bluuebunny/crossref_metadata_2025 huggingface dataset:
Why double ovarian stimulation in an in vitro fertilization cycle is potentially unsafe
Authors: Tocci Angelo
Published: November 2021

The occurrence of two antral follicle recruitment waves in a single inter-ovulatory interval has been detected in ovaries of normal women. This data supports the claim that a double ovarian stimulation in the same cycle may benefit poor responder patients with an increased recovery of mature oocytes and good quality embryos per single cycle. The double stimulation protocol was the object of several published studies in which, surprisingly, the mechanism and the safety of the double stimulation in the same cycle were poorly addressed. We propose that in the double stimulation protocol, the first stimulation impacts more committed oocytes progenitors ready to differentiate into mature oocytes. Conversely, the protracted exposure of developmentally earlier less-committed ovarian stem cells to FSH, which occurs in the double stimulation protocol, impacts the less differentiated stem cells which take longer to differentiate into oocytes. The proposed mechanism has broad implications for the safety of the double stimulation strategy.
Analysis of a model of a natural gas pipeline—a transfer function approach
Authors: Baker Luke , Armbruster Dieter , Scaglione Anna , Platte Rodrigo B
Published: November 2021

A framework for natural gas pipelines is developed in a context similar to the theory of electric transmission lines. The system of semi-linear partial differential equations describing the time-dependent flow of natural gas is linearized around the steady-state flow. Additional approximations lead to a constant coefficient linear system that is equivalent to an electrical circuit that is analytically solvable and admits an ABCD matrix representation of input and output. The sinusoidal steady-state operation of natural gas pipelines is analysed including the distortion of waves. It is shown that the timing of the propagation of phases and other events is accurately represented in the approximation. The quantitative accuracy for flux and gas density of the approximation depending on different operating scenarios and depending on the frequency of the disturbances is documented.
Severe Acute Respiratory Syndrome Coronavirus 2 Monoclonal Antibody Combination Therapy in Patients With Coronavirus Disease 2019 and Primary Antibody Deficiency
Authors: Pulvirenti Federica , Milito Cinzia , Cinetto Francesco , Fernandez Salinas Ane , Terreri Sara , Piano Mortari Eva , Auria Stefania , Soccodato Valentina , Miriam Lichtner , Nicastri Emanuele , Vincenzi Laura , Carsetti Rita , D’Offizi Gianpiero , Quinti Isabella
Published: November 2021

Background

Previous reports highlighted the efficacy of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific monoclonal antibodies (mAbs) against coronavirus disease 2019.

Methods

We conducted a prospective study on the clinical outcome and antiviral effects of mAbs added to standard of care therapy in SARS-CoV-2-infected patients with primary antibody defects.

Results

Median time of SARS-CoV-2 quantitative polymerase chain reaction (qPCR) positivity was shorter in 8 patients treated with mAbs (22 days) than in 10 patients treated with standard of care therapy only (37 days, P=.026). Median time of SARS-CoV-2 qPCR positivity from mAb administration was 10 days.

Conclusions

The SARS-CoV-2 mAbs treatment was effective and well tolerated in patients with primary antibody defects.
Simulating grass phenotypic plasticity as an emergent property of growth zone responses to carbon and nitrogen metabolites
Authors: Gauthier Marion , Barillot Romain , Andrieu Bruno
Published: November 2021

Phenotypic plasticity—the ability of one genotype to produce different phenotypes depending on growth conditions—is a core aspect of the interactions between plants and the environment. The model CN-Wheat simulates the functioning of a grass culm and the construction of traits as properties emerging from the feedback loops between morphogenesis, the environmental factors and source–sink activities. The plant is seen as a self-regulated system where leaf growth is driven by carbon and nitrogen metabolism within each leaf and by coordination rules between successive leaves. Here, we investigated the ability of this approach to simulate realistic grass phenotypic plasticity and explored plant behaviour in a wide range of growth conditions. The growth of grass monoculms, with traits similar to a wheat stem, was simulated for highly contrasting conditions of soil nitrogen concentration, incident light and planting density. The monoculms were kept vegetative and produced ~15 mature leaves at the end of the simulations. The model simulated highly contrasting phenotypes. Overall, the simulated trends and the magnitude of responses of leaf and plant traits to growth conditions were consistent with the literature on grass species. These results demonstrate that integrating plant functioning at organ scale can simulate, as an emergent property, the phenotypic plasticity of plants in contrasting light and nitrogen conditions. Besides, simulations of the internal variables of plants gave access to plant trophic status across plant ontogeny and plant environments. In conclusion, this framework is a significant step towards better integration of the genotype–environment interactions.
BSAC Vanguard Series: AMR diagnostics in light of evolving technologies and access in low- and middle-income countries
Authors: Berman Daniel , Neale Ruth
Published: November 2021

Rapid point-of-care tests are needed to control antimicrobial consumption, as recognized by the Longitude Prize. However, in addition to bacterial pathogen identification, clinicians need more information, such as which antimicrobial will be effective and how severe the infection really is. This technology is beginning to emerge, but both economic and technological challenges remain before it can be delivered, especially in low- and middle-income countries. This article outlines these challenges and how we might overcome them.
In vitro activity of the orally bioavailable ceftibuten/VNRX-7145 (VNRX-5236 etzadroxil) combination against a challenge set of Enterobacterales pathogens carrying molecularly characterized β-lactamase genes
Authors: Mendes Rodrigo E , Rhomberg Paul R , Watters Amy A , Castanheira Mariana
Published: November 2021

Objectives

This study assessed the activity of ceftibuten, ceftibuten combined with the active form (VNRX-5236) of the β-lactamase inhibitor VNRX-7145 and comparators against a challenge set of Gram-negative pathogens.

