bluuebunny/crossref_metadata_2025 huggingface dataset:
Massive rhizobial genomic variation associated with partner quality in Lotus–Mesorhizobium symbiosis
Authors: Bamba Masaru , Aoki Seishiro , Kajita Tadashi , Setoguchi Hiroaki , Watano Yasuyuki , Sato Shusei , Tsuchimatsu Takashi
Published: September 2020

Variation in partner quality is commonly observed in diverse cooperative relationships, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variation. Here, we investigated how genetic variation in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variation in the core genome and the similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using 9 sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variation represented by plant growth phenotypes, including genotype-by-genotype interactions. Variation in quality was not associated with the presence/absence variation in known symbiosis-related genes in the symbiosis island; rather, it showed significant correlation with the core genome variation. Given the recurrent HGT of the symbiosis islands into diverse Mesorhizobium strains, local Mesorhizobium communities could serve as a major source of variation for core genomes, which might prevent variation in partner quality from fixing, even in the presence of selection favoring high-quality partners. These findings highlight the novel role of HGT of symbiosis islands in maintaining partner quality variation in the legume–rhizobia symbiosis.
Bacterial microbiota associated with insect vectors of grapevine Bois noir disease in relation to phytoplasma infection
Authors: Moussa Abdelhameed , Passera Alessandro , Sanna Francesco , Faccincani Monica , Casati Paola , Bianco Piero Attilio , Mori Nicola , Quaglino Fabio
Published: September 2020

Bois noir is a grapevine disease causing severe yield loss in vineyards worldwide. It is associated with ‘Candidatus Phytoplasma solani’, a phloem-limited bacterium transmitted by polyphagous insects. Due to its complex epidemiology, it is difficult to organize effective containment measures. This study aimed to describe the bacterial microbiota associated with ‘Candidatus Phytoplasma solani’ infected and non-infected insect hosts and vectors to investigate if phytoplasma presence can shape the microbiota. Alpha-diversity analysis showed a low microbiota diversity in these insects, in which few genera were highly abundant. Beta-diversity analysis revealed that the xylem- and phloem-feeding behavior influences the microbiota structure. Moreover, it highlighted that phytoplasma infection is associated with a restructuring of microbiota exclusively in Deltocephalinae insect vectors. Obtained data showed that ‘Candidatus Phytoplasma solani’ may have adverse effects on the endosymbionts Sulcia and Wolbachia, suggesting a possible fitness modification in the insects. The phytoplasma-antagonistic Dyella was not found in any of the examined insect species. The results indicate an interesting perspective regarding the microbial signatures associated with xylem- and phloem-feeding insects, and determinants that could be relevant to establish whether an insect species can be a vector or not, opening up new avenues for developing microbial resource management-based approaches.
‘Candidatus Oscillochloris kuznetsovii’ a novel mesophilic filamentous anoxygenic phototrophic Chloroflexales bacterium from Arctic coastal environments
Authors: Gaisin Vasil A , Grouzdev Denis S , Krutkina Maria S , Ashikhmin Aleksandr A , Sinetova Maria A , Osipova Natalya S , Koziaeva Veronika V , Gorlenko Vladimir M
Published: September 2020

