bluuebunny/crossref_metadata_2025 huggingface dataset:
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data
Authors: Rodríguez-Pérez Héctor , Ciuffreda Laura , Flores Carlos
Published: October 2020

NanoCLUST is an analysis pipeline for the classification of amplicon-based full-length 16S rRNA nanopore reads. It is characterized by an unsupervised read clustering step, based on Uniform Manifold Approximation and Projection (UMAP), followed by the construction of a polished read and subsequent Blast classification. Here, we demonstrate that NanoCLUST performs better than other state-of-the-art software in the characterization of two commercial mock communities, enabling accurate bacterial identification and abundance profile estimation at species-level resolution.

Availability and implementation

Source code, test data and documentation of NanoCLUST are freely available at https://github.com/genomicsITER/NanoCLUST under MIT License.

Supplementary information

Supplementary data are available at Bioinformatics online.
Only males care about their environment: sex-biased dispersal in the asp viper (Vipera aspis)
Authors: Zwahlen Valerie , Nanni-Geser Silvia , Kaiser Laura , Golay Joaquim , Dubey Sylvain , Ursenbacher Sylvain
Published: October 2020

Sex-biased dispersal is common among vertebrates and numerous studies have documented a tendency towards male-biased dispersal in mammals and female-biased dispersal in birds. A few studies have demonstrated that male-biased dispersal seems to be prevalent in reptiles. However, most of these studies considered only a single study site without taking into account possible local variability. We investigated sex-biased dispersal in Vipera aspis in four study sites in Switzerland using microsatellite markers and we predicted a higher dispersal in males than females. In two study sites, females were more spatially autocorrelated and showed a stronger isolation by distance compared with males, which suggests male-biased dispersal. In the other two study sites, the absence of sex-biased dispersal could have been the result of habitat fragmentation. Surprisingly, the dispersal ability of females was similar in the four sites, regardless of habitat fragmentation. This finding suggests a limited impact of habitat on female dispersal and the opposite for male dispersal. Our study demonstrates the importance of inferring sex-biased dispersal in different habitats, because local barriers can affect the outcome of such studies. Hence, general conclusions about patterns of sex-biased dispersal should be drawn with caution when studies are conducted at a single study site.
Comment on: Low Health Literacy Exists in the Inflammatory Bowel Disease Population and Is Disproportionately Prevalent in Older African Americans
Authors: Languido Lauren S , Salwen-Deremer Jessica K
Published: October 2020

Lay Summary

Dos Santos Margues and colleagues found that African Americans with IBD may have more difficulty with understanding and making decisions about health information. We discuss their work and give suggestions on how to create a supportive clinic environment.
The physiological and pathological functions of VEGFR3 in cardiac and lymphatic development and related diseases
Authors: Monaghan Richard M , Page Donna J , Ostergaard Pia , Keavney Bernard D
Published: October 2020

Vascular endothelial growth factor receptors (VEGFRs) are part of the evolutionarily conserved VEGF signalling pathways that regulate the development and maintenance of the body’s cardiovascular and lymphovascular systems. VEGFR3, encoded by the FLT4 gene, has an indispensable and well-characterized function in development and establishment of the lymphatic system. Autosomal dominant VEGFR3 mutations, that prevent the receptor functioning as a homodimer, cause one of the major forms of hereditary primary lymphoedema; Milroy disease. Recently, we and others have shown that FLT4 variants, distinct to those observed in Milroy disease cases, predispose individuals to Tetralogy of Fallot, the most common cyanotic congenital heart disease, demonstrating a novel function for VEGFR3 in early cardiac development. Here, we examine the familiar and emerging roles of VEGFR3 in the development of both lymphovascular and cardiovascular systems, respectively, compare how distinct genetic variants in FLT4 lead to two disparate human conditions, and highlight the research still required to fully understand this multifaceted receptor.
Quantitative fluorescence-guided perfusion assessment of the gastric conduit to predict anastomotic complications after esophagectomy
Authors: Slooter M D , de Bruin D M , Eshuis W J , Veelo D P , van Dieren S , Gisbertz S S , van Berge Henegouwen M I
Published: October 2020

Background: Fluorescence angiography (FA) assesses anastomotic perfusion during esophagectomy with gastric conduit reconstruction, but its interpretation is subjective. This study evaluated time to fluorescent enhancement in the gastric conduit, with the aim to determine a threshold to predict postoperative anastomotic complications.

Methods: In a prospective cohort study, all consecutive patients undergoing esophagectomy with gastric conduit reconstruction from July 2018 to October 2019 were included. FA was performed before anastomotic reconstruction following injection of indocyanine green (ICG). During FA, the following time points were recorded: ICG injection, first fluorescent enhancement in the lung, at the base of the gastric conduit, at the planned anastomotic site, and at ICG watershed or in the tip of the gastric conduit. Anastomotic complications including anastomotic leakage and clinically relevant strictures were documented.

