bluuebunny/crossref_metadata_2025 huggingface dataset:
THE MINIMUM NUMBER OF GENES CONTRIBUTING TO QUANTITATIVE VARIATION BETWEEN AND WITHIN POPULATIONS
Authors: Lande Russell
Published: April 2021

A procedure is outlined for estimating the minimum number of freely segregating genetic factors, nE,contributing to the difference in a quantitative character between two populations that have diverged by artificial or natural selection. If certain simple criteria are satisfied approximately on an appropriate scale of measurement, nEcan be estimated by comparing the phenotypic means and variances in the two parental populations and in their F1 and F2 hybrids (and backcrosses). This generalizes the method of WRIGHtTo genetically heterogeneous (or wild) parental populations, as well as inbred lines. Standard errors of the estimates are derived for large samples. The minimum number of genes involved in producing a large difference between populations in a quantitative trait is typically estimated to be about 5 or IO, with occasional values up to 20. This strongly supports the neo-Darwinian theory that large evolutionary changes usually occur by the accumulation of multiple genetic factors with relatively small effects.
Amyrel, a novel glucose-forming α-amylase from Drosophila with 4-α-glucanotransferase activity by disproportionation and hydrolysis of maltooligosaccharides
Authors: Feller Georges , Bonneau Magalie , Da Lage Jean-Luc
Published: April 2021

The α-amylase paralogue Amyrel present in true flies (Diptera Muscomorpha) has been classified as a glycoside hydrolase in CAZy family GH13 on the basis of its primary structure. Here, we report that, in fact, Amyrel is currently unique among animals as it possesses both the hydrolytic α-amylase activity (EC 3.2.1.1) and a 4-α-glucanotransferase (EC 2.4.1.25) transglycosylation activity. Amyrel reacts specifically on α-(1–4) glycosidic bonds of starch and related polymers but produces a complex mixture of maltooligosaccharides, which is in sharp contrast with canonical animal α-amylases. With model maltooligosaccharides G2 (maltose) to G7, the Amyrel reaction starts by a disproportionation leading to Gn − 1 and Gn + 1 products, which by themselves become substrates for new disproportionation cycles. As a result, all detectable odd- and even-numbered maltooligosaccharides, at least up to G12, were observed. However, hydrolysis of these products proceeds simultaneously, as shown by p-nitrophenyl-tagged oligosaccharides and microcalorimetry, and upon prolonged reaction, glucose is the major end-product followed by maltose. The main structural determinant of these atypical activities was found to be a Gly-His-Gly-Ala deletion in the so-called flexible loop bordering the active site. Indeed, engineering this deletion in porcine pancreatic and Drosophila melanogaster α-amylases results in reaction patterns similar to those of Amyrel. It is proposed that this deletion provides more freedom to the substrate for subsites occupancy and allows a less-constrained action pattern resulting in versatile activities at the active site.
Estrogenic Modulation of Retinal Sensitivity in Reproductive Female Túngara Frogs
Authors: Leslie Caitlin E , Walkowski Whitney , Rosencrans Robert F , Gordon William C , Bazan Nicolas G , Ryan Michael J , Farris Hamilton E
Published: April 2021

Although mate searching behavior in female túngara frogs (Physalaemus pustulosus) is nocturnal and largely mediated by acoustic cues, male signaling includes visual cues produced by the vocal sac. To compensate for these low light conditions, visual sensitivity in females is modulated when they are in a reproductive state, as retinal thresholds are decreased. This study tested whether estradiol (E2) plays a role in this modulation. Female túngara frogs were injected with either human chorionic gonadotropin (hCG) or a combination of hCG and fadrozole. hCG induces a reproductive state and increases retinal sensitivity, while fadrozole is an aromatase inhibitor that blocks hCG-induced E2 synthesis. In an analysis of scotopic electroretinograms (ERGs), hCG treatment lowered the threshold for eliciting a b-wave response, whereas the addition of fadrozole abolished this effect, matching thresholds in non-reproductive saline-injected controls. This suggests that blocking E2 synthesis blocked the hCG-mediated reproductive modulation of retinal sensitivity. By implicating E2 in control of retinal sensitivity, our data add to growing evidence that the targets of gonadal steroid feedback loops include sensory receptor organs, where stimulus sensitivity may be modulated, rather than more central brain nuclei, where modulation may affect mechanisms involved in motivation.
Behavioral Sex Differences and Hormonal Control in a Bird with an Elaborate Courtship Display
Authors: Schlinger Barney A , Chiver Ioana
Published: April 2021

Synopsis

Gonadal hormones can activate performance of reproductive behavior in adult animals, but also organize sex-specific neural circuits developmentally. Few studies have examined the hormonal basis of sex differences in the performance of elaborate, physically complex, and energetic male courtship displays. Here we describe our studies over more than 20 years examining sex difference and hormonal control of courtship in Golden-collared manakins (Manacus vitellinus) of Panamanian rainforests. Our recent studies of birds studied in an artificial “lek” in a rainforest aviary provide many new insights. Wild and captive males and females differ markedly in their performance of male-typical behaviors. Testosterone (T) treatment augments performance of virtually all of these behaviors in juvenile males with low levels of circulating T. By contrast, T-treatment of females (with low circulating T) either failed to activate some behaviors or activated male behaviors weakly or strongly. These results are discussed within a framework of our appreciation for hormonal versus genetic basis for sex differences in behavior with speculation about the neural mechanisms producing these patterns of hormonal activation.
Gelfand’s Trick for the Spherical Derived Hecke Algebra
Authors: Gehrmann Lennart
Published: April 2021