Chloroflexales bacteria are mostly known as filamentous anoxygenic phototrophs that thrive as members of the microbial communities of hot spring cyanobacterial mats. Recently, we described many new Chloroflexales species from non-thermal environments and showed that mesophilic Chloroflexales are more diverse than previously expected. Most of these species were isolated from aquatic environments of mid-latitudes. Here, we present the comprehensive characterization of a new filamentous multicellular anoxygenic phototrophic Chloroflexales bacterium from an Arctic coastal environment (Kandalaksha Gulf, the White Sea). Phylogenomic analysis and 16S rRNA phylogeny indicated that this bacterium belongs to the Oscillochloridaceae family as a new species. We propose that this species be named ‘Candidatus Oscillochloris kuznetsovii’. The genomes of this species possessed genes encoding sulfide:quinone reductase, the nitrogenase complex and the Calvin cycle, which indicate potential for photoautotrophic metabolism. We observed only mesophilic anaerobic anoxygenic phototrophic growth of this novel bacterium. Electron microphotography showed the presence of chlorosomes, polyhydroxyalkanoate-like granules and polyphosphate-like granules in the cells. High-performance liquid chromatography also revealed the presence of bacteriochlorophylls a, c and d as well as carotenoids. In addition, we found that this bacterium is present in benthic microbial communities of various coastal environments of the Kandalaksha Gulf.
Characterizing offspring of Dutch elm disease-resistant trees (Ulmus minorMill.)
Authors: Martín Juan A , Solla Alejandro , Oszako Tomasz , Gil Luis
Published: September 2020

Populations of Ulmus minor in Europe were severely damaged by Dutch elm disease (DED) pandemics. However, elm breeding programmes have permitted selection of resistant elm varieties currently used for reforestation. In restored elm forests, resistant (R) and susceptible (S) trees interbreed, but little is known about resistance in their offspring. In this work, growth, DED resistance and xylem anatomy in the offspring of two resistant U. minor trees (R1 and R2) were studied. To verify whether transmission of traits in offspring is determined by maternal or paternal trees, a complete randomized plot was established with clonal material from controlled crosses (R1 × S and R2 × S) and parent trees (R1, R2 and S). Trees were inoculated with O. novo-ulmi firstly at age 4 years and again at 5 years. Growth, susceptibility to DED and vessel size in offspring were closer to the traits of maternal than of paternal trees. This association disappeared after the second inoculation when symptoms increased. The more resistant trees in R1 × S and R2 × S had wide and narrow earlywood vessels, respectively, suggesting that water-conducting strategies and resistance mechanisms vary in offspring. Tylosis formation was related to resistance only in R2 × S offspring, possibly due to the narrow earlywood vessles of trees. Latewood vessels were normally narrower in the more resistant trees. This study sheds light on anatomical resistance mechanisms of elms against DED: (1) offspring exhibit high variability in responses among individuals, (2) narrow earlywood vessels are not a prerequisite for DED resistance and (3) barrier zones are not fully associated with tree resistance in offspring.
Renal-function change after transjugular intra-hepatic portosystemic shunt placement and its relationship with survival: a single-center experience
Authors: Lang Min , Lang Angela L. , Tsui Brian Q. , Wang Weiping , Erly Brian K. , Shen Bo , Kapoor Baljendra
Published: September 2020

Background

The effect of transjugular intra-hepatic portosystemic shunt (TIPS) placement on renal function and the correlation of post-TIPS Cr with mortality remain unclear. This study aimed to assess the effect of TIPS placement on renal function and to examine the relationship between post-TIPS Cr and mortality risk.

Methods

A total of 593 patients who underwent de novo TIPS placement between 2004 and 2017 at a single institution were included in the study. The pre-TIPS Cr level (T0; within 7 days before TIPS placement) and post-TIPS Cr levels, at 1–2 days (T1), 5–12 days (T2), and 15–40 days (T3), were collected. Predictors of Cr change after TIPS placement and the 1-year mortality rate were analysed using multivariable linear-regression and Cox proportional-hazards models, respectively.

Results

Overall, 21.4% of patients (n = 127) had elevated baseline Cr (≥1.5 mg/dL; mean, 2.51 ± 1.49 mg/dL) and 78.6% (n = 466) had normal baseline Cr (<1.5 mg/dL; mean, 0.92 ± 0.26 mg/dL). Patients with elevated pre-TIPS Cr demonstrated a decrease in post-TIPS Cr (difference, −0.60 mg/dL), whereas patients with normal baseline Cr exhibited no change (difference, <0.01 mg/dL). The 30-day, 90-day, and 1-year mortality rates were 13%, 20%, and 32%, respectively. Variceal bleeding as a TIPS-placement indication (hazard ratio = 1.731; P = 0.036), higher T0 Cr (hazard ratio = 1.834; P = 0.012), and higher T3 Cr (hazard ratio = 3.524; P < 0.001) were associated with higher 1-year mortality risk.