Results: Eighty-four patients were included, the majority (67 out of 84, 80%) of which underwent an Ivor Lewis procedure. After a median follow-up of 297 days, anastomotic leakage was observed in 12 out of 84 (14.3%) and anastomotic stricture in 12 out of 82 (14.6%). Time between ICG injection and enhancement in the tip was predictive for anastomotic leakage (P = 0.174, area under the curve = 0.731), and a cut-off value of 98 seconds was derived (specificity: 98%). All times to enhancement at the planned anastomotic site and ICG watershed were significantly predictive for the occurrence of a stricture, however area under the curves were <0.7.

Conclusions: The identified fluorescent threshold can be used for intraoperative decision making or to identify potentially high-risk patients for anastomotic leakage after esophagectomy with gastric conduit reconstruction.
Effect of surgical start time on short- and long-term outcomes after minimally invasive esophagectomy: a propensity-score matching analysis
Authors: Bao Tao , Zhao Xiao-Long , Li Kun-Kun , Wang Ying-Jian , Guo Wei
Published: October 2020

There is growing focus on the relationship between surgical start time and postoperative outcomes. However, the extent to which the operation start time affects the surgical and oncological outcomes of patients undergoing esophagectomy has not previously been studied. The purpose of this retrospective study was to investigate the potential effect of surgical start time on the short- and long-term outcomes for patients who underwent thoracoscopic–laparoscopic McKeown esophagectomy. From September 2009 to June 2019, a total of 700 consecutive patients suffering from esophageal cancer underwent thoracoscopic–laparoscopic McKeown esophagectomy in the Department of Thoracic Surgery at Daping Hospital. Among these patients, 166 esophagectomies were performed on the same day and were classified as the first- or second-start group. Patients in the first-start group were more likely to be older than those in the second-start group: (64.73 vs. 61.28, P = 0.002). In addition, patients with diabetes mellitus were more likely to be first-start cases (8.4 vs. 1.2%). After propensity score matching (52 matched patients in first-start cases and 52 matched patients in second-start cases), these findings were no longer statistically significant. There was no difference in the incidence rate of peri- or postoperative adverse events between the first- and second-start groups. The disease-specific survival rates and disease-free survival rates were comparable between the two groups (P = 0.236 and 0.292, respectively). On the basis of the present results, a later start time does not negatively affect the short- or long-term outcomes of patients undergoing minimally invasive McKeown esophagectomy.
Protect right: right ventricular failure prevention strategy for left ventricular assist device implantation
Authors: Kawabori Masashi , Nordan Taylor , Kapur Navin K , Couper Gregory S
Published: October 2020

Right ventricular failure imparts poor prognosis following left ventricular assist device implantation. We present a strategy for the primary prevention of right ventricular failure after left ventricular assist device implantation in a high-risk patient.
IRF6,MSX1,TGFA, dental anomalies, and skeletal malocclusion
Authors: Fernandez Clarissa C A , Pereira Christiane V C A , Ferreira Fernanda F C F , Maciel José V B , Modesto Adriana , Costa Marcelo C , Vieira Alexandre R
Published: October 2020

Objective

Verify the presence of association between four variables—transforming growth factor α (TGFA; C/T rs1523305), interferon regulatory factor 6 (IRF6; A/C rs2013162), muscle segment homeobox 1 (MSX1; A/G rs12532), and dental anomalies—with skeletal malocclusion by comparing these four variables with Angle Classes I, II, and III, and normal, hyperdivergent, and hypodivergent growth patterns.

Methods

A total of 505 orthodontic records of patients older than 8 years were evaluated. The sample consisted of 285 (56.4 per cent) females, 220 (43.6 per cent) males, 304 (60.2 per cent) Whites (the rest were mixed Blacks with Whites), with a mean age of 20.28 (±10.35) years (ranging from 8 to 25 years). Eight cephalometric points, which served as the anatomical framework for obtaining angles and cephalometric measurements, were used for skeletal characterization using the Dolphin Software. Samples of saliva were collected and the DNA was extracted, diluted and quantified. Markers in TGFA, IRF6, and MSX1 were used and genotypes were obtained using TaqMan chemistry. Odds ratio (OR) and 95 per cent confidence interval (CI) calculations, chi-square, Fisher’s Exact, Mann–Whitney, and correlation coefficient tests (significance level: 95 per cent) were performed. Bonferroni correction was applied and an alpha of 0.0006 was considered statistically significant.

Results

There was no statistically significant associations between markers in TGFA or IRF6 with skeletal malocclusions. Tooth agenesis was associated with facial convexity (P < 0.001). MSX1 was associated with Class II skeletal malocclusion (P = 0.0001, OR = 0.6, CI = 0.46–0.78).

Conclusion

Individuals with tooth agenesis were more likely to have a convex face. MSX1 was associated with Class II skeletal malocclusion.
Public support for European cooperation in the procurement, stockpiling and distribution of medicines
Authors: Beetsma Roel , Burgoon Brian , Nicoli Francesco , de Ruijter Anniek , Vandenbroucke Frank
Published: October 2020

Background

The COVID-19 outbreak has heightened ongoing political debate about the international joint procurement of medicines and medical countermeasures. The European Union (EU) has developed what remains largely contractual and decentralized international procurement cooperation. The corona crisis has broadened and deepened public debate on such cooperation, in particular on the scope of cooperation, solidarity in the allocation of such cooperation, and delegation of cooperative decision-making. Crucial to political debate about these issues are public attitudes that constrain and undergird international cooperation.