Methods

Two hundred and five Enterobacterales carrying plasmid AmpC (53 isolates), ESBL (50), KPC (50), OXA-48-like (49) or OXA-48-like with KPC (3) encoding genes were selected. Susceptibility was determined by broth microdilution. VNRX-5236 and avibactam were tested at a fixed concentration of 4 mg/L.

Results

Ceftibuten/VNRX-5236 (MIC50/90 0.12/1 mg/L) MIC values were 256-fold lower than those of ceftibuten (MIC50/90 32/256 mg/L) for all Enterobacterales and 2- to 4-fold lower than those of ceftazidime/avibactam (MIC50/90 0.5/2 mg/L). For isolates producing a plasmid-encoded AmpC, VNRX-5236 decreased ceftibuten MIC (MIC50/90 0.12/1 mg/L) by at least 512-fold compared with ceftibuten (MIC50/90 128/>256 mg/L). Ceftibuten/VNRX-5236 (MIC50/90 0.06/0.12 mg/L) and meropenem (MIC50/90 ≤0.03/0.06 mg/L; 100% susceptible) showed comparable activities against ESBL isolates and these agents had MIC90 values 4- to 8-fold lower than that of ceftazidime/avibactam (MIC50/90 0.25/0.5 mg/L; 100% susceptible). Ceftibuten/VNRX-5236 (MIC50/90 0.12/0.5 mg/L) had the lowest MIC for KPC producers, followed by ceftazidime/avibactam (MIC50/90 2/4 mg/L; 98.0% susceptible). The same MIC90 values were obtained for ceftibuten/VNRX-5236 (MIC50/90 0.25/1 mg/L) and ceftazidime/avibactam (MIC50/90 1/1 mg/L; 100.0% susceptible) for isolates carrying blaOXA-48-like. VNRX-5236 decreased the ceftibuten MIC at least 16-fold for three isolates carrying blaOXA-48-like and blaKPC.

Conclusions

VNRX-5236 rescued the in vitro activity of ceftibuten against Enterobacterales carrying common serine β-lactamases, including ESBL, AmpC and the KPC and OXA-48-like carbapenemases. Ceftibuten/VNRX-5236 may have potential as an oral treatment for infections caused by resistant Enterobacterales, while sparing carbapenems.
Comparative Evaluation of Two NGAL Automated Immunoassays in Urine and Plasma
Authors: Whitehead Simon J , Chadwick Katie , Ford Clare , Giri Ramesh , Luckraz Heyman , Gama Rousseau
Published: November 2021

Background

Acute kidney injury (AKI), a frequent and serious complication of hospitalized patients, is associated with increased mortality and morbidity. Neutrophil gelatinase-associated lipocalin (NGAL) is a biomarker for the early identification of AKI. We report a comparative laboratory verification of the Abbott Diagnostics (ARCHITECT® urine NGAL) and BioPorto Diagnostics (NGAL TestTM) assays including an assessment of the Abbott assay’s performance in EDTA plasma.

Methods

Intra-/interbatch imprecision, linearity, recovery, and limit of quantitation (LoQ) were assessed and an interassay comparison performed (n = 51). Between-laboratory agreement was assessed against other laboratories using the Abbott (n = 48) and BioPorto (n = 94) assays. Plasma NGAL (pNGAL) levels were measured in non-AKI patients with a range of estimated glomerular filtration rates (n = 80).

Results

Coefficients of variation (CVs) for intra- and interbatch imprecision were 0.7%–12.4% and 1.9%–27.5% for the BioPorto assay, respectively, and 1.4%–6.3%/3.4%–6.8%, respectively, for the Abbott assay. The BioPorto assay exhibited a higher LoQ (27.5 ng/mL vs 1.2 ng/mL). Both assays were linear over the range 5–6000 ng/mL. Recovery of recombinant NGAL was 113.1 ± 7.1% and 96.5 ± 7.8% for the Abbott and BioPorto assays, respectively. On average, the Abbott assay gave results 9.2% lower than the BioPorto assay. Mean differences of 0.2% (Abbott) and 20.2% (BioPorto) were observed in the between-laboratory comparison. In patients without AKI, pNGAL levels were inversely proportional to eGFR.

Conclusions

Performance of the Abbott and BioPorto assays was similar although the latter performed less well at lower NGAL concentrations. The Abbott assay tended to yield lower results, exhibited a lower LoQ and over-recovered NGAL. Although only Conformité Européenne-marked and marketed for use in urine, the Abbott assay demonstrated equivalent performance to the BioPorto assay with EDTA plasma.
Understanding enterprise data warehouses to support clinical and translational research: enterprise information technology relationships, data governance, workforce, and cloud computing
Authors: Knosp Boyd M , Craven Catherine K , Dorr David A , Bernstam Elmer V , Campion Thomas R
Published: November 2021

Objective

Among National Institutes of Health Clinical and Translational Science Award (CTSA) hubs, effective approaches for enterprise data warehouses for research (EDW4R) development, maintenance, and sustainability remain unclear. The goal of this qualitative study was to understand CTSA EDW4R operations within the broader contexts of academic medical centers and technology.