Gelfand’s trick shows that the spherical Hecke algebra of a $p$-adic split reductive group is commutative. We adapt this strategy in order to show that the spherical derived Hecke algebra is graded commutative under mild assumptions on the coefficient ring.
A Combination of N and S Antigens With IgA and IgG Measurement Strengthens the Accuracy of SARS-CoV-2 Serodiagnostics
Authors: Jalkanen Pinja , Pasternack Arja , Maljanen Sari , Melén Krister , Kolehmainen Pekka , Huttunen Moona , Lundberg Rickard , Tripathi Lav , Khan Hira , Ritvos Mikael A , Naves Rauno , Haveri Anu , Österlund Pamela , Kuivanen Suvi , Jääskeläinen Anne J , Kurkela Satu , Lappalainen Maija , Rantasärkkä Kaisa , Vuorinen Tytti , Hytönen Jukka , Waris Matti , Tauriainen Sisko , Ritvos Olli , Kakkola Laura , Julkunen Ilkka
Published: April 2021

Background

Primary diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is based on detection of virus RNA in nasopharyngeal swab samples. In addition, analysis of humoral immunity against SARS-CoV-2 has an important role in viral diagnostics and seroprevalence estimates.

Methods

We developed and optimized an enzyme immunoassays (EIA) using SARS-CoV-2 nucleoprotein (N), S1 and receptor binding domain (RBD) of the viral spike protein, and N proteins from SARS, Middle East respiratory syndrome (MERS), and 4 low-pathogenic human CoVs. Neutralizing antibody activity was compared with SARS-CoV-2 IgG, IgA, and IgM EIA results.

Results

The sensitivity of EIA for detecting immune response in COVID-19 patients (n = 101) was 77% in the acute phase and 100% in the convalescent phase of SARS-CoV-2 infection when N and RBD were used as antigens in IgG and IgA specific EIAs. SARS-CoV-2 infection significantly increased humoral immune responses against the 229E and NL63 N proteins. S1 and RBD-based EIA results had a strong correlation with microneutralization test results.

Conclusions

The data indicate a combination of SARS-CoV-2 S1 or RBD and N proteins and analysis of IgG and IgA immunoglobulin classes in sera provide an excellent basis for specific and sensitive serological diagnostics of COVID-19.
Pharmacokinetic modelling to estimate intracellular favipiravir ribofuranosyl-5′-triphosphate exposure to support posology for SARS-CoV-2
Authors: Pertinez Henry , Rajoli Rajith K R , Khoo Saye H , Owen Andrew
Published: April 2021

Objectives

Favipiravir has discrepant activity against SARS-CoV-2 in vitro, concerns about teratogenicity and pill burden, and an unknown optimal dose. This analysis used available data to simulate the intracellular pharmacokinetics of the favipiravir active metabolite [favipiravir ribofuranosyl-5′-triphosphate (FAVI-RTP)].

Methods

Published in vitro data for intracellular production and elimination of FAVI-RTP in Madin–Darby canine kidney cells were fitted with a mathematical model describing the time course of intracellular FAVI-RTP as a function of favipiravir concentration. Parameter estimates were then combined with a published population pharmacokinetic model in Chinese patients to predict human intracellular FAVI-RTP. In vitro FAVI-RTP data were adequately described as a function of concentrations with an empirical model, noting simplification and consolidation of various processes and several assumptions.

Results

Parameter estimates from fittings to in vitro data predict a flatter dynamic range of peak to trough for intracellular FAVI-RTP (peak to trough ratio of ∼1 to 1) when driven by a predicted free plasma concentration profile, compared with the plasma profile of parent favipiravir (ratio of ∼2 to 1). This approach has important assumptions, but indicates that, despite rapid clearance of the parent from plasma, sufficient intracellular FAVI-RTP may be maintained across the dosing interval because of its long intracellular half-life.

Conclusions

Population mean intracellular FAVI-RTP concentrations are estimated to be maintained above the Km for the SARS-CoV-2 polymerase for 9 days with a 1200 mg twice-daily regimen (following a 1600 mg twice-daily loading dose on day 1). Further evaluation of favipiravir as part of antiviral combinations for SARS-CoV-2 is warranted.
Association Between Alcohol, Substance Use, and Inpatient Burn Outcomes
Authors: Williams Felicia N , Chrisco Lori , Strassle Paula D , Navajas Emma , Laughon Sarah L , Sljivic Sanja , Nizamani Rabia , Charles Anthony , King Booker
Published: April 2021