Methods

Our survey includes a randomized survey experiment (conjoint analysis) on a representative sample in five European countries in March 2020, informed by legal and policy debate on medical cooperation. Respondents choose and rate policy packages containing randomized mixes of policy attributes with respect to the scope of medicines covered, the solidarity in conferring priority access and the level of delegation.

Results

In all country populations surveyed, the experiment reveals considerable popular support for European cooperation. Significant majorities preferred cooperation packages with greater rather than less scope of medicines regulated; with priority given to most in-need countries; and with delegation to EU-level rather than national expertise.

Conclusion

Joint procurement raises delicate questions with regard to its scope, the inclusion of cross-border solidarity and the delegation of decision-making, that explain reluctance toward joint procurement among political decision-makers. This research shows that there is considerable public support across different countries in favor of centralization, i.e. a large scope and solidarity in the allocation and delegation of decision-making.
Tripartite relationship between gut microbiota, intestinal mucus and dietary fibers: towards preventive strategies against enteric infections
Authors: Sauvaitre Thomas , Etienne-Mesmin Lucie , Sivignon Adeline , Mosoni Pascale , Courtin Christophe M , Van de Wiele Tom , Blanquet-Diot Stéphanie
Published: October 2020

The human gut is inhabited by a large variety of microorganims involved in many physiological processes and collectively referred as to gut microbiota. Disrupted microbiome has been associated with negative health outcomes and especially could promote the onset of enteric infections. To sustain their growth and persistence within the human digestive tract, gut microbes and enteric pathogens rely on two main polysaccharide compartments, namely dietary fibers and mucus carbohydrates. Several evidences suggest that the three-way relationship between gut microbiota, dietary fibers and mucus layer could unravel the capacity of enteric pathogens to colonise the human digestive tract and ultimately lead to infection. The review starts by shedding light on similarities and differences between dietary fibers and mucus carbohydrates structures and functions. Next, we provide an overview of the interactions of these two components with the third partner, namely, the gut microbiota, under health and disease situations. The review will then provide insights into the relevance of using dietary fibers interventions to prevent enteric infections with a focus on gut microbial imbalance and impaired-mucus integrity. Facing the numerous challenges in studying microbiota–pathogen–dietary fiber-mucus interactions, we lastly describe the characteristics and potentialities of currently available in vitro models of the human gut.
On the use of adjoints in the inversion of observed quasi-static deformation
Authors: Vasco D W , Mali Gwyn
Published: October 2020

An adjoint-based conjugate gradient algorithm provides an efficient means for imaging sources of deformation within the Earth, such as volume stresses associated with fluid flow in aquifers and reservoirs. For time intervals over which the overburden deforms elastically, one can calculate the gradient elements for a single model update using just two numerical simulations. The first is a forward run that is used to compute the residuals associated with the given iteration. The second simulation is to evaluate the application of the adjoint operator to the residuals. In this adjoint calculation, the residual displacements are applied as sources at the measurement locations, driving the deformation in the simulation. The volume stress on the source grid blocks, in response to the residual displacements, provide the gradient components. We apply this technique to satellite-based interferometric synthetic aperture radar (InSAR) line-of-sight displacements that were observed over an oil reservoir in California’s Central Valley. We find that the adjoint-based gradient estimates, requiring 18 CPU seconds, agree with conventional numerical calculations that take over 3700 CPU seconds to compute. Conjugate gradient algorithms utilizing the conventional approach and adjoint-based gradient computations give roughly the same reductions in misfit and similar final estimates of reservoir volume change.
Mucosal glycan degradation of the host by the gut microbiota
Authors: Bell Andrew , Juge Nathalie
Published: October 2020

The gut microbiota plays a major role in human health and an alteration in gut microbiota structure and function has been implicated in several diseases. In the colon, mucus covering the epithelium is critical to maintain a homeostatic relationship with the gut microbiota by harboring a microbial community at safe distance from the epithelium surface. The mucin glycans composing the mucus layer provide binding sites and a sustainable source of nutrients to the bacteria inhabiting the mucus niche. Access to these glycan chains requires a complement of glycoside hydrolases (GHs) produced by bacteria across the phyla constituting the human gut microbiota. Due to the increased recognition of the role of mucus-associated microbes in human health, how commensal bacteria breakdown and utilize host mucin glycans has become of increased interest and is reviewed here. This short review provides an overview of the strategies evolved by gut commensal bacteria to access this rich source of the nutrient with a focus on the GHs involved in mucin degradation.
Lessons From Bacille Calmette-Guérin for SARS-CoV-2 Vaccine Candidates
Authors: Behr Marcel A , Divangahi Maziar , Schurr Erwin
Published: October 2020

Developers of severe acute respiratory syndrome coronavirus 2 vaccines should consider some of the lessons from a “new” vaccine introduced in 1921, namely bacille Calmette-Guérin.
Development and Validation of a Method for the Detection and Quantification of Antidepressants and Antipsychotics in Bone Samples by GC–MS
Authors: Laudani Antonino , Sangregorio Deborah , Zuccarello Pietro , Licciardello Teresa , Grasso Stephanie , Romano Guido , Barbera Nunziata
Published: October 2020