Materials and Methods

We performed a directed content analysis of transcripts generated from semistructured interviews with informatics leaders from 20 CTSA hubs.

Results

Respondents referred to services provided by health system, university, and medical school information technology (IT) organizations as “enterprise information technology (IT).” Seventy-five percent of respondents stated that the team providing EDW4R service at their hub was separate from enterprise IT; strong relationships between EDW4R teams and enterprise IT were critical for success. Managing challenges of EDW4R staffing was made easier by executive leadership support. Data governance appeared to be a work in progress, as most hubs reported complex and incomplete processes, especially for commercial data sharing. Although nearly all hubs (n = 16) described use of cloud computing for specific projects, only 2 hubs reported using a cloud-based EDW4R. Respondents described EDW4R cloud migration facilitators, barriers, and opportunities.

Discussion

Descriptions of approaches to how EDW4R teams at CTSA hubs work with enterprise IT organizations, manage workforces, make decisions about data, and approach cloud computing provide insights for institutions seeking to leverage patient data for research.

Conclusion

Identification of EDW4R best practices is challenging, and this study helps identify a breadth of viable options for CTSA hubs to consider when implementing EDW4R services.
Molecular Identification and Functional Characterization of Vitellogenin Receptor From Harmonia axyridis (Coleoptera: Coccinellidae)
Authors: Han Hui , Han ShiPeng , Qin QiuJu , Chen Jie , Wang Da , He Yunzhuan
Published: November 2021

Vitellogenin receptors (VgRs) have vital roles in reproduction by mediating endocytosis of the vitellogenin (Vg) in oviparous insects. Same as most insect species that possess only one VgR, in this study, a single VgR mRNA (HmVgR) was identified in an important natural enemy ladybeetle, Harmonia axyridis (Pallas). The open reading frame of HmVgR was 5,340 bases encoding a protein of 1,779 amino acids. Bioinformatic analyses showed that HmVgR had conserved domain motifs of low-density lipoprotein receptor family. Based on phylogenetic analysis, HmVgR had highly homologous within the Coleoptera. The transcriptional level of HmVgR was initially detected in the newly emerged female adults, gradually increased from day 3 to day 9, peaked on day 13, and then sharply decreased on day 15. Similar to most insects, HmVgR was expressed specifically in ovarian tissue. Moreover, RNA interference (RNAi) clearly decreased the transcription levels of HmVgR, which blocked the deposition of yolk protein in the ovaries, shortened the ovarian length, and led to negative impacts on reproductive-related parameters (i.e., prolonged preoviposition periods, reduced spawning and depressed hatchability). In sum, these results indicated that HmVgR may be critical for yolk protein deposition of oocytes and can play a key role in reproduction of female adults of H. axyridis. Our results provide conclusive proof for the important roles of HmVgR in fecundity, and establish a basis for further research on its interaction with vitellogenin.
Reproduction of Black Soldier Fly (Diptera: Stratiomyidae) Under Different Adult Densities and Light Regimes
Authors: Liu Zhongyi , Najar-Rodriguez Adriana J , Morel Patrick C H , Minor Maria A
Published: November 2021

The black soldier fly (BSF) Hermetia illucens (L.) (Diptera: Stratiomyidae) has been recognized as a promising insect species for sustainable management of organic waste and by-products. Indoor breeding of BSF with artificial lighting has been proved successful, but efforts are still needed to optimize BSF reproductive output. Increasing adult density seems an option to exploit space, whereas decreasing artificial lighting duration may reduce unnecessary power consumption. This study aimed at investigating the effects of adult density (10, 25, and 50 pairs per 30 × 30 × 30 cm cage; i.e., 370, 926, and 1,852 pairs/m3), light regime (8:16, 12:12, and 16:8 [L:D] h), and their possible interactions, on some BSF life history traits relevant to reproduction. The results show that the overall BSF reproductive output increased with increasing adult density but was not affected by light regimes per se. With the highest BSF adult density tested, an average of more than 20,000 neonate larvae were produced from a cage within 10 d. At this density, increasing photoperiod increased neonate production, but also decreased the number of neonates per watt used for artificial illumination. The temporal oviposition patterns, mean individual female reproductive output, mating success, egg hatching rate, and insect survival rate were not affected by adult density or light regime as simple effects. However, the interaction between adult density and light regime was significant for the first oviposition peak, mean individual female reproductive output, and insect survival rate. The possible mechanisms behind our results are discussed.
Seasonal Distribution of Halyomorpha halys (Hemiptera: Pentatomidae) Captures in Woods-to-Orchard Pheromone Trap Transects in Virginia
Authors: Hadden Whitney T , Nixon Laura J , Leskey Tracy C , Bergh J Christopher
Published: November 2021

The invasive brown marmorated stink bug, Halyomorpha halys (Stål), is a pest of numerous economically important crops in the USA. In the Mid-Atlantic region, it is a significant, direct pest in tree fruit orchards, many of which are bordered by woodlots containing a variety of its deciduous tree and shrub hosts. During the growing season, H. halys moves from woodland habitats into crops, but seasonal changes in its relative abundance between these adjacent habitats have not been examined. Using linear transects of six pheromone-baited pyramid traps that extended from 100 m into the interior of woodlots to 100 m into the interior of adjacent commercial apple orchards in Virginia, spatiotemporal changes in H. halys captures were measured during three growing seasons. Captures of H. halys adults and nymphs were recorded weekly from May through October, and annual data were separated into early, mid, and late-season captures. Only adults were captured during the early season, and there was no indication of a spatial trend in captures across traps in the transects among years. Beginning in mid-season and becoming increasingly apparent by late season, captures of H. halys adults and nymphs tended to become most frequent in traps at the woods and orchard edges and at 50 m into the orchard interior. These findings conform with and expand upon previous research documenting an edge effect for H. halys relative abundance and can inform and support the optimization of perimeter-based management strategies for H. halys in Mid-Atlantic apple orchards.
Long-Term Care Services and Inter-American Human Rights in Argentina
Authors: Dabove Maria Isolina
Published: November 2021

Currently, long-term care services are considered socially accepted alternatives that meet the need for assistance and accommodation of older persons, especially in situations of dependency. Their design and expansion are conditioned by a new phenomenon: global aging and the multi-generational society. This article looks at the current situation of long-term care services in Argentina. It identifies the new standards of Elder Law set by the Inter American Convention on the Protecting of Human Rights of Older Persons and contrasts them with the Argentinian legal system on long-term care. It then analyses the clash between the way these services are currently provided and the new human rights approach, and considers the pioneering Argentinian judicial criteria concerning long-term care facilities. Finally, it points out the main aspects that need to be considered in order to implement the necessary social change and legal reform in Argentina.
Identification and Functional Analysis of Differentially Expressed Genes in Myzus persicae (Hemiptera: Aphididae) in Response to Trans-anethole
Authors: Ding Chao-Yang , Ma Yu-Meng , Li Bin , Wang Yun , Zhao Le , Peng Jiang-Nan , Li Mao-Ye , Liu Su , Li Shi-Guang
Published: November 2021

Plant essential oils, with high bioactivity and biodegradability, provide promising alternatives to synthetic pesticides for pest control. Trans-anethole is the major component of essential oil from star anise, Illicium verum Hook. The compound has a strong contact toxicity against the green peach aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae), which is a major insect pest of many vegetables and crops. However, little information is known about how M. persicae responds to trans-anethole at the molecular level. We conducted a comparative transcriptome analysis of M. persicae in response to a LD50 dose of trans-anethole. A total of 559 differentially expressed genes were detected in the treated individuals, with 318 genes up-regulated, and 241 genes down-regulated. Gene ontology (GO) analysis revealed that these genes were classified into different biological processes and pathways. We also found that genes encoding ATP-binding cassette (ABC) transporters, DnaJ, and cuticle proteins were dramatically up-regulated in response to trans-anethole. To study the function of these genes, we performed RNA interference (RNAi) analysis. Knockdown of an ABC transporter gene (ABCG4) and a DnaJ gene (DnaJC1) resulted in a significantly increased mortality rate in M. persicae following trans-anethole exposure, indicating the involvement of these two genes in the toxicity response to trans-anethole. The findings provide new insights into the mechanisms of M. persicae in coping with plant essential oils.
Seasonality in daily movement patterns of mandrills revealed by combining direct tracking and camera traps
Authors: Hongo Shun , Nakashima Yoshihiro , Akomo-Okoue Etienne François , Mindonga-Nguelet Fred Loïque
Published: November 2021

Movement is a fundamental characteristic of animals, but challenging to measure noninvasively. Noninvasive methods for measuring travel have different weaknesses, so multiple techniques need to be applied multiple techniques for reliable inferences. We used two methods, direct tracking and camera trapping, to examine the variation in time and seasonal differences in movement rates of mandrills (Mandrillus sphinx), an elusive primate that lives in large groups in central Africa. In a 400-km2 rainforest area in Moukalaba-Doudou National Park, Gabon, we tracked unidentified groups 46 times from 2009 to 2013. We systematically placed 157 terrestrial camera traps in the same area from 2012 to 2014 and recorded groups 309 times. Generalized additive mixed models (GAMMs) of the tracking data indicated that the group travel speed varied with time and season. In the fruiting season, the movement rate fluctuated with time in a bimodal pattern, whereas in the nonfruiting season, it increased monotonously with time. The predicted day range was longer in the fruiting season (6.98 km) than in the nonfruiting season (6.06 km). These seasonal differences suggest responses to changes in food resources and temperature. Camera-trap detection rates showed similar temporal and seasonal patterns to the tracking data, allowing us to generalize our findings to the population level. Moreover, cameras never detected mandrills at night, and we observed that they slept high in trees and hardly moved until the next morning, all suggesting their strict avoidance of nighttime movement. This study demonstrated the significance of the multiple-method approach in drawing robust conclusions on temporal patterns of animal movement.
Damages and ISDS Reform: Between Procedure and Substance
Authors: Bonnitcha Jonathan , Langford Malcolm , Alvarez-Zarate Jose M , Behn Daniel
Published: November 2021

