bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhancement mechanisms of sub-bandgap broadband absorption in pyramid-structured silicon
Authors: Li Zhe , Zhang Tieyan , Yu Jiachen , Wulan Qiqige , Zhou Xiangru , Liu Zhijun
Published: October 2021

Structure-engineered silicon exhibits a wealth of unique optical properties below its bandgap, which holds promise for mid-infrared and terahertz applications such as photodetection, thermophotovoltaics, radiative cooling, and spectroscopy. In this paper, we investigate enhancement mechanisms of sub-bandgap absorption of black silicon fabricated into periodic pyramids. Our measurements indicate that the pyramid structure leads to an enhanced broadband absorption in the wavelength region from 1.5 to 13.07 μm with an efficiency of over 80%. The broadband absorption enhancement is shown to originate from the Rayleigh–Wood anomaly, localized magnetic plasmonic resonance, and graded-index effect, which together facilitate the interaction between light and free-carriers in silicon. These results are helpful for understanding the interaction between light and black silicon.
Advanced x-ray spectroscopy of actinide trichlorides
Authors: Butorin Sergei M.
Published: October 2021

The application of core-to-core (3d-to-4f) resonant inelastic x-ray scattering (RIXS) and high-energy-resolution fluorescence-detected x-ray absorption (HERFD-XAS) at actinide M4,5 edges, as techniques with the enhanced sensitivity to changes in the chemical state, was analyzed for trivalent actinide compounds. As an example, a series of actinide chlorides AnCl3 (An = U, Np, Pu, Am, Cm, Bk, and Cf) was used. The crystal-field multiplet formalism was applied to calculate the 3d-4f RIXS maps, and the HERFD-XAS spectra were extracted as cuts of these RIXS maps along the incident energy axis at the constant emitted energy, corresponding to the maximum of the RIXS intensity. A relation between HERFD and conventional XAS methods was also examined. Despite some differences between profiles of the An M5 HERFD and conventional XAS spectra of trivalent actinides, the results of calculations indicate that the HERFD method can be used at the An M5 edge for monitoring even small variations in the An chemical state. As a whole, better agreement between the HERFD and XAS spectra was found for the An M4 edges as compared to the An M5 edges. By using the point charge electrostatic model, the dependence of the An M4,5 HERFD-XAS spectra on the An coordination number was studied, which indicates the significant sensitivity of the distribution of the An 5f states to the ligand structural arrangement around the An sites.
Striped patterns in radially driven suspensions with open boundaries
Authors: Mohammadi Mahdieh , Maleki Maniya , Wysocki Adam , Shaebani M. Reza
Published: October 2021

We study the motion of radially driven fluid–immersed particles in a novel Hele–Shaw cell with open boundaries. The initially uniform suspension forms a striped pattern within a specific range of horizontal oscillation frequencies and for sufficiently large amplitudes. We observe that the initial coarsening dynamics of the stripes gradually slows down and the pattern reaches a steady state after a few minutes. The distance between the stripes in the steady state exhibits an exponentially saturating increase with increased oscillation amplitude or frequency. The width of the stripes decreases as a power-law with the frequency, while its amplitude dependence follows a logistic function. We propose a mechanism—based on the interplay between shear stress, hydrodynamic interactions, and frictional forces—to link the structural characteristics of the stripes to the properties of the oscillatory external drive.
Ceramide accumulation induces mitophagy and impairs β-oxidation in PINK1 deficiency
Authors: Vos Melissa , Dulovic-Mahlow Marija , Mandik Frida , Frese Lisa , Kanana Yuliia , Haissatou Diaw Sokhna , Depperschmidt Julia , Böhm Claudia , Rohr Jonas , Lohnau Thora , König Inke R. , Klein Christine
Published: October 2021

Significance

Ceramide accumulates in Parkinson’s disease–related PINK1 deficiency to initiate ceramide-mediated mitophagy as an alternative pathway to overcome defective PINK1-related mitophagy and the concomitant increased requirements for mitochondrial clearance. Increased ceramide levels negatively correlate with β-oxidation and thus decrease efficiency of the electron transport chain, further increasing the need for mitochondrial clearance. Interfering with this vicious cycle can constitute a novel therapeutic strategy as suggested by our data showing that a reduction of ceramide levels or stimulation of β-oxidation improve the
PINK1
-mutant phenotypes.
An ELISA-based method for rapid genetic screens in
Drosophila
Authors: Jay Taylor R. , Kang Yunsik , Jefferson Amanda , Freeman Marc R.
Published: October 2021

Significance

Forward genetic screens in
Drosophila
have played an integral role in elucidating cellular and molecular pathways that govern almost every facet of biology. However, current screening methods in
Drosophila
are either fast, but limited in their specificity, or rely on imaging, requiring substantial expertise, time, and cost. We developed a rapid GFP-based ELISA that, when paired with the wealth of genetic tools available in
Drosophila
, can be used to screen for regulators of many subpopulations of cells, transcriptional programs, and proteins. Using this assay, we identified genes required for astrocytic synapse elimination. This technique provides a screening platform that is fast, accessible, and broadly applicable to many pathways and processes, making
Drosophila
an even more powerful screening platform.
Soft hydraulics: from Newtonian to complex fluid flows through compliant conduits
Authors: Christov Ivan C
Published: October 2021