Conclusion

TIPS placement improved renal function in patients with baseline renal dysfunction and the post-TIPS Cr level was a strong predictor of 1-year mortality risk.
The Evolution of Phenotypic Plasticity in Response to Temperature Stress
Authors: Mallard Francois , Nolte Viola , Schlötterer Christian
Published: September 2020

Phenotypic plasticity is the ability of a single genotype to produce different phenotypes in response to environmental variation. The importance of phenotypic plasticity in natural populations and its contribution to phenotypic evolution during rapid environmental change is widely debated. Here, we show that thermal plasticity of gene expression in natural populations is a key component of its adaptation: evolution to novel thermal environments increases ancestral plasticity rather than mean genetic expression. We determined the evolution of plasticity in gene expression by conducting laboratory natural selection on a Drosophila simulans population in hot and cold environments. After more than 60 generations in the hot environment, 325 genes evolved a change in plasticity relative to the natural ancestral population. Plasticity increased in 75% of these genes, which were strongly enriched for several well-defined functional categories (e.g., chitin metabolism, glycolysis, and oxidative phosphorylation). Furthermore, we show that plasticity in gene expression of populations exposed to different temperatures is rather similar across species. We conclude that most of the ancestral plasticity can evolve further in more extreme environments.
Sex-Specific Protective Effects ofAPOEε2 on Cognitive Performance
Authors: Lamonja-Vicente Noemí , Dacosta-Aguayo Rosalia , López-Olóriz Jorge , Prades-Senovilla Laia , Roig-Coll Francesca , Castells-Sánchez Alba , Soriano-Raya Juan José , Clemente Inmaculada , Miralbell Júlia , Barrios Maite , López-Cancio Elena , Cáceres Cynthia , Arenillas Juan Francisco , Millán Mónica , Torán Pere , Pera Guillem , Fores Rosa , Alzamora Maria Teresa , Mataró Maria , Via Marc
Published: September 2020

Apolipoprotein E (APOE) has an important role in the multiple trajectories of cognitive aging. However, environmental variables and other genes mediate the impact of APOE on cognition. Our main objective was to analyze the effect of APOE genotype on cognition and its interactions and relationships with sex, age, lipid profile, C-reactive protein, and Brain-derived neurotrophic factor (BDNF) genotype in a sample of 648 healthy participants over 50 years of age with a comprehensive neuropsychological assessment. Our results showed that APOE ε2 carriers performed better in the Verbal Memory (p = .002) and Fluency Domains (p = .001). When we studied the effect of sex, we observed that the beneficial effect of APOE ε2 on the normalized values of these cognitive domains occurred only in females (β = 0.735; 95% confidence interval, 0.396–1.074; p = 3.167·10−5 and β = 0.568; 95% confidence interval, 0.276–0.861; p = 1.853·10−4, respectively). Similarly, the sex-specific effects of APOE ε2 were further observed on lipidic and inflammation biomarkers. In the whole sample, APOE ε2 carriers showed significantly lower levels of total cholesterol, low-density lipoprotein cholesterol, and C-reactive protein. These differences were found only among females. Furthermore, total cholesterol and low-density lipoprotein cholesterol mediated the protective effect of APOE ε2 on cognition in the whole sample and total cholesterol in females, providing candidate physiological mechanisms for the observed genetic effects. Our results show that the neuroprotective role of APOE ε2 in cognition varies with sex and that the lipidic profile partially mediates this protection. Age-related cognitive and functional decline is a continuous biological process with different cognitive trajectories (1). Complex interactions between heritability, environmental influence, and cognitive functions in aging have been highlighted (2). In particular, genetic differences explain around 15%–25% of the variance in life expectancy (3). Therefore, the identification of susceptibility genes and their biological effects on cognitive aging is required to establish interindividual differences in this process and promote early personalized interventions to delay cognitive decline and minimize the financial burden of aging in the health care system.
An extensible big data software architecture managing a research resource of real-world clinical radiology data linked to other health data from the whole Scottish population
Authors: Nind Thomas , Sutherland James , McAllister Gordon , Hardy Douglas , Hume Ally , MacLeod Ruairidh , Caldwell Jacqueline , Krueger Susan , Tramma Leandro , Teviotdale Ross , Abdelatif Mohammed , Gillen Kenny , Ward Joe , Scobbie Donald , Baillie Ian , Brooks Andrew , Prodan Bianca , Kerr William , Sloan-Murphy Dominic , Herrera Juan F R , McManus Dan , Morris Carole , Sinclair Carol , Baxter Rob , Parsons Mark , Morris Andrew , Jefferson Emily
Published: September 2020