Monetary damages is the ordinary remedy in investor-state dispute settlement (ISDS). As such, arbitral practice relating to damages has direct, practical relevance for states and investors. The size of damages awards is also amongst the core critiques of ISDS. It is somewhat surprising, then, that the issue of damages has not figured prominently in discussions on reform of investment treaties and the ISDS mechanism, including those currently underway in Working Group III of the United Nations Commission on International Trade Law (UNCITRAL). In this context, this article makes three contributions. First, it provides an overview of empirical trends in damages in ISDS. Secondly, it considers the extent to which tribunals’ approaches to damages raise the sorts of concerns with ISDS identified by UNCITRAL Working Group III, focusing specifically on concerns of correctness, consistency, legal and expert costs, and independence and impartiality. Thirdly, it identifies a range of possible procedural and substantive reform options that might alleviate these concerns.
Drill-guided femoral nail extraction: a novel technique
Authors: Misailidis Alexandros I , Aifantis Ioannis D , Pallis Dimitrios , Mitsikostas Pantelis K , Gourtzelidis Georgios , Tsivelekas Konstantinos , Papadakis Stamatios A
Published: November 2021

Femoral nail extraction, although it is considered a challenging procedure for orthopedic surgeons, can be simplified. We present a new technique to aid the removal of a proximally (antegrade) inserted femoral nail by applying drilling consecutively in order to identify the margins and depth of the nail into the intramedyllary canal of the femur. The damage to the bone is minimal as we use k-wires or drilling and in our practice was uneventful. This technique is the first to be reported in literature. Most authors suggest techniques that enable radiolucent table and fluoroscopy techniques using C-arm. With this technique, traction table and fluoroscopy techniques seem to be less essential to accomplish the removal of a proximally (antegrade) inserted femoral nail.
Differential response of the photosynthetic machinery to dehydration in older and younger resurrection plants
Authors: Oung Hui Min Olivia , Mukhopadhyay Roma , Svoboda Vaclav , Charuvi Dana , Reich Ziv , Kirchhoff Helmut
Published: November 2021

A group of vascular plants called homoiochlorophyllous resurrection plants evolved unique capabilities to protect their photosynthetic machinery against desiccation-induced damage. This study examined whether the ontogenetic status of the resurrection plant Craterostigma pumilum has an impact on how the plant responds to dehydration at the thylakoid membrane level to prepare cells for the desiccated state. Thus, younger plants (<4 months) were compared with their older (>6 months) counterparts. Ultrastructural analysis provided evidence that younger plants suppressed senescence-like programs that are realized in older plants. During dehydration, older plants degrade specific subunits of the photosynthetic apparatus such as the D1 subunit of PSII and subunits of the cytochrome b6f complex. The latter leads to a controlled down-regulation of linear electron transport. In contrast, younger plants increased photoprotective high-energy quenching mechanisms and maintained a high capability to replace damaged D1 subunits. It follows that depending on the ontogenetic state, either more degradation-based or more photoprotective mechanisms are employed during dehydration of Craterostigma pumilum.
Searching for low radio-frequency gravitational wave counterparts in wide-field LOFAR data
Authors: Gourdji K , Rowlinson A , Wijers R A M J , Broderick J W , Shulevski A , Jonker P G
Published: November 2021

The electromagnetic counterparts to gravitational wave (GW) merger events are highly sought after, but difficult to find owing to large localization regions. In this study, we present a strategy to search for compact object merger radio counterparts in wide-field data collected by the Low-Frequency Array (LOFAR). In particular, we use multi-epoch LOFAR observations centred at 144 MHz spanning roughly 300 deg2 at optimum sensitivity of a since retracted neutron star–black hole merger candidate detected during O2, the second Advanced Ligo–Virgo GW observing run. The minimum sensitivity of the entire (overlapping) 1809 deg2 field searched is 50 mJy and the false negative rate is 0.1 per cent above 200 mJy. We do not find any transients and thus place an upper limit at 95 per cent confidence of 0.02 transients per square degree above 20 mJy on one, two, and three month time-scales, which are the most sensitive limits available to date. Finally, we discuss the prospects of observing GW events with LOFAR in the upcoming GW observing run and show that a single multibeam LOFAR observation can probe the full projected median localization area of binary neutron star mergers down to a median sensitivity of at least 8 mJy.
Polarimetric properties of the near-Sun asteroid (155140) 2005 UD in comparison with other asteroids and meteoritic samples
Authors: Ishiguro Masateru , Bach Yoonsoo P , Geem Jooyeon , Naito Hiroyuki , Kuroda Daisuke , Im Myungshin , Lee Myung Gyoon , Seo Jinguk , Jin Sunho , Kwon Yuna G , Oono Tatsuharu , Takagi Seiko , Sato Mitsuteru , Kuramoto Kiyoshi , Ito Takashi , Hasegawa Sunao , Yoshida Fumi , Arai Tomoko , Akitaya Hiroshi , Sekiguchi Tomohiko , Okazaki Ryo , Imai Masataka , Ohtsuka Katsuhito , Watanabe Makoto , Takahashi Jun , Devogèle Maxime , Fedorets Grigori , Siltala Lauri , Granvik Mikael
Published: November 2021