Microfluidic devices manufactured from soft polymeric materials have emerged as a paradigm for cheap, disposable and easy-to-prototype fluidic platforms for integrating chemical and biological assays and analyses. The interplay between the flow forces and the inherently compliant conduits of such microfluidic devices requires careful consideration. While mechanical compliance was initially a side-effect of the manufacturing process and materials used, compliance has now become a paradigm, enabling new approaches to microrheological measurements, new modalities of micromixing, and improved sieving of micro- and nano-particles, to name a few applications. This topical review provides an introduction to the physics of these systems. Specifically, the goal of this review is to summarize the recent progress towards a mechanistic understanding of the interaction between non-Newtonian (complex) fluid flows and their deformable confining boundaries. In this context, key experimental results and relevant applications are also explored, hand-in-hand with the fundamental principles for their physics-based modeling. The key topics covered include shear-dependent viscosity of non-Newtonian fluids, hydrodynamic pressure gradients during flow, the elastic response (deformation and bulging) of soft conduits due to flow within, the effect of cross-sectional conduit geometry on the resulting fluid–structure interaction, and key dimensionless groups describing the coupled physics. Open problems and future directions in this nascent field of soft hydraulics, at the intersection of non-Newtonian fluid mechanics, soft matter physics, and microfluidics, are noted.
Smart personal protective equipment (PPE): current PPE needs, opportunities for nanotechnology and e-textiles
Authors: Basodan Rayan A M , Park Byoungyoul , Chung Hyun-Joong
Published: October 2021

Smart personal protective equipment (PPE) is the future of improved occupational health and safety, and nanotechnology facilitates the development of critical smart PPE components such as smart textiles, wearable/flexible electronics, and augmented reality among others. Smart PPE utilizes sensing and communication technology in a way that is non-intrusive to either improve workplace safety or enhance occupational capabilities. The development of such smart PPE requires a multidisciplinary approach. This paper investigates the current state of PPE technologies for firefighters, healthcare workers, police/military, and construction workers. The modern PPE needs are identified from both end user surveys as well as expert third-party studies. There are already some smart PPE solutions for the challenges identified. Recent advances in stretchable and textile-based electronics, enabled by nanotechnology, demonstrate almost all imaginable solutions to the unmet needs that PPE users and expert advisor groups have identified. However, integration into smart PPE requires attention to the unique harsh conditions of hazardous workplaces. This review aims to inspire researchers in the field of flexible and printed electronics to develop and improve future smart PPE.
Biological activity validation of a computationally designed Rituximab/CD3 T cell engager targeting CD20+ cancers with multiple mechanisms of action
Authors: Cai Wenyan , Dong Jianbo , Gallolu Kankanamalage Sachith , Titong Allison , Shi Jiadong , Jia Zhejun , Wang Bo , Huang Cai , Zhang Jing , Lin Jun , Kan Steven Z , Han Shuhua , Zhou Joe , Liu Yue
Published: October 2021

Background

Bispecific T cell engaging antibodies (TEAs) with one arm targeting a cancer antigen and another arm binding to CD3 have demonstrated impressive efficacy in multiple clinical studies. However, establishing a safety/efficacy balance remains challenging. For instance, some TEAs have severe safety issues. Additionally, not all patients or all cancer cells of one patient respond equally to TEAs.

Methods

Here, we developed a next-generation bispecific TEA with better safety/efficacy balance and expanded mechanisms of action. Using the computer-aided antibody design strategy, we replaced heavy chain complementarity-determining regions (HCDRs) in one Rituximab arm with HCDRs from a CD3 antibody and generated a novel CD20/CD3 bispecific antibody.

Results

After series of computer-aided sequence optimization, the lead molecule, GB261, showed great safety/efficacy balance both in vitro and in animal studies. GB261 exhibited high affinity to CD20 and ultra-low affinity to CD3. It showed comparable T cell activation and reduced cytokine secretion compared with a benchmark antibody (BM). ADCC and CDC caused by GB261 only killed CD20+ cells but not CD3+ cells. It exhibited better RRCL cell killing than the BM in a PBMC-engrafted, therapeutic treatment mouse model and good safety in cynomolgus monkeys.

Conclusions

Thus, GB261 is a promising novel TEA against CD20+ cancers.
Case report: Stepwise transition from subcutaneous treprostinil to epoprostenol in high-risk pulmonary arterial hypertension
Authors: Mori Ana Laura , Rodríguez Andrea , Gagliardi Juan Alberto , Stewart Harris Alejandro
Published: October 2021

Background

Idiopathic pulmonary arterial hypertension is associated with high morbidity and mortality. In recent years, the use of targeted therapies has led to an improvement in prognosis. Prostacyclin analogues treprostinil and epoprostenol require continuous subcutaneous or intravenous infusion and are generally administered in a stepwise approach. However, there are no clear recommendations for transition in high-risk patients requiring high doses of prostacyclin analogues.

Case summary

In this report, we describe the case of a 20-year-old woman under combined treatment with sildenafil, macitentan, and treprostinil who required transition from subcutaneous treprostinil therapy to intravenous epoprostenol due to erratic drug absorption and functional class progression. The transition was performed over 48 h in a stepwise approach reducing treprostinil dose 4 ng/kg/min every 3 h while increasing epoprostenol infusion 2 ng/kg/min until achieving a maintenance dose of 32 ng/kg/min. There were no side effects requiring changes in the infusion rate.