The use of alcohol and illicit substances has been associated with impaired judgment and health, but the effect on inpatient outcomes after burn injury remains unsettled. Our objective was to evaluate the effect of alcohol and illicit substance use on our inpatient burn outcomes. Adult patients admitted with burn injury—including inhalation injury only—between January 1, 2014 and June 30, 2019 were eligible for inclusion. Alcohol use and illicit drug use were identified on admission. Outcomes of interest included requiring mechanical ventilation, admission to the intensive care unit, length of stay, and inpatient mortality. Multivariable linear and logistic regression models were used to estimate the effects of use on inpatient outcomes. A total of 3476 patients were included in our analyses; 8% (n = 284) tested positive for alcohol, 10% (n = 364) tested positive for cocaine, and 27% (n = 930) tested positive for marijuana and at admission. Two hundred and eighty adults (18% of all positive patients) tested positive for at least two substances. Patients who tested positive for alcohol had longer lengths of stay and were more likely to be admitted to the intensive care unit. Patients who tested positive for cocaine had longer overall and intensive care unit lengths of stay. No differences in inpatient outcomes were seen among patients who tested positive for marijuana. Neither alcohol nor illicit substance use appears to affect inpatient mortality after burns. Alcohol and cocaine use significantly increased overall length of stay. Marijuana use had no impact on inpatient outcomes.
Exploring Grower-sourced Data to Understand Spatiotemporal Trends in the Occurrence of a Vector, Pseudococcus maritimus (Hemiptera: Pseudococcidae) and Improve Grapevine Leafroll Disease Management
Authors: MacDonald Sarah L , Schartel Tyler E , Cooper Monica L
Published: April 2021

Grapevine leafroll disease is a significant concern in the wine grape industry, as it spreads rapidly and contributes to economically significant reductions in yield and grape quality. Our objective was to utilize 5 yr of grower-sourced data from Napa (California, USA) to improve local and regional disease management efforts. Specifically, we applied a spatially integrated multivariate clustering technique to improve understanding of spatiotemporal trends in Pseudococcus maritimus (Ehrhorn) male populations—the primary vector in the region. We also implemented generalized linear mixed models to evaluate the effects of two key practices, insecticide sprays and roguing, on disease incidence. Results show P. maritimus has a biannual flight pattern in the study area, with the first flight peaking in early May and the second between early August and early September. Clusters of P. maritimus flight data fall largely within the vineyard footprints of individual growers, but also showed clear neighborhood effects. We found that when disease incidence within a block is <1%, consistent monitoring and removal of diseased vines is required to contain within-block spread. As within-block disease incidence grows to 1–20%, both insecticide applications and roguing are effective practices to reduce spread. At incidence levels >20%, roguing is a critical practice. Our results emphasize the importance of individual management efforts, but also the value of programs that engage the wider neighboring community and highlight the power of community data collection to guide decision-making.
Expression Profiles of Digestive Genes in the Gut and Salivary Glands of Tarnished Plant Bug (Hemiptera: Miridae)
Authors: Perera Omaththage P , Shelby Kent S , Pierce Calvin A , Snodgrass Gordon L
Published: April 2021

Host plant preference of agricultural pests may shift throughout the growing season, allowing the pests to persist on wild hosts when crops are not available. Lygus Hahn (Hemiptera: Miridae) bugs are severe pests of cotton during flowering and fruiting stages, but can persist on alternative crops, or on weed species. Diversity of digestive enzymes produced by salivary glands and gut tissues play a pivotal role in an organism’s ability to utilize various food sources. Polyphagous insects produce an array of enzymes that can process carbohydrates, lipids, and proteins. In this study, the digestive enzyme repertoire of the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois), was identified by high-throughput sequencing followed by cDNA cloning and sequencing. This study identified 87 digestive genes, including 30 polygalacturonases (PG), one β-galactosidase, three α-glucosidases, six β-glucosidases, 28 trypsin-like proteases, three serine proteases, one apyrase-like protease, one cysteine protease, 12 lipases, and two transcripts with low similarity to a xylanase A-like genes. RNA-Seq expression profiles of these digestive genes in adult tarnished plant bugs revealed that 57 and 12 genes were differentially expressed in the salivary gland and gut (≥5-fold, P ≤ 0.01), respectively. All polygalacturonase genes, most proteases, and two xylanase-like genes were differentially expressed in salivary glands, while most of the carbohydrate and lipid processing enzymes were differentially expressed in the gut. Seven of the proteases (KF208689, KF208697, KF208698, KF208699, KF208700, KF208701, and KF208702) were not detected in either the gut or salivary glands.
Personalized medicine drugs and the burden of disease in Germany
Authors: Kohler Stefan
Published: April 2021

Objectives

This study aimed to assess the burden attributable to diseases with subtypes that are indications for the personalized medicine (PM) drugs approved in Germany.

Methods

A secondary analysis of a PM drug database and Global Burden of Disease (GBD) Study 2019 data was conducted. Indications of the PM drugs approved in Germany for biomarker-targeted therapy were matched with disease burden causes to quantify the portion of the disease burden attributable to causes that, in some instances, may be treated with PM drugs.

Results

Between 1995 and 2020, the number of PM drugs approved in Germany rose from 0 to 83. Accordingly, the portion of the disease burden due to causes of disease with subtypes that are PM drug indications has risen. Indications for use of the 83 PM drugs approved in Germany by the end of 2020 related to 39 of 369 GBD causes, to which 7825 disability-adjusted life years (DALYs) or 24.3% of the total burden of 32 162 DALYs per 100 000 population in Germany were attributed. Twenty years earlier, in 2000, 5 PM drugs related to 2 GBD causes, to which 978 DALYs (3.1%) of a total burden of 31 878 DALYs per 100 000 population were attributed. Considering the median frequency of biomarkers that can change pharmacological treatment resulted in estimating that not more than 3.0% (interquartile range: 1.1–7.3) of the current German disease burden is affected by personalized pharmacotherapy.

Conclusions

Mapping PM drug indications to disease burden causes allowed to quantify the disease burden within and outside the domain of personalized pharmacotherapy in Germany.
Totally implanted chemotherapy port catheters: literature review and report of four cases
Authors: Farshidmehr Pezhman , Omrani Zahra , Cheraghali Roozbeh
Published: April 2021

Totally implantable catheters tend to be the most popular choice because once installed they allow permanent access to a deep vein, which is gained by puncturing the port rather than a vein.

In this article, we explain four cases of chemotherapy port complications: superior vena cava (SVC) syndrome in a metastatic colorectal cancer patient who presented with bilateral mastitis, snare technique for removal of migrated catheter line, carotid artery placement of a port in a 5-year-old child that was referred to our hospital from a pediatric center and adhesive port tip in the heart that finally we left the port in situ.

In SVC syndrome, treatment should be guided by the severity of symptoms, etiology of the obstruction, prognosis of the patient and treatment goals. We propose timely removal of port-a-cath following completion of intended chemotherapeutic regimen.
Laparoscopic liver cyst fenestration with real-time indocyanine green fluorescence-guided surgery: a case report
Authors: Une Norikazu , Fujio Atsushi , Mitsugashira Hiroaki , Kanai Norifumi , Saitoh Yoshikatsu , Ohta Mineto , Sasaki Kengo , Miyazawa Koji , Kashiwadate Toshiaki , Nakanishi Wataru , Tokodai Kazuaki , Miyagi Shigehito , Unno Michiaki , Kamei Takashi
Published: April 2021

Laparoscopic fenestration (LF) has recently been considered a standard procedure for nonparasitic symptomatic liver cysts. Here, we report a case of LF that was safely performed using real-time indocyanine green (ICG) fluorescence-guided surgery. A 74-year-old woman presented with right upper abdominal pain and poor dietary intake. The patient was diagnosed with symptomatic liver cysts and underwent LF. One hour before surgery, ICG (2.5 mg) was intravenously administered to the patient. ICG fluorescence imaging clearly showed the biliary ducts and distinguished the cysts from the liver parenchyma. We could resect only the cyst walls as wide as possible under the guidance of both white light and fluorescence imaging. There were no signs of postoperative symptom recurrence. Detection of ICG fluorescence in the liver parenchyma is as important as ICG cholangiography for fenestration. Laparoscopic liver cyst fenestration with real-time ICG fluorescence-guided surgery is safe and can be used as a standard procedure.
Psychiatric Conditions During Pregnancy and Postpartum in a Universally Insured American Population
Authors: Andriotti Tomas , Ranjit Anju , Hamlin Lynette , Koehlmoos Tracey , Robinson Julian N , Lutgendorf Monica A
Published: April 2021

Background

Mental health conditions are common and can have significant effects during the perinatal period. Our objective was to determine the incidences and predictors of psychiatric conditions during pregnancy and postpartum among universally insured American women.

Material and Methods

This was an Institutional Review Board (IRB)-approved protocol using a retrospective cohort of 104,866 deliveries covered by TRICARE from 2005 to 2014. We used TRICARE claims data to identify pregnant women without current psychiatric conditions who developed new psychiatric condition(s) during pregnancy or postpartum compared with those who did not, as identified by International Classification of Diseases (ICD)-9 CM codes. Predictors of psychiatric conditions during pregnancy or postpartum were determined using stepwise logistic regression models.

Results

A total of 104,866 women met the inclusion criteria; of these, 35% (n = 36,192) were diagnosed with a new psychiatric condition during pregnancy or within 1 year of delivery, 15% (n = 15,636) with a psychiatric condition during pregnancy, and 20% (n = 20,556) with a psychiatric condition within 1 year of delivery. We demonstrated that the African-American race (odds ratio [OR] 1.16, 95% CI 1.10-1.22), active duty status (OR 1.20, 95% CI 1.14-1.25), and severe maternal morbidity during delivery (OR 1.18, 95% CI 1.02-1.35) were significantly associated with the occurrence of a psychiatric condition within 1 year of delivery. For Asian women, there was a 28% higher odds of developing a psychiatric disorder during pregnancy (adjusted OR 1.28, 95% CI 1.17-1.40) compared with White women. Active duty women were twice as likely to be diagnosed with post-traumatic stress disorder (adjusted OR 2.31, 95% CI 1.83–2.90).

Conclusion

In a universally insured population, the incidences of psychiatric conditions in pregnancy and within a year of delivery were similar to the American population. Additionally, the development of psychiatric conditions in pregnancy and within a year of delivery may be associated with race, active duty status, and complicated births.
Non-Measurability, Imprecise Credences, and Imprecise Chances
Authors: Isaacs Yoaav , Hájek Alan , Hawthorne John
Published: April 2021

Abstract–

We offer a new motivation for imprecise probabilities. We argue that there are propositions to which precise probability cannot be assigned, but to which imprecise probability can be assigned. In such cases the alternative to imprecise probability is not precise probability, but no probability at all. And an imprecise probability is substantially better than no probability at all. Our argument is based on the mathematical phenomenon of non-measurable sets. Non-measurable propositions cannot receive precise probabilities, but there is a natural way for them to receive imprecise probabilities. The mathematics of non-measurable sets is arcane, but its epistemological import is far-reaching; even apparently mundane propositions are liable to be affected by non-measurability. The phenomenon of non-measurability dramatically reshapes the dialectic between critics and proponents of imprecise credence. Non-measurability offers natural rejoinders to prominent critics of imprecise credence. Non-measurability even reverses some of the critics’ arguments—by the very lights that have been used to argue against imprecise credences, imprecise credences are better than precise credences.
Capturing the Zeitgeist: Dvořák’s Prague Debut and the Politics of Patriotism
Authors: Branda Eva
Published: April 2021

While Dvořák’s Hymnus: Heirs of the White Mountain (1872) for chorus and orchestra is largely unknown today, its Prague premiere in 1873 was a landmark event in Dvořák’s career. This study shows that the work’s success at its first performance depended on cultural expectations and political circumstances that were particular to Prague in the 1870s. Audiences were accustomed to choral concerts of modest proportions, and the spectacle delivered by the Hlahol choral society on this occasion caught the public by surprise, as did Dvořák’s seemingly sudden emergence onto the scene. The performance also came in the midst of heated debates on the nature of Czech music, and Hymnus was harnessed in the service of certain critical agendas. Moreover, the work explores the aftermath of a crucial seventeenth-century Czech military defeat; this reference was timely in 1873, as Czech politicians had recently waged and lost their own battle in the Austrian parliament, leading audiences to relate in a unique way to Hymnus.
AstroSat/UVIT observations of IC 4329A: constraining the accretion disc inner radius
Authors: Dewangan Gulab C , Tripathi P , Papadakis I E , Singh K P
Published: April 2021

We present a study of far- and near ultraviolet (UV) emission from the accretion disc in a powerful Seyfert 1 galaxy IC 4329A using observations performed with the Ultraviolet Imaging Telescope (UVIT) onboard AstroSat. These data provide the highest spatial resolution and deepest images of IC 4329A in the far- and near UV bands acquired to date. The excellent spatial resolution of the UVIT data has allowed us to accurately separate the extended emission from the host galaxy and the AGN emission in the far- and near UV bands. We derive the intrinsic AGN flux after correcting for the Galactic and internal reddening, as well as for the contribution of emission lines from the broad and narrow-line regions. The intrinsic UV continuum emission shows a marked deficit compared to that expected from the ‘standard’ models of the accretion disc around an estimated black hole mass of $1-2\times 10^8\, {\rm M}_{\odot }$ when the disc extends to the innermost stable circular orbit. We find that the intrinsic UV continuum is fully consistent with the standard disc models, but only if the disc emits from distances larger than ∼80–150 gravitational radii.
Rapid modification of neutron star surface magnetic field: a proposed mechanism for explaining radio emission state changes in pulsars
Authors: Geppert U , Basu R , Mitra D , Melikidze G I , Szkudlarek M
Published: April 2021

The radio emission in many pulsars shows sudden changes, usually within a period, that cannot be related to the steady state processes within the inner acceleration region (IAR) above the polar cap. These changes are often quasi-periodic in nature, where regular transitions between two or more stable emission states are seen. The durations of these states show a wide variety ranging from several seconds to hours at a time. There are strong, small-scale magnetic field structures and huge temperature gradients present at the polar cap surface. We have considered several processes that can cause temporal modifications of the local magnetic field structure and strength at the surface of the polar cap. Using different magnetic field strengths and scales, and also assuming realistic scales of the temperature gradients, the evolutionary time-scales of different phenomena affecting the surface magnetic field were estimated. We find that the Hall drift results in faster changes in comparison to both Ohmic decay and thermoelectric effects. A mechanism based on the partially screened gap (PSG) model of the IAR has been proposed, where the Hall and thermoelectric oscillations perturb the polar cap magnetic field to alter the sparking process in the PSG. This is likely to affect the observed radio emission resulting in the observed state changes.
The peculiar WAT NGC 2329 with Seyfert/FR I-like radio lobes
Authors: Das S , Kharb P , Morganti R , Nandi S
Published: April 2021

We report the complex radio properties of the radio galaxy NGC 2329 that resides in the centre of the galaxy cluster Abell 569. For this study, we have used archival data from the Very Large Array (VLA) at various resolutions and frequencies, as well as the Very Long Baseline Array (VLBA). While the wide-angle tailed (WAT) Fanaroff–Riley type I (FR I) radio morphology of the source has been discussed widely in the literature, the nature of the inner lobes has not been as widely discussed. In particular, we note that the inner lobes resemble the bubble-like radio structures observed in Seyfert galaxies. Polarization-sensitive data from the VLA clearly show magnetic field structures consistent with FR Is for the outer lobes and Seyferts for the inner lobes in NGC 2329. FR Is are classified as radio-loud (RL) active galactic nuclei (AGN) and Seyferts as radio-quiet (RQ) AGN, making this source unique. The VLBA shows a one-sided radio jet suggesting a relativistic pc-scale outflow, leading into the inner lobes. Electron lifetime estimates suggest that the outer FR I-like lobes are nearly twice as old (∼45 Myr) as the inner Seyfert-like lobes (∼25 Myr). Gas inflow in this merging cluster seems to have rejuvenated the AGN about ∼25 Myr ago, and may have caused a change in the accretion disc state. The complex composite radio morphology of NGC 2329 suggests that the RL/RQ dichotomy is a function of time in the lifecycle of an AGN.
Observational constraints to the dynamics of dust particles in the coma of comet 67P/Churyumov–Gerasimenko
Authors: Frattin E , Bertini I , Ivanovski S L , Marzari F , Fulle M , Zakharov V V , Moreno F , Naletto G , Lazzarin M , Cambianica P , Cremonese G , Ferrari S , Ferri F , Güttler C , La Forgia F , Lucchetti A , Pajola M , Penasa L , Rotundi A , Sierks H , Tubiana C
Published: April 2021

In this work, we aim to characterize the dust motion in the inner coma of comet 67P/Churyumov–Gerasimenko to provide constraints for theoretical 3D coma models. The OSIRIS camera on-board the Rosetta mission was able for the first time to acquire images of single dust particles from inside the cometary coma, very close to the nucleus. We analyse a large number of particles, performing a significant statistic of their behaviour during the post-perihelion period, when the spacecraft covered distances from the nucleus ranging between 80 and 400 km. We describe the particle trajectories, investigating their orientation and finding highly radial motion with respect to the nucleus. Then, from the particle brightness profiles, we derive a particle rotational frequency of ν < 3.6 Hz, revealing that they are slow rotators and do not undergo fragmentation. We use scattering models to compare the observed spectral radiance of the particles with the simulated ones in order to estimate their size, finding values that range from millimetres up to centimetres. The statistics performed in this paper provide useful parameters to constrain the cometary coma dynamical models.
Recovering the wedge modes lost to 21-cm foregrounds
Authors: Gagnon-Hartman Samuel , Cui Yue , Liu Adrian , Ravanbakhsh Siamak
Published: April 2021

One of the critical challenges facing imaging studies of the 21-cm signal at the Epoch of Reionization (EoR) is the separation of astrophysical foreground contamination. These foregrounds are known to lie in a wedge-shaped region of (k⊥, k∥) Fourier space. Removing these Fourier modes excises the foregrounds at grave expense to image fidelity, since the cosmological information at these modes is also removed by the wedge filter. However, the 21-cm EoR signal is non-Gaussian, meaning that the lost wedge modes are correlated to the surviving modes by some covariance matrix. We have developed a machine learning-based method that exploits this information to identify ionized regions within a wedge-filtered image. Our method reliably identifies the largest ionized regions and can reconstruct their shape, size, and location within an image. We further demonstrate that our method remains viable when instrumental effects are accounted for, using the Hydrogen EoR Array and the Square Kilometre Array as fiducial instruments. The ability to recover spatial information from wedge-filtered images unlocks the potential for imaging studies using current- and next-generation instruments without relying on detailed models of the astrophysical foregrounds themselves.
Isocyanic acid (HNCO) in the hot molecular core G331.512-0.103: observations and chemical modelling
Authors: Canelo Carla M , Bronfman Leonardo , Mendoza Edgar , Duronea Nicolas , Merello Manuel , Carvajal Miguel , Friaça Amâncio C S , Lepine Jacques
Published: April 2021

Isocyanic acid (HNCO) is a simple molecule with a potential to form prebiotic and complex organic species. Using a spectral survey collected with the Atacama Pathfinder EXperiment, in this work we report the detection of 42 transitions of HNCO in the hot molecular core/outflow G331.512-0.103 (hereafter G331). The spectral lines were observed in the frequency interval ∼160–355 GHz. By means of Local Thermodynamic Equilibrium analyses, applying the rotational diagram method, we studied the excitation conditions of HNCO. The excitation temperature and column density are estimated to be Tex= 58.8 ± 2.7 K and N = (3.7 ± 0.5) × 1015 cm−2, considering beam dilution effects. The derived relative abundance is between (3.8 ± 0.5) × 10−9 and (1.4 ± 0.2) × 10−8. In comparison with other hot molecular cores, our column densities and abundances are in agreement. An update of the internal partition functions of the four CHNO isomers: HNCO; cyanic acid, HOCN; fulminic acid, HCNO; and isofulminic acid, HONC is provided. We also used the astrochemical code Nautilus to model and discuss HNCO abundances. The simulations could reproduce the abundances with a simple zero-dimensional model at a temperature of 60 K and for a chemical age of ∼105 yr, which is larger than the estimated dynamical age for G331. This result could suggest the need for a more robust model and even the revision of chemical reactions associated with HNCO.
A spectral survey of WASP-19b with ESPRESSO
Authors: Sedaghati Elyar , MacDonald Ryan J , Casasayas-Barris Núria , Hoeijmakers H Jens , Boffin Henri M J , Rodler Florian , Brahm Rafael , Jones Matías , Sánchez-López Alejandro , Carleo Ilaria , Figueira Pedro , Mehner Andrea , López-Puertas Manuel
Published: April 2021

High-resolution precision spectroscopy provides a multitude of robust techniques for probing exoplanetary atmospheres. We present multiple VLT/ESPRESSO transit observations of the hot-Jupiter exoplanet WASP-19b with previously published but disputed atmospheric features from low resolution studies. Through spectral synthesis and modelling of the Rossiter–McLaughlin (RM) effect we calculate stellar, orbital and physical parameters for the system. From narrow-band spectroscopy we do not detect any of H i, Fe i, Mg i, Ca i, Na i, and K i neutral species, placing upper limits on their line contrasts. Through cross-correlation analyses with atmospheric models, we do not detect Fe i and place a 3σ upper limit of $\log \, (X_{\textrm {Fe}}/X_\odot) \approx -1.83\, \pm \, 0.11$ on its mass fraction, from injection and retrieval. We show the inability to detect the presence of H2O for known abundances, owing to lack of strong absorption bands, as well as relatively low S/N ratio. We detect a barely significant peak (3.02 ± 0.15 σ) in the cross-correlation map for TiO, consistent with the sub-solar abundance previously reported. This is merely a hint for the presence of TiO and does not constitute a confirmation. However, we do confirm the presence of previously observed enhanced scattering towards blue wavelengths, through chromatic RM measurements, pointing to a hazy atmosphere. We finally present a reanalysis of low-resolution transmission spectra of this exoplanet, concluding that unocculted starspots alone cannot explain previously detected features. Our reanalysis of the FORS2 spectra of WASP-19b finds a ∼100× sub-solar TiO abundance, precisely constrained to $\log \, X_{\textrm {TiO}} \approx -7.52 \pm 0.38$, consistent with the TiO hint from ESPRESSO. We present plausible paths to reconciliation with other seemingly contradicting results.
Statistical exploration of halo anisotropic clustering and intrinsic alignments with the mass-Peak Patch algorithm
Authors: Regaldo-Saint Blancard Bruno , Codis Sandrine , Bond J Richard , Stein George
Published: April 2021

The anisotropy or triaxiality of massive dark matter haloes largely defines the structure of the cosmic web, in particular the filaments that join the haloes together. Here, we investigate such oriented correlations in mass-Peak Patch halo catalogues by using the initial strain tensor of spherical proto-halo regions to orient the haloes. To go beyond the spherically averaged two-point correlation function of haloes, we use oriented stacks to compute oriented two-point correlations: we explicitly break isotropy by imposing a local frame set by the strain tensor of the reference halo before stacking neighbouring haloes. Beyond the exclusion zone of the reference halo, clustering is found to be strongly enhanced along the major direction of the strain tensor as expected. This anisotropic clustering of haloes along filaments is further quantified by using a spherical harmonics decomposition. Furthermore, we compute the evolution of cluster-scale halo principal directions relative to those of their neighbours and show that there are strong correlations extending up to very large scales. In order to provide calculations more suitable to observational confrontations, we also utilize 2D projected versions of some equivalent correlation functions. Finally, we show that the multipole structure of the mass-peak patch halo’s anisotropic clustering can be qualitatively captured in an analytic treatment based on peak theory. Though highly informative, giving the same qualitative features as the oriented correlations found from the simulation catalogue, analytic evaluation involves extensive use of Monte Carlo methods, which is also what the simulated catalogue uses, taking into account as they do the adaptive nature of the mass-peak patch mass hierarchy and all non-local complexities associated with the exclusion of smaller haloes overlapping with larger ones: there is no substitute for the mass-Peak Patch simulation-based determination of oriented and anisotropic correlations.
Cosmological cross-correlations and nearest neighbour distributions
Authors: Banerjee Arka , Abel Tom
Published: April 2021

Cross-correlations between data sets are used in many different contexts in cosmological analyses. Recently, k-nearest neighbour cumulative distribution functions (kNN-CDF) were shown to be sensitive probes of cosmological (auto) clustering. In this paper, we extend the framework of NN measurements to describe joint distributions of, and correlations between, two data sets. We describe the measurement of joint kNN-CDFs, and show that these measurements are sensitive to all possible connected N-point functions that can be defined in terms of the two data sets. We describe how the cross-correlations can be isolated by combining measurements of the joint kNN-CDFs and those measured from individual data sets. We demonstrate the application of these measurements in the context of Gaussian density fields, as well as for fully non-linear cosmological data sets. Using a Fisher analysis, we show that measurements of the halo-matter cross-correlations, as measured through NN measurements are more sensitive to the underlying cosmological parameters, compared to traditional two-point cross-correlation measurements over the same range of scales. Finally, we demonstrate how the NN cross-correlations can robustly detect cross-correlations between sparse samples – the same regime where the two-point cross-correlation measurements are dominated by noise.
Molecular and morphological evidence for a unified, inclusiveSinotaia quadrata(Caenogastropoda: Viviparidae: Bellamyinae)
Authors: Ye Bin , Hirano Takahiro , Saito Takumi , Dong Zhengzhong , Do Van Tu , Chiba Satoshi
Published: April 2021

The taxonomy of species in the caenogastropod genus Sinotaia (Viviparidae: Bellamyinae) has been a complex and controversial issue since the 19th century. Sinotaia quadrata, the type species of Sinotaia, comprises many named forms and transitions between them, and the taxonomic validity of some species similar to S. quadrata also requires clarification. To clarify relationships in this common and significant member of the freshwater benthos, we reconstructed a phylogeny for species related to S. quadrata based on the 16S rRNA and cytochrome c oxidase subunit I genes to test which classifications are robust using modern data and interpretation. We also compared the shell outline morphology of type material of most species in the genus Sinotaia from the original literature. The combination of phylogenetic and shape variance data suggests that seven currently recognized species of Sinotaia should be synonymized with S. quadrata. We used microsatellite markers and landmark-based geometric morphometric analysis to examine the genetic differentiation and shell shape variation of S. quadrata populations in both China and Japan. Genetic and shape variations were not congruent, suggesting that minor variations in shell shape do not indicate distinct Sinotaia species. Shell shape variation shows no clear separations and shows environmental plasticity. Using data on molecular phylogenetics, genetic diversity and shell morphology, we provide a more inclusive species concept for S. quadrata. This provides a basis to formally revise this taxon and the seven closely related nominal species that are widely distributed in China and East Asia.
PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing
Authors: Hwang Gue-Ho , Jeong You Kyeong , Habib Omer , Hong Sung-Ah , Lim Kayeong , Kim Jin-Soo , Bae Sangsu
Published: April 2021

Prime editing technology is capable of generating targeted insertions, deletions, and base conversions. However, the process of designing prime editing guide RNAs (pegRNAs), which contain a primer binding site and a reverse-transcription template at the 3′ end, is more complex than that for the single guide RNAs used with CRISPR nucleases or base editors. Furthermore, the assessment of high-throughput sequencing data after prime editors (PEs) have been employed should consider the unique feature of PEs; thus, pre-existing assessment tools cannot directly be adopted for PEs. Here, we present two user-friendly web-based tools for PEs, named PE-Designer and PE-Analyzer. PE-Designer, a dedicated tool for pegRNA selection, provides all possible target sequences, pegRNA extension sequences, and nicking guide RNA sequences together with useful information, and displays the results in an interactive image. PE-Analyzer, a dedicated tool for PE outcome analysis, accepts high-throughput sequencing data, summarizes mutation-related information in a table, and provides interactive graphs. PE-Analyzer was mainly written using JavaScript so that it can analyze several data sets without requiring that huge sequencing data (>100MB) be uploaded to the server, reducing analysis time and increasing personal security. PE-Designer and PE-Analyzer are freely available at http://www.rgenome.net/pe-designer/ and http://www.rgenome.net/pe-analyzer/ without a login process.
LitSuggest: a web-based system for literature recommendation and curation using machine learning
Authors: Allot Alexis , Lee Kyubum , Chen Qingyu , Luo Ling , Lu Zhiyong
Published: April 2021

Searching and reading relevant literature is a routine practice in biomedical research. However, it is challenging for a user to design optimal search queries using all the keywords related to a given topic. As such, existing search systems such as PubMed often return suboptimal results. Several computational methods have been proposed as an effective alternative to keyword-based query methods for literature recommendation. However, those methods require specialized knowledge in machine learning and natural language processing, which can make them difficult for biologists to utilize. In this paper, we propose LitSuggest, a web server that provides an all-in-one literature recommendation and curation service to help biomedical researchers stay up to date with scientific literature. LitSuggest combines advanced machine learning techniques for suggesting relevant PubMed articles with high accuracy. In addition to innovative text-processing methods, LitSuggest offers multiple advantages over existing tools. First, LitSuggest allows users to curate, organize, and download classification results in a single interface. Second, users can easily fine-tune LitSuggest results by updating the training corpus. Third, results can be readily shared, enabling collaborative analysis and curation of scientific literature. Finally, LitSuggest provides an automated personalized weekly digest of newly published articles for each user's project. LitSuggest is publicly available at https://www.ncbi.nlm.nih.gov/research/litsuggest.
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure
Authors: Dieckmann Marius Alfred , Beyvers Sebastian , Nkouamedjo-Fankep Rudel Christian , Hanel Patrick Harald Georg , Jelonek Lukas , Blom Jochen , Goesmann Alexander
Published: April 2021

The EDGAR platform, a web server providing databases of precomputed orthology data for thousands of microbial genomes, is one of the most established tools in the field of comparative genomics and phylogenomics. Based on precomputed gene alignments, EDGAR allows quick identification of the differential gene content, i.e. the pan genome, the core genome, or singleton genes. Furthermore, EDGAR features a wide range of analyses and visualizations like Venn diagrams, synteny plots, phylogenetic trees, as well as Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI) matrices. During the last few years, the average number of genomes analyzed in an EDGAR project increased by two orders of magnitude. To handle this massive increase, a completely new technical backend infrastructure for the EDGAR platform was designed and launched as EDGAR3.0. For the calculation of new EDGAR3.0 projects, we are now using a scalable Kubernetes cluster running in a cloud environment. A new storage infrastructure was developed using a file-based high-performance storage backend which ensures timely data handling and efficient access. The new data backend guarantees a memory efficient calculation of orthologs, and parallelization has led to drastically reduced processing times. Based on the advanced technical infrastructure new analysis features could be implemented including POCP and FastANI genomes similarity indices, UpSet intersecting set visualization, and circular genome plots. Also the public database section of EDGAR was largely updated and now offers access to 24,317 genomes in 749 free-to-use projects. In summary, EDGAR 3.0 provides a new, scalable infrastructure for comprehensive microbial comparative gene content analysis. The web server is accessible at http://edgar3.computational.bio.