Aim

To enable a world-leading research dataset of routinely collected clinical images linked to other routinely collected data from the whole Scottish national population. This includes more than 30 million different radiological examinations from a population of 5.4 million and >2 PB of data collected since 2010.

Methods

Scotland has a central archive of radiological data used to directly provide clinical care to patients. We have developed an architecture and platform to securely extract a copy of those data, link it to other clinical or social datasets, remove personal data to protect privacy, and make the resulting data available to researchers in a controlled Safe Haven environment.

Results

An extensive software platform has been developed to host, extract, and link data from cohorts to answer research questions. The platform has been tested on 5 different test cases and is currently being further enhanced to support 3 exemplar research projects.

Conclusions

The data available are from a range of radiological modalities and scanner types and were collected under different environmental conditions. These real-world, heterogenous data are valuable for training algorithms to support clinical decision making, especially for deep learning where large data volumes are required. The resource is now available for international research access. The platform and data can support new health research using artificial intelligence and machine learning technologies, as well as enabling discovery science.
Multifault complex rupture and afterslip associated with the 2018 Mw 6.4 Hualien earthquake in northeastern Taiwan
Authors: Zhao Dezheng , Qu Chunyan , Shan Xinjian , Bürgmann Roland , Gong Wenyu , Tung Hsin , Zhang Guohong , Song Xiaogang , Qiao Xin
Published: September 2020

We investigate the coseismic and post-seismic deformation due to the 6 February 2018 Mw 6.4 Hualien earthquake to gain improved insights into the fault geometries and complex regional tectonics in this structural transition zone. We generate coseismic deformation fields using ascending and descending Sentinel-1A/B InSAR data and GPS data. Analysis of the aftershocks and InSAR measurements reveal complex multifault rupture during this event. We compare two fault model joint inversions of SAR, GPS and teleseismic body waves data to illuminate the involved seismogenic faults, coseismic slip distributions and rupture processes. Our preferred fault model suggests that both well-known active faults, the dominantly left-lateral Milun and Lingding faults, and previously unrecognized oblique-reverse west-dipping and north-dipping detachment faults, ruptured during this event. The maximum slip of ∼1.6 m occurred on the Milun fault at a depth of ∼2–5 km. We compute post-seismic displacement time series using the persistent scatterer method. The post-seismic range-change fields reveal large surface displacements mainly in the near-field of the Milun fault. Kinematic inversions constrained by cumulative InSAR displacements along two tracks indicate that the afterslip occurred on the Milun and Lingding faults and the west-dipping fault just to the east. The maximum cumulative afterslip of 0.4–0.6 m occurred along the Milun fault within ∼7 months of the main shock. The main shock-induced static Coulomb stress changes may have played an important role in driving the afterslip adjacent to coseismic high-slip zones on the Milun, Lingding and west-dipping faults.
Slc26a3 (DRA) in the Gut: Expression, Function, Regulation, Role in Infectious Diarrhea and Inflammatory Bowel Disease
Authors: Yu Qin
Published: September 2020

Background

The transport of transepithelial Cl- and HCO3- is crucial for the function of the intestinal epithelium and maintains the acid-based homeostasis. Slc26a3 (DRA), as a key chloride-bicarbonate exchanger protein in the intestinal epithelial luminal membrane, participates in the electroneutral NaCl absorption of intestine, together with Na+/H+ exchangers. Increasing recent evidence supports the essential role of decreased DRA function or expression in infectious diarrhea and inflammatory bowel disease (IBD).