Discussion

Patients with advanced pulmonary arterial hypertension may necessitate switching from subcutaneous treprostinil to epoprostenol. Although many protocols have been used to date, there are no guidelines to direct this process safely. This 48-h scheme based on the pharmacokinetic properties of each drug was successful and well-tolerated.
Myocardial infarction versus COVID-19 blood secretome
Authors: Sadykov V F , Bogdanova A A , Sergeev A A , Konovalova M V , Konstantinova E , Pyregov A V , Poltavtseva R A , Gilyarov M Y , Svirshchevskaya E V
Published: October 2021

Background

Both myocardial infarction (MI) and COVID-19 are characterized by cytokine storm in blood.

Purpose

The objective of this study was to compare the concentration of 39 cytokines, chemokines, and growth factors in blood sera of patients with MI, COVID-19 (COV), and healthy donors.

Methods

Patients' blood was collected within 1–2 days after hospitalization in the cardiovascular or COVID intensive care units. All COV patients were in a severe condition; all had increased C reactive protein, 86 and 95% had increased ferritin and D-dimers levels accordingly, 8–10 times decreased lymphocyte numbers. The analysis of the humoral factors in blood serum of MI (n=22), COV (n=23) and donors (n=27) was performed using a 39-plex cytometric analysis.

Results

Among all factors analyzed TGFa, IL-1b, 2, 3, 5, 9, 13, 17A were almost not detectable both in patient and donor sera. The concentrations of the other 31 humoral factors in normal sera differed significantly from 0 to 22000 pg/mL. We divided them into house-keeping factors HKF ranged from 1000 to 22000 pg/mL; sentinel innate immunity factors SIF (30–200 pg/mL), and acute phase factors APF (0–30 pg/mL). HKF were detected in all samples. Among SIF and APF IL-1a, G-CSF, IFNa2, IL-7, MIP-1a, IL-12, and IFNg were detected in 56–80% donor blood while IL-1RA, MCP-3, IL-2, 6, 10, 12, 15, FLT-3F, GM-CSF, TNF-b – only in 10–55%. At the same time all MI patients were 100% positive in all these factors showing extensive activation of blood secretome. Among low incidence APF cytokines in COV patients, percentage of IL-1RA, MCP-3, IFNa2, IL-6, 10, 15, FLT-3L negative sera decreased 3–5 times; and all sera were positive for MIP-1a and IL-12. At the same time TNF-a level decreased significantly from 0 in control to 85% of negative sera in COV patients. Summarized results are shown as the ratios of factor concentrations in MI or COV sera to normal control (Fig). Blood secretome of MI changed more significantly than of COV patients. The major factors (shown in red) in MI were IL-6, IL-12, IFNg, FLT-3L, GM-CSF, and IL-15, which increased 12, 9, 6, 6, 6, and 5 times accordingly. In COV sera IL-6, IL-10, IP-10, and MCP-3 increased by 28, 12, 10, and 9 times accordingly. Less expressed however significant increases are marked with asterisks.

Conclusions

Acute MI is characterized by severe disturbances in blood secretome with an increased level of 25 out of 39 factors studied. Contrary to it, in COV patients the levels of IL-6, 10, IP-10, and MCP-3 were more enhanced while only 15 out of 31 exceeded normal levels.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Public Institution
Population genomic screening of young adults for familial hypercholesterolaemia: a cost-effectiveness analysis
Authors: Marquina Clara , Lacaze Paul , Tiller Jane , Riaz Moeen , Sturm Amy C , Nelson Mark R , Ference Brian A , Pang Jing , Watts Gerald F , Nicholls Stephen J , Zoungas Sophia , Liew Danny , McNeil John , Ademi Zanfina
Published: October 2021

Aims

The aim of this study was to assess the impact and cost-effectiveness of offering population genomic screening to all young adults in Australia to detect heterozygous familial hypercholesterolaemia (FH).

Methods and results

We designed a decision analytic Markov model to compare the current standard of care for heterozygous FH diagnosis in Australia (opportunistic cholesterol screening and genetic cascade testing) with the alternate strategy of population genomic screening of adults aged 18–40 years to detect pathogenic variants in the LDLR/APOB/PCSK9 genes. We used a validated cost-adaptation method to adapt findings to eight high-income countries. The model captured coronary heart disease (CHD) morbidity/mortality over a lifetime horizon, from healthcare and societal perspectives. Risk of CHD, treatment effects, prevalence, and healthcare costs were estimated from published studies. Outcomes included quality-adjusted life years (QALYs), costs and incremental cost-effectiveness ratio (ICER), discounted 5% annually. Sensitivity analyses were undertaken to explore the impact of key input parameters on the robustness of the model. Over the lifetime of the population (4 167 768 men; 4 129 961 women), the model estimated a gain of 33 488years of life lived and 51 790 QALYs due to CHD prevention. Population genomic screening for FH would be cost-effective from a healthcare perspective if the per-test cost was ≤AU$250, yielding an ICER of <AU$28 000 per QALY gained. From a societal perspective, population genomic screening would be cost-saving. ICERs from societal perspective remained cost-saving after adaptation to other countries.

Conclusion

Based on our model, offering population genomic screening to all young adults for FH could be cost-effective, at testing costs that are feasible.
The Besnus transition in 4C pyrrhotite revisited
Authors: Gehring Andreas U , Firlus Alexander , Koulialias Dimitrios , Weidler Peter G , Löffler Jörg F
Published: October 2021

Ferrimagnetic, monoclinic 4C pyrrhotite (Fe7S8) is the only iron sulphide with high relevance for palaeomagnetism and rock magnetism that can be identified in rock materials by its characteristic low-temperature anomaly. Despite its relevance in natural magnetism and the many magnetic studies over the last decades, the physics and the crystallography behind this anomaly, also denoted Besnus transition, is a matter of debate. In this study, we analyse the static and dynamic magnetization associated with the Besnus transition in conjunction with low-temperature structural data of 4C pyrrhotite reported in the literature. The correlation between the Fe–Fe bonds causing spin-orbit coupling and the dynamic magnetic properties show that the magnetic characteristics of the Besnus transition stem from the interaction of two magnetocrystalline anisotropy systems triggered by thermally induced structural changes on an atomic level in monoclinic 4C pyrrhotite. This refutes the widespread view that the Besnus transition is caused by a crystallographic change from monoclinic to triclinic.
An efficient algorithm for sampling the shear-modulus reduction curve in the context of wave propagation using the elastoplastic Iwan model
Authors: Chabot S , Mercerat E D , Glinsky N , Bonilla L F
Published: October 2021

The elastoplastic Iwan model has been used since the end of the 1970s to simulate nonlinear soil behaviour in seismic wave propagation. In this work, we present an automatic algorithm to efficiently sample the shear-modulus reduction curve in function of shear deformation, which constitutes the exclusive ingredient of the elastoplastic model. This model requires the data from the shear- modulus reduction as a function of shear deformation, which are readily available in the literature and from specific laboratory tests. The method involves a discretization and interpolation of these data to be used. The quality of the solution depends on the number of interpolated points. However, a larger number of them produce an increase of the computational time. To overcome this, we present an automatic algorithm to efficiently sample the shear-modulus reduction curve. We numerically prove that the chosen discretization of the curve has a strong impact on the calculation load, in addition to the well-known dependence on the input motion amplitude level. Two tests of nonlinear wave propagation in 1-D and 3-D media show the clear gain in computation time when using the proposed automatic sampling algorithm.
GPS-derived interseismic fault locking along the Jalisco–Colima segment of the Mexico subduction zone
Authors: Cosenza-Muralles B , DeMets C , Márquez-Azúa B , Sánchez O , Stock J , Cabral-Cano E , McCaffrey R
Published: October 2021

Northeastward subduction of the oceanic Rivera and Cocos plates in western Mexico poses a poorly understood seismic hazard to the overlying areas of the North America plate. We estimate the magnitude and distribution of interseismic locking along the northern ∼500 km of the Mexico subduction zone, with a series of elastic half-space inversions that optimize the fits to the velocities of 57 GPS stations in western Mexico. All velocities were corrected for the co-seismic, afterslip and viscoelastic rebound effects of the 1995 Colima–Jalisco and 2003 Tecomán earthquakes. We explore the robustness of interseismic locking estimates to a variety of mantle Maxwell times that are required for the viscoelastic corrections, to the maximum permitted depth for locking of the subduction interface and to the location assigned to the Rivera–Cocos–North America plate triple junction offshore from western Mexico. The best-fitting locking solutions are associated with a maximum locking depth of 40 km, a triple junction location ∼50 km northwest of the Manzanillo Trough and a mantle Maxwell time of 15 yr (viscosity of 2 × 1019 Pa s). Checkerboard tests show that the locking distribution is best resolved at intermediate depths (10–40 km). All of our inversions define a gradual transition from strong locking (i.e. 70–100 per cent) of most (70 per cent) of the Rivera–North America subduction interface to strong but less uniform locking below the Manzanillo Trough, where oceanic lithosphere transitional between the Cocos and Rivera plate subducts, to weak to moderate locking (averaging 55 per cent) of the Michoacán segment of the Cocos–North America interface. Strong locking of the ∼125-km-long trench segment offshore from Puerto Vallarta and other developed coastal areas, where our modelling indicates an average annual elastic slip-rate deficit of ∼20 mm yr−1, implies that ∼1.8 m of unrelieved plate slip has accrued since the segment last ruptured in 1932, sufficient for an M ∼ 8.0 earthquake.
Comparing the performance of stacking-based methods for microearthquake location: a case study from the Burträsk fault, northern Sweden
Authors: Beckel Ruth A , Lund Björn , Eggertsson Gunnar A , Juhlin Christopher
Published: October 2021

Traditional earthquake location relying on first arrival picking is challenging for microseismic events with low signal-to-noise ratio. Over the past years, alternative procedures have been explored based on the idea of migrating the energy of an earthquake back into its source position by stacking along theoretical traveltime curves. To avoid destructive interference of signals with opposite polarity, it is common to transform the input signals into positive time-series. Stacking-based source location has been successfully applied at various scales, but existing studies differ considerably in the choice of characteristic function, the amount of pre-processing and the phases used in the analysis. We use a data set of 62 natural microearthquakes recorded on a 2-D seismic array of 145 vertical geophones across the glacially triggered Burträsk fault to compare the performance of five commonly used characteristic functions: the noise filtered seismograms and the semblance, the envelope, the short-term average/long-term average ratio and the kurtosis gradient of the seismograms. We obtain the best results for a combined P- and S-wave location using a polarity-sensitive characteristic function, that is the filtered seismograms or the semblance. In contrast, the absolute functions often fail to align the signals properly, yielding biased location estimates. Moreover, we observe that the success of the procedure is very sensitive to noise suppression and signal shaping prior to stacking. Our study demonstrates the usefulness of including lower quality S-wave data to improve the location estimates. Furthermore, our results illustrate the benefits of retaining the phase information for location accuracy and noise suppression. To ensure optimal location results, we recommend carefully pre-processing the data and test different characteristic functions for each new data set. Despite the suboptimal array geometry, we obtain good locations for most events within ∼30–40 km of the survey and the locations are consistent with an image of the fault trace from an earlier reflection seismic survey.
Does unionization and working under collective agreements promote health?
Authors: Muller Jessica , Raphael Dennis
Published: October 2021

Health promoters recognize the social determinants of health (SDOH) shape health outcomes yet generally neglect how unionization and collective agreements (CAs) shape these SDOH. This is surprising since extensive evidence indicates unions and CAs influence wages and benefits, job security, working conditions and income inequality, which go on to affect additional SDOH of food and housing security, child development and social exclusion. We argue unions and CAs should be a health promotion focus by examining how they influence the SDOH and health outcomes in wealthy developed nations in four ways. First, we consider how union density (UD) and CA coverage (CAC) are associated with differences between wealthy western nations in percentage of low-waged workers, extent of income inequality, and low birthweight and infant mortality rates. Second, we bring together literature that shows greater UD and CAC within national sub-jurisdictions are associated over time with more equitable distribution of the SDOH and better health outcomes. Third, we document—also using available literature—how within nations, union membership and working under a CA shape the SDOH one experiences. Fourth, we carry out a Canadian case study—applying a political economy lens—to examine how power relations, working through economic and political systems, determine extent of unionization and CAC and the inclination of health promoters to consider these issues. Implications for health promoters are considered.
Advanced Virtual Support for Operational Forces: A 3-Year Summary
Authors: McLeroy Robert D , Kile Michael T , Yourk Daniel , Hipp Sean , Pamplin Jeremy C
Published: October 2021

Introduction

The Military Health System mission is to provide medical care throughout the globe to service members and beneficiaries. To achieve this mission in the most austere of locations, telemedical support is an essential force multiplier when robust in-person medical support is not feasible. This led to the development of a telemedical solution initially known as the Virtual Critical Care Consultation service which provided tele-critical care assistance to downrange providers. The VC3 system then expanded to include multiple medical specialties available for consultation. The current version of this telemedical solution is the ADvanced VIrtual Support for OpeRational Forces (ADVISOR) program which is a synchronous and asynchronous telemedicine system that was developed to provide 24/7 remote expert support to military clinicians engaged in casualty care in austere and operational environments.

Materials and Methods

This manuscript reviews the ADVISOR program data collected from 2017 to 2020 and provides a rough order of magnitude for return on investment. We reviewed data collected by Operational Virtual Health Reports and Operational Virtual Health Evaluations following synchronous consultations. Part of the data reviewed was available patient demographic data, local caregiver information, the purpose of the consult, recommendations made during the consult, the technology used during the consult, and the patient disposition. They also recorded the evacuation plan for the patient and whether a medical evacuation was escalated (e.g. changed from routine to urgent, or from urgent to critical care air transport), downgraded (e.g. urgent to routine), or avoided altogether based on the telephonic consultation.

Results

There were a total of 156 real-world calls during the evaluation period. The total cost savings for these calls was $1,097,027 (3-year program costs of $909,973 less an average of $87,261+/- $28,633 per call or $2,007,000 total) from downgrading or avoidance of planned evacuations. The unmeasured value associated with ADVISOR consultations should also be commented on. For example, when evacuation plans are escalated based on remote expert consultation, it is probable that the escalation increases patient safety and may avoid medical complications that would result in longer term medical costs to the government.

Conclusions

Based on the collected information, the financial return on investment has exceeded costs and the system is perceived as being valued added for both local caregivers and remote experts. The system appears to help optimize evacuation planning, specifically by downgrading or eliminating unnecessary evacuations.
Large H i optical depth and redshifted 21-cm signal from cosmic dawn
Authors: Datta Kanan K , Ghara Raghunath , Hoque Ariful , Majumdar Suman
Published: October 2021

The atomic neutral hydrogen (H i) 21-cm optical depth (τb) can be considerably large as the kinetic and spin temperature of the intergalactic medium is expected to be very low during cosmic dawn. It will be particularly higher at regions with H i overdensity. We revisit the validity of the widely used linearized equation for estimating the H i 21-cm differential brightness temperature (Tb) which assumes τb ≪ 1 and approximates [1 − exp (− τb)] as τb. We consider two scenarios, one without any additional cooling mechanism or radio background (referred as standard scenario) and the other (referred as excess-cooling scenario) assumes the EDGES like absorption profile and an excess cooling mechanism. We find that given a measured global absorption signal, consistent with the standard (excess-cooling) scenario, the linearized equation overestimates the spin temperature by $\sim\!{5}\,\mathrm{ per}\,\mathrm{ cent}\ (10\,\mathrm{ per}\,\mathrm{ cent})$. Further, using numerical simulations, we study impact that the large optical depth has on various signal statistics. We observe that the variance, skewness, and kurtosis, calculated at simulation resolution ($\sim\!{0.5} \,h^{-1} \, {\rm Mpc}$), are overpredicted up to $\sim\!{30}$, $30$, and $15\,\mathrm{ per}\,\mathrm{ cent}$, respectively, for the standard and up to $\sim\!90$, $50$, and $50\,\mathrm{ per}\,\mathrm{ cent}$, respectively, for the excess-cooling scenario. Moreover, we find that the probability distribution function of Tb is squeezed and becomes more Gaussian in shape if no approximation is made. The spherically averaged H i power spectrum is overpredicted by up to $\sim\!25$ and $80\,\mathrm{ per}\,\mathrm{ cent}$ at all scales for the standard and excess-cooling scenarios, respectively.
H i absorption at z ∼ 0.7 against the lobe of the powerful radio galaxy PKS 0409−75
Authors: Mahony Elizabeth K , Allison James R , Sadler Elaine M , Ellison Sara L , Mao Sui Ann , Morganti Raffaella , Moss Vanessa A , Seta Amit , Tadhunter Clive N , Weng Simon , Whiting Matthew T , Yoon Hyein , Bell Martin , Bunton John D , Harvey-Smith Lisa , Kimball Amy , Koribalski Bärbel S , Voronkov Max A
Published: October 2021

We present results from a search for the H i 21-cm line in absorption towards 16 bright radio sources with the six-antenna commissioning array of the Australian Square Kilometre Array Pathfinder. Our targets were selected from the 2-Jy sample, a flux-limited survey of the southern radio sky with extensive multiwavelength follow-up. Two sources were detected in H i absorption including a new detection towards the bright Fanaroff–Riley Type II radio galaxy PKS 0409−75 at a redshift of $z$ = 0.674. The H i absorption line is blueshifted by ∼3300 km s−1 compared to the optical redshift of the host galaxy of PKS 0409−75 at $z$ = 0.693. Deep optical imaging and spectroscopic follow-up with the GMOS instrument on the Gemini-South telescope reveal that the H i absorption is associated with a galaxy in front of the southern radio lobe with a stellar mass of 3.2–6.8 × 1011 M⊙, a star formation rate of ∼1.24 M⊙ yr−1, and an estimated H i column density of 2.16 × 1021 cm−2, assuming a spin temperature of Tspin = 500 K and source covering factor of Cf = 0.3. Using polarization measurements of PKS 0409−75 from the literature, we estimate the magnetic field of the absorbing galaxy to be ∼14.5 $\mu$G, consistent with field strengths observed in nearby spiral galaxies but larger than expected for an elliptical galaxy. Results from this pilot study can inform future surveys as new wide-field telescopes allow us to search for 21-cm H i absorption towards all bright radio sources as opposed to smaller targeted samples.
Bolometric luminosity estimators using infrared hydrogen lines for dust obscured active galactic nuclei
Authors: Kim Dohyeong , Lee Daye , Im Myungshin
Published: October 2021

Bolometric luminosity is an important quantity that tells us the radiative energy output of an active galactic nucleus (AGN). A common way to estimate bolometric luminosity is to use ultraviolet (UV) or optical luminosities as its proxies, but the UV- or optical-based-bolometric luminosity estimators can be easily affected by dust extinction. In this study, we present new methods for estimating bolometric luminosities using infrared (IR) hydrogen Paschen and Brackett line luminosities to alleviate the dust extinction effects. We show that there exist tight correlations between the bolometric luminosities and the IR hydrogen line luminosities, and present the IR hydrogen line-based-bolometric luminosity estimators. As an example, we apply the relation to dust obscured red AGNs, confirming previous results that red AGNs have higher Eddington rations than unobscured AGNs. The new bolometric luminosity estimator will be useful for studying obscured AGNs (e.g. red AGNs, Compton thick AGNs, and Type 2 AGNs), during the coming era of sensitive near-infrared (NIR) and mid-infrared (MIR) missions, such as the James Webb Space Telescope.
The circumbinary rings of GG Carinae: indications of disc eccentricity growth in the B[e] supergiant’s atomic emission lines
Authors: Porter Augustus , Blundell Katherine , Lee Steven
Published: October 2021

B[e] supergiants have unusual circumstellar environments which may include thin, concentric rings displaying atomic line emission. GG Carinae is a B[e] supergiant binary which exhibits such a geometry in its circumbinary environment. We study atomic emission lines arising from GG Carinae’s circumbinary disc in FEROS spectra collected between 1998 and 2015. We find that semiforbidden Fe ii] and permitted Ca ii emission are formed in the same thin circumbinary ring previously reported to have forbidden [O i] and [Ca ii] emission. We find that there are two circumbinary rings orbiting with projected velocities of 84.6 ± 1.0 and 27.3 ± 0.6 $\rm km\, s^{-1}$. Deprojecting these velocities from the line of sight, and using updated binary masses presented by Porter et al. (2021a), we find that the radii of the circumbinary rings are $2.8^{+0.9}_{-1.1}$ and $27^{+9}_{-10}$ au for the inner ring and outer ring, respectively. We find evidence of subtle dynamical change in the inner circumbinary ring over the 17 yr spanned by the data, manifesting in variability in the ratio of the intensity of the blueshifted peak to the redshifted peak of its emission lines and the central velocity becoming more blueshifted. We perform smoothed-particle hydrodynamic simulations of the system which suggest that these observed changes are consistent with pumping of the eccentricity of a radially thin circumbinary ring by the inner binary. We find a systemic velocity of the GG Carinae system of −23.2 ± 0.4 $\rm km\, s^{-1}$.
CARPool Covariance: Fast, unbiased covariance estimation for large-scale structure observables
Authors: Chartier Nicolas , Wandelt Benjamin D
Published: October 2021

The covariance matrix $\boldsymbol{\Sigma }$ of non-linear clustering statistics that are measured in current and upcoming surveys is of fundamental interest for comparing cosmological theory and data and a crucial ingredient for the likelihood approximations underlying widely used parameter inference and forecasting methods. The extreme number of simulations needed to estimate $\boldsymbol{\Sigma }$ to sufficient accuracy poses a severe challenge. Approximating $\boldsymbol{\Sigma }$ using inexpensive but biased surrogates introduces model error with respect to full simulations, especially in the non-linear regime of structure growth. To address this problem we develop a matrix generalization of Convergence Acceleration by Regression and Pooling (CARPool) to combine a small number of simulations with fast surrogates and obtain low-noise estimates of $\boldsymbol{\Sigma }$ that are unbiased by construction. Our numerical examples use CARPool to combine GADGET-III N-body simulations with fast surrogates computed using COmoving Lagrangian Acceleration (COLA). Even at the challenging redshift z = 0.5, we find variance reductions of at least $\mathcal {O}(10^1)$ and up to $\mathcal {O}(10^4)$ for the elements of the matter power spectrum covariance matrix on scales 8.9 × 10−3 < kmax < 1.0 hMpc−1. We demonstrate comparable performance for the covariance of the matter bispectrum, the matter correlation function and probability density function of the matter density field. We compare eigenvalues, likelihoods, and Fisher matrices computed using the CARPool covariance estimate with the standard sample covariance and generally find considerable improvement except in cases where $\boldsymbol{\Sigma }$ is severely ill-conditioned.
SAbDab in the age of biotherapeutics: updates including SAbDab-nano, the nanobody structure tracker
Authors: Schneider Constantin , Raybould Matthew I J , Deane Charlotte M
Published: October 2021

In 2013, we released the Structural Antibody Database (SAbDab), a publicly available repository of experimentally determined antibody structures. In the interim, the rapid increase in the number of antibody structure depositions to the Protein Data Bank, driven primarily by increased interest in antibodies as biotherapeutics, has led us to implement several improvements to the original database infrastructure. These include the development of SAbDab-nano, a sub-database that tracks nanobodies (heavy chain-only antibodies) which have seen a particular growth in attention from both the academic and pharmaceutical research communities over the past few years. Both SAbDab and SAbDab-nano are updated weekly, comprehensively annotated with the latest features described here, and are freely accessible at opig.stats.ox.ac.uk/webapps/newsabdab/.
Cyclophilin acts as a ribosome biogenesis factor by chaperoning the ribosomal protein (PlRPS15) in filamentous fungi
Authors: Mo Chenmi , Xie Chong , Wang Gaofeng , Tian Tian , Liu Juan , Zhu Chunxiao , Xiao Xueqiong , Xiao Yannong
Published: October 2021

The rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into pre-ribosomal particles are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, whose expression is up-regulated during abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 co-translationally interacted with the unassembled small ribosomal subunit protein, PlRPS15 (uS19). PlRPS15 contained an eukaryote-specific N-terminal extension that mediated the interaction with PlCYP5. PlCYP5 increased the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. Consistently, the phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g. growth and ribosome biogenesis defects). PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botrytis cinerea and Metarhizium anisopliae were identified. Notably, PlCYP5-PlRPS15 homologs from three filamentous fungi interacted with each other but not those from other species. In summary, our data disclosed a unique dedicated chaperone system for RPs by cyclophilin in filamentous fungi.
Estimating 24-hour urinary excretion using spot urine measurements in kidney stone formers
Authors: Ferraro Pietro Manuel , Lopez Fernando , Petrarulo Michele , Barbarini Silvia , Curhan Gary C , Marangella Martino , Taylor Eric N
Published: October 2021

Background

One limitation of the use of 24-hour collection is impracticality. We analysed the performance of spot urine measurements to estimate 24-hour excretion in patients with kidney stones.

Methods

A total of 74 adult patients from two centres performed a 24-hour urine collection. A sample of the last micturition was sent for spot urine analysis. Twenty patients were asked to collect two additional spot urine samples, one before dinner and the other after dinner. Urinary concentrations of creatinine, calcium, oxalate, uric acid, citrate and magnesium were measured in the 24-hour and each of the spot urine samples. Four approaches were used to estimate 24-hour urinary excretion, multiplying the ratio of the spot urinary analyte to creatinine concentration by (i) measured 24-hour urinary creatinine excretion (Prediction 1), (ii) estimated 24-hour urinary creatinine excretion (Prediction 2), (iii) assumed 1-g 24-hour urinary creatinine excretion (Prediction 3) or (iv) assumed 1.5-g 24-hour urinary creatinine excretion (Prediction 4). For each parameter we computed Lin's concordance correlation coefficients (CCCs), Bland–Altman plots and 95% limits of agreement.

Results

The performance of estimates obtained with Prediction 1 and Prediction 2 was similar, except for citrate and uric acid, for which Prediction 2 performed worse. Both approaches performed moderately well: citrate CCC {0.82 [95% confidence interval (CI) 0.75–0.90]}, oxalate [0.66 (95% CI 0.55–0.78)], magnesium [0.66 (95% CI 0.54–0.77)], calcium [0.63 (95% CI 0.50–0.75)] and uric acid [0.52 (95% CI 0.36–0.68)]. The performance of Predictions 3 and 4 was worse.

Conclusions

Although spot urine samples may hold promise for clinical and population-based research, at present they have limited utility in clinical practice. Measuring or estimating 24-hour creatinine, rather than assuming a given creatinine excretion, will be necessary in future studies of spot urine samples.
SOCS3-mediated activation of p53-p21-NRF2 axis and cellular adaptation to oxidative stress in SOCS1-deficient hepatocellular carcinoma
Authors: Khan Md Gulam Musawwir , Boufaied Nadia , Yeganeh Mehdi , Ghosh Amit , Kandhi Rajani , Bagheri Rezvan , Petkiewicz Stephanie , Sharma Ankur , Yoshimura Akihiko , Ferbeyre Gerardo , Labbé David P. , Ramanathan Sheela , Ilangumaran Subburaj
Published: October 2021

SOCS1andSOCS3genes, frequently repressed in hepatocellular carcinoma (HCC), function as tumor suppressors in hepatocytes. However, TCGA transcriptomic data revealed thatSOCS1-low/SOCS3-highspecimens displayed more aggressive HCC thanSOCS1-low/SOCS3-lowcases. We show that hepatocyte-specificSocs1-deficient livers upregulateSocs3expression following genotoxic stress. Whereas deletion ofSocs1orSocs3increased HCC susceptibility, ablation of both genes attenuated HCC growth. SOCS3 promotes p53 activation in SOCS1-deficient livers, leading to increased expression of CDKN1A (p21WAF1/CIP1), which coincides with elevated expression and transcriptional activity of NRF2. DeletingCdkn1ain SOCS1-deficient livers diminished NRF2 activation, oxidative stress and HCC progression. ElevatedCDKN1Aexpression and enrichment of antioxidant response genes also characterizedSOCS1-low/SOCS3-highHCC. SOCS1 expression in HCC cell lines reduced oxidative stress, p21 expression and NRF2 activation. Our findings demonstrate that SOCS1 controls the oncogenic potential of SOCS3-driven p53-p21-NRF2 axis and suggest that NRF2-mediated antioxidant response represents a drug target in SOCS1-deficient HCC.
Visualization of Sympathetic Neural Innervation in Human White Adipose Tissue
Authors: Perdikari Aliki , Cacciottolo Tessa , Henning Elana , de Oliveira Edson Mendes , Keogh Julia M. , Farooqi I. Sadaf
Published: October 2021

Obesity, defined as an excess of adipose tissue that adversely affects health, is a major cause of morbidity and mortality. However, understanding the structure and function of human adipose tissue has been limited by the inability to visualize cellular components due to the innate structure of adipocytes, which are characterized by large lipid droplets. Combining the iDISCO and the CUBIC protocols for whole tissue staining and optical clearing, we developed a protocol to enable immunostaining and clearing of human subcutaneous white adipose tissue (WAT) obtained from individuals with severe obesity. We were able to perform immunolabeling of sympathetic nerve terminals in whole white adipose tissue and subsequent optical clearing by eliminating lipids to render the opaque tissue completely transparent. We then used light sheet confocal microscopy to visualize innervation of human WAT from obese individuals in a 3D manner.We demonstrate the visualization of sympathetic nerve terminals in human WAT. This protocol can be modified to visualize other structures such as blood vessels involved in the development, maintenance and function of human adipose tissue in health and disease.
Gramicidin S and Melittin - Potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection
Authors: Ghalib Mohammed , Parekh Yash , Banu Sarena , Ram Sushma , Nagaraj Ramakrishnan , Kumar Bokara Kiran , Idris Mohammed M
Published: October 2021

The COVID19 pandemic has resulted in multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of gramicidin S and melittin peptides obtained from Bacillus brevis and bee venom respectively. Our in vitro antiviral assay results showed significant decrease in the viral load compared to the untreated group with no/very less cytotoxicity. The EC50 values for gramicidin S and melittin are calculated as 1.571μg and 0.656μg respectively. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 hours onwards with a maximal clearance after 24 hours post infection. Based on proteome analysis it was found that more than 250 proteins were found to be differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 hours post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.