bluuebunny/crossref_metadata_2025 huggingface dataset:
The Evolution of Chromosome Numbers: Mechanistic Models and Experimental Approaches
Authors: Mayrose Itay , Lysak Martin A
Published: October 2020

Chromosome numbers have been widely used to describe the most fundamental genomic attribute of an organism or a lineage. Although providing strong phylogenetic signal, chromosome numbers vary remarkably among eukaryotes at all levels of taxonomic resolution. Changes in chromosome numbers regularly serve as indication of major genomic events, most notably polyploidy and dysploidy. Here, we review recent advancements in our ability to make inferences regarding historical events that led to alterations in the number of chromosomes of a lineage. We first describe the mechanistic processes underlying changes in chromosome numbers, focusing on structural chromosomal rearrangements. Then, we focus on experimental procedures, encompassing comparative cytogenomics and genomics approaches, and on computational methodologies that are based on explicit models of chromosome-number evolution. Together, these tools offer valuable predictions regarding historical events that have changed chromosome numbers and genome structures, as well as their phylogenetic and temporal placements.
Variability in Hourly Activity Levels: Statistical Noise or Insight Into Older Adult Frailty?
Authors: Huisingh-Scheetz Megan , Wroblewski Kristen , Waite Linda , Huang Elbert S , Schumm L Philip , Hedeker Donald
Published: October 2020

Background

Frailty is associated with lower mean activity; however, hourly activity is highly variable among older individuals. We aimed to relate frailty to hourly activity variance beyond frailty’s association with mean activity.

Method

Using the 2010–2011 National Social Life, Health and Aging Project wrist accelerometry data (n = 647), we employed a mixed-effects location scale model to simultaneously determine whether an adapted phenotypic frailty scale (0–4) was associated with the log10-mean hourly counts per minute (cpm) and between-and within-subject hourly activity variability, adjusting for demographics, health characteristics, season, day-of-week, and time-of-day. We tested the significance of a Frailty × Time-of-day interaction and whether adjusting for sleep time altered relationships.

Results

Each additional frailty point was associated with a 7.6% (10–0.0343, β = −0.0343; 95% CI: −0.05, −0.02) lower mean hourly cpm in the morning, mid-day, and late afternoon but not evening. Each frailty point was also associated with a 24.5% (e0.219, β = 0.219; 95% CI: 0.09, 0.34) greater between-subject hourly activity variance across the day; a 7% (e0.07, β = 0.07; 95% CI: 0.01¸ 0.13), 6% (e0.06, β = 0.06; 95% CI: 0, 0.12), and 10% (e0.091, β = 0.091; 95% CI: 0.03, 0.15) greater within-subject hourly activity variance in the morning, mid-day, and late afternoon, respectively; and a 6% (e−0.06, β = −0.06; 95% CI: −0.12, −0.003) lower within-subject hourly activity variance in the evening. Adjusting for sleep time did not alter results.

Conclusions

Frail adults have more variable hourly activity levels than robust adults, a potential novel marker of vulnerability. These findings suggest a need for more precise activity assessment in older adults.
The Finite-interval Spectral Power method for detecting underground cavities using seismic ambient noise
Authors: Kristekova Miriam , Kristek Jozef , Moczo Peter , Labak Peter
Published: October 2020

Undetected natural and man-made cavities pose a serious geotechnical hazard to human safety. It is therefore important to develop methods for identifying and locating underground cavities in urban development and civil construction. Another important type of cavity is the one generated by an underground nuclear explosion. Identification and location of such cavities is an important proof in case of suspicion of violating the Comprehensive Nuclear-Test-Ban Treaty (CTBT), an international treaty banning nuclear weapon test explosion or any other nuclear explosion which is yet to come into force. We present a new method for detecting and locating a horizontal position of cavity which uses the Finite-interval Spectral Power of seismic ambient noise. The method makes it possible to use single-station measurements at a set of potentially irregularly distributed points in the area on the Earth's free surface over a suspected cavity. Because the method gives better results for undistorted segments of noise records, we also present a method of automatic identification of such segments. We tested our method using records of noise from a site near the Felsőpetény, Hungary, which were collected for the CTBT Organization during a field test in the framework of developing on-site inspection capabilities. The method is ready for further tests in different cavity conditions and applications.
SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity
Authors: Reske Jake J , Wilson Mike R , Holladay Jeanne , Wegener Marc , Adams Marie , Chandler Ronald L
Published: October 2020

Although ARID1A mutations are a hallmark feature, mutations in other SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin remodeling subunits are also observed in endometrial neoplasms. Here, we interrogated the roles of Brahma/SWI2-related gene 1 (BRG1, SMARCA4), the SWI/SNF catalytic subunit, in the endometrial epithelium. BRG1 loss affects more than one-third of all active genes and highly overlaps with the ARID1A gene regulatory network. Chromatin immunoprecipitation studies revealed widespread subunit-specific differences in transcriptional regulation, as BRG1 promoter interactions are associated with gene activation, while ARID1A binding is associated with gene repression. However, we identified a physiologically relevant subset of BRG1 and ARID1A co-regulated epithelial identity genes. Mice were genetically engineered to inactivate BRG1 specifically in the endometrial epithelium. Endometrial glands were observed embedded in uterine myometrium, indicating adenomyosis-like phenotypes. Molecular similarities were observed between BRG1 and ARID1A mutant endometrial cells in vivo, including loss of epithelial cell adhesion and junction genes. Collectively, these studies illustrate overlapping contributions of multiple SWI/SNF subunit mutations in the translocation of endometrium to distal sites, with loss of cell integrity being a common feature in SWI/SNF mutant endometrial epithelia.
Conditional deletion of SMN in cell culture identifies functional SMN alleles
Authors: Blatnik Anton J , McGovern Vicki L , Le Thanh T , Iyer Chitra C , Kaspar Brian K , Burghes Arthur H M
Published: October 2020