Method

In this review, we give an overview of the current knowledge of Slc26a3, including its cloning and expression, function, roles in infectious diarrhea and IBD, and mechanisms of actions. A better understanding of the physiological and pathophysiological relevance of Slc26a3 in infectious diarrhea and IBD may reveal novel targets for future therapy.

Conclusion

Understanding the physiological function, regulatory interactions, and the potential mechanisms of Slc26a3 in the pathophysiology of infectious diarrhea and IBD will define novel therapeutic approaches in future.
Conservation restocking of the imperilled European eel does not necessarily equal conservation
Authors: Rohtla Mehis , Silm Maidu , Tulonen Jouni , Paiste Päärn , Wickström Håkan , Kielman-Schmitt Melanie , Kooijman Ellen , Vaino Väino , Eschbaum Redik , Saks Lauri , Verliin Aare , Vetemaa Markus
Published: September 2020

To stop the decline of the European eel population, one of the measures taken is translocating eels for restocking, despite its conservational value being largely unknown. We aimed to contribute to this knowledge gap by (i) investigating the origin of eels caught in coastal waters of Estonia and Finland using otolith microchemistry and (ii) directly estimating restocked eel escapement from Narva River Basin District (NRBD), which is part of the primary Eel Management Unit in Estonia. In Estonia, 74% of the sampled eels (n = 140) were natural recruits and 26% were restocked. In Finland, 27% of the sampled eels (n = 235) were natural recruits and 73% were restocked. Only 1% of all the coastally collected eels were originally restocked to NRBD. These new data together with the reported commercial landings from the escapement route conflict with the current silver eel escapement estimation for NRBD and question the accuracy and value of such indirect calculations compiled for most Eel Management Units throughout the European Union. It is concluded that restocking eels to freshwaters may be futile as a conservation measure in some situations, and better escapement is likely achieved in restocking eels to coastal waters or undammed freshwater systems with a direct connection to the sea.
Development and validation of a prognostic model based on comorbidities to predict COVID-19 severity: a population-based study
Authors: Gude-Sampedro Francisco , Fernández-Merino Carmen , Ferreiro Lucía , Lado-Baleato Óscar , Espasandín-Domínguez Jenifer , Hervada Xurxo , Cadarso Carmen M , Valdés Luis
Published: September 2020

Background

The prognosis of patients with COVID-19 infection is uncertain. We derived and validated a new risk model for predicting progression to disease severity, hospitalization, admission to intensive care unit (ICU) and mortality in patients with COVID-19 infection (Gal-COVID-19 scores).

Methods

This is a retrospective cohort study of patients with COVID-19 infection confirmed by reverse transcription polymerase chain reaction (RT-PCR) in Galicia, Spain. Data were extracted from electronic health records of patients, including age, sex and comorbidities according to International Classification of Primary Care codes (ICPC-2). Logistic regression models were used to estimate the probability of disease severity. Calibration and discrimination were evaluated to assess model performance.

Results

The incidence of infection was 0.39% (10 454 patients). A total of 2492 patients (23.8%) required hospitalization, 284 (2.7%) were admitted to the ICU and 544 (5.2%) died. The variables included in the models to predict severity included age, gender and chronic comorbidities such as cardiovascular disease, diabetes, obesity, hypertension, chronic obstructive pulmonary disease, asthma, liver disease, chronic kidney disease and haematological cancer. The models demonstrated a fair–good fit for predicting hospitalization {AUC [area under the receiver operating characteristics (ROC) curve] 0.77 [95% confidence interval (CI) 0.76, 0.78]}, admission to ICU [AUC 0.83 (95%CI 0.81, 0.85)] and death [AUC 0.89 (95%CI 0.88, 0.90)].