The investigation of asteroids near the Sun is important for understanding the final evolutionary stage of primitive Solar system objects. A near-Sun asteroid (NSA), (155140) 2005 UD, has orbital elements similar to those of (3200) Phaethon (the target asteroid for the JAXA’s DESTINY+ mission). We conducted photometric and polarimetric observations of 2005 UD and found that this asteroid exhibits a polarization phase curve similar to that of Phaethon over a wide range of observed solar phase angles (α = 20–105°) but different from those of (101955) Bennu and (162173) Ryugu (asteroids composed of hydrated carbonaceous materials). At a low phase angle (α ≲ 30°), the polarimetric properties of these NSAs (2005 UD and Phaethon) are consistent with anhydrous carbonaceous chondrites, while the properties of Bennu are consistent with hydrous carbonaceous chondrites. We derived the geometric albedo, pV ∼ 0.1 (in the range of 0.088–0.109); mean V-band absolute magnitude, HV = 17.54 ± 0.02; synodic rotational period, $T_\mathrm{rot} = 5.2388 \pm 0.0022 \, \mathrm{h}$ (the two-peaked solution is assumed); and effective mean diameter, $D_\mathrm{eff} = 1.32 \pm 0.06 \, \mathrm{km}$. At large phase angles (α ≳ 80°), the polarization phase curve are likely explained by the dominance of large grains and the paucity of small micron-sized grains. We conclude that the polarimetric similarity of these NSAs can be attributed to the intense solar heating of carbonaceous materials around their perihelia, where large anhydrous particles with small porosity could be produced by sintering.
Energetic pickup proton population downstream of the termination shock as revealed by IBEX-Hi data
Authors: Baliukin I I , Izmodenov V V , Alexashov D B
Published: November 2021

Pickup protons originate as a result of the ionization of hydrogen atoms in the supersonic solar wind, forming the suprathermal component of protons in the heliosphere. While they are being picked by the heliospheric magnetic field and convected into the heliosheath, the pickup protons may suffer stochastic acceleration from the solar wind turbulence in the region from the Sun up to the heliospheric termination shock, where they can also experience shock-drift acceleration or reflection from the cross-shock potential. These processes create a high-energy tail in the pickup ion energy distribution. The properties of this energetic pickup proton population are still not well defined, in spite of the fact that they are vital for models that simulate energetic neutral atom fluxes. We consider two scenarios for the pickup proton velocity distribution downstream of the heliospheric termination shock (a filled shell with an energetic power-law tail, and bi-Maxwellian). Based on a numerical kinetic model and observations of the energetic neutral atom fluxes from the inner heliosheath by the IBEX-Hi instrument, we characterize the pickup proton distribution and provide estimations of the properties of the energetic pickup proton population downstream of the termination shock.
Machine learning astrophysics from 21 cm lightcones: impact of network architectures and signal contamination
Authors: Prelogović David , Mesinger Andrei , Murray Steven , Fiameni Giuseppe , Gillet Nicolas
Published: November 2021

Imaging the cosmic 21 cm signal will map out the first billion years of our Universe. The resulting 3D lightcone (LC) will encode the properties of the unseen first galaxies and physical cosmology. Here, we build on previous work using neural networks (NNs) to infer astrophysical parameters directly from 21 cm LC images. We introduce recurrent neural networks (RNNs), capable of efficiently characterizing the evolution along the redshift axis of 21 cm LC images. Using a large database of simulated cosmic 21 cm LCs, we compare the relative performance in parameter estimation of different network architectures. These including two types of RNNs, which differ in their complexity, as well as a more traditional convolutional neural network (CNN). For the ideal case of no instrumental effects, our simplest and easiest to train RNN performs the best, with a mean squared parameter estimation error (MSE) that is lower by a factor of ≳2 compared with the other architectures studied here, and a factor of ≳8 lower than the previously-studied CNN. We also corrupt the cosmic signal by adding noise expected from a 1000 h integration with the Square Kilometre Array, as well as excising a foreground-contaminated ‘horizon wedge’. Parameter prediction errors increase when the NNs are trained on these contaminated LC images, though recovery is still good even in the most pessimistic case (with R2 ≳ 0.5−0.95). However, we find no notable differences in performance between network architectures on the contaminated images. We argue this is due to the size of our data set, highlighting the need for larger data sets and/or better data augmentation in order to maximize the potential of NNs in 21 cm parameter estimation.
Scintillation time-scale measurement of the highly active FRB20201124A
Authors: Main R A , Hilmarsson G H , Marthi V R , Spitler L G , Wharton R S , Bethapudi S , Li D Z , Lin H-H
Published: November 2021

Scintillation of compact radio sources results from the interference between images caused by multipath propagation, and probes the intervening scattering plasma and the velocities of the emitting source and scattering screen. In FRB20201124A, a repeating fast radio burst (FRB) that entered a period of extreme activity, we obtained many burst detections in observations at the upgraded Giant Metrewave Radio Telescope (uGMRT) and the Effelsberg 100-m Radio Telescope. Bursts nearby in time show similar scintillation patterns, and we measure a scintillation time-scale of 14.3 ± 1.2 and 7 ± 2 min at Effelsberg (1370 MHz) and uGMRT (650 MHz), respectively, by correlating burst pair spectra. The scintillation bandwidth scaled to 1 GHz is 0.5 ± 0.1 MHz, and the inferred scintillation velocity at Effelsberg is $V_{\mathrm{ISS}}\approx (59\pm 7) \sqrt{d_{\mathrm{ l}}/2\, \rm {kpc}}~{\rm km~s}^{-1}$, higher than Earth’s velocity for any screen beyond a lens distance of $d_{\mathrm{ l}} \gtrsim 400\,$ pc. From the measured scintillation bandwidth, FRB20201124A has comparatively lower scattering than nearby pulsars, and is underscattered by a factor of ∼30 or ∼1200 compared to the NE2001 and YMW16 model predictions, respectively. This underscattering together with the measured scintillation velocity is consistent with a scattering screen more nearby the Earth at $d_{\mathrm{ l}} \sim 400\,$ pc, rather than at 2 kpc spiral arm that NE2001 predicts to be the dominant source of scattering. With future measurements, the distance, geometry, and velocity of the scattering screen could be obtained through modelling of the annual variation in VISS, or through interstation time delays or interferometric observations. Scintillation/scattering measurements of FRBs could help improve Galactic electron density models, particularly in the Galactic halo or at high Galactic latitudes.
Cosmic shear beyond 2-point statistics: Accounting for galaxy intrinsic alignment with projected tidal fields
Authors: Harnois-Déraps Joachim , Martinet Nicolas , Reischke Robert
Published: November 2021

Developing analysis pipelines based on statistics beyond two-point functions is critical for extracting a maximal amount of cosmological information from current and upcoming weak lensing surveys. In this paper, we study the impact of the intrinsic alignment of galaxies (IA) on three promising probes measured from aperture mass maps – the lensing peaks, minima, and full PDF. Our 2D IA infusion method converts the light-cone-projected mass sheets into projected tidal tensors, which are then linearly coupled to an intrinsic ellipticity component with a strength controlled by the coupling parameter AIA. We validate our method with the γ-2PCFs statistics, recovering well the linear alignment model of Bridle & King in a full tomographic setting, and for different AIA values. We next use our method to infuse at the galaxy catalogue level a non-linear IA model that includes the density-weighting term introduced in Blazek et al., and compute the impact on the three aperture mass map statistics. We find that large $\mathcal {S}/\mathcal {N}$ peaks are maximally affected, with deviations reaching 30 per cent (10 per cent) for a Euclid-like (KiDS-like) survey. Modelling the signal in a wCDM cosmology universe with N-body simulations, we forecast the cosmological bias caused by unmodelled IA for 100 deg2 of Euclid-like data, finding very large offsets in w0 (5-10σstat), Ωm (4-6σstat), and $S_8 \equiv \sigma _8\sqrt{\Omega _{\rm m}/0.3}$ (∼3σstat). The method presented in this paper offers a compelling avenue to account for IA in beyond-two-point weak lensing statistics, with a flexibility comparable to that of current γ-2PCFs IA analytical models.
(H)DPGMM: a hierarchy of Dirichlet process Gaussian mixture models for the inference of the black hole mass function
Authors: Rinaldi Stefano , Del Pozzo Walter
Published: November 2021

We introduce (H)DPGMM, a hierarchical Bayesian non-parametric method based on the Dirichlet process Gaussian mixture model, designed to infer data-driven population properties of astrophysical objects without being committal to any specific physical model. We investigate the efficacy of our model on simulated data sets and demonstrate its capability to reconstruct correctly a variety of population models without the need of fine-tuning of the algorithm. We apply our method to the problem of inferring the black hole mass function given a set of gravitational wave observations from LIGO and Virgo, and find that the (H)DPGMM infers a binary black hole mass function that is consistent with previous estimates without the requirement of a theoretically motivated parametric model. Although the number of systems observed is still too small for a robust inference, (H)DPGMM confirms the presence of at least two distinct modes in the observed merging black hole mass function, hence suggesting in a model-independent fashion the presence of at least two classes of binary black hole systems.
Galaxy And Mass Assembly (GAMA): z ~ 0 galaxy luminosity function down to L ~ 106 L⊙ via clustering based redshift inference
Authors: Karademir Geray S , Taylor Edward N , Blake Chris , Baldry Ivan K , Bellstedt Sabine , Bilicki Maciej , Brown Michael J I , Cluver Michelle E , Driver Simon P , Hildebrandt Hendrik , Holwerda Benne W , Hopkins Andrew M , Loveday Jonathan , Phillipps Steven , Wright Angus H
Published: November 2021

In this study, we present a new experimental design using clustering-based redshift inference to measure the evolving galaxy luminosity function (GLF) spanning 5.5 decades from L ∼ 1011.5 to 106 L⊙. We use data from the Galaxy And Mass Assembly (GAMA) survey and the Kilo-Degree Survey (KiDS). We derive redshift distributions in bins of apparent magnitude to the limits of the GAMA-KiDS photometric catalogue: mr ≲ 23; more than a decade in luminosity beyond the limits of the GAMA spectroscopic redshift sample via clustering-based redshift inference. This technique uses spatial cross-correlation statistics for a reference set with known redshifts (in our case, the main GAMA sample) to derive the redshift distribution for the target ensemble. For the calibration of the redshift distribution, we use a simple parametrization with an adaptive normalization factor over the interval 0.005 < z < 0.48 to derive the clustering redshift results. We find that the GLF has a relatively constant power-law slope α ≈ −1.2 for −17 ≲ Mr ≲ −13, and then appears to steepen sharply for −13 ≲ Mr ≲ −10. This upturn appears to be where globular clusters (GCs) take over to dominate the source counts as a function of luminosity. Thus, we have mapped the GLF across the full range of the z ∼ 0 field galaxy population from the most luminous galaxies down to the GC scale.
Quenching, bursting, and galaxy shapes: colour transformation as a function of morphology
Authors: de Sá-Freitas C , Gonçalves T S , de Carvalho R R , Menéndez-Delmestre K , Barchi P H , Sampaio V M , Basu-Zych Antara , Darvish Behnam , Martin Christopher
Published: November 2021

Different mechanisms for quenching star formation in galaxies are commonly invoked in the literature, but the relative impact of each one at different cosmic epochs is still unknown. In particular, the relation between these processes and morphological transformation remains poorly understood. In this work, we measure the effectiveness of changes in star formation rates by analysing a new parameter, the Star Formation Acceleration (SFA), as a function of galaxy morphology. This methodology is capable of identifying both bursting and quenching episodes that occurred in the preceding 300 Myr. We use morphological classification catalogues based on Deep Learning techniques. Our final sample has ∼14 200 spirals and ∼2500 ellipticals. We find that elliptical galaxies in the transition region have median shorter quenching time-scales (τ < 1 Gyr) than spirals (τ ≥ 1 Gyr). This result conforms to the scenario in which major mergers and other violent processes play a fundamental role in galaxy evolution for most ellipticals, not only quenching star formation more rapidly but also playing a role in morphological transformation. We also find that ∼two-thirds of galaxies bursting in the green valley in our sample are massive spirals ($M_\star \ge 10^{11.0}\, \mathrm{M}_\odot$) with signs of disturbance. This is in accordance with the scenario where low-mass galaxies are losing their gas in an interaction with a massive galaxy: while the former is quenching, the last is being refueled and going through a burst, showing signs of recent interaction.
Massive black hole evolution models confronting the n-Hz amplitude of the stochastic gravitational wave background
Authors: Izquierdo-Villalba David , Sesana Alberto , Bonoli Silvia , Colpi Monica
Published: November 2021

We estimate the amplitude of the nano-Hz stochastic gravitational wave background (GWB) resulting from an unresolved population of inspiralling massive black hole binaries (MBHBs). To this aim, we use the L-Galaxies semi-analytical model applied on top of the Millennium merger trees. The dynamical evolution of MBHBs includes dynamical friction, stellar and gas binary hardening, and gravitational wave (GW) feedback. At the frequencies proved by the Pulsar Timing Array experiments, our model predicts an amplitude of ${\sim }1.2 \times 10^{-15}$ at ${\sim }3 \times 10^{-8}\, \rm Hz$ in agreement with current estimations. The contribution to the background comes primarily from equal-mass binaries with chirp masses above $\rm 10^{8}\, M_{\odot }$. We then consider the recently detected common red noise in NANOGrav, PPTA, and EPTA data, working under the hypothesis that it is indeed a stochastic GWB coming from MBHBs. By boosting the massive black hole growth via gas accretion, we show that our model can produce a signal with an amplitude $A\approx (2\!-\!3) \times 10^{-15}$. There are, however, difficulties in predicting this background level without mismatching key observational constraints such as the quasar bolometric luminosity functions or the local black hole mass function. This highlights how current and forthcoming GW observations can, for the first time, confront galaxy and black hole evolution models.
CoCoNet—boosting RNA contact prediction by convolutional neural networks
Authors: Zerihun Mehari B , Pucci Fabrizio , Schug Alexander
Published: November 2021

Co-evolutionary models such as direct coupling analysis (DCA) in combination with machine learning (ML) techniques based on deep neural networks are able to predict accurate protein contact or distance maps. Such information can be used as constraints in structure prediction and massively increase prediction accuracy. Unfortunately, the same ML methods cannot readily be applied to RNA as they rely on large structural datasets only available for proteins. Here, we demonstrate how the available smaller data for RNA can be used to improve prediction of RNA contact maps. We introduce an algorithm called CoCoNet that is based on a combination of a Coevolutionary model and a shallow Convolutional Neural Network. Despite its simplicity and the small number of trained parameters, the method boosts the positive predictive value (PPV) of predicted contacts by about 70% with respect to DCA as tested by cross-validation of about eighty RNA structures. However, the direct inclusion of the CoCoNet contacts in 3D modeling tools does not result in a proportional increase of the 3D RNA structure prediction accuracy. Therefore, we suggest that the field develops, in addition to contact PPV, metrics which estimate the expected impact for 3D structure modeling tools better. CoCoNet is freely available and can be found at https://github.com/KIT-MBS/coconet.
Position 34 of tRNA is a discriminative element for m5C38 modification by human DNMT2
Authors: Huang Zhi-Xuan , Li Jing , Xiong Qing-Ping , Li Hao , Wang En-Duo , Liu Ru-Juan
Published: November 2021

Dnmt2, a member of the DNA methyltransferase superfamily, catalyzes the formation of 5-methylcytosine at position 38 in the anticodon loop of tRNAs. Dnmt2 regulates many cellular biological processes, especially the production of tRNA-derived fragments and intergenerational transmission of paternal metabolic disorders to offspring. Moreover, Dnmt2 is closely related to human cancers. The tRNA substrates of mammalian Dnmt2s are mainly detected using bisulfite sequencing; however, we lack supporting biochemical data concerning their substrate specificity or recognition mechanism. Here, we deciphered the tRNA substrates of human DNMT2 (hDNMT2) as tRNAAsp(GUC), tRNAGly(GCC) and tRNAVal(AAC). Intriguingly, for tRNAAsp(GUC) and tRNAGly(GCC), G34 is the discriminator element; whereas for tRNAVal(AAC), the inosine modification at position 34 (I34), which is formed by the ADAT2/3 complex, is the prerequisite for hDNMT2 recognition. We showed that the C32U33(G/I)34N35 (C/U)36A37C38 motif in the anticodon loop, U11:A24 in the D stem, and the correct size of the variable loop are required for Dnmt2 recognition of substrate tRNAs. Furthermore, mammalian Dnmt2s possess a conserved tRNA recognition mechanism.