Bone marrow is the tissue contained inside the bones and can be considered one of the potential alternative tissues in forensic toxicology. This matrix could be particularly useful in those cases where the routine sample is not available due to an advanced state of decomposition or skeletonization of the corpse. The aim of this study was to develop, validate and apply an analytical method of extraction and analysis of different antidepressants and antipsychotics, commonly used in therapy, from spiked pig ribs. Pig ribs, each of 5 g and 5 cm long, were spiked at three concentration levels (100, 200 and 500 ng/g). For each concentration, 10 pig ribs were prepared. The method involves the leaching by ethanol at different pHs of nine drugs from the inside of ribs, in particular from the bone marrow, without the fragmentation of bone tissue. Following a liquid–liquid purification and extraction, analysis was performed by gas chromatography coupled with mass spectrometry in selected ion monitoring mode. For method validation was assessed linearity, sensitivity, precision and accuracy, matrix interferences and, finally, carryover. Analytical method performance was acceptable respect to acceptance criteria for validation. No matrix interferences were detected; for this reason, it is possible to affirm that this method has a good selectivity. Moreover, the method was not affected by carryover. Considering that the study conducted on pig ribs has given encouraging results, it can be assumed that this method can be used in forensic toxicological protocols (human autopsy cases) as alternative to classic procedures.
Appropriate Extent of Lymphadenectomy in Segmentectomy: A Multicenter Study
Authors: Handa Yoshinori , Tsutani Yasuhiro , Mimae Takahiro , Miyata Yoshihiro , Ito Hiroyuki , Nakayama Haruhiko , Ikeda Norihiko , Okada Morihito
Published: October 2020

Background

The significance of lymphadenectomy is yet to be fully examined in segmentectomy. We compared the oncological outcomes of mediastinal lymph node dissection (LND) and hilar LND for lung cancer treated with segmentectomy via a multicenter database using propensity score-matched analysis.

Methods

We reviewed 357 clinical stage IA radiologically solid-dominant lung cancer patients who underwent segmentectomy with lymphadenectomy. The extent of LND was classified into systematic/lobe-specific mediastinal LND and hilar LND only groups. Postoperative results after segmentectomy with mediastinal LND (n = 179) and hilar LND (n = 178) were analyzed for all patients and their propensity score-matched pairs.

Results

Cancer-specific survival (CSS) and recurrence-free interval (RFI) rates for the mediastinal LND group were determined to be not significantly different compared with the hilar LND group in all non-adjusted cohorts. In the propensity score-matched cohort (129 pairs), mediastinal LND harvested more lymph nodes compared with hilar LND, and both groups had significantly different pathological stages (P = 0.015). Adjuvant chemotherapy was performed in 10 (7.8%) patients in the mediastinal LND group and 4 (3.1%) in the hilar LND group. The mediastinal LND group tended to have better prognosis than the hilar LND group (5-year CSS rates, 97.4% vs 93.2%; 5-year RFI rates, 93.5% vs 88.5%).

Conclusions

Mediastinal LND was found to provide more appropriate pathological staging compared with hilar LND in patients with segmentectomy by harvesting more lymph nodes. In addition, mediastinal LND might lead to better oncological outcome than hilar LND in segmentectomy.
A Comparison of Tick Collection Materials and Methods in Southeastern Virginia
Authors: Espada Christina , Cummins Hannah , Gonzales Jon A , Notto Leo , Gaff Holly D
Published: October 2020

In field studies of tick ecology, observed patterns may be biased by sampling methods. Results can vary by species, life stage, and habitat, and understanding these biases will improve comparisons of data across studies as well as assessment of human disease risk. A direct comparison of flagging versus dragging was conducted in southeastern Virginia. Transects were surveyed over a 6-wk period to identify differences in species and life stage collected, as well as differences between corduroy and denim material and inspection method for drags. Flagging collected more Ixodes affinis Neumann (Acari: Ixodidae) adults and Amblyomma americanum L. (Acari: Ixodidae) adults than dragging. Ground inspection was more efficient than tree inspection for collection of I. affinis adults, with no significant difference in inspection method for any other species or life stage. Corduroy was found to be more effective than denim in collecting nymphal A. americanum, although this may be an artifact of three large samples for corduroy collection of these ticks. There was no significant difference in Ixodes scapularis Say (Acari: Ixodidae) collection in any comparison. Dragging, tree inspection, and denim were not found to be more efficient in any scenario. This is the first comparison of flagging and dragging conducted in the southeastern United States. The community composition of ticks in this region greatly differs from regions where studies of these commonly used sampling techniques have been conducted. As the distributions of ticks continue to change over time, it will be important to evaluate best practices annually.
BES1/BZR1 Homolog 3 cooperates with E3 ligase AtRZF1 to regulate osmotic stress and brassinosteroid responses in Arabidopsis
Authors: Van Nguyen Tinh , Park Cho-Rong , Lee Kyeong-Hwan , Lee Sungbeom , Kim Cheol Soo
Published: October 2020