Spinal muscular atrophy (SMA) is caused by mutation or deletion of survival motor neuron 1 (SMN1) and retention of SMN2 leading to SMN protein deficiency. We developed an immortalized mouse embryonic fibroblast (iMEF) line in which full-length wild-type Smn (flwt-Smn) can be conditionally deleted using Cre recombinase. iMEFs lacking flwt-Smn are not viable. We tested the SMA patient SMN1 missense mutation alleles A2G, D44V, A111G, E134K and T274I in these cells to determine which human SMN (huSMN) mutant alleles can function in the absence of flwt-Smn. All missense mutant alleles failed to rescue survival in the conditionally deleted iMEFs. Thus, the function lost by these mutations is essential to cell survival. However, co-expression of two different huSMN missense mutants can rescue iMEF survival and small nuclear ribonucleoprotein (snRNP) assembly, demonstrating intragenic complementation of SMN alleles. In addition, we show that a Smn protein lacking exon 2B can rescue iMEF survival and snRNP assembly in the absence of flwt-Smn, indicating exon 2B is not required for the essential function of Smn. For the first time, using this novel cell line, we can assay the function of SMN alleles in the complete absence of flwt-Smn.
Variants in RABL2A causing male infertility and ciliopathy
Authors: Ding Xinbao , Fragoza Robert , Singh Priti , Zhang Shu , Yu Haiyuan , Schimenti John C
Published: October 2020

Approximately 7% of men worldwide suffer from infertility, with sperm abnormalities being the most common defect. Though genetic causes are thought to underlie a substantial fraction of idiopathic cases, the actual molecular bases are usually undetermined. Because the consequences of most genetic variants in populations are unknown, this complicates genetic diagnosis even after genome sequencing of patients. Some patients with ciliopathies, including primary ciliary dyskinesia and Bardet–Biedl syndrome, also suffer from infertility because cilia and sperm flagella share several characteristics. Here, we identified two deleterious alleles of RABL2A, a gene essential for normal function of cilia and flagella. Our in silico predictions and in vitro assays suggest that both alleles destabilize the protein. We constructed and analyzed mice homozygous for these two single-nucleotide polymorphisms, Rabl2L119F (rs80006029) and Rabl2V158F (rs200121688), and found that they exhibit ciliopathy-associated disorders including male infertility, early growth retardation, excessive weight gain in adulthood, heterotaxia, pre-axial polydactyly, neural tube defects and hydrocephalus. Our study provides a paradigm for triaging candidate infertility variants in the population for in vivo functional validation, using computational, in vitro and in vivo approaches.
Homological Percolation: The Formation of Giant k-Cycles
Authors: Bobrowski Omer , Skraba Primoz
Published: October 2020

In this paper we introduce and study a higher dimensional analogue of the giant component in continuum percolation. Using the language of algebraic topology, we define the notion of giant $k$-dimensional cycles (with $0$-cycles being connected components). Considering a continuum percolation model in the flat $d$-dimensional torus, we show that all the giant $k$-cycles ($1\le k \le d-1$) appear in the regime known as the thermodynamic limit. We also prove that the thresholds for the emergence of the giant $k$-cycles are increasing in $k$ and are tightly related to the critical values in continuum percolation. Finally, we provide bounds for the exponential decay of the probabilities of giant cycles appearing.
The Burden of Malaria in the Democratic Republic of the Congo
Authors: Deutsch-Feldman Molly , Parr Jonathan B , Keeler Corinna , Brazeau Nicholas F , Goel Varun , Emch Michael , Edwards Jessie K , Kashamuka Melchior , Tshefu Antoinette K , Meshnick Steven R
Published: October 2020

Despite evidence that older children and adolescents bear the highest burden of malaria, large malaria surveys focus on younger children. We used polymerase chain reaction data from the 2013–2014 Demographic and Health Survey in the Democratic Republic of Congo (including children aged <5 years and adults aged ≥15 years) and a longitudinal study in Kinshasa Province (participants aged 6 months to 98 years) to estimate malaria prevalence across age strata. We fit linear models and estimated prevalences for each age category; adolescents aged 10–14 years had the highest prevalence. We estimate approximately 26 million polymerase chain reaction–detectable infections nationally. Adolescents and older children should be included in surveillance studies.
A Novel Approach to Hematology Testing at the Point of Care
Authors: Bransky Avishay , Larsson Anders , Aardal Elisabeth , Ben-Yosef Yaara , Christenson Robert H
Published: October 2020

Background

The need for rapid point-of-care (POC) diagnostics is now becoming more evident due to the increasing need for timely results and improvement in healthcare service. With the recent COVID-19 pandemic outbreak, POC has become critical in managing the spread of disease. Applicable diagnostics should be readily deployable, easy to use, portable, and accurate so that they fit mobile laboratories, pop-up treatment centers, field hospitals, secluded wards within hospitals, or remote regions, and can be operated by staff with minimal training. Complete blood count (CBC), however, has not been available at the POC in a simple-to-use device until recently. The HemoScreen, which was recently cleared by the FDA for POC use, is a miniature, easy-to-use instrument that uses disposable cartridges and may fill this gap.