Conclusions

The Gal-COVID-19 scores provide risk estimates for predicting severity in COVID-19 patients. The ability to predict disease severity may help clinicians prioritize high-risk patients and facilitate the decision making of health authorities.
The Hessian Map
Authors: Ciliberto Ciro , Ottaviani Giorgio
Published: September 2020

In this paper, we study the Hessian map $h_{d,r}$, which associates to any hypersurface of degree $d$ in ${{\mathbb{P}}}^r$ its Hessian hypersurface, and the general properties of this map and prove that $h_{d,1}$ is birational onto its image if $d\geqslant 5.$ We also study in detail the maps $h_{3,1}$, $h_{4,1}$, and $h_{3,2}$ and the restriction of the Hessian map to the locus of hypersurfaces of degree $d$ with Waring rank $r+2$ in ${{\mathbb{P}}}^r$, proving that this restriction is injective as soon as $r\geqslant 2$ and $d\geqslant 3$, which implies that $h_{3,3}$ is birational onto its image. We also prove that the differential of the Hessian map is of maximal rank on the generic hypersurfaces of degree $d$ with Waring rank $r+2$ in ${{\mathbb{P}}}^r$, as soon as $r\geqslant 2$ and $d\geqslant 3$.
Feasibility of upfront mobile money transfers for transportation reimbursement to promote retention among patients receiving lymphoma treatment in Malawi
Authors: Ellis Grace K , Manda Agness , Topazian Hillary , Stanley Christopher C , Seguin Ryan , Minnick Caroline E , Tewete Blessings , Mtangwanika Asekanadziwa , Chawinga Mena , Chiyoyola Sara , Chikasema Maria , Salima Ande , Kimani Stephen , Kasonkanji Edwards , Mithi Victor , Kaimila Bongani , Painschab Matthew S , Gopal Satish , Westmoreland Katherine D
Published: September 2020

Background

Cancer outcomes in sub-Saharan Africa (SSA) remain suboptimal, in part due to poor patient retention. Many patients travel long distances to receive care, and transportation costs are often prohibitively expensive. These are well-known and established causes of delayed treatment and care abandonment in Malawi and across SSA.

Methods

We sent visit reminder texts and offered upfront money to cover transportation costs through a mobile money transfer (MMT) platform to lymphoma patients enrolled in a prospective cohort in Malawi. The primary aim was to test the feasibility of upfront MMTs.

Results

We sent 1034 visit reminder texts to 189 participating patients. Of these texts, 614 (59%) were successfully delivered, with 536 (52%) responses. 320/536 (60%) MMTs were sent to interested patients and 312/320 (98%) came to their appointment on time. Of 189 total patients, 120 (63%) were reached via text and 84 (44%) received MMTs a median of three times (IQR 2–5). Median age of reachable patients was 41 (IQR 30–50), 75 (63%) were male, 62 (52%) were HIV+ and 79 (66%) resided outside of Lilongwe.

Conclusion

MMTs were a feasible way to cover upfront transportation costs for patients reachable via text, however many of our patients were unreachable. Future studies exploring barriers to care, particularly among unreachable patients, may help improve the efficacy of MMT initiatives and guide retention strategies throughout SSA.
Understanding Patient Anxiety and Pain During Initial Image-guided Breast Biopsy
Authors: Maimone Santo , Morozov Andrey P , Wilhelm Annamaria , Robrahn Inna , Whitcomb Tedra D , Lin Kathryn Y , Maxwell Robert W
Published: September 2020

Objective

Image-guided breast biopsies are safe, efficient, and reliable. However, patients are often anxious about these procedures, particularly those who have never undergone a prior biopsy.

Methods

This prospective IRB-approved study surveyed 163 patients undergoing their first breast biopsy. Participants provided informed consent and completed a short written survