledge Infrastructure) and Wanfang Database. Randomized controlled trials
(RCTs) and prospective studies with control/placebo groups were
included. Five studies were included with a total of 244 participants (121
patients in the raloxifene group and 123 patients in the placebo/control
group). The median duration of treatment was 12 months. The incidence rate of
side effects of raloxifene was 0/121 (0%). There was a
significant improvement of lumbar spine bone mineral density (BMD) levels in the
raloxifene group compared with the placebo group (MD: 33.88, 95% CI:
10.93, 56.84, p=0.004). There was no significant difference concerning
the improvement of femoral neck BMD (MD: 8.42, 95% CI: –10.21,
27.04, p=0.38), intact parathyroid hormone (iPTH) (MD: –12.62,
95% CI: –35.36, 10.13, p=0.28), calcium (MD: -0.08,
95% CI: –0.61, 0.44, p=0.76), phosphorus (MD: 0.18,
95% CI: –0.12, 0.48, p=0.23) or bone alkaline
phosphatase (BAP) (MD: –4.33, 95% CI: –14.44, 5.79,
p=0.40). Raloxifene seems to be effective in improving the lumbar spine
BMD in postmenopausal women with ESRD. More large RCTs are necessary to evaluate
the long-term safety of raloxifene in uremic patients.
Spin–orbit torque magnetization switching in a perpendicularly magnetized full Heusler alloy Co2FeSi
Authors: Jiang Miao , Matsushita Eisuke , Takamura Yota , Anh Le Duc , Nakagawa Shigeki , Ohya Shinobu , Tanaka Masaaki 
Published: November 2021

To optimize the writing and reading performance of magnetic random-access memory (MRAM) devices, achieving current-induced spin–orbit torque (SOT) magnetization switching in perpendicularly magnetized full Heusler alloys is vitally important. For conventional SOT-metal bilayer systems, heavy metals (HMs) with a large spin Hall angle (θSH) are generally used for generating a spin current, which is injected into the adjacent ferromagnet (FM) layer and exerts a torque on the magnetization to switch it. However, the large resistivity of generally used HMs such as β-Ta and β-W can increase the Ohmic loss. In this article, we achieve full SOT switching in Heusler alloy Co2FeSi using low-resistivity Pd as a spin current generation source. The critical switching current density is found to be 3.7 × 107 A cm−2, which is in the same order of magnitude as that required for conventional HM/FM systems even though Pd has a smaller θSH than that of generally used HMs. Using harmonic Hall measurements, the damping-like and field-like effective fields per unit current density are estimated to be 56.9 (10−7 Oe A−1 cm2) and 39.8 (10−7 Oe A−1 cm2), respectively. This high efficiency can be attributed to the excellent lattice matching between Co2FeSi and Pd (only 2% mismatch), to a slight Pd diffusion, and possibly to the additional SOTs induced by the in-plane spin component generated in the Co2FeSi layer. Our finding will advance the development of SOT-MRAM devices with both better reading and writing performance.
An ITO–graphene heterojunction integrated absorption modulator on Si-photonics for neuromorphic nonlinear activation
Authors: Amin Rubab , George Jonathan K. , Wang Hao , Maiti Rishi , Ma Zhizhen , Dalir Hamed , Khurgin Jacob B. , Sorger Volker J. 
Published: November 2021

The high demand for machine intelligence of doubling every three months is driving novel hardware solutions beyond charging of electrical wires, given a resurrection to application specific integrated circuit (ASIC)-based accelerators. These innovations include photonic-based ASICs (P-ASICs) due to prospects of performing optical linear (and also nonlinear) operations, such as multiply–accumulate for vector matrix multiplications or convolutions, without iterative architectures. Such photonic linear algebra enables picosecond delay when photonic integrated circuits are utilized via “on-the-fly” mathematics. However, the neuron’s full function includes providing a nonlinear activation function, known as thresholding, to enable decision making on inferred data. Many P-ASIC solutions perform this nonlinearity in the electronic domain, which brings challenges in terms of data throughput and delay, thus breaking the optical link and introducing increased system complexity via domain crossings. This work follows the notion of utilizing enhanced light–matter interactions to provide efficient, compact, and engineerable electro-optic neuron nonlinearity. Here, we introduce and demonstrate a novel electro-optic device to engineer the shape of this optical nonlinearity to resemble a leaky rectifying linear unit—the most commonly used nonlinear activation function in neural networks. We combine the counter-directional transfer functions from heterostructures made out of two electro-optic materials to design a diode-like nonlinear response of the device. Integrating this nonlinearity into a photonic neural network, we show how the electrostatics of this thresholder’s gating junction improves machine learning inference accuracy and the energy efficiency of the neural network.
Automated feeding of sheep. 2. Feeding behaviour influences the methane emissions of sheep offered restricted diets
Authors: Muir S. K. , Behrendt R. , Moniruzzaman M. , Kearney G. , Knight M. I. 
Published: November 2021

Context During the non-growing season of pastures and during droughts, the dry-matter intake (DMI) of sheep is often constrained due to low pasture availability and the need to feed for weight loss or maintenance. Below-maintenance feeding may have consequences for methane (CH4) production and yield in farm systems. Aims The effect of six restricted feeding levels on CH4 emissions measured using portable accumulation chambers (PACs) was examined in relation to DMI, oxygen consumption (O2) and carbon dioxide (CO2) emissions and observed changes in feeding behaviour in sheep fed with automated feeders. Methods An automated feeding system was used to apply daily feeding levels to Maternal Composite ewes (n = 126). Sheep were adapted to the automated feeding system over 19 days, with unlimited access to feed. Following adaptation, sheep were allocated to restricted daily feed levels at 40%, 80%, 100%, 140% and 180% of estimated maintenance requirements (MR) for 41 days. Methane, CO2 and O2 emissions from ewes were measured using PACs on Days 30 and 31 of the restricted feeding period. Key results Methane production (g/day) increased (P < 0.001) with the level of feeding. However, time since the last meal decreased with the level of feeding and was associated with CH4 production. Sheep on lower levels of feeding tended to consume meals earlier in the day and had longer times since their last meal at PAC measurement and lower CH4 production. These two factors explained 58.7% of the variance in CH4 production in an additive linear model. Methane yield (g CH4/kg DMI) decreased as the level of feeding was increased. Conclusions Methane emissions were affected not only by daily DMI, but also time since the last meal. An understanding of the effect of feeding behaviour and time since the last meal should be incorporated into feeding protocols prior to CH4 measurements when PACs are being used to measure CH4 emissions from sheep fed restricted diets. Implications Utilising automated feeders may improve the accuracy of PAC measurements of sheep CH4 emissions fed both ad libitum and restricted feed amounts, by increasing understanding of DMI and feeding behaviour.
Towards a (re)imagined posture on (im)migration
Authors: Gavilanes Vianney A. 
Published: November 2021

AbstractThe hegemonic production of knowledge on (im)migration from the geopolitical and epistemic location of the United States has made legible and knowable a particular conception of (im)migration shaping in turn how (im)migrant subjects are made and remade. As a corpus these dominant conceptions of (im)migration are legible through a dominant discourse that has, in the particular case of the U.S., contributed to a racialized (im)migrant personhood and to the study ofoutsiders coming in to settle. In a two-pronged approach the piece (a) shows the settler colonial logics embedded in (im)migration discourse while (b) simultaneously enacting work of (re)imagining by putting in conversation the work on discourse and racialization within the contexts of (im)migration with Indigenous scholars’ work on borders, settlement, and sovereignty. As such the goals are to disrupt the naturalized ways whereby the racialized (im)migrant and (im)migration are conceptualized within the U.S. context and to offer an aperture for a (re)imagined posture on (im)migration. These initial and fragmentary dialogic exchanges offer a potential path towards a (re)imagined posture on (im)migration that does not reproduce settler colonial logics while sustaining the coexistence of antagonisms and tensions in our quotidian interactions needed to live with the discomfort of contradictions.