Content

The HemoScreen’s analysis method, in contrast to standard laboratory analyzers, is based on machine vision (image-based analysis) and artificial intelligence (AI). We discuss the different methods currently used and compare their results to the vision-based one. The HemoScreen is found to correlate well to laser and impedance-based methods while emphasis is given to mean cell volume (MCV), mean cell hemoglobin (MCH), and platelets (PLT) that demonstrate better correlation when the vision-based method is compared to itself due to the essential differences between the underlying technologies.

The HemoScreen analyzer demonstrates lab equivalent performance, tested at different clinical settings and sample characteristics, and might outperform standard techniques in the presence of certain interferences. This new approach to hematology testing has great potential to improve quality of care in a variety of settings.
Trophic relationships within the genusCarollia(Chiroptera, Phyllostomidae) in a premontane forest of central Peru
Authors: Pellón Juan J , Rivero Jorge , Williams Marta , Flores Mercedes
Published: October 2020

Assemblages of Neotropical frugivorous bats are structured as a function of the fruit diets of species; however, ecological relationships among closely related species largely remain unknown. This study evaluated the trophic relations among three species of Carollia in a premontane forest of central Peru. To accomplish this, we first determined the diet composition of frugivorous bats to build a bat–fruit interaction network. We then assessed the trophic structure of the bat assemblage using a modularity analysis in the network. Carollia brevicauda and Carollia perspicillata were grouped apart from Carollia benkeithi. This partition occurred because the diet of C. benkeithi was more specialized, characterized by two Piper species, a Cyclanthaceae species, and Banara guianensis. Moreover, C. benkeithi, in contrast to its congeners, did not consume fruits of Ficus or Cecropia (canopy resources). This result and available information on the ecology of Carollia species suggest that small species of Carollia are more likely to carry out most of their feeding activities in the understory than are large species of the genus.
Detection ofPintomyia fischeri(Diptera: Psychodidae) WithLeishmania infantum(Trypanosomatida: Trypanosomatidae) Promastigotes in a Focus of Visceral Leishmaniasis in Brazil
Authors: Galvis-Ovallos Fredy , Ueta Adriele Eiko , Marques Gabriella de Oliveira , Sarmento Ana Maria Casagrande , Araujo Gabriela , Sandoval Carmen , Tomokane Thaíse Yumie , da Matta Vânia Lúcia Ribeiro , Laurenti Márcia Dalastra , Galati Eunice Aparecida Bianchi
Published: October 2020

Visceral leishmaniasis is spreading in Brazil where the main vector of its agent, Leishmania infantum Nicolle, 1908, is the Lutzomyia longipalpis (Lutz & Neiva, 1912) species complex (Diptera: Psychodidae: Phlebotominae), on which many of the activities of the visceral leishmaniasis surveillance program are based. However, there are areas where canine, and/or human cases have been occurring without the presence of this species complex as in the western part of the Greater São Paulo Metropolitan region, where Embu das Artes municipality is situated. In this area, Pintomyia fischeri (Pinto, 1926) has been implicated as potential vector of Le. infantum but so far its natural infection with this parasite has not yet been ascertained. Therefore, the present study sought to investigate the natural infection in sand flies of a CVL focus in Embu das Artes. The sand fly collections were undertaken with Shannon and CDC traps, monthly, between 1800 and 2100 hours from November 2018 to October 2019, inclusive. A total of 951 sand flies (457 males and 494 females), belonging to 10 species, were captured. Pintomyia fischeri was the predominant species (89.5%); of which 426 females were dissected and one of them (0.23%) was found to be harboring flagellates in its midgut. A sample of these flagellates was isolated in culture and characterized by a 234 base pair fragment of Leishmania heat-shock protein 70 gene (hsp70) and restriction fragment length polymorphism with Hae III restriction enzyme as Le. infantum. This finding reinforces previous evidence of Pi. fischeri as a vector of Le. infantum in foci of visceral leishmaniasis and highlights the importance of vector surveillance in areas where this species occurs.
After All This Time? The Impact of Media and Authoritarian History on Political News Coverage in Twelve Western Countries
Authors: de Leeuw Sjifra E , Azrout Rachid , Rekker Roderik S B , Van Spanje Joost H P
Published: October 2020

Historical classifications of journalistic traditions are the backbone of comparative explanations for political news coverage. This study assesses the validity of the dominant media systems framework and proposes and tests a novel framework, which states that a history of authoritarianism affects today’s coverage. To facilitate a clean cross-national comparison, we focus on the same person and measurement in 12 Western democracies, that is, the use of the pejorative terms “sexist,” “racist,” “dictator,” and equivalents to describe Donald Trump. Our manually validated automated content analysis (2016–2018; N = 27,830) shows that content varies along with countries’ media and authoritarian history: pejoration is more common in countries with a polarized pluralist media system and former authoritarian countries than elsewhere. Newspapers’ ideology does not matter, irrespective of countries’ level of political parallelism or experiences with authoritarianism. Combined, we provide new methodological and theoretical handles to further comparative communication research in Western democracies.
Operative approach to intestinal malrotation encountered during laparoscopic gastric bypass
Authors: Shockcor Nicole , Nzara Rumbidzayi , Pal Anam , Lo Menzo Emanuele , Kligman Mark D
Published: October 2020

Congenital anomalies of midgut rotation are uncommon with a 0.2–0.5% incidence. Intestinal malrotation (IM) presents a unique challenge in bariatric surgery during laparoscopic gastric bypass (LRYGB), and familiarity with alternatives allows for safe laparoscopic intervention. IM was encountered in 5 of 1183 (0.4%) patients undergoing surgery. Once IM was suspected, a standardized approach was applied: rightward shift of ports, confirmation of IM by the absence of the ligament of Treitz, identification of the duodenojejunal junction, lysis of Ladd’s bands, mirror-image construction of the Roux limb and construction of the gastrojejunal anastomosis. Forty percent were male, age 33 ± 8 years, with body mass index 50 kg/m2 (37–75 kg/m2). IM was identified preoperatively in two patients (40%). All operations were completed laparoscopically. Despite the finding of IM, successful laparoscopic completion of gastric bypass can be anticipated if the surgeon has an understanding of the anatomic alterations and a strategy for intraoperative management.
An Arabidopsis downy mildew non-RxLR effector suppresses induced plant cell death to promote biotroph infection
Authors: Dunker Florian , Oberkofler Lorenz , Lederer Bernhard , Trutzenberg Adriana , Weiberg Arne
Published: October 2020

Our understanding of obligate biotrophic pathogens is limited by lack of knowledge concerning the molecular function of virulence factors. We established Arabidopsis host-induced gene silencing (HIGS) to explore gene functions of Hyaloperonospora arabidopsidis, including CYSTEINE-RICH PROTEIN (HaCR)1, a potential secreted effector gene of this obligate biotrophic pathogen. HaCR1 HIGS resulted in H. arabidopsidis-induced local plant cell death and reduced pathogen reproduction. We functionally characterized HaCR1 by ectopic expression in Nicotiana benthamiana. HaCR1 was capable of inhibiting effector-triggered plant cell death. Consistent with this, HaCR1 expression in N. benthamiana led to stronger disease symptoms caused by the hemibiotrophic oomycete pathogen Phytophthora capsici, but reduced disease symptoms caused by the necrotrophic fungal pathogen Botrytis cinerea. Expressing HaCR1 in transgenic Arabidopsis confirmed higher susceptibility to H. arabidopsidis and to the bacterial hemibiotrophic pathogen Pseudomonas syringae. Increased H. arabidopsidis infection was in accordance with reduced PATHOGENESIS RELATED (PR)1 induction. Expression of full-length HaCR1 was required for its function, which was lost if the signal peptide was deleted, suggesting its site of action in the plant apoplast. This study provides phytopathological and molecular evidence for the importance of this widespread, but largely unexplored class of non-RxLR effectors in biotrophic oomycetes.
Short-term effects of increased CO2, nitrate and temperature on photosynthetic activity in Ulva rigida (Chlorophyta) estimated by different pulse amplitude modulated fluorometers and oxygen evolution
Authors: Figueroa Felix L , Bonomi-Barufi Jose , Celis-Plá Paula S M , Nitschke Udo , Arenas Francisco , Connan Solene , Abreu Maria Helena , Malta Erik-J , Conde-Álvarez Rafael , Chow Fungyi , Mata Maria Teresa , Meyerhoff O , Robledo Daniel , Stengel Dagmar B
Published: October 2020

Short-term effects of pCO2 (700–380 ppm; High carbon (HC) and Low carbon (LC), respectively) and nitrate content (50–5 µM; High nitrogen (HN) and Low nitrogen (LN), respectively on photosynthesis were investigated in Ulva rigida (Chlorophyta) under solar radiation (in-situ) and in the laboratory under artificial light (ex-situ). After six days of incubation at ambient temperature (AT), algae were subjected to a 4 °C temperature increase (AT+4 °C) for 3 d. Both in-situ and ex-situ maximal electron transport rate (ETRmax) and in situ gross photosynthesis (GP), measured by O2 evolution, presented highest values under HCHN, and lowest under HCLN, across all measuring systems. Maximal quantum yield (Fv/Fm), and ETRmax of photosystem (PS) II [ETR(II)max] and PSI [ETR(I)max], decreased under HCLN at AT+4 °C. Ex situ ETR was higher than in situ ETR. At noon, Fv/Fm decreased (indicating photoinhibition), whereas ETR(II)max and maximal non-photochemical quenching (NPQmax) increased. ETR(II)max decreased under AT+ 4 °C in contrast to Fv/Fm, photosynthetic efficiency (α ETR) and saturated irradiance (EK). Thus, U. rigida exhibited a decrease in photosynthesis under acidification, changing LN, and AT+4 °C. These results emphasize the importance of studying the interaction between environmental parameters using in-situ versus ex-situ conditions, when aiming to evaluate the impact of global change on marine macroalgae.
Recent insights into the metabolic adaptations of phosphorus-deprived plants
Authors: Dissanayaka D M S B , Ghahremani Mina , Siebers Meike , Wasaki Jun , Plaxton William C
Published: October 2020

Inorganic phosphate (Pi) is an essential macronutrient required for many fundamental processes in plants, including photosynthesis and respiration, as well as nucleic acid, protein, and membrane phospholipid synthesis. The huge use of Pi-containing fertilizers in agriculture demonstrates that the soluble Pi levels of most soils are suboptimal for crop growth. This review explores recent advances concerning the understanding of adaptive metabolic processes that plants have evolved to alleviate the negative impact of nutritional Pi deficiency. Plant Pi starvation responses arise from complex signaling pathways that integrate altered gene expression with post-transcriptional and post-translational mechanisms. The resultant remodeling of the transcriptome, proteome, and metabolome enhances the efficiency of root Pi acquisition from the soil, as well as the use of assimilated Pi throughout the plant. We emphasize how the up-regulation of high-affinity Pi transporters and intra- and extracellular Pi scavenging and recycling enzymes, organic acid anion efflux, membrane remodeling, and the remarkable flexibility of plant metabolism and bioenergetics contribute to the survival of Pi-deficient plants. This research field is enabling the development of a broad range of innovative and promising strategies for engineering phosphorus-efficient crops. Such cultivars are urgently needed to reduce inputs of unsustainable and non-renewable Pi fertilizers for maximum agronomic benefit and long-term global food security and ecosystem preservation.
Evidence for a role of nitric oxide in iron homeostasis in plants
Authors: Tewari Rajesh Kumar , Horemans Nele , Watanabe Masami
Published: October 2020

Nitric oxide (NO), once regarded as a poisonous air pollutant, is now understood as a regulatory molecule essential for several biological functions in plants. In this review, we summarize NO generation in different plant organs and cellular compartments, and also discuss the role of NO in iron (Fe) homeostasis, particularly in Fe-deficient plants. Fe is one of the most limiting essential nutrient elements for plants. Plants often exhibit Fe deficiency symptoms despite sufficient tissue Fe concentrations. NO appears to not only up-regulate Fe uptake mechanisms but also makes Fe more bioavailable for metabolic functions. NO forms complexes with Fe, which can then be delivered into target cells/tissues. NO generated in plants can alleviate oxidative stress by regulating antioxidant defense processes, probably by improving functional Fe status and by inducing post-translational modifications in the enzymes/proteins involved in antioxidant defense responses. It is hypothesized that NO acts in cooperation with transcription factors such as bHLHs, FIT, and IRO to regulate the expression of enzymes and proteins essential for Fe homeostasis. However, further investigations are needed to disentangle the interaction of NO with intracellular target molecules that leads to enhanced internal Fe availability in plants.
A phylogenetic analysis of galaxies in the Coma Cluster and the field: a new approach to galaxy evolution
Authors: Martínez-Marín M , Demarco R , Cabrera-Vives G , Cerulo P , Leigh N W C , Herrera-Camus R
Published: October 2020

We propose a phylogenetic approach (PA) as a novel and robust tool to detect galaxy populations (GPs) based on their chemical composition. The branches of the tree are interpreted as different GPs and the length between nodes as the internal chemical variation along a branch. We apply the PA using 30 abundance indices from the Sloan Digital Sky Survey to 475 galaxies in the Coma Cluster and 438 galaxies in the field. We find that a dense environment, such as Coma, shows several GPs, which indicates that the environment is promoting galaxy evolution. Each population shares common properties that can be identified in colour–magnitude space, in addition to minor structures inside the red sequence. The field is more homogeneous, presenting one main GP. We also apply a principal component analysis (PCA) to both samples, and find that the PCA does not have the same power in identifying GPs.
A new approach to observational cosmology using the scattering transform
Authors: Cheng (程思浩) Sihao , Ting (丁源森) Yuan-Sen , Ménard Brice , Bruna Joan
Published: October 2020

Parameter estimation with non-Gaussian stochastic fields is a common challenge in astrophysics and cosmology. In this paper, we advocate performing this task using the scattering transform, a statistical tool sharing ideas with convolutional neural networks (CNNs) but requiring neither training nor tuning. It generates a compact set of coefficients, which can be used as robust summary statistics for non-Gaussian information. It is especially suited for fields presenting localized structures and hierarchical clustering, such as the cosmological density field. To demonstrate its power, we apply this estimator to a cosmological parameter inference problem in the context of weak lensing. On simulated convergence maps with realistic noise, the scattering transform outperforms classic estimators and is on a par with the state-of-the-art CNN. It retains advantages of traditional statistical descriptors, has provable stability properties, allows to check for systematics, and importantly, the scattering coefficients are interpretable. It is a powerful and attractive estimator for observational cosmology and the study of physical fields in general.
Hot gaseous atmospheres of rotating galaxies observed with XMM–Newton
Authors: Juráňová A , Werner N , Nulsen P E J , Gaspari M , Lakhchaura K , Canning R E A , Donahue M , Hroch F , Voit G M
Published: October 2020

X-ray emitting atmospheres of non-rotating early-type galaxies and their connection to central active galactic nuclei have been thoroughly studied over the years. However, in systems with significant angular momentum, processes of heating and cooling are likely to proceed differently. We present an analysis of the hot atmospheres of six lenticulars and a spiral galaxy to study the effects of angular momentum on the hot gas properties. We find an alignment between the hot gas and the stellar distribution, with the ellipticity of the X-ray emission generally lower than that of the optical stellar emission, consistent with theoretical predictions for rotationally supported hot atmospheres. The entropy profiles of NGC 4382 and the massive spiral galaxy NGC 1961 are significantly shallower than the entropy distribution in other galaxies, suggesting the presence of strong heating (via outflows or compressional) in the central regions of these systems. Finally, we investigate the thermal (in)stability of the hot atmospheres via criteria such as the TI- and C-ratio, and discuss the possibility that the discs of cold gas present in these objects have condensed out of the hot atmospheres.
The mid-infrared Leavitt law for classical Cepheids in the Magellanic Clouds
Authors: Chown Abigail H , Scowcroft Victoria , Wuyts Stijn
Published: October 2020

The Cepheid Leavitt Law (LL), also known as the Period–Luminosity relation, is a crucial tool for assembling the cosmic distance ladder. By combining data from the OGLE-IV catalogue with mid-infrared photometry from the Spitzer Space Telescope, we have determined the 3.6 and 4.5 $\mu$m LLs for the Magellanic Clouds using ∼5000 fundamental-mode classical Cepheids. Mean magnitudes were determined using a Monte Carlo Markov Chain (MCMC) template fitting procedure, with template light curves constructed from a subsample of these Cepheids with fully phased, well-sampled light curves. The dependence of the Large Magellanic Cloud LL coefficients on various period cuts was tested, in addition to the linearity of the relationship. The zero-point of the LL was calibrated using the parallaxes of Milky Way Cepheids from the Hubble Space Telescope and Gaia Data Release 2. Our final calibrated relations are M[3.6] = −3.246(±0.008)(log (P) − 1.0) − 5.784(±0.030) and M[4.5] = −3.162(±0.008)(log (P) − 1.0) − 5.751(±0.030).
Reconciling galaxy cluster shapes, measured by theorists versus observers
Authors: Harvey David , Robertson Andrew , Tam Sut-Ieng , Jauzac Mathilde , Massey Richard , Rhodes Jason , McCarthy Ian G
Published: October 2020

If properly calibrated, the shapes of galaxy clusters can be used to investigate many physical processes: from feedback and quenching of star formation, to the nature of dark matter. Theorists frequently measure shapes using moments of inertia of simulated particles’. We instead create mock (optical, X-ray, strong-, and weak-lensing) observations of the 22 most massive ($\sim 10^{14.7}\, \mathrm{ M}_\odot$) relaxed clusters in the BAHAMAS simulations. We find that observable measures of shape are rounder. Even when moments of inertia are projected into 2D and evaluated at matched radius, they overestimate ellipticity by 56 per cent (compared to observable strong lensing) and 430 per cent (compared to observable weak lensing). Therefore, we propose matchable quantities and test them using observations of eight relaxed clusters from the Hubble Space Telescope (HST) and Chandra X-Ray Observatory. We also release our HST data reduction and lensing analysis software to the community. In real clusters, the ellipticity and orientation angle at all radii are strongly correlated. In simulated clusters, the ellipticity of inner (<rvir/20) regions becomes decoupled: for example, with greater misalignment of the central cluster galaxy. This may indicate overly efficient implementation of feedback from active galactic nuclei. Future exploitation of cluster shapes as a function of radii will require better understanding of core baryonic processes. Exploitation of shapes on any scale will require calibration on simulations extended all the way to mock observations.
Thermal and photochemical study of CH3OH and CH3OH–O2 astrophysical ices
Authors: Leroux Killian , Krim Lahouari
Published: October 2020

Methanol, which is one of the most abundant organic molecules in the interstellar medium, plays an important role in the complex grain surface chemistry that is believed to be a source of many organic compounds. Under energetic processing such as ultraviolet (UV) photons or cosmic rays, methanol may decompose into CH4, CO2, CO, HCO, H2CO, CH3O and CH2OH, which in turn lead to complex organic molecules such as CH3OCHO, CHOCH2OH and HOCH2CH2OH through radical recombination reactions. However, although molecular oxygen and its detection, abundance and role in the interstellar medium have been the subject of many debates, few experiments on the oxidation of organic compounds have been carried out under interstellar conditions. The present study shows the behaviour of solid methanol when treated by UV light and thermal processing in oxygen-rich environments. Methanol has been irradiated in the absence and presence of O2 at different concentrations in order to study how oxidized complex organic molecules may form and also to investigate the O-insertion reaction in the C–H bound to form methanediol HOCH2OH through a CH3OH + O(1D) solid-state reaction. The adding of O2 in the thermal and photochemical reaction of solid methanol leads to the formation of O3, H2O and HO2, in addition to three main organics, HCOOH, CHOCHO and HOCH2OH. We show that in an O2-rich environment, species such as CO, CH4, HCO, CH3OH and CHOCH2OH are oxidized into CO2, CH3OH, HC(O)OO, HOCH2OH and CHOCHO, respectively, while HCOOH might be formed through the H2CO + O(3P) → (OH + HCO)cage → HCOOH hydrogen-abstraction reaction.
Search for radio emission from the exoplanets Qatar-1b and WASP-80b near 150 MHz using the giant metrewave radio telescope
Authors: Green D A , Madhusudhan N
Published: October 2020

We present radio observations made towards the exoplanets Qatar-1b and WASP-80b near 150 MHz with the Giant Meterwave Radio Telescope (GMRT). These targets are relatively nearby irradiated giant exoplanets, a hot Jupiter and a hot Saturn, with sizes comparable to Jupiter but different masses and lower densities. Both the targets are expected to host extended H/He envelopes like Jupiter, with comparable or larger magnetic moments. No radio emission was detected from these exoplanets, with 3σ limits of 5.9 and 5.2 mJy for Qatar-1b and WASP-80b, respectively, from these targeted observations. These are considerably deeper limits than those available for exoplanets from wide-field surveys at similar frequencies. We also present archival Very Large Array (VLA) observations of a previously reported radio source close to 61 Vir (which has three exoplanets). The VLA observations resolve the source, which we identify as an extragalactic radio source, i.e. a chance association with 61 Vir. Additionally, we cross-match a recent exoplanet catalogue with the TIFR GMRT Sky Survey ADR1 radio catalogue, but do not find any convincing associations.
Primordial nucleosynthesis constraints on high-z energy releases
Authors: De Zotti Gianfranco , Bonato Matteo
Published: October 2020

The cosmic microwave background (CMB) spectrum provides tight constraints on the thermal history of the universe up to z ∼ 2 × 106. At higher redshifts, thermalization processes become very efficient so that even large energy releases do not leave visible imprints in the CMB spectrum. In this paper, we show that the consistency between the accurate determinations of the specific entropy at primordial nucleosynthesis and at the electron–photon decoupling implies that no more than 7.8 per cent of the present-day CMB energy density could have been released in the post-nucleosynthesis era. As pointed out by previous studies, primordial nucleosynthesis complements model independent constraints provided by the CMB spectrum, extending them by two orders of magnitude in redshift.
The role of ZFP57 and additional KRAB-zinc finger proteins in the maintenance of human imprinted methylation and multi-locus imprinting disturbances
Authors: Monteagudo-Sánchez Ana , Hernandez Mora Jose Ramon , Simon Carlos , Burton Adam , Tenorio Jair , Lapunzina Pablo , Clark Stephen , Esteller Manel , Kelsey Gavin , López-Siguero Juan Pedro , de Nanclares Guiomar Perez , Torres-Padilla Maria-Elena , Monk David
Published: October 2020

Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation that is resistant to embryonic reprogramming, resulting in parental origin-specific monoallelic gene expression. A subset of individuals affected by imprinting disorders (IDs) displays multi-locus imprinting disturbances (MLID), which may result from aberrant establishment of imprinted differentially methylated regions (DMRs) in gametes or their maintenance in early embryogenesis. Here we investigated the extent of MLID in a family harbouring a ZFP57 truncating variant and characterize the interactions between human ZFP57 and the KAP1 co-repressor complex. By ectopically targeting ZFP57 to reprogrammed loci in mouse embryos using a dCas9 approach, we confirm that ZFP57 recruitment is sufficient to protect oocyte-derived methylation from reprogramming. Expression profiling in human pre-implantation embryos and oocytes reveals that unlike in mice, ZFP57 is only expressed following embryonic-genome activation, implying that other KRAB-zinc finger proteins (KZNFs) recruit KAP1 prior to blastocyst formation. Furthermore, we uncover ZNF202 and ZNF445 as additional KZNFs likely to recruit KAP1 to imprinted loci during reprogramming in the absence of ZFP57. Together, these data confirm the perplexing link between KZFPs and imprint maintenance and highlight the differences between mouse and humans in this respect.
4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogenLeptospira interrogans
Authors: Gaultney Robert A , Vincent Antony T , Lorioux Céline , Coppée Jean-Yves , Sismeiro Odile , Varet Hugo , Legendre Rachel , Cockram Charlotte A , Veyrier Frédéric J , Picardeau Mathieu
Published: October 2020

