bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving the connectivity of MgB2 bulk superconductors by a novel liquid phase sintering process
Authors: Matthews G A B , Mousavi T , Santra S , Grovenor C R M , Grant P S , Speller S
Published: February 2022

This work investigates a new processing method developed to improve the connectivity of ex-situ MgB2 bulks at low sintering temperatures. Mg additions (1–10 wt.%) were mixed to pre-synthesised MgB2 to make composite powders that were sintered at 900 ∘C by the field assisted sintering technique. Addition of 10 wt.% Mg resulted in a substantial increase in density from 68% to 79% and a dramatic reduction in MgB4 from 11 to ∼0 wt.%. Pressure and dilatometry data recorded in-situ during the sintering process revealed that Mg additions led to different sintering mechanisms depending on the Mg fraction. For large Mg fractions (6 and 10 wt.%) a Mg liquid phase was formed and led to significant density improvements, and all pre-existing MgB4 was transformed into MgB2. A small amount of residual Mg remained in the bulks after the sintering process. Connectivity was improved with Mg additions, increasing four fold in the 10 wt.% Mg-MgB2 sample compared to unmodified MgB2. J

c
values at low field were also significantly improved by Mg additions, in particular the 6 and 10 wt.% Mg-MgB2 specimens showed J

c
(20 K, 0 T) values 4–5 times higher than for unmodified MgB2.
Prospects for assembling ultracold radioactive molecules from laser-cooled atoms
Authors: Kłos Jacek , Li Hui , Tiesinga Eite , Kotochigova Svetlana
Published: February 2022

Molecules with unstable isotopes often contain heavy and deformed nuclei and thus possess a high sensitivity to parity-violating effects, such as the Schiff moments. Currently the best limits on Schiff moments are set with diamagnetic atoms. Polar molecules with quantum-enhanced sensing capabilities, however, can offer better sensitivity. In this work, we consider the prototypical 223Fr107Ag molecule, as the octupole deformation of the unstable 223Fr francium nucleus amplifies the nuclear Schiff moment of the molecule by two orders of magnitude relative to that of spherical nuclei and as the silver atom has a large electron affinity. To develop a competitive experimental platform based on molecular quantum systems, 223Fr atoms and 107Ag atoms have to be brought together at ultracold temperatures. That is, we explore the prospects of forming 223Fr107Ag from laser-cooled Fr and Ag atoms. We have performed fully relativistic electronic-structure calculations of ground and excited states of FrAg that account for the strong spin-dependent relativistic effects of Fr and the strong ionic bond to Ag. In addition, we predict the nearest-neighbor densities of magnetic-field Feshbach resonances in ultracold 223Fr + 107Ag collisions with coupled-channel calculations. These resonances can be used for magneto-association into ultracold, weakly-bound FrAg. We also determine the conditions for creating 223Fr107Ag molecules in their absolute ground state from these weakly-bound dimers via stimulated Raman adiabatic passage using our calculations of the relativistic transition electric dipole moments.
Efficient rotational cooling of a cold beam of barium monofluoride
Authors: Courageux T , Cournol A , Comparat D , Viaris de Lesegno B , Lignier H
Published: February 2022

The ability to cool and trap a large number of molecules is currently a crucial challenge for the implementation of various applications in fundamental physics and cold chemistry. We here present an optical cooling of the internal degrees of freedom which maximizes the number of molecules in a minimum number of rotational states. Our demonstration is achieved on a supersonic beam of barium monofluoride seeded in argon, a process that leads to a rotational temperature T
rot ≈ 12 K. The rotation is then cooled by our optical pumping to approximately T
rot ≈ 0.8 K which, compared to the initial rotational distribution, corresponds to an increase of the number of molecules in the lowest rotational state by one order of magnitude. Our method employs two light sources coming from tapered amplifiers. The first source, dedicated to the rotational cooling of molecules occupying the fundamental vibrational level, is optimized thanks to a spectral shaping whose resolution is comparable to the separation of the relevant rotational levels. The second source is used to pump the molecules back to the fundamental vibrational level when they escape from it. This work focuses on the relevant features of these two types of optical pumping.
Al0.30Ga0.70N /GaN MODFET with triple-teeth metal for RF and high-power applications
Authors: Dubey Shashank Kumar , Islam Aminul
Published: February 2022

A modulation-doped field-effect transistor (MODFET) has been investigated in this paper. It is also called HEMT (high electron mobility transistor). The proposed MODFET is made up of Al0.30Ga0.70N as supply layer and GaN as channel or buffer layer, in which floating metal is embedded. Its T-gate is recessed to obtain higher gm, which results in improved RF characteristics. T-gate is used to minimize the gate resistance which reduces the power consumption of the proposed HEMT. A floating metal having triple teeth (TT), which resembles a comb is developed in GaN channel/buffer layer between the gate and drain electrodes to improve the device performance without increasing the dimensions of the device. The transition or cutoff frequency (f
T) of 125 GHz and unity power gain (also called) maximum oscillation) frequency (f
MAX) of 530 GHz at V
DS = 10 V with V
GS = 0.4 V have been reported in this paper. Analysis of power consumption of the proposed FET such as power gain (A
P), output power (P
OUT), and power-added efficiency (PAE) have been analyzed at 10 GHz in continuous wave mode and V
DS = 35 V have been analyzed. The value obtained for P
OUT, A
P, and PAE is 67.5 dBmW, 11.6 dB, and 24.6%, respectively. All the obtained results from the Silvaco TCAD software have been verified with the mathematical model.
Reflection and refraction of photons
Authors: Bersons Imants , Veilande Rita , Balcers Ojars
Published: February 2022

Three linear equations are proposed as quantum-mechanical equations for the free propagating photons. The solution of these equations is the vector potential of the electromagnetic field and it is a product of the Gaussian functions for the transverse coordinates and the eigenfunction of the harmonic oscillator for the longitudinal coordinate. This solutions is used to describe the reflection and refraction of photons on the boundary between two dielectrics. The amplitude of the reflected field coincides with the Fresnel formulae for the plane waves, but the amplitude of the refracted field is different. These amplitudes are the probability’s amplitudes of reflection and refraction of photons—like in the quantum mechanics. The photons propagated from the first into the second medium increase (decrease) their transverse size in the plane of incidence, if the refraction index of the second medium is greater (smaller) than in the first medium. The increasing or decreasing grow when increasing the angle of incidence. The difference between the quantum mechanics of the particles with a mass and the photons, as well as the interpretation of the wave function of photons, is discussed.
Constraints for electric charge from Maxwell’s equations and boundary conditions
Authors: Cameron Robert P
Published: February 2022

Certain boundary conditions constrain the forms that the electromagnetic field can take in a theory, in particular the boundary conditions inherent to closed spaces. According to Maxwell’s equations, this can give rise to constraints for the electric charge in the theory. We identify three such ‘boundary constraints’ for electric charge and highlight some of their myriad implications, touching upon a wealth of topics including the self-consistency of practical calculations, the nature of dark matter, the origin of electric-charge quantisation and the shape of the Universe. Furthermore, we explain that magnetic analogues of our boundary constraints offer new insights into the possible existence of magnetic monopoles and dyons.
A fully Lagrangian, non-parametric bias model for dark matter halos
Authors: Wu Xiaohan , Muñoz Julian B. , Eisenstein Daniel
Published: February 2022

We present a non-parametric Lagrangian biasing model and fit the ratio of the halo and mass densities at the field level using the mass-weighted halo field in the AbacusSummit simulations at z=0.5. Unlike the perturbative halo bias model that has been widely used in interpreting the observed large-scale structure traced by galaxies, we find a non-negative halo-to-mass ratio that increases monotonically with the linear overdensity δ1 in the initial Lagrangian space. The bias expansion, however, does not guarantee non-negativity of the halo counts, and may lead to rising halo number counts at negative overdensities. The shape of the halo-to-mass ratio is unlikely to be described by a polynomial function of δ1 and other quantities. Especially for massive halos with 6×1012 h-1 M⊙, the halo-to-mass ratio starts soaring up at δ1>0, substantially different from the predictions of the bias expansion. We show that for the halo masses we consider (M>3×1011 h-1 M⊙) a non-parametric halo-to-mass ratio as a function of δ1 and its local derivative ∇^2δ1 can recover the halo power spectra to sub-percent level accuracy for wavenumbers k=0.01-0.1 h Mpc-1 given a proper smoothing scale to filter the initial density field, even though we do not fit the power spectrum directly. However, there is mild dependence of the recovery of the halo power spectrum on the smoothing scale and other input parameters. At k<0.01 h Mpc-1 and for massive halos with M>6×1012 h-1 M⊙, our non-parametric model leads to a few percent overestimation of the halo power spectrum, indicating the need for larger or multiple smoothing scales. The halo-to-mass ratios obtained qualitatively agree with intuitions from extended Press-Schechter theory. We compare our framework to the bias expansion and discuss possible extensions.
Clustering of Gravitational Wave and Supernovae events: a multitracer analysis in Luminosity Distance Space
Authors: Libanore S. , Artale M.C. , Karagiannis D. , Liguori M. , Bartolo N. , Bouffanais Y. , Mapelli M. , Matarrese S.
Published: February 2022

We study the clustering of Gravitational Wave (GW) merger events and Supernovae IA (SN), as cosmic tracers in Luminosity Distance Space. We modify the publicly available CAMB code to numerically evaluate auto- and cross- power spectra for the different sources, including Luminosity Distance Space distortion effects generated by peculiar velocities and lensing convergence. We perform a multitracer Fisher analysis to forecast expected constraints on cosmological and GW bias coefficients, using outputs from hydrodynamical N-body simulations to determine the bias fiducial model and considering future observations from the Vera Rubin Observatory and Einstein Telescope (ET), both single and in a 3 detector network configuration. We find that adding SN to the GW merger dataset considerably improves the forecast, mostly by breaking significant parameter degeneracies, with final constraints comparable to those obtainable from a Euclid-like survey. GW merger bias is forecasted to be detectable with good significance even in the single ET case.
jULIEs: nanostructured polytrodes for low traumatic extracellular recordings and stimulation in the mammalian brain
Authors: Racz Romeo R , Kollo Mihaly , Racz Gabriella , Bulz Ciprian , Ackels Tobias , Warner Tom , Wray William , Kiskin Nikolai , Chen Chi , Ye Zhiwen , de Hoz Livia , Rancz Ede , Schaefer Andreas T
Published: February 2022

