bluuebunny/crossref_metadata_2025 huggingface dataset:
Allele-specific multi-sample copy number segmentation in ASCAT
Authors: Ross Edith M. , Haase Kerstin , Van Loo Peter , Markowetz Florian
Published: May 2020

Motivation

Allele-specific copy number alterations are commonly used to trace the evolution of tumours. A key step of the analysis is to segment genomic data into regions of constant copy number. For precise phylogenetic inference, breakpoints shared between samples need to be aligned to each other.

Results

Here, we present asmultipcf, an algorithm for allele-specific segmentation of multiple samples that infers private and shared segment boundaries of phylogenetically related samples. The output of this algorithm can directly be used for allele-specific copy number calling using ASCAT.

Availability and implementation

asmultipcf is available as part of the ASCAT R package (version ≥2.5) from github.com/Crick-CancerGenomics/ascat/.
TissUUmaps: interactive visualization of large-scale spatial gene expression and tissue morphology data
Authors: Solorzano Leslie , Partel Gabriele , Wählby Carolina
Published: May 2020

Motivation

Visual assessment of scanned tissue samples and associated molecular markers, such as gene expression, requires easy interactive inspection at multiple resolutions. This requires smart handling of image pyramids and efficient distribution of different types of data across several levels of detail.

Results

We present TissUUmaps, enabling fast visualization and exploration of millions of data points overlaying a tissue sample. TissUUmaps can be used both as a web service or locally in any computer, and regions of interest as well as local statistics can be extracted and shared among users.

Availability and implementation

TissUUmaps is available on github at github.com/wahlby-lab/TissUUmaps. Several demos and video tutorials are available at http://tissuumaps.research.it.uu.se/howto.html.

Supplementary information

Supplementary data are available at Bioinformatics online.
Dopamine is associated with prioritization of reward-associated memories in Parkinson’s disease
Authors: Sharp Madeleine E , Duncan Katherine , Foerde Karin , Shohamy Daphna
Published: May 2020

Patients with Parkinson’s disease have reduced reward sensitivity related to dopaminergic neuron loss, which is associated with impairments in reinforcement learning. Increasingly, however, dopamine-dependent reward signals are recognized to play an important role beyond reinforcement learning. In particular, it has been shown that reward signals mediated by dopamine help guide the prioritization of events for long-term memory consolidation. Meanwhile, studies of memory in patients with Parkinson’s disease have focused on overall memory capacity rather than what is versus what isn’t remembered, leaving open questions about the effect of dopamine replacement on the prioritization of memories by reward and the time-dependence of this effect. The current study sought to fill this gap by testing the effect of reward and dopamine on memory in patients with Parkinson’s disease. We tested the effect of dopamine modulation and reward on two forms of long-term memory: episodic memory for neutral objects and memory for stimulus-value associations. We measured both forms of memory in a single task, adapting a standard task of reinforcement learning with incidental episodic encoding events of trial-unique objects. Objects were presented on each trial at the time of feedback, which was either rewarding or not. Memory for the trial-unique images and for the stimulus-value associations, and the influence of reward on both, was tested immediately after learning and 2 days later. We measured performance in Parkinson’s disease patients tested either ON or OFF their dopaminergic medications and in healthy older control subjects. We found that dopamine was associated with a selective enhancement of memory for reward-associated images, but that it did not influence overall memory capacity. Contrary to predictions, this effect did not differ between the immediate and delayed memory tests. We also found that while dopamine had an effect on reward-modulated episodic memory, there was no effect of dopamine on memory for stimulus-value associations. Our results suggest that impaired prioritization of cognitive resource allocation may contribute to the early cognitive deficits of Parkinson’s disease.
Impact of Intrapartum Oral Azithromycin on the Acquired Macrolide Resistome of Infants’ Nasopharynx: A Randomized Controlled Trial
Authors: Bojang Abdoulie , Baines Sarah L , Camara Bully , Guerillot Romain , Donovan Liam , Marqués Raquel Sánchez , Secka Ousman , D’Alessandro Umberto , Bottomley Christian , Howden Benjamin P , Roca Anna
Published: May 2020

In a post hoc analysis of samples from an intrapartum azithromycin randomized clinical trial, we found that children whose mothers had been treated with the drug had higher prevalence of macrolide-resistance genes msr(A) and ermC at 28 days but not at 12 months. The 2 genes were positively associated in the nasopharynx.

Clinical Trials Registration

NCT1800942.
Declines in Pneumonia Mortality Following the Introduction of Pneumococcal Conjugate Vaccines in Latin American and Caribbean Countries
Authors: de Oliveira Lucia H , Shioda Kayoko , Valenzuela Maria Tereza , Janusz Cara B , Rearte Analía , Sbarra Alyssa N , Warren Joshua L , Toscano Cristiana M , Weinberger Daniel M ,   Multinational Study for PCV Impact in Mortality Study Team
Published: May 2020

Background

Pneumococcal conjugate vaccines (PCVs) are recommended for use in pediatric immunization programs worldwide. Few data are available on their effect against mortality. We present a multicountry evaluation of the population-level impact of PCVs against death due to pneumonia in children < 5 years of age.

Methods

We obtained national-level mortality data between 2000 and 2016 from 10 Latin American and Caribbean countries, using the standardized protocol. Time series models were used to evaluate the decline in all-cause pneumonia deaths during the postvaccination period while controlling for unrelated temporal trends using control causes of death.

Results

The estimated declines in pneumonia mortality following the introduction of PCVs ranged from 11% to 35% among children aged 2–59 months in 5 countries: Colombia (24% [95% credible interval {CrI}, 3%–35%]), Ecuador (25% [95% CrI, 4%–41%]), Mexico (11% [95% CrI, 3%–18%]), Nicaragua (19% [95% CrI, 0–34%]), and Peru (35% [95% CrI, 20%–47%]). In Argentina, Brazil, and the Dominican Republic, the declines were not detected in the aggregated age group but were detected in certain age strata. In Guyana and Honduras, the estimates had large uncertainty, and no declines were detected. Across the 10 countries, most of which have low to moderate incidence of pneumonia mortality, PCVs have prevented nearly 4500 all-cause pneumonia deaths in children 2–59 months since introduction.

Conclusions

Although the data quality was variable between countries, and the patterns varied across countries and age groups, the balance of evidence suggests that mortality due to all-cause pneumonia in children declined after PCV introduction. The impact could be greater in populations with a higher prevaccine burden of pneumonia.
Decreased Time From Human Immunodeficiency Virus Diagnosis to Care, Antiretroviral Therapy Initiation, and Virologic Suppression during the Citywide RAPID Initiative in San Francisco
Authors: Bacon Oliver , Chin Jennie , Cohen Stephanie E , Hessol Nancy A , Sachdev Darpun , Coffey Susa , Scheer Susan , Buchbinder Susan , Havlir Diane V , Hsu Ling
Published: May 2020

Background

Early virologic suppression (VS) after human immunodeficiency virus (HIV) infection improves individual health outcomes and decreases onward transmission. In San Francisco, immediate antiretroviral therapy (ART) at HIV diagnosis was piloted in 2013–2014 and expanded citywide in 2015 in a rapid start initiative to link all new diagnoses to care within 5 days and start ART at the first care visit.

Methods

HIV providers and linkage navigators were trained on a rapid start protocol with sites caring for vulnerable populations prioritized. Dates of HIV diagnosis, first care visit, ART initiation, and VS were abstracted from the San Francisco Department of Public Health HIV surveillance registry.

Results

During 2013–2017, among 1354 new HIV diagnoses in San Francisco, median days from diagnosis to first VS decreased from 145 to 76 (48%; P < .0001) and from first care visit to ART initiation decreased from 28 to 1 (96%; P < .0001). By 2017, 28% of new diagnoses had a rapid start, which was independently associated with Latinx ethnicity (AOR, 1.73; 95% CI, 1.15–2.60) and recent year of diagnosis (2017; AOR, 16.84; 95% CI, 8.03–35.33). Persons with a rapid ART start were more likely to be virologically suppressed within 12 months of diagnosis than those with a non-rapid start (RR, 1.17; 95% CI, 1.10–1.24).

Conclusions

During a multisector initiative to optimize ART initiation, median time from diagnosis to VS decreased by nearly half. Immediate ART at care initiation was achieved across many, but not all, populations, and was associated with improved suppression rates.
Clinical Correlations of Programmed Cell Death Ligand 1 Status in Liquid and Standard Biopsies in Breast Cancer
Authors: Jacot William , Mazel Martine , Mollevi Caroline , Pouderoux Stéphane , D’Hondt Véronique , Cayrefourcq Laure , Bourgier Céline , Boissiere-Michot Florence , Berrabah Fella , Lopez-Crapez Evelyne , Bidard François-Clément , Viala Marie , Maudelonde Thierry , Guiu Séverine , Alix-Panabières Catherine
Published: May 2020

Background

Data regarding the prognostic value of programmed cell death ligand 1 (PD-L1) expression on circulating tumor cells (CTCs) are lacking. However, CTCs could represent an alternative approach to serial biopsies, allowing real-time monitoring of cancer phenotype.

Methods

We evaluated, in a dedicated prospective clinical trial, the clinicopathological correlations and prognostic value of PD-L1(+)-CTCs in 72 patients with metastatic breast cancer (MBC).

Results

Eighteen of 56 patients with available archival tissue presented at least one positive (≥1%) PD-L1 tumor sample. Baseline CTCs and PD-L1(+)-CTCs were detected in 57 (79.2%) and 26 (36.1%) patients. No significant correlation was found between PD-L1 tumors and CTC expression. In univariate analysis, triple negative (TN) phenotype, number of metastatic treatments, >2 metastatic sites, ≥5 CTCs and PD-L1(+)-CTCs were significantly associated with progression-free survival, while tissue PD-L1 expression was not. In multivariate analysis, TN phenotype, number of metastatic treatments and of metastatic sites were the only 3 variables independently associated with progression-free survival. Progesterone receptor negativity, TN phenotype, >2 metastatic sites and ≥5 CTCs were significantly associated with overall survival in univariate analysis. In multivariable analysis, TN phenotype and >2 metastatic sites were the only 2 independent variables.

Conclusions

Unlike PD-L1(+)-tumor, PD-L1(+)-CTCs correlate to survival in MBC. Reappraisal of the role of PD-L1 expression by tumor tissue and by CTCs under anti-PD-1/PD-L1 treatment is necessary to evaluate its predictive value and potential role as a stratifying factor in strategies and trials for MBC patients with MBC.

Clinical trial registration

NCT02866149
The Vanishing Procyclicality of Labour Productivity
Authors: Galí Jordi , van Rens Thijs
Published: May 2020

We document two changes in post-war US macroeconomic dynamics: the procyclicality of labour productivity vanished, and the relative volatility of employment rose. We propose an explanation for these changes that is based on reduced hiring frictions due to improvements in information about the quality of job matches and the resulting decline in turnover. We develop a simple model with hiring frictions and variable effort to illustrate the mechanisms underlying our explanation. We show that our model qualitatively and quantitatively matches the observed changes in business cycle dynamics.
Agents of Socialization and Female Migrants’ Employment: The Influence of Mothers and the Country Context
Authors: Krieger Magdalena
Published: May 2020

Women around the world are on the move but find it difficult to secure jobs. Employment is vital for migrant integration as it affords financial security, autonomy in the family and helps to establish social contacts. Besides human capital, previous research has looked into ethnic origin and specific source country aspects as drivers of female migrant employment. By contrast, ideas of adolescence as the ‘impressionable’ years and individuals’ exposure to female employment at that time have not yet entered the discussion. However, these theoretical notions have previously been found to be highly predictive of employment in adulthood for natives. This study further investigates these theoretical ideas by using data on 2,047 female immigrants from the German Socio-Economic Panel. Female migrants’ employment and hours worked are analysed in multivariate regressions. The analyses focus on female migrants’ adolescent experiences with female employment in their family—namely, whether their mother worked—and in the broader labour market—measured by the female to male labour force participation rate—as explanatory variables. These two experiences are retrospectively captured for respondents at age 15. Analyses highlight the deep embeddedness of individuals in home country social norms and the power of role models during youth for later employment.
Performance of A Priori and A Posteriori Calibration Strategies in Divergence Time Estimation
Authors: Beavan Alan J S , Donoghue Philip C J , Beaumont Mark A , Pisani Davide
Published: May 2020

Relaxed molecular clock methods allow the use of genomic data to estimate divergence times across the tree of life. This is most commonly achieved in Bayesian analyses where the molecular clock is calibrated a priori through the integration of fossil information. Alternatively, fossil calibrations can be used a posteriori, to transform previously estimated relative divergence times that were inferred without considering fossil information, into absolute divergence times. However, as branch length is the product of the rate of evolution and the duration in time of the considered branch, the extent to which a posteriori calibrated, relative divergence time methods can disambiguate time and rate, is unclear. Here, we use forward evolutionary simulations and compare a priori and a posteriori calibration strategies using different molecular clock methods and models. Specifically, we compare three Bayesian methods, the strict clock, uncorrelated clock and autocorrelated clock, and the non-Bayesian algorithm implemented in RelTime. We simulate phylogenies with multiple, independent substitution rate changes and show that correct timescales cannot be inferred without the use of calibrations. Under our simulation conditions, a posteriori calibration strategies almost invariably inferred incorrect rate changes and divergence times. The a priori integration of fossil calibrations is fundamental in these cases to improve the accuracy of the estimated divergence times. Relative divergence times and absolute timescales derived by calibrating relative timescales to geological time a posteriori appear to be less reliable than a priori calibrated, timescales.
Recurrent Loss of abaA, a Master Regulator of Asexual Development in Filamentous Fungi, Correlates with Changes in Genomic and Morphological Traits
Authors: Mead Matthew E , Borowsky Alexander T , Joehnk Bastian , Steenwyk Jacob L , Shen Xing-Xing , Sil Anita , Rokas Antonis
Published: May 2020

Gene regulatory networks (GRNs) drive developmental and cellular differentiation, and variation in their architectures gives rise to morphological diversity. Pioneering studies in Aspergillus fungi, coupled with subsequent work in other filamentous fungi, have shown that the GRN governed by the BrlA, AbaA, and WetA proteins controls the development of the asexual fruiting body or conidiophore. A specific aspect of conidiophore development is the production of phialides, conidiophore structures that are under the developmental control of AbaA and function to repetitively generate spores. Fungal genome sequencing has revealed that some filamentous fungi lack abaA, and also produce asexual structures that lack phialides, raising the hypothesis that abaA loss is functionally linked to diversity in asexual fruiting body morphology. To examine this hypothesis, we carried out an extensive search for the abaA gene across 241 genomes of species from the fungal subphylum Pezizomycotina. We found that abaA was independently lost in four lineages of Eurotiomycetes, including from all sequenced species within the order Onygenales, and that all four lineages that have lost abaA also lack the ability to form phialides. Genetic restoration of abaA from Aspergillus nidulans into Histoplasma capsulatum, a pathogenic species from the order Onygenales that lacks an endogenous copy of abaA, did not alter Histoplasma conidiation morphology but resulted in a marked increase in spore viability. We also discovered that species lacking abaA contain fewer AbaA binding motifs in the regulatory regions of orthologs of some AbaA target genes, suggesting that the asexual fruiting body GRN of organisms that have lost abaA has likely been rewired. Our results provide an illustration of how repeated losses of a key regulatory transcription factor have contributed to the diversity of an iconic fungal morphological trait.
Proteomics of Osmoregulatory Responses in Threespine Stickleback Gills
Authors: Li Johnathon , Kültz Dietmar
Published: May 2020

Synopsis

The gill proteome of threespine sticklebacks (Gasterosteus aculeatus) differs greatly in populations that inhabit diverse environments characterized by different temperature, salinity, food availability, parasites, and other parameters. To assess the contribution of a specific environmental parameter to such differences it is necessary to isolate its effects from those of other parameters. In this study the effect of environmental salinity on the gill proteome of G. aculeatus was isolated in controlled mesocosm experiments. Salinity-dependent changes in the gill proteome were analyzed by Liquid chromatography/Tandem mass spectrometry data-independent acquisition (DIA) and Skyline. Relative abundances of 1691 proteins representing the molecular phenotype of stickleback gills were quantified using previously developed MSMS spectral and assay libraries in combination with DIA quantitative proteomics. Non-directional stress responses were distinguished from osmoregulatory protein abundance changes by their consistent occurrence during both hypo- and hyper-osmotic salinity stress in six separate mesocosm experiments. If the abundance of a protein was consistently regulated in opposite directions by hyper- versus hypo-osmotic salinity stress, then it was considered an osmoregulatory protein. In contrast, if protein abundance was consistently increased irrespective of whether salinity was increased or decreased, then it was considered a non-directional response protein. KEGG pathway analysis revealed that the salivary secretion, inositol phosphate metabolism, valine, leucine, and isoleucine degradation, citrate cycle, oxidative phosphorylation, and corresponding endocrine and extracellular signaling pathways contain most of the osmoregulatory gill proteins whose abundance is directly proportional to environmental salinity. Most proteins that were inversely correlated with salinity map to KEGG pathways that represent proteostasis, immunity, and related intracellular signaling processes. Non-directional stress response proteins represent fatty and amino acid degradation, purine metabolism, focal adhesion, mRNA surveillance, phagosome, endocytosis, and associated intracellular signaling KEGG pathways. These results demonstrate that G. aculeatus responds to salinity changes by adjusting osmoregulatory mechanisms that are distinct from transient non-directional stress responses to control compatible osmolyte synthesis, transepithelial ion transport, and oxidative energy metabolism. Furthermore, this study establishes salinity as a key factor for causing the regulation of numerous proteins and KEGG pathways with established functions in proteostasis, immunity, and tissue remodeling. We conclude that the corresponding osmoregulatory gill proteins and KEGG pathways represent molecular phenotypes that promote transepithelial ion transport, cellular osmoregulation, and gill epithelial remodeling to adjust gill function to environmental salinity.
Surfacing and vertical behaviour of Atlantic bluefin tuna (Thunnus thynnus) in the Mediterranean Sea: implications for aerial surveys
Authors: Bauer Robert Klaus , Forget Fabien , Fromentin Jean-Marc , Capello Manuela
Published: May 2020

Atlantic bluefin tuna (Thunnus thynnus) (ABFT) frequently engage in surface basking and foraging behaviour that makes them detectable from afar. This behaviour is utilized for the development of fisheries-independent abundance indices based on aerial surveys, although changes in the surface-feeding dynamics of ABFT are not yet accounted for. We investigated the daytime surfacing behaviour of ABFT at different temporal and vertical resolutions based on 24 individuals (117–158 cm fork length), tagged with pop-up archival tags in the Gulf of Lion, NW-Mediterranean Sea between 2015 and 2016. The results suggest that ABFT remain usually <2 min continuously within the visible surface (0–1 m) during daytime. ABFT presence in the 0–1 and 0–20 m layers varied over time and between individuals but showed a seasonal decline towards autumn with the breakdown of thermal stratification. Furthermore, the rate of surfacing events was highly correlated with the time spent in the 0–20 m layer. Geolocation estimates confirm a strong site fidelity of ABFT during the aerial survey period (August–October) in the Gulf of Lion. Our results support the choice of the survey region and period, but related indices should account for the seasonality of ABFT surface behaviour [i.e. the time spent in the 0–20 m layer.
Regional Survey of Diamondback Moth (Lepidoptera: Plutellidae) Response to Maximum Dosages of Insecticides in Georgia and Florida
Authors: Riley David , Smith Hugh , Bennett John , Torrance Philip , Huffman Evan , Sparks Alton , Gruver Charles , Dunn Thomas , Champagne Donald
Published: May 2020

We conducted maximum dose bioassays of insecticide for the control of diamondback moth (DBM), Plutella xylostella (Linnaeus), in cole crops, from 2016 to 2019 at several commercial locations in Georgia and Florida. The nominal maximum dose was defined as the highest labeled rate of an insecticide at the beginning of the survey in the equivalent of 935 liters/ha dilution. The results indicated low insecticide efficacy for high labeled rates of the following insecticides by common name (Insecticide Resistance Action Committee group number in parentheses). Our 4-yr survey identified very low levels of DBM larval control (<47%) by lambda-cyhalothrin (3), methoxyfenozide (18), pyriproxyfen (7C), novaluron (15), bifenthrin (3), chlorantraniliprole (28), indoxacarb (22A), and methomyl (1A). The best products for DBM control (>74%) listed in decreasing average levels of efficacy were naled (1B), cyclaniliprole (28), tolfenpyrad (21A), emamectin benzoate (6), and cyantraniliprole (28). Intermediate levels of control (61–71%) were obtained with Bacillus thuringiensis subspecies aizawai (11A), Bacillus thuringiensis, subsp. kurstaki, strain ABTS-351 (11A), and spinetoram (5). This rapid bioassay provided the grower with a ranking of insecticide efficacy for the control the DBM population for that farm site. These data allowed growers to make an informed decision on control quickly and plan for resistance management rotations for DBM that season.
Effectiveness of planned surveillance for detecting second primary head and neck cancers after endoscopic resection of esophageal squamous cell carcinoma
Authors: Shinozaki Takeshi , Katada Chikatoshi , Shiga Kiyoto , Asakage Takahiro , Yokoyama Tetsuji , Yano Tomonori , Oda Ichiro , Shimizu Yuichi , Takemura Kenichi , Ishikawa Hideki , Yokoyama Akira , Muto Manabu
Published: May 2020

Background

Second primary head and neck cancers after endoscopic resection of esophageal squamous cell carcinoma adversely affect patients’ outcomes and the quality of life; however, an adequate surveillance schedule remains unclear.

Methods

We analyzed 330 patients with early esophageal squamous cell carcinoma who underwent endoscopic resection and were registered in the multicenter cohort study to evaluate adequate surveillance for detection of second primary head and neck cancers. Gastrointestinal endoscopists examined the head and neck regions after 3–6 months of endoscopic resection for esophageal squamous cell carcinoma and subsequently every 6 months. An otolaryngologist also examined the head and neck regions at the time of endoscopic resection for esophageal squamous cell carcinoma and at 12 months intervals thereafter.

Results

During the median follow-up period of 49.4 months (1.3–81.2 months), 33 second primary head and neck cancers were newly detected in 20 patients (6%). The tumor site was as follows: 22 lesions in the hypopharynx, eight lesions in the oropharynx, two lesions in larynx and one lesion in the oral cavity. The 2-year cumulative incidence rate of second primary head and neck cancers was 3.7%. Among them, 17 patients with 29 lesions were treated by transoral surgery. One patient with two synchronous lesions was treated by radiotherapy. Two lesions in two patients were not detected after biopsy. All patients were cured with preserved laryngeal function.

Conclusions

Surveillance by gastrointestinal endoscopy every 6 months and surveillance by an otolaryngologist every 12 months could detect second primary head and neck cancers at an early stage, thereby facilitating minimally invasive treatment.
Ultrastructural Analysis of Mouthparts of Adult Horn Fly (Diptera: Muscidae) From the Brazilian Midwest Region
Authors: Fernandes Fernando de Freitas , Bahia Ana Cristina , Secundino Nágila Francinete Costa , Pimenta Paulo Filemon Paolucci
Published: May 2020

The ultrastructure of the mouthparts of Haematobia irritans (L.) was investigated by scanning electron microscopy. The morphological characteristics of the maxillary palps, labium (prementum and postmentum), labrum, hypopharynx, haustellum, and labellar lobes are described, as well as of the sensilla evidenced on all the surface of the mouthparts, and the set of different positions assumed by the mouth apparatus of this fly. Based on their morphology, 12 well-differentiated sensilla were identified, among three types of cuticular sensilla: trichoidea, coeloconica, and campaniformia. A slight sexual dimorphism in the sensilla patterns found in the mouthparts of H. irritans was evidenced. These observations are discussed with reference to the current literature on the functional morphology of sense organs of Insecta. These results could facilitate the recognition of the chemosensory sensilla by electrophysiological techniques, and foment future taxonomic and phylogenetic studies to better elucidate the evolution of Diptera, Muscomorpha.
Protection status as determinant of carbon stock drivers in Cerrado sensu stricto
Authors: Pereira Kelly Marianne Guimarães , Cordeiro Natielle Gomes , Terra Marcela de Castro Nunes Santos , Pyles Marcela Venelli , Cabacinha Christian Dias , de Mello José Márcio , van den Berg Eduardo
Published: May 2020

Aims

Natural vegetation plays an important role in global carbon cycling and storage. Thus, the Cerrado (Brazilian savannah) is considered a carbon sink because of its intrinsic characteristics. Our aim was to evaluate how the aboveground biomass and biodiversity relationship change between three Cerrado remnants with different protection status: a ‘control area’ (Legal Reserve area), a protected area (PA) and a non-protected area (Non-PA).

Methods

All three studied fragments are situated in northern Minas Gerais state, Brazil. We estimated the aboveground carbon stocks based on the forest inventory. We also measured three dimensions of biodiversity metrics for each plot: functional trait dominance, taxonomic diversity and functional diversity. The following functional traits were evaluated for the species: wood density, maximum diameter and seed size. We carried out generalized linear models seeking to evaluate how carbon stocks, community-weighted mean (CWM) trait values, species richness and diversity, and functional diversity indices differ among the remnants.

Important Findings

The Cerrado areas without protection status had lower carbon stocks, species richness, species diversity, functional richness and functional dispersion, whereas both PA and Non-PA had lower CWM maximum diameter and seed size compared with the Legal Reserve control area. Generalized linear models showed that carbon stocks, species and functional richness metrics were correlated within and across sites, and thus, species richness could serve as a good proxy for functional richness and carbon stocks. The carbon stocks were positively driven by species richness and CWM maximum diameter, while they were negatively driven by functional dispersion. Functional richness, species diversity and CWM seed size appeared in the set of best models, but with no significant direct effect on carbon stocks. Thus, we concluded that absence of protection in the Cerrado areas decreases both species richness and carbon stocks.
The Three Hundred project: the stellar and gas profiles
Authors: Li Qingyang , Cui Weiguang , Yang Xiaohu , Rasia Elena , Dave Romeel , De Petris Marco , Knebe Alexander , Peacock John A , Pearce Frazer , Yepes Gustavo
Published: May 2020

Using the catalogues of galaxy clusters from The Three Hundred project, modelled with both hydrodynamic simulations (gadget-x and gadget-music), and semi-analytical models (SAMs), we study the scatter and self-similarity of the profiles and distributions of the baryonic components of the clusters: the stellar and gas mass, metallicity, the stellar age, gas temperature, and the (specific) star formation rate. Through comparisons with observational results, we find that the shape and the scatter of the gas density profiles matches well the observed trends including the reduced scatter at large radii which is a signature of self-similarity suggested in previous studies. One of our simulated sets, gadget-x, reproduces well the shape of the observed temperature profile, while gadget-music has a higher and flatter profile in the cluster centre and a lower and steeper profile at large radii. The gas metallicity profiles from both simulation sets, despite following the observed trend, have a relatively lower normalization. The cumulative stellar density profiles from SAMs are in better agreement with the observed result than both hydrodynamic simulations which show relatively higher profiles. The scatter in these physical profiles, especially in the cluster centre region, shows a dependence on the cluster dynamical state and on the cool-core/non-cool-core dichotomy. The stellar age, metallicity, and (s)SFR show very large scatter, which are then presented in 2D maps. We also do not find any clear radial dependence of these properties. However, the brightest central galaxies have distinguishable features compared to the properties of the satellite galaxies.
The local Universe in the era of large surveys – I. Spectral classification of S0 galaxies
Authors: Tous J L , Solanes J M , Perea J D
Published: May 2020

This is the first paper in a series devoted to review the main properties of galaxies designated S0 in the Hubble classification system. Our aim is to gather abundant and, above all, robust information on the most relevant physical parameters of this poorly understood morphological type and their possible dependence on the environment, which could later be used to assess their possible formation channel(s). The adopted approach combines the characterization of the fundamental features of the optical spectra of $68\, 043$ S0 with heliocentric z ≲ 0.1 with the exploration of a comprehensive set of their global attributes. A principal component analysis is used to reduce the huge number of dimensions of the spectral data to a low-dimensional space facilitating a bias-free machine-learning-based classification of the galaxies. This procedure has revealed that objects bearing the S0 designation consist, despite their similar morphology, of two separate subpopulations with statistically inconsistent physical properties. Compared to the absorption-dominated S0, those with significant nebular emission are, on average, somewhat less massive, more luminous with less concentrated light profiles, have a younger, bluer, and metal-poorer stellar component, and avoid high-galaxy-density regions. Noteworthy is the fact that the majority of members of this latter class, which accounts for at least a quarter of the local S0 population, show star formation rates and spectral characteristics entirely similar to those seen in late spirals. Our findings suggest that star-forming S0 might be less rare than hitherto believed and raise the interesting possibility of identifying them with plausible progenitors of their quiescent counterparts.
Zinc finger protein ZFP36L1 inhibits influenza A virus through translational repression by targeting HA, M and NS RNA transcripts
Authors: Lin Ren-Jye , Huang Chih-Heng , Liu Ping-Cheng , Lin I-Chieh , Huang Yu-Ling , Chen An-Yu , Chiu Hsin-Ping , Shih Shin-Ru , Lin Li-Hsiung , Lien Shu-Pei , Yen Li-Chen , Liao Ching-Len
Published: May 2020

ZFP36L1, a CCCH-type zinc finger protein, is an RNA-binding protein that participates in controlling cellular mRNA abundance and turnover by posttranscriptional regulation. Here, we demonstrated that ZFP36L1 has an important role in host defense against influenza A virus (IAV) infection. Overexpression of ZFP36L1 reduced IAV replication via translational repression of HA, M and NS RNA segment transcripts. IAV infection upregulated cellular ZFP36L1 expression, and endogenous ZFP36L1 knockdown significantly enhanced IAV replication. ZFP36L1 directly binds to IAV NS1 mRNA in the cytoplasm and blocks the expression and function of NS1 protein. Mutation of CCCH-type zinc finger domains of ZFP36L1 lost its antiviral potential and NS1 mRNA binding. Thus, ZFP36L1 can act as a host innate defense by targeting HA, M and NS mRNA transcripts to suppress viral protein translation.
Picture of a pandemic: visual aids in the COVID-19 crisis
Authors: Hamaguchi Ryoko , Nematollahi Saman , Minter Daniel J
Published: May 2020

As a global crisis, COVID-19 has underscored the challenge of disseminating evidence-based public health recommendations amidst a rapidly evolving, often uncensored information ecosystem—one fueled in part by an unprecedented degree of connected afforded through social media. In this piece, we explore an underdiscussed intersection between the visual arts and public health, focusing on the use of validated infographics and other forms of visual communication to rapidly disseminate accurate public health information during the COVID-19 pandemic. We illustrate our arguments through our own experience in creating a validated infographic for patients, now disseminated through social media and other outlets across the world in nearly 20 translations. Visual communication offers a creative and practical medium to bridge critical health literacy gaps, empower diverse patient communities through evidence-based information and facilitate public health advocacy during this pandemic and the ‘new normal’ that lies ahead.
Capillary-gravity waves on the interface of two dielectric fluid layers under normal electric fields
Authors: Doak A , Gao T , Vanden-Broeck J -M , Kandola J J S
Published: May 2020

In this article, we consider capillary-gravity waves propagating on the interface of two dielectric fluids under the influence of normal electric fields. The density of the upper fluid is assumed to be much smaller than the lower one. Linear and weakly nonlinear theories are studied. The connection to the results in other limit configurations is discussed. Fully nonlinear computations for travelling wave solutions are achieved via a boundary integral equation method. Periodic waves, solitary waves and generalised solitary waves are presented. The bifurcation of generalised solitary waves is discussed in detail.
A rare type of skeletal dysplasia resembling rheumatoid arthritis
Authors: Elsayed S , Gamal R
Published: May 2020

Progressive pseudorheumatoid dysplasia is a rare type of spondylo-epi-metaphyseal dysplasia that can be confused clinically and radiologically with juvenile idiopathic arthritis. Precise diagnosis is essential to avoid unnecessary investigation and treatment. The disease is characterized by predominant involvement of joints with progressive limitation of movement with absence of clinical and biochemical markers of inflammation.

Here we report three children (two boys and one girl) with this rare disease. Their age of presentation ranged from 3-5 years with pain, swelling and deformities of interphalangeal joints of both hands which progressed with time to joint contractures. Other affected joints included elbows and knees. Back was involved in the oldest patient with lumbar lordosis. All three patients had short stature and normal mentality.

The patients had several misdiagnoses before referral to the genetics clinic including rheumatoid arthritis and Morquio syndrome which was excluded by proper investigations.

In conclusion, Progressive pseudorheumatoid dysplasia can be confused with Juvenile rheumatoid arthritis as well as other MPS diseases, both clinically and radiologically. Early diagnosis is mandatory to avoid associated disabilities and to avoid unnecessary investigations and treatment
Contrast Enhanced Mammography: The added value in the assessment of Suspicious Breast Lesions
Authors: Abdullah R , Abdelmonem L , Nasry N , Ayoub M
Published: May 2020

Background

Breast cancer in women is a major public health problem throughout the world, being the second most common cancer worldwide. Sonomammography has been always recommended as the basic breast imaging modality for early detection and diagnosis of breast cancer. Some malignant tumors have been missed, specially in dense breasts, and high false-negative rate have been reported. Contrast enhanced spectral mammography is a new modality, used to depict the tumor vascularity and neoangiogenesis; a classic sign of malignant tumors.

Aim of Work

The purpose of this study is to determine the added value of dual energy contrast mammography to sono-mammography in the assessment of suspicious breast lesions.

Patients and Methods

36 patients were included in the study, referred from outpatient clinics in private settings and from Demerdash Hospitals. Contrast enhanced spectral mammography CESM was performed by using a digital mammography unit (Seno DS; GE, Buc, France) that had been adapted to obtain two images for each view: a low-energy image (below the k edge of iodine, 33.2 keV) and a high-energy image (above the k edge of iodine) at 45 to 49 kVp.

Results: CEDM versus sonomammography shows p (0.021) value less than 0.05. Also the area under the ROC curve was higher for MX+CEDM (94.4%) than that was for sonomammography (63.8%) compared to pathology analysis with 100% sensitivity, 88.2 % specificity, 90.48 %PPV and 100 % NPV in diagnosis of suspicious lesions.

Conclusion

The diagnostic accuracy of CEDM+ MX for the detection of breast carcinoma has proven to be superior to sonomammography alone. CEDM had a better diagnostic accuracy mainly due to improved positive and negative predictive values (Positive predictive value about 90.48, negative predictive value 100). The role of CEDM in detection of multifocal / multicentric carcinomas with particular interest for the assessment of the extent of disease specially in dense breasts is appreciated.
Role of magnetic resonance in evaluation of anterior knee pain
Authors: Abdalraowf M , Derwaish E A , Osman A A
Published: May 2020

Background

The knee joint is one of the most commonly injured joints in the body. Because of its complex structure, this joint is subjected to numerous pathologies and due to the recent increase in various sport activities, there has been a parallel increase in sport-induced internal derangements of the knee. Acute knee pain is the most common complaint of the knee joint, which can be secondary to a variety of etiologies.

Aim of the Work

To review several of the most common causes of AKP, with emphasis on their MRI findings with the goal of allowing more accurate diagnosis and grading of some of the most common pathologies, for understanding, better treatment and improvement of this common complaint.

Patients and Methods

This study was conducted on in Ain Shams university hospitals and other private centers on 32 patients with ages ranging between 10-60 years. All presented by anterior knee pain and were referred to radiology department for MRI examination after orthopedic consultation.

Results

The majority of patients are female (63%) and the symptom most commonly occurs in the second and third decades of life.

Conclusion

MRI is generally safe, accurate, and specific modality which has been proven to be the modality of choice in the diagnosis of different knee pathologies that cause anterior knee pain in different age groups. Also it has a high specification in detecting the grades and types of some of these diseases or factors predispose to them as patella alta and trochlear dysplasia.
Role of Ultrasound and Magnetic Resonance Imaging in Assessment of Müllerian Duct Anomalies
Authors: Ali S B , Salama A M , Mahmoud Z A
Published: May 2020

Background

Müllerian duct anomalies (MDAs) occur as a result from abnormal development of the uterus, cervix, and upper vagina. Many classification systems are presented, aiming to provide a more suitable and accurate categorization of female genital anomalies. Ultrasonography (US), Magnetic Resonance Imaging (MRI), or a combination of both are considered the gold standard in evaluation of uterine anomalies.

Aim of the Work

The main purpose of the study is to determine the diagnostic role of MRI and US in assessment of Müllerian duct anomalies and its subtypes.

Patients and Methods

This prospective analytical study was conducted at 14 patients suspected to have MDAs at Al-Demerdash Hospital-Ain Shams University in the period from September 2017 to May 2018, Their ages ranged from 15-40 year-old. All cases underwent Pelvic U/S and MRI, findings were correlated with laparoscopy.

Results

In this study the Mullerian duct anomalies were categorized into four groups: (a) congenital absence of the Müllerian ducts, or the Mayer-Rokitansky-Kuster-Hauser syndrome (n = 8), (b) disorders of vertical fusion (n = 1),(c) disorders of lateral fusion (n = 3) and (d) MDAs mimics(n = 2).MRI allowed correct diagnosis of 14 uterine anomalies (accuracy 100%) whereas US was correct in 13 out of 14 cases (accuracy 92.8%).

Conclusion

Two dimensional ultrasound stands as the first imaging modality of choice. MRI remains the reference imaging modality in diagnosis of Mullerian anomalies and it is subtypes and should be preserved for doubtful or complex cases.
Role of Magnetic Resonance Imaging Including Diffusion- Weighted MRI Imaging in Characterization of Parotid Gland Tumors
Authors: Elgaafary S M , Darwish E A , Hussein D Y
Published: May 2020

Introduction

The parotid gland is the largest salivary gland and parotid cancer accounts for 5% of the incidence rate of all head and neck tumors and 80% the salivary gland tumors. Benign tumors account for 80–85% and malignant tumors account for 15–20%. About 25% of untreated parotid pleomorphic adenoma shows malignant degeneration after a long history of disease, especially in multiple pleomorphic adenoma, but Warthin’s tumors are rarely malignant, with a rate of less than 1%.

Objectives

This review aim to assess the role of magnetic resonance imaging and diffusion weighted MR Imaging in diagnosis and characterization of parotid gland tumors.

Data Sources

Medline databases (PubMed, Medscape, Science Direct. EMF-Portal) and all materials available in the Internet till 2018.

Study Selection

This search presented 70 articles. The articles studied the role of MRI and diffusion weighted image in parotid tumors and to purify the most recent studies in this field.

Data Extraction

If the studies did not fulfill the inclusion criteria, they were excluded. Study quality assessment included whether ethical approval was gained, eligibility criteria specified, appropriate controls, and adequate information and defined assessment measures.

Data Synthesis

Comparisons were made by structured review with the results tabulated.

Conclusion

The combination of conventional MR imaging with advanced multiparametric MR assessment can enable accurate characterization of parotid gland tumors non –invasively.
Role of diffusion weighted MR imaging in diagnosis of acute pancreatitis
Authors: Sabry K A A , Kamel O F , Ahmed A Y , Abuzeid H M
Published: May 2020

Purpose

to assess the role of Diffusion-weighted MRI in diagnosis of acute pancreatitis by measure the apparent diffusion coefficient (ADC) values detected by diffusion-weighted imaging (DWI) in acute pancreatitis and compare them with the control group

Methods and Material

sixteen patients with acute pancreatitis and sixteen normal controls underwent DWI with b values (0,200 & 800). Apparent diffusion coefficient (ADC) maps are generated from DWI and ADC values were calculated for pancreas and compared the results between the two groups

Results

The mean pancreatic ADC in the AP group (1.17 × 10(-3) mm(2)/s ± 0.2) was significantly lower than in the normal group (1.6 × 10(-3) mm(2)/s ± 0.32). There was no significant difference in mean ADCs between each of the pancreatic segments in the controls. A threshold ADC value of 1.38 × 10-3 mm(2)/s yielded a sensitivity of 93% and specificity of 87% for detecting acute pancreatitis. Pancreatic ADCs are significantly lower in patients with AP than normal controls.

Conclusion

MR diffusion imaging could be an important supportive tool in diagnosis of acute pancreatitis
Role of Ultrasound-Guided Platelet Rich Plasma Injection in Treatment of Chronic Rotator Cuff Muscles Tendinopathy
Authors: Nassef M A , Allam A E , Mohammed H M N
Published: May 2020

Background

shoulder pain is the third most common musculoskeletal complaint. And rotator cuff muscles tendinopathy is one of the most common causes for shoulder pain.

Aim of the Work

to evaluate the effectiveness of the percutaneous ultrasound guided PRP injection in improving or treating chronic Rotator Cuff muscles tendinopathy.

Patients and Methods

this study was conducted on 33 patients presented to Police Hospital Nasr City and diagnosed as cases of rotator cuff tendinopathy for more than 6 months and not responding to NSAIDs.

Results

there is high significant improvement of the ultrasound findings and clinical manifestations of patients as regard pain, range of motion and power comparing to the base line start. According to this study, PRP was found to be more effective on the long term then short term “comparing results after one and five month”.

Conclusion

ultrasound guided PRP injection is a safe and an effective treatment modality for rotator cuff tendinopathy as evidenced by decreased pain and improved range of motion across the shoulder joint after the application and follow up of the PRP.