In bacteria, DNA methylation can be facilitated by ‘orphan’ DNA methyltransferases lacking cognate restriction endonucleases, but whether and how these enzymes control key cellular processes are poorly understood. The effects of a specific modification, 4-methylcytosine (4mC), are even less clear, as this epigenetic marker is unique to bacteria and archaea, whereas the bulk of epigenetic research is currently performed on eukaryotes. Here, we characterize a 4mC methyltransferase from the understudied pathogen Leptospira spp. Inactivating this enzyme resulted in complete abrogation of CTAG motif methylation, leading to genome-wide dysregulation of gene expression. Mutants exhibited growth defects, decreased adhesion to host cells, higher susceptibility to LPS-targeting antibiotics, and, importantly, were no longer virulent in an acute infection model. Further investigation resulted in the discovery of at least one gene, that of an ECF sigma factor, whose transcription was altered in the methylase mutant and, subsequently, by mutation of the CTAG motifs in the promoter of the gene. The genes that comprise the regulon of this sigma factor were, accordingly, dysregulated in the methylase mutant and in a strain overexpressing the sigma factor. Our results highlight the importance of 4mC in Leptospira physiology, and suggest the same of other understudied species.
Single-molecule DNA sequencing of widely varying GC-content using nucleotide release, capture and detection in microdroplets
Authors: Puchtler Tim J , Johnson Kerr , Palmer Rebecca N , Talbot Emma L , Ibbotson Lindsey A , Powalowska Paulina K , Knox Rachel , Shibahara Aya , M. S. Cunha Pedro , Newell Oliver J , Wu Mei , Chana Jasmin , Athanasopoulou Evangelia-Nefeli , Waeber Andreas M , Stolarek Magdalena , Silva Ana-Luisa , Mordaka Justyna M , Haggis-Powell Michael , Xyrafaki Christina , Bush James , Topkaya Ibrahim S , Sosna Maciej , Ingham Richard J , Huckvale Thomas , Negrea Aurel , Breiner Boris , Šlikas Justinas , Kelly Douglas J , Dunning Alexander J , Bell Neil M , Dethlefsen Mark , Love David M , Dear Paul H , Kuleshova Jekaterina , Podd Gareth J , Isaac Tom H , Balmforth Barnaby W , Frayling Cameron A
Published: October 2020

Despite remarkable progress in DNA sequencing technologies there remains a trade-off between short-read platforms, having limited ability to sequence homopolymers, repeated motifs or long-range structural variation, and long-read platforms, which tend to have lower accuracy and/or throughput. Moreover, current methods do not allow direct readout of epigenetic modifications from a single read. With the aim of addressing these limitations, we have developed an optical electrowetting sequencing platform that uses step-wise nucleotide triphosphate (dNTP) release, capture and detection in microdroplets from single DNA molecules. Each microdroplet serves as a reaction vessel that identifies an individual dNTP based on a robust fluorescence signal, with the detection chemistry extended to enable detection of 5-methylcytosine. Our platform uses small reagent volumes and inexpensive equipment, paving the way to cost-effective single-molecule DNA sequencing, capable of handling widely varying GC-bias, and demonstrating direct detection of epigenetic modifications.
iCSDB: an integrated database of CRISPR screens
Authors: Choi Ahyoung , Jang Insu , Han Heewon , Kim Min-Seo , Choi Jinhyuk , Lee Jieun , Cho Sung-Yup , Jun Yukyung , Lee Charles , Kim Jaesang , Lee Byungwook , Lee Sanghyuk
Published: October 2020

High-throughput screening based on CRISPR-Cas9 libraries has become an attractive and powerful technique to identify target genes for functional studies. However, accessibility of public data is limited due to the lack of user-friendly utilities and up-to-date resources covering experiments from third parties. Here, we describe iCSDB, an integrated database of CRISPR screening experiments using human cell lines. We compiled two major sources of CRISPR-Cas9 screening: the DepMap portal and BioGRID ORCS. DepMap portal itself is an integrated database that includes three large-scale projects of CRISPR screening. We additionally aggregated CRISPR screens from BioGRID ORCS that is a collection of screening results from PubMed articles. Currently, iCSDB contains 1375 genome-wide screens across 976 human cell lines, covering 28 tissues and 70 cancer types. Importantly, the batch effects from different CRISPR libraries were removed and the screening scores were converted into a single metric to estimate the knockout efficiency. Clinical and molecular information were also integrated to help users to select cell lines of interest readily. Furthermore, we have implemented various interactive tools and viewers to facilitate users to choose, examine and compare the screen results both at the gene and guide RNA levels. iCSDB is available at https://www.kobic.re.kr/icsdb/.
The Dual Function of OsSWEET3a as a Gibberellin and Glucose Transporter Is Important for Young Shoot Development in Rice
Authors: Morii Minami , Sugihara Akihiko , Takehara Sayaka , Kanno Yuri , Kawai Kyosuke , Hobo Tokunori , Hattori Masako , Yoshimura Hisako , Seo Mitsunori , Ueguchi-Tanaka Miyako
Published: October 2020

Translocation and long-distance transport of phytohormones are considered important processes for phytohormone responses, as well as their synthesis and signaling. Here, we report on the dual function of OsSWEET3a, a bidirectional sugar transporter from clade I of the rice SWEET family of proteins, as both a gibberellin (GA) and a glucose transporter. OsSWEET3a efficiently transports GAs in the C13-hydroxylation pathway of GA biosynthesis. Both knockout and overexpression lines of OsSWEET3a showed defects in germination and early shoot development, which were partially restored by GA, especially GA20. Quantitative reverse transcription PCR, GUS staining and in situ hybridization revealed that OsSWEET3a was expressed in vascular bundles in basal parts of the seedlings. OsSWEET3a expression was co-localized with OsGA20ox1 expression in the vascular bundles but not with OsGA3ox2, whose expression was restricted to leaf primordia and young leaves. These results suggest that OsSWEET3a is expressed in the vascular tissue of basal parts of seedlings and is involved in the transport of both GA20 and glucose to young leaves, where GA20 is possibly converted to the bioactive GA1 form by OsGA3ox2, during early plant development. We also indicated that such GA transport activities of SWEET proteins have sporadically appeared in the evolution of plants: GA transporters in Arabidopsis have evolved from sucrose transporters, while those in rice and sorghum have evolved from glucose transporters.