Proline (Pro) metabolism plays important roles in protein synthesis, redox balance, and abiotic stress response. However, it is not known if cross-talk occurs between proline and brassinosteroid (BR) signaling pathways. Here, an Arabidopsis intergenic enhancer double mutant, namely proline content alterative 41 (pca41), was generated by inserting a T-DNA tag in the Arabidopsis thaliana ring zinc finger 1 (atrzf1 ) mutant background. pca41 had a T-DNA inserted at the site of the gene encoding BES1/BZR1 Homolog 3 (BEH3). pca41 has a drought-insensitive phenotype that is stronger than atrzf1 under osmotic stress, including high Pro accumulation and decreased amounts of reactive oxygen species. Analysis of physiological, genetic, and molecular networks revealed that negative regulation of BEH3 during abiotic stress was linked to the BR signaling pathway. Our data also suggest that AtRZF1, an E3 ubiquitin ligase, might control osmotic stress, abscisic acid, and BR responses in a BEH3-dependent manner. Under darkness, pca41 displays a long hypocotyl phenotype, which is similar to atrzf1 and beh3, suggesting that BEH3 acts in the same pathway as AtRZF1. Overexpression of BEH3 results in an osmotic stress-sensitive phenotype, which is reversed by exogenous BR application. Taken together, our results indicate that AtRZF1 and BEH3 may play important roles in the osmotic stress response via ubiquitination and BR signaling.
Hemispherical variance anomaly and reionization optical depth
Authors: O’Dwyer Márcio , Copi Craig J , Nagy Johanna M , Netterfield C Barth , Ruhl John , Starkman Glenn D
Published: October 2020

Cosmic microwave background (CMB) full-sky temperature data show a hemispherical asymmetry in power nearly aligned with the Ecliptic, with the Northern hemisphere displaying an anomalously low variance, while the Southern hemisphere appears consistent with expectations from the best-fitting theory, Lambda Cold Dark Matter (ΛCDM). The low signal-to-noise ratio in current polarization data prevents a similar comparison. Polarization realizations constrained by temperature data show that in ΛCDM the lack of variance is not expected to be present in polarization data. Therefore, a natural way of testing whether the temperature result is a fluke is to measure the variance of CMB polarization components. In anticipation of future CMB experiments that will allow for high-precision large-scale polarization measurements, we study how the variance of polarization depends on ΛCDM-parameter uncertainties by forecasting polarization maps with Planck’s Markov chain Monte Carlo chains. We show that polarization variance is sensitive to present uncertainties in cosmological parameters, mainly due to current poor constraints on the reionization optical depth τ, which drives variance at low multipoles. We demonstrate how the improvement in the τ measurement seen between Planck’s two latest data releases results in a tighter constraint on polarization variance expectations. Finally, we consider even smaller uncertainties on τ and how more precise measurements of τ can drive the expectation for polarization variance in a hemisphere close to that of the cosmic-variance-limited distribution.
Gas-phase formation of acetaldehyde: review and new theoretical computations
Authors: Vazart Fanny , Ceccarelli Cecilia , Balucani Nadia , Bianchi Eleonora , Skouteris Dimitrios
Published: October 2020

Among all the interstellar complex organic molecules, acetaldehyde is one of the most widely detected species. The question of its formation route(s) is, therefore, of a major interest regarding astrochemical models. In this paper, we provide an extensive review of the gas-phase formation paths that were, or are, reported in the literature and the major astrochemical data bases. Four different gas-phase formation routes stand out : (1) CH3OCH3  + H+/CH3CHOH+  + e−, (2) C2H5  + O(3P), (3) CH3OH  + CH, and (4) CH3CH2OH  + OH/CH3CHOH  + O(3P). Paths (2) and (3) were not studied neither via laboratory nor theoretical works in the low temperature and density regime valid for the interstellar medium (ISM). Thus, we carried out new accurate quantum chemistry computations. A theoretical kinetics study at low temperatures (7 ÷ 300 K), adopting the Rice–Ramsperger–Kassel–Marcus scheme, was also performed. We confirm that reaction (2) is efficient in forming acetaldehyde in the 7–300 temperature range (α  = 1.21 × 10−10 cm3 s−1 and β = 0.16). On the contrary, our new computations disprove the formation of acetaldehyde through reaction (3) (α = 1.84 ÷ 0.67 × 10−13 cm3 s−1 and β = −0.07 ÷ −0.95). Path (1) was showed to be inefficient too by recent computations, while path (4) was formerly considered for glycolaldehyde formation, having acetaldehyde as a byproduct. In conclusions, of the four above paths, only two, the (2) and (4), are potentially efficient gas-phase reaction routes for the formation of acetaldehyde and we encourage astrochemical modellers to consider only them. Comparison with astronomical observations suggests that path (4) may actually play the major role.
A pair of Jovian Trojans at the L4 Lagrange point
Authors: Holt Timothy R , Vokrouhlický David , Nesvorný David , Brož Miroslav , Horner Jonathan
Published: October 2020

Asteroid pairs, two objects that are not gravitationally bound to one another, but share a common origin, have been discovered in the Main belt and Hungaria populations. Such pairs are of major interest, as the study of their evolution under a variety of dynamical influences can indicate the time since the pair was created. To date, no asteroid pairs have been found in the Jovian Trojans, despite the presence of several binaries and collisional families in the population. The search for pairs in the Jovian Trojan population is of particular interest, given the importance of the Trojans as tracers of planetary migration during the Solar system’s youth. Here we report a discovery of the first pair, (258656) 2002 ES76 and 2013 CC41, in the Jovian Trojans. The two objects are approximately the same size and are located very close to the L4 Lagrange point. Using numerical integrations, we find that the pair is at least 360 Myr old, though its age could be as high as several Gyrs. The existence of the (258656) 2002 ES76–2013 CC41 pair implies there could be many such pairs scattered through the Trojan population. Our preferred formation mechanism for the newly discovered pair is through the dissociation of an ancient binary system, triggered by a sub-catastrophic impact, but we can not rule out rotation fission of a single object driven by YORP torques. A by-product of our work is an up-to-date catalogue of Jovian Trojan proper elements, which we have made available for further studies.
On the vanishing orbital X-ray variability of the eclipsing binary millisecond pulsar 47 Tuc W
Authors: Hebbar P R , Heinke C O , Kandel D , Romani R W , Freire P C C
Published: October 2020

Redback millisecond pulsars (MSPs) typically show pronounced orbital variability in their X-ray emission due to our changing view of the intrabinary shock (IBS) between the pulsar wind and stellar wind from the companion. Some redbacks (‘transitional’ MSPs) have shown dramatic changes in their multiwavelength properties, indicating a transition from a radio pulsar state to an accretion-powered state. The redback MSP 47 Tuc W showed clear X-ray orbital variability in the Chandra ACIS-S observations in 2002, which were not detectable in the longer Chandra HRC-S observations in 2005–06, suggesting that it might have undergone a state transition. However, the Chandra observations of 47 Tuc in 2014–15 show similar X-ray orbital variability as in 2002. We explain the different X-ray light curves from these epochs in terms of two components of the X-ray spectrum (soft X-rays from the pulsar versus harder X-rays from the IBS), and different sensitivities of the X-ray instruments observing in each epoch. However, when we use our best-fitting spectra with HRC response files to model the HRC light curve, we expect a more significant and shorter dip than that observed in the 2005–06 Chandra data. This suggests an intrinsic change in the IBS of the system. We use the icarus stellar modelling software, including calculations of heating by an IBS, to model the X-ray, optical, and UV light curves of 47 Tuc W. Our best-fitting parameters point towards a high-inclination system ($i \sim 60 \deg$), which is primarily heated by the pulsar radiation, with an IBS dominated by the companion wind momentum.
The relative orientation between the magnetic field and gas density structures in non-gravitating turbulent media
Authors: Körtgen Bastian , Soler Juan D
Published: October 2020

Magnetic fields are a dynamically important agent for regulating structure formation in the interstellar medium. The study of the relative orientation between the local magnetic field and gas (column-) density gradient has become a powerful tool to analyse the magnetic field’s impact on the dense gas formation in the Galaxy. In this study, we perform numerical simulations of a non-gravitating, isothermal gas, where the turbulence is driven either solenoidally or compressively. We find that only simulations with an initially strong magnetic field (plasma-β < 1) show a change in the preferential orientation between the magnetic field and isodensity contours, from mostly parallel at low densities to mostly perpendicular at higher densities. Hence, compressive turbulence alone is not capable of inducing the transition observed towards nearby molecular clouds. At the same high initial magnetization, we find that solenoidal modes produce a sharper transition in the relative orientation with increasing density than compressive modes. We further study the time evolution of the relative orientation and find that it remains unchanged by the turbulent forcing after one dynamical time-scale.
Mitogenomes Reveal Alternative Initiation Codons and Lineage-Specific Gene Order Conservation in Echinoderms
Authors: Quek Zheng Bin Randolph , Chang Jia Jin Marc , Ip Yin Cheong Aden , Chan Yong Kit Samuel , Huang Danwei
Published: October 2020

The mitochondrial genetic code is much more varied than the standard genetic code. The invertebrate mitochondrial code, for instance, comprises six initiation codons, including five alternative start codons. However, only two initiation codons are known in the echinoderm and flatworm mitochondrial code, the canonical ATG and alternative GTG. Here, we analyzed 23 Asteroidea mitogenomes, including ten newly sequenced species and unambiguously identified at least two other start codons, ATT and ATC, both of which also initiate translation of mitochondrial genes in other invertebrates. These findings underscore the diversity of the genetic code and expand upon the suite of initiation codons among echinoderms to avoid erroneous annotations. Our analyses have also uncovered the remarkable conservation of gene order among asteroids, echinoids, and holothuroids, with only an interchange between two gene positions in asteroids over ∼500 Ma of echinoderm evolution.
REDIportal: millions of novel A-to-I RNA editing events from thousands of RNAseq experiments
Authors: Mansi Luigi , Tangaro Marco Antonio , Lo Giudice Claudio , Flati Tiziano , Kopel Eli , Schaffer Amos Avraham , Castrignanò Tiziana , Chillemi Giovanni , Pesole Graziano , Picardi Ernesto
Published: October 2020

RNA editing is a relevant epitranscriptome phenomenon able to increase the transcriptome and proteome diversity of eukaryotic organisms. ADAR mediated RNA editing is widespread in humans in which millions of A-to-I changes modify thousands of primary transcripts. RNA editing has pivotal roles in the regulation of gene expression or modulation of the innate immune response or functioning of several neurotransmitter receptors. Massive transcriptome sequencing has fostered the research in this field. Nonetheless, different aspects of the RNA editing biology are still unknown and need to be elucidated. To support the study of A-to-I RNA editing we have updated our REDIportal catalogue raising its content to about 16 millions of events detected in 9642 human RNAseq samples from the GTEx project by using a dedicated pipeline based on the HPC version of the REDItools software. REDIportal now allows searches at sample level, provides overviews of RNA editing profiles per each RNAseq experiment, implements a Gene View module to look at individual events in their genic context and hosts the CLAIRE database. Starting from this novel version, REDIportal will start collecting non-human RNA editing changes for comparative genomics investigations. The database is freely available at http://srv00.recas.ba.infn.it/atlas/index.html.
DrugSpaceX: a large screenable and synthetically tractable database extending drug space
Authors: Yang Tianbiao , Li Zhaojun , Chen Yingjia , Feng Dan , Wang Guangchao , Fu Zunyun , Ding Xiaoyu , Tan Xiaoqin , Zhao Jihui , Luo Xiaomin , Chen Kaixian , Jiang Hualiang , Zheng Mingyue
Published: October 2020

One of the most prominent topics in drug discovery is efficient exploration of the vast drug-like chemical space to find synthesizable and novel chemical structures with desired biological properties. To address this challenge, we created the DrugSpaceX (https://drugspacex.simm.ac.cn/) database based on expert-defined transformations of approved drug molecules. The current version of DrugSpaceX contains >100 million transformed chemical products for virtual screening, with outstanding characteristics in terms of structural novelty, diversity and large three-dimensional chemical space coverage. To illustrate its practical application in drug discovery, we used a case study of discoidin domain receptor 1 (DDR1), a kinase target implicated in fibrosis and other diseases, to show DrugSpaceX performing a quick search of initial hit compounds. Additionally, for ligand identification and optimization purposes, DrugSpaceX also provides several subsets for download, including a 10% diversity subset, an extended drug-like subset, a drug-like subset, a lead-like subset, and a fragment-like subset. In addition to chemical properties and transformation instructions, DrugSpaceX can locate the position of transformation, which will enable medicinal chemists to easily integrate strategy planning and protection design.
Missing the forest because of the trees: slower alternations during binocular rivalry are associated with lower levels of visual detail during ongoing thought
Authors: Ho Nerissa Siu Ping , Baker Daniel , Karapanagiotidis Theodoros , Seli Paul , Wang Hao Ting , Leech Robert , Bernhardt Boris , Margulies Daniel , Jefferies Elizabeth , Smallwood Jonathan
Published: October 2020

Conscious awareness of the world fluctuates, either through variation in how vividly we perceive the environment, or when our attentional focus shifts away from information in the external environment towards information that we generate via imagination. Our study combined individual differences in experience sampling, psychophysical reports of perception and neuroimaging descriptions of structural connectivity to better understand these changes in conscious awareness. In particular, we examined (i) whether aspects of ongoing thought—indexed via multi-dimensional experience sampling during a sustained attention task—are associated with the white matter fibre organization of the cortex as reflected by their relative degree of anisotropic diffusion and (ii) whether these neurocognitive descriptions of ongoing experience are related to a more constrained measure of visual consciousness through analysis of bistable perception during binocular rivalry. Individuals with greater fractional anisotropy in right hemisphere white matter regions involving the inferior fronto-occipital fasciculus, the superior longitudinal fasciculus and the cortico-spinal tract, described their ongoing thoughts as lacking external details. Subsequent analysis indicated that the combination of low fractional anisotropy in these right hemisphere regions, with reports of thoughts with high levels of external details, was associated with the shortest periods of dominance during binocular rivalry. Since variation in binocular rivalry reflects differences between bottom-up and top-down influences on vision, our study suggests that reports of ongoing thoughts with vivid external details may occur when conscious precedence is given to bottom-up representation of perceptual information.
Coherency and Constructions for Monoids
Authors: Dandan Yang , Gould Victoria , Hartmann Miklós , Ruškuc Nik , Zenab Rida-E
Published: October 2020

A monoid S is right coherent if every finitely generated subact of every finitely presented right S-act is finitely presented. This is a finiteness condition, and we investigate whether or not it is preserved under some standard algebraic and semigroup theoretic constructions: subsemigroups, homomorphic images, direct products, Rees matrix semigroups, including Brandt semigroups, and Bruck–Reilly extensions. We also investigate the relationship with the property of being weakly right noetherian, which requires all right ideals of S to be finitely generated.
Flat ring epimorphisms and universal localizations of commutative rings
Authors: Angeleri Hügel Lidia , Marks Frederik , Št’ovíček Jan , Takahashi Ryo , Vitória Jorge
Published: October 2020

We study different types of localizations of a commutative noetherian ring. More precisely, we provide criteria to decide: (a) if a given flat ring epimorphism is a universal localization in the sense of Cohn and Schofield; and (b) when such universal localizations are classical rings of fractions. In order to find such criteria, we use the theory of support and we analyse the specialization closed subset associated to a flat ring epimorphism. In case the underlying ring is locally factorial or of Krull dimension one, we show that all flat ring epimorphisms are universal localizations. Moreover, it turns out that an answer to the question of when universal localizations are classical depends on the structure of the Picard group. We furthermore discuss the case of normal rings, for which the divisor class group plays an essential role to decide if a given flat ring epimorphism is a universal localization. Finally, we explore several (counter)examples which highlight the necessity of our assumptions.
Counting Algebraic Points in Expansions of O-Minimal Structures by a Dense Set
Authors: Eleftheriou Pantelis E
Published: October 2020

The Pila–Wilkie theorem states that if a set $X\subseteq \mathbb{R}^n$ is definable in an o-minimal structure $\mathcal{R}$ and contains ‘many’ rational points, then it contains an infinite semialgebraic set. In this paper, we extend this theorem to an expansion $\widetilde{\mathcal{R}}=\langle {\mathcal{R}}, P\rangle$ of ${\mathcal{R}}$ by a dense set P, which is either an elementary substructure of ${\mathcal{R}}$, or it is $\mathrm{dcl}$-independent, as follows. If X is definable in $\widetilde{\mathcal{R}}$ and contains many rational points, then it is dense in an infinite semialgebraic set. Moreover, it contains an infinite set which is ${\emptyset}$-definable in $\langle \overline{\mathbb{R}}, P\rangle$, where $\overline{\mathbb{R}}$ is the real field.

Along the way we introduce the notion of the ‘algebraic trace part’ $X^{{\, alg}}_t$ of any set $X\subseteq \mathbb{R}^n$, and we show that if X is definable in an o-minimal structure, then $X^{{\, alg}}_t$ coincides with the usual algebraic part of X.
Biomass partitioning and photosynthesis in the quest for nitrogen- use efficiency for citrus tree species
Authors: Dovis Veronica L , Erismann Norma M , Machado Eduardo C , Quaggio Jose A , Boaretto Rodrigo M , Mattos Júnior Dirceu
Published: October 2020

Optimizing the use of nitrogen (N) for food production is a major challenge in agricultural systems. The transformation of N into crop production results from intricate pathways, depending on plants, as well as the environment and fertilization regimes, which affect the N-use efficiency (NUE) of plants. In this context, lemon trees [Citrus limon (L.) Burm. f.] attain maximum harvest index at lower leaf N concentrations compared with sweet orange trees [Citrus sinensis (L.) Osbeck], and the processes governing these plant responses are not well known. The aim of this study was to understand how the higher NUE in lemons trees is constructed based on growth and biomass partitioning evaluation, as well as photochemical and biochemical characteristics of photosynthesis. To attain this goal, we evaluated growth, photosynthesis and biochemical characteristics in lemon and sweet orange trees under two different N levels over 14 months. We hypothesized that higher NUE in lemon trees is affected by plant capacity to grow with economy on nutrient resources. Furthermore, lemon trees could be more efficient in CO2 assimilation in non-limiting environmental conditions. We found that higher NUE in lemon trees was explained in part by the ability of trees to invest greater biomass in leaves instead of roots, even though this species exhibited lower relative recovery efficiency of N from the substrate than the sweet orange. We also found that lemon trees had a higher relative growth rate than sweet oranges, despite the fact that net CO2 assimilation and dark respiration were similar between the two species. As a consequence, we suggested that lemons could exhibit a lower biomass construction cost than oranges. Because lemon presented lower N concentration than sweet orange trees, the former exhibited better photosynthetic N-use efficiency (PNUE: 55–120 mmol CO2 g N−1 day−1) compared with the sweet orange (PNUE: 31–68 mmol CO2 g N−1 day−1). Lemon trees also exhibited a higher relative rate of electron transport per unit of chlorophyll (ETR/chlor: 350–850) compared with orange trees (ETR/chlor: 300–550) at both low and at high N supply. These characteristics were likely associated with transport facilitation of CO2 to the catalytic sites of plants. In fact, improved growth of lemon trees results from an array of events explained mostly by increase in leaf area and associated low construction cost despite N supply.
A Clinician’s Guide to Functional Hypothalamic Amenorrhea
Authors: RUIZ-ZAMBRANA ALVARO , BERGA SARAH L.
Published: October 2020

Patients and clinicians alike want to know if stress causes infertility. Stress could impair with reproductive function by a variety of mechanisms, including compromise of ovarian function, spermatogenesis, fertilization, endometrial development, implantation, and placentation. Herein we focus on the pathogenesis and treatment of stress-induced anovulation, which is often termed functional hypothalamic amenorrhea (FHA), with the objective of summarizing the actual knowledge as a clinical guide. FHA is a reversible form of anovulation due to slowing of gonadotropin-releasing hormone pulse frequency that results in insufficient pituitary secretion of gonadotropins to support full folliculogenesis. Importantly, FHA heralds a constellation of neuroendocrine alterations with health concomitants. The activity of the hypothalamic-pituitary-adrenal axis is increased in women with FHA and this observation supports the notion that stress is the cause. The extent of reproductive suppression relates to individual endocrinological and physiological sensitivity to stressors, both metabolic and psychogenic, and chronicity.