Objective. Extracellular microelectrode techniques are the most widely used approach to interrogate neuronal populations. However, regardless of the manufacturing method used, damage to the vasculature and circuit function during probe insertion remains a concern. This issue can be mitigated by minimising the footprint of the probe used. Reducing the size of probes typically requires either a reduction in the number of channels present in the probe, or a reduction in the individual channel area. Both lead to less effective coupling between the probe and extracellular signals of interest. Approach. Here, we show that continuously drawn SiO2-insulated ultra-microelectrode fibres offer an attractive substrate to address these challenges. Individual fibres can be fabricated to >10 m continuous stretches and a selection of diameters below 30 µm with low resistance (<100 Ω mm−1) continuously conductive metal core of <10 µm and atomically flat smooth shank surfaces. To optimize the properties of the miniaturised electrode-tissue interface, we electrodeposit rough Au structures followed by ∼20 nm IrOx film resulting in the reduction of the interfacial impedance to <500 kΩ at 1 kHz. Main results. We demonstrate that these ultra-low impedance electrodes can record and stimulate both single and multi-unit activity with minimal tissue disturbance and exceptional signal-to-noise ratio in both superficial (∼40 µm) and deep (∼6 mm) structures of the mouse brain. Further, we show that sensor modifications are stable and probe manufacturing is reproducible. Significance. Minimally perturbing bidirectional neural interfacing can reveal circuit function in the mammalian brain in vivo.
A network information theoretic framework to characterise muscle synergies in space and time
Authors: Ó’ Reilly David , Delis Ioannis
Published: February 2022

Objective. Current approaches to muscle synergy extraction rely on linear dimensionality reduction algorithms that make specific assumptions on the underlying signals. However, to capture nonlinear time varying, large-scale but also muscle-specific interactions, a more generalised approach is required. Approach. Here we developed a novel framework for muscle synergy extraction that relaxes model assumptions by using a combination of information and network theory and dimensionality reduction. We first quantify informational dynamics between muscles, time-samples or muscle-time pairings using a novel mutual information formulation. We then model these pairwise interactions as multiplex networks and identify modules representing the network architecture. We employ this modularity criterion as the input parameter for dimensionality reduction, which verifiably extracts the identified modules, and also to characterise salient structures within each module. Main results. This novel framework captures spatial, temporal and spatiotemporal interactions across two benchmark datasets of reaching movements, producing distinct spatial groupings and both tonic and phasic temporal patterns. Readily interpretable muscle synergies spanning multiple spatial and temporal scales were identified, demonstrating significant task dependence, ability to capture trial-to-trial fluctuations and concordance across participants. Furthermore, our framework identifies submodular structures that represent the distributed networks of co-occurring signal interactions across scales. Significance. The capabilities of this framework are illustrated through the concomitant continuity with previous research and novelty of the insights gained. Several previous limitations are circumvented including the extraction of functionally meaningful and multiplexed pairwise muscle couplings under relaxed model assumptions. The extracted synergies provide a holistic view of the movement while important details of task performance are readily interpretable. The identified muscle groupings transcend biomechanical constraints and the temporal patterns reveal characteristics of fundamental motor control mechanisms. We conclude that this framework opens new opportunities for muscle synergy research and can constitute a bridge between existing models and recent network-theoretic endeavours.
The radial phase variation of reversed-shear and toroidicity-induced Alfvén eigenmodes in DIII-D
Authors: Heidbrink W.W. , Hansen E.C. , Austin M.E. , Kramer G.J. , Van Zeeland M.A.
Published: February 2022

The eigenfunction of an instability contains information about energy flow in the wave. In this study, the amplitude and phase of electron cyclotron emission radiometer data from hundreds of DIII-D reversed shear Alfvén eigenmodes (RSAE) and toroidicity-induced Alfvén eigenmodes (TAE) are analyzed along the outboard horizontal midplane. The radial phase profile can be flat, linearly rising or falling, convex or concave; in other words, a wide variety of shapes is observed. For a particular mode, often the radial phase profile remains approximately constant as the mode evolves in time but sometimes it changes rapidly. Many TAEs and some RSAEs have phase profiles that are rather flat where the mode amplitude is largest but rise steadily by

∼
2
π

at large major radius. Rapid phase changes are observed when the frequencies of an RSAE and TAE overlap and the modes couple. The phase profile depends weakly on the fast-ion gradient that would appear in the absence of wave-induced transport. Linear and quadratic fits to the phase profiles, together with many plasma parameters, are assembled into RSAE and TAE databases. In both cases, large variability is observed. For RSAEs, the strongest phase dependencies are on electron temperature T
e, RSAE mode frequency, and the density of carbon impurities. For TAEs, the strongest dependencies are on beam power and major radius of the mode. In general, the average RSAE radial phase profile is essentially flat but the TAE profile has non-zero slope and curvature.
Pairs of commuting quadratic elements in the universal enveloping algebra of Euclidean algebra and integrals of motion*
Authors: Marchesiello A , Šnobl L
Published: February 2022

Motivated by the consideration of integrable systems in three spatial dimensions in Euclidean space with integrals quadratic in the momenta we classify three-dimensional Abelian subalgebras of quadratic elements in the universal enveloping algebra of the Euclidean algebra under the assumption that the Casimir invariant

p

→

⋅

l

→

vanishes in the relevant representation. We show by means of an explicit example that in the presence of magnetic field, i.e. terms linear in the momenta in the Hamiltonian, this classification allows for pairs of commuting integrals whose leading order terms cannot be written in the famous classical form of Makarov et al [17]. We consider limits simplifying the structure of the magnetic field in this example and corresponding reductions of integrals, demonstrating that singularities in the integrals may arise, forcing structural changes of the leading order terms.
Design of a broadband reflection mirror for the water window region using a stacked multilayer with optimized structure
Authors: Yang Taolve , Chen Shujing , Lin Chengyou
Published: February 2022

A broadband reflection mirror that can realize maximum uniform reflectivity is an important optical element in the water window region. In this paper, a stacked multilayer (SM) mirror with optimized structure for achieving broadband reflection in the water window region is presented. A genetic algorithm with a two-parametric merit function is employed to achieve maximum uniform reflection in the desired spectral band. A 4.90% average reflectivity with 0.25% root-mean-square deviation in the range of 370–390 eV is achieved by a Cr/Sc SM with 40 periodic multilayer structures. Compared with aperiodic multilayers, proposed SMs exhibit better optimization efficiency, design robustness, and thickness error tolerance. This research provides an efficient method for designing broadband reflection mirrors in the water window region, and may be helpful for steering broadband water window sources, such as high order harmonics and attosecond pulse.
Cut and project sets with polytopal window II: linear repetitivity
Authors: Koivusalo Henna , Walton James
Published: February 2022

In this paper we give a complete characterisation of linear repetitivity for cut and project schemes with convex polytopal windows satisfying a weak homogeneity condition. This answers a question of Lagarias and Pleasants from the 90s for a natural class of cut and project schemes which is large enough to cover almost all such polytopal schemes which are of interest in the literature. We show that a cut and project scheme in this class has linear repetitivity exactly when it has the lowest possible patch complexity and satisfies a Diophantine condition. Finding the correct Diophantine condition is a major part of the work. To this end we develop a theory, initiated by Forrest, Hunton and Kellendonk, of decomposing polytopal cut and project schemes to factors. We also demonstrate our main theorem on a wide variety of examples, covering all classical examples of canonical cut and project schemes, such as Penrose and Ammann–Beenker tilings.
Positivity of the CM line bundle for K-stable log Fanos
Authors: Posva Quentin
Published: February 2022

We prove the bigness of the Chow–Mumford line bundle associated to a

Q

\mathbb {Q}

-Gorenstein family of log Fano varieties of maximal variation with uniformly K-stable general geometric fibers. This result generalizes a theorem of Codogni and Patakfalvi to the logarithmic setting.
Residual equidistribution of modular symbols and cohomology classes for quotients of hyperbolic 𝑛-space
Authors: Constantinescu Petru , Nordentoft Asbjørn
Published: February 2022

We provide a new and simple automorphic method using Eisenstein series to study the equidistribution of modular symbols modulo primes, which we apply to prove an average version of a conjecture of Mazur and Rubin. More precisely, we prove that modular symbols corresponding to a Hecke basis of weight 2 cusp forms are asymptotically jointly equidistributed mod

p
p

while we allow restrictions on the location of the cusps. As an application, we obtain a residual equidistribution result for Dedekind sums. Furthermore, we calculate the variance of the distribution and show a surprising bias with connections to perturbation theory. Additionally, we prove the full conjecture in some particular cases using a connection to Eisenstein congruences. Finally, our methods generalise to equidistribution results for cohomology classes of finite volume quotients of

n
n

-dimensional hyperbolic space.
Glucagon-Like Peptide 1 Receptor Agonists and Risk of Anaphylactic Reaction Among Patients With Type 2 Diabetes: A Multisite Population-Based Cohort Study
Authors: Pradhan Richeek , Patorno Elisabetta , Tesfaye Helen , Schneeweiss Sebastian , Yin Hui , Franklin Jessica , Pawar Ajinkya , Santella Christina , Yu Oriana H Y , Renoux Christel , Azoulay Laurent
Published: February 2022

Case reports and a pharmacovigilance analysis have linked glucagon-like peptide 1 receptor agonists (GLP-1 RAs) with anaphylactic reactions, but real-world evidence for this possible association is lacking. Using databases from the United Kingdom (Clinical Practice Research Datalink) and the United States (Medicare, Optum (Optum, Inc., Eden Prairie, Minnesota), and IBM MarketScan (IBM, Armonk, New York)), we employed a new-user, active comparator study design wherein initiators of GLP-1 RAs were compared with 2 different active comparator groups (initiators of dipeptidyl peptidase 4 (DPP-4) inhibitors and initiators of sodium-glucose cotransporter 2 (SGLT-2) inhibitors) between 2007 and 2019. Propensity score fine stratification weighted Cox proportional hazards models were fitted to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for an anaphylactic reaction. Database-specific HRs were pooled using random-effects models. Compared with the use of DPP-4 inhibitors (n = 1,641,520), use of GLP-1 RAs (n = 324,098) generated a modest increase in the HR for anaphylactic reaction, with a wide 95% CI (36.9 per 100,000 person-years vs. 32.1 per 100,000 person-years, respectively; HR = 1.15, 95% CI: 0.94, 1.42). Compared with SGLT-2 inhibitors (n = 366,067), GLP-1 RAs (n = 259,929) were associated with a 38% increased risk of anaphylactic reaction (40.7 per 100,000 person-years vs. 29.4 per 100,000 person-years, respectively; HR = 1.38, 95% CI: 1.02, 1.87). In this large, multisite population-based cohort study, GLP-1 RAs were associated with a modestly increased risk of anaphylactic reaction when compared with DPP-4 inhibitors and SGLT-2 inhibitors.
Research on Health Disparities: Strategies and Findings From the Black Women’s Health Study
Authors: Palmer Julie R , Cozier Yvette C , Rosenberg Lynn
Published: February 2022

The American Journal of Epidemiology has been a platform for findings from the Black Women’s Health Study (BWHS) that are relevant to health disparities. Topics addressed have included methods of follow-up of a large cohort of Black women, disparities in health-care delivery, modifiable risk factors for health conditions that disproportionately affect Black women, associations with exposures that are highly prevalent in Black women, and methods for genetic research. BWHS papers have also highlighted the importance of considering social context, including perceived experiences of racism, in understanding health disparities. In the future, BWHS investigators will contribute to documentation of the role that structural racism plays in health disparities.
A Differential Response to Antihypertensive Therapy in African Men and Women: Insights From the CREOLE Trial
Authors: Ojji Dike B , Shedul Gabriel L , Sani Mahmoud , Ogah Okechukwu S , Dzudie Anastase , Barasa Felix , Mondo Charles , Ingabire Prossie M , Jones Erika S W , Rayner Brian , Albertino Damasceno , Ogola Elijah , Smythe Wynand , Hickman Nicky , Francis Veronica , Shahiemah Pandie , Shedul Grace , Aje Akinyemi , Sliwa Karen , Stewart Simon
Published: February 2022

Background

We sought to address the paucity of data to support the evidence-based management of hypertension to achieve optimal blood pressure (BP) control on a sex-specific basis in Africa.

Methods

We undertook a post hoc analysis of the multicenter, randomized CREOLE (Comparison of Three Combination Therapies in Lowering Blood Pressure in Black Africans) Trial to test the hypothesis that there would be clinically important differences in office BP control between African men and women. We compared the BP levels of 397 and 238 hypertensive women (63%, 50.9 ± 10.5 years) and men (51.2 ± 11.3 years) from 10 sites across sub-Saharan Africa who completed baseline and 6-month profiling according to their randomly allocated antihypertensive treatment.

Results

Overall, 442/635 (69.6%) participants achieved an office BP target of <140/90 mm Hg at 6 months; comprising more women (286/72.0%) than men (156/65.5%) (adjusted odds ratio [OR] 1.59, 95% confidence interval [CI] 1.07–2.39; P = 0.023). Women randomized to amlodipine–hydrochlorothiazide (HCTZ) (adjusted OR 3.03, 95% CI 1.71–5.35; P < 0.001) or amlodipine–perindopril (adjusted OR 2.62, 95% CI 1.49–4.58; P = 0.01) were more likely to achieve this target compared with perindopril–HCTZ. Among men, there were no equivalent treatment differences—amlodipine–HCTZ (OR 1.54, 95% CI 0.76–3.12; P = 0.23) or amlodipine–perindopril (OR 1.32, 95% CI 0.65–2.67; P = 0.44) vs. perindopril–HCTZ. Among the 613 participants (97%) with 24-hour ambulatory BP monitoring, women had significantly lower systolic (124.1 ± 18.1 vs. 127.3 ± 16.9; P = 0.028) and diastolic (72.7 ± 10.4 vs. 75.1 ± 10.5; P = 0.007) BP levels at 6 months compared with men.

Conclusions

These data suggest clinically important differences in the therapeutic response to antihypertensive combination therapy among African women compared with African men.
Biosynthetic machineries of anthraquinones and bisanthraquinones in Talaromyces islandicus
Authors: Fukaya Mitsunori , Ozaki Taro , Minami Atsushi , Oikawa Hideaki
Published: February 2022

Talaromyces islandicus is a unique fungus that produces more than 20 numbers of anthraquinones (AQs) and their dimeric natural products, bisanthraquinones (BQs). These compounds share a 9,10-anthracenedione core derived from emodin. The biosynthetic pathway of emodin has been firmly established, while that of other AQs and BQs is still unclear. In this study, we identified the biosynthetic gene clusters for chrysophanol and skyrin. The function of key modification enzymes was examined by performing biotransformation experiments and in vitro enzymatic reactions with emodin and its derivatives, allowing us to propose a mechanism for the modification reactions. The present study provides insight into the biosynthesis of AQs and BQs in T. islandicus.
BDK knockout skeletal muscle satellite cells exhibit enhanced protein translation initiation signal in response to BCAA in vitro
Authors: Nakai Naoya , Iida Noriko , Kitai Saki , Shimomura Yoshiharu , Kitaura Yasuyuki , Higashida Kazuhiko
Published: February 2022

We examined the effects of branched-chain amino acids (BCAAs) and electrical pulse stimulation (EPS) on the mTORC1 pathway in muscle satellite cells (MSCs) isolated from branched-chain α-keto acid dehydrogenase kinase (BDK) knockout (KO) mice in vitro. MSCs were isolated from BDK KO and wild-type (WT) mice, proliferated, and differentiated into myotubes. BCAA stimulation increased the phosphorylation of p70 S6 kinase (p70S6K), a marker of protein translation initiation, in MSCs from WT and BDK KO mice, but the rate of the increase was higher in MSCs isolated from BDK KO mice. Contrarily, there was no difference in the increase in p70S6K phosphorylation by EPS. Acute BDK knockdown in MSCs from WT mice using shRNA decreased p70S6K phosphorylation in response to BCAA stimulation. Collectively, the susceptibility of mTORC1 to BCAA stimulation was elevated by chronic, but not acute, enhancement of BCAA catabolism.
A multi-label learning framework for predicting antibiotic resistance genes via dual-view modeling
Authors: Zhao Weizhong , Luo Shujie , Wu Haifang , Jiang Xingpeng , He Tingting , Hu Xiaohua
Published: February 2022

The increasing prevalence of antibiotic resistance has become a global health crisis. For the purpose of safety regulation, it is of high importance to identify antibiotic resistance genes (ARGs) in bacteria. Although culture-based methods can identify ARGs relatively more accurately, the identifying process is time-consuming and specialized knowledge is required. With the rapid development of whole genome sequencing technology, researchers attempt to identify ARGs by computing sequence similarity from public databases. However, these computational methods might fail to detect ARGs due to the low sequence identity to known ARGs. Moreover, existing methods cannot effectively address the issue of multidrug resistance prediction for ARGs, which is a great challenge to clinical treatments. To address the challenges, we propose an end-to-end multi-label learning framework for predicting ARGs. More specifically, the task of ARGs prediction is modeled as a problem of multi-label learning, and a deep neural network-based end-to-end framework is proposed, in which a specific loss function is introduced to employ the advantage of multi-label learning for ARGs prediction. In addition, a dual-view modeling mechanism is employed to make full use of the semantic associations among two views of ARGs, i.e. sequence-based information and structure-based information. Extensive experiments are conducted on publicly available data, and experimental results demonstrate the effectiveness of the proposed framework on the task of ARGs prediction.
Drug repositioning based on multi-view learning with matrix completion
Authors: Yan Yixin , Yang Mengyun , Zhao Haochen , Duan Guihua , Peng Xiaoqing , Wang Jianxin
Published: February 2022

Determining drug indications is a critical part of the drug development process. However, traditional drug discovery is expensive and time-consuming. Drug repositioning aims to find potential indications for existing drugs, which is considered as an important alternative to the traditional drug discovery. In this article, we propose a multi-view learning with matrix completion (MLMC) method to predict the potential associations between drugs and diseases. Specifically, MLMC first learns the comprehensive similarity matrices from five drug similarity matrices and two disease similarity matrices based on the multi-view learning (ML) with Laplacian graph regularization, and updates the drug-disease association matrix simultaneously. Then, we introduce matrix completion (MC) to add some positive entries in original association matrix based on low-rank structure, and re-execute the multi-view learning algorithm for association prediction. At last, the prediction results of the above two operations are integrated as the final output. Evaluated by 10-fold cross-validation and de novo tests, MLMC achieves higher prediction accuracy than the current state-of-the-art methods. Moreover, case studies confirm the ability of our method in novel drug-disease association discovery. The codes of MLMC are available at https://github.com/BioinformaticsCSU/MLMC. Contact: jxwang@mail.csu.edu.cn
Unfolding Social Work Research to Address the COVID-19 Impact: A Text Mining literature Analysis
Authors: Casquilho-Martins Inês , Belchior-Rocha Helena , Moro Sérgio
Published: February 2022

This article aims to contribute to understanding the main social impacts of the pandemic caused by COVID-19 by highlighting the present and future challenges of social intervention and proposing a research agenda for social workers. Based on main indicators collected from international reports, we categorise the terms associated and analyse 284 Scopus articles that address social work issues in face of the COVID-19 through a text mining literature analysis. By applying topic modelling, we are able to identify relations within the body of knowledge between the main indicators. The results enable to highlight the current trends of research, contributing to leverage knowledge in social work in face of a complex and uncertain society. We find that most articles are focused on professional practice, as well as areas such as health, education and employment. In contrast, we argue that issues related to women or migrants have been less explored. These aspects could bring new perspectives in future research within the pandemic context.
Single-Cell Phenotypic and Molecular Characterization of Circulating Tumor Cells Isolated from Cryopreserved Peripheral Blood Mononuclear Cells of Patients with Lung Cancer and Sarcoma
Authors: Vismara Marta , Reduzzi Carolina , Silvestri Marco , Murianni Fabio , Lo Russo Giuseppe , Fortunato Orazio , Motta Rosita , Lanzoni Davide , Giovinazzo Francesca , Miodini Patrizia , Pasquali Sandro , Suatoni Paola , Pastorino Ugo , Roz Luca , Sozzi Gabriella , Cappelletti Vera , Bertolini Giulia
Published: February 2022

Background

The isolation of circulating tumor cells (CTCs) requires rapid processing of the collected blood due to their inherent fragility. The ability to recover CTCs from peripheral blood mononuclear cells (PBMCs) preserved from cancer patients could allow for retrospective analyses or multicenter CTC studies.

Methods

We compared the efficacy of CTC recovery and characterization using cryopreserved PMBCs vs fresh whole blood from patients with non-small cell lung cancer (NSCLC; n = 8) and sarcoma (n = 6). Two epithelial cellular adhesion molecule (EpCAM)-independent strategies for CTC enrichment, based on Parsortix® technology or immunomagnetic depletion of blood cells (AutoMACS®) were tested, followed by DEPArray™ single-cell isolation. Phenotype and genotype, assessed by copy number alterations analysis, were evaluated at a single-cell level. Detection of target mutations in CTC-enriched samples from frozen NSCLC PBMCs was also evaluated by digital PCR (dPCR).

Results

The use of cryopreserved PBMCs from cancer patients allowed for the retrospective enumeration of CTCs and their molecular characterization, using both EpCAM-independent strategies that performed equally in capturing CTC. Cells isolated from frozen PBMCs were representative of whole blood-derived CTCs in terms of number, phenotype, and copy number aberration profile/target mutations. Long-term storage (≥3 years) did not affect the efficacy of CTC recovery. Detection of target mutations was also feasible by dPCR in CTC-enriched samples derived from stored PBMCs.

Conclusions

Isolating CTCs from longitudinally collected PBMCs using an unbiased selection strategy can offer a wider range of retrospective genomic/phenotypic analyses to guide patients’ personalized therapy, paving the way for sample sharing in multicenter studies.
Highly Specific Droplet-Digital PCR Detection of Universally Methylated Circulating Tumor DNA in Endometrial Carcinoma
Authors: Beinse Guillaume , Borghese Bruno , Métairie Marie , Just Pierre-Alexandre , Poulet Geoffroy , Garinet Simon , Parfait Beatrice , Didelot Audrey , Bourreau Camille , Agueeff Natacha , Lavollé Alexandre , Terris Benoit , Chapron Charles , Goldwasser François , Leroy Karen , Blons Helene , Laurent-Puig Pierre , Taly Valérie , Alexandre Jérôme
Published: February 2022

Background

No circulating biomarker is available for endometrial carcinoma (EC). We aimed to identify DNA positions universally hypermethylated in EC, and to develop a digital droplet PCR (ddPCR) assay for detection of hypermethylated circulating tumor DNA (meth-ctDNA) in plasma from patients with EC.

Methods

DNA positions hypermethylated in EC, and without unspecific hypermethylation in tissue/cell types releasing circulating cell-free DNA in plasma, were identified in silico from TCGA/Gene Expression Omnibus (GEO) data. A methylation-specific ddPCR (meth-ddPCR) assay following bisulfite conversion of DNA extracted from plasma was optimized for detection of meth-ctDNA according to dMIQE guidelines. Performances were validated on a retrospective cohort (n = 78 tumors, n = 30 tumor-adjacent tissues), a prospective pilot cohort (n = 33 stage I–IV patients), and 55 patients/donors without cancer.

Results

Hypermethylation of zinc finger and SCAN domain containing 12 (ZSCAN12) and/or oxytocin (OXT) classified EC samples from multiple noncancer samples with high diagnostic specificity/sensitivity [>97%; area under the curve (AUC) = 0.99; TCGA/GEO tissues/blood samples]. These results were confirmed in the independent retrospective cohort (AUC = 0.99). Meth-ddPCR showed a high analytical specificity (limit of blank = 2) and sensitivity (absolute lower threshold of detection = 50 pgmethDNA/mLplasma). In the pilot cohort, meth-ctDNA was detected in pretreatment plasma samples from 9/11 and 5/20 patients with advanced and non-advanced EC, respectively. 2 of 9 patients had ctDNA detected after macroscopic complete surgery and experienced progression within 6 months. No healthy donors had any copy of hypermethylated DNA detected in plasma.

Conclusions

Meth-ddPCR of ZSCAN12/OXT allows a highly specific and sensitive detection of ctDNA in plasma from patients with EC and appears promising for personalized approaches for these patients.
The genome of the Paleogene relic treeBretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs
Authors: Liu Hai-Lin , Harris A J , Wang Zheng-Feng , Chen Hong-Feng , Li Zhi-An , Wei Xiao
Published: February 2022

Among relic species, genomic information may provide the key to inferring their long-term survival. Therefore, in this study, we investigated the genome of the Paleogene relic tree species, Bretschneidera sinensis, which is a rare endemic species within southeastern Asia. Specifically, we assembled a high-quality genome for B. sinensis using PacBio high-fidelity and high-throughput chromosome conformation capture reads and annotated it with long and short RNA sequencing reads. Using the genome, we then detected a trade-off between active and passive disease defences among the gene families. Gene families involved in salicylic acid and MAPK signalling pathways expanded as active defence mechanisms against disease, but families involved in terpene synthase activity as passive defences contracted. When inferring the long evolutionary history of B. sinensis, we detected population declines corresponding to historical climate change around the Eocene–Oligocene transition and to climatic fluctuations in the Quaternary. Additionally, based on this genome, we identified 388 single nucleotide polymorphisms (SNPs) that were likely under selection, and showed diverse functions in growth and stress responses. Among them, we further found 41 climate-associated SNPs. The genome of B. sinensis and the SNP dataset will be important resources for understanding extinction/diversification processes using comparative genomics in different lineages.
Spatialized ecological network analysis for ecosystem-based management: effects of climate change, marine renewable energy, and fishing on ecosystem functioning in the Bay of Seine
Authors: Nogues Quentin , Araignous Emma , Bourdaud Pierre , Halouani Ghassen , Raoux Aurore , Foucher Éric , Loc'h François Le , Loew-Turbout Frédérique , Ben Rais Lasram Frida , Dauvin Jean-Claude , Niquil Nathalie
Published: February 2022

Integrative and spatialized tools for studying the effects of a wide variety of ecosystem drivers are needed to implement ecosystem-based management and marine spatial planning. We developed a tool for analyzing the direct and indirect effects of anthropic activities on the structure and functioning of coastal and marine ecosystems. Using innovative modelling techniques, we ran a spatially explicit model to carry out an ecological network analysis (ENA) of the effects of climate change (CC), of an offshore wind farm (OWF) and of multiple fishing scenarios on the Bay of Seine (eastern part of the English Channel) ecosystem. ENA indices described the effects of those different drivers in a holistic and spatial way. The spatial analysis of ecosystem properties revealed local and global patterns of modifications attributed to CC, while the OWF resulted in localized changes in the ecosystem. This ability of ENA indicators to detect human-induced changes in ecosystem functioning at various spatial scales allows for a more integrative view of the effects of human activities on ecosystems. ENA indices could be used to link both local and global ecosystem changes, for a more cross-scale approach to ecosystem management.
Increased Breadth of Group A Streptococcus Antibody Responses in Children With Acute Rheumatic Fever Compared to Precursor Pharyngitis and Skin Infections
Authors: Whitcombe Alana L , McGregor Reuben , Bennett Julie , Gurney Jason K , Williamson Deborah A , Baker Michael G , Moreland Nicole J
Published: February 2022

Background

Group A Streptococcus (GAS) causes superficial pharyngitis and skin infections as well as serious autoimmune sequelae such as acute rheumatic fever (ARF) and subsequent rheumatic heart disease. ARF pathogenesis remains poorly understood. Immune priming by repeated GAS infections is thought to trigger ARF, and there is growing evidence for the role of skin infections in this process.

Methods

We utilized our recently developed 8-plex immunoassay, comprising antigens used in clinical serology for diagnosis of ARF (SLO, DNase B, SpnA), and 5 conserved putative GAS vaccine antigens (Spy0843, SCPA, SpyCEP, SpyAD, Group A carbohydrate), to characterize antibody responses in sera from New Zealand children with a range of clinically diagnosed GAS disease: ARF (n = 79), GAS-positive pharyngitis (n = 94), GAS-positive skin infection (n = 51), and matched healthy controls (n = 90).

Results

The magnitude and breadth of antibodies in ARF was very high, giving rise to a distinct serological profile. An average of 6.5 antigen-specific reactivities per individual was observed in ARF, compared to 4.2 in skin infections and 3.3 in pharyngitis.

Conclusions

ARF patients have a unique serological profile, which may be the result of repeated precursor pharyngitis and skin infections that progressively boost antibody breadth and magnitude.
A Biomass Pyrolysis Oil as a Novel Insect Growth Regulator Mimic for a Variety of Stored Product Beetles
Authors: Bruce Alexander , Wilson A Nolan , Ranabhat Sabita , Montgomery Jaden , Nicholson Scott , Harris Kylee , Morrison William R
Published: February 2022

As fumigants face increasing regulatory restrictions, resistance, and consumer pushback, it is vital to expand the integrated pest management (IPM) chemical toolkit for stored products. The production of biomass derived insecticides (e.g., bio-oil fraction) from byproducts of biofuel production may be a promising alternative source of chemistries for controlling stored product insects. These potential insecticidal bio-oils were fractionated based on boiling points (ranging from 115 to 230°C in one series and 245–250°C in another). Fractions were analyzed using GC-MS, and were found to be unique in composition. The lethality of these fractions was tested on Tribolium castaneum, Tribolium confusum, and Oryzaephilus surinamensis (L.) (Coleoptera: Silvanidae). Fractions were tested at concentrations ranging from 5–260 mg/ml to screen for efficacy against adults for durations of 2–8 hr sprayed on concrete arenas. In addition, a separate assay evaluated adult emergence of larvae after 6 wk with supplemental food in arenas, while repellency was evaluated against four stored product insect species in a laminar wind tunnel. A greenhouse gas (GHG) emissions life cycle assessment was also performed, which found the use of the bio-oil fraction could reduce GHG emissions associated with the insecticide supply chain by 25–61% relative to a fossil-fuel based insecticide or pyrethroid. While adults were largely unaffected, we found that larval emergence was significantly suppressed compared to controls by roughly half or more. We also determined that there was minimal repellency to most fractions by most species. We conclude that the use of bio-oil fractions is a climate-friendly choice that may support IPM programs.
Powerful Identification of Large Quantitative Trait Loci Using Genome-Wide R/glmnet-Based Regression
Authors: Yang Li’ang , Qu Qiannan , Hao Zhiyu , Sha Ke , Li Ziyu , Li Shuling
Published: February 2022

R/glmnet has been successfully applied to jointly mapped multiple quantitative trait loci for linkage analysis, along with statistical inference for quantitative trait loci candidates with nonzero genetic effects using R/lm for normally distributed traits, R/glm for discrete traits, and R/coxph for survival times. In this study, we extended R/glmnet to a genome-wide association study by means of parallel computation. A multi-locus genome-wide association study for high-throughput single-nucleotide polymorphisms was implemented in the “Multi-Runking” software written within the R workspace. This software can better detect common and large quantitative trait nucleotides and more accurately estimate than genome-wide mixed model analysis for one single-nucleotide polymorphism at a time and linear mixed models-least absolute shrinkage and selection operator. Its applicability and utility were demonstrated by multi-locus genome-wide association studies for the simulated and real traits distributed normally, binary traits, and survival times.
In a Storm of Lies and Half-truths
Authors: Anderson Janet , Duerr Benjamin
Published: February 2022

Media professionals are increasingly confronted with misinformation and disinformation, which impedes their professional responsibility to communicate the truth. Institutions such as the International Criminal Court are critically dependent on public legitimacy and state support to achieve their function, and yet, may be vulnerable to harmful narratives which erode these vital pillars. Using the example of the Kenya situation, this comment describes how such narratives may be constructed and employed and identifies lessons for the ICC in working better with media professionals to ensure that these false information storms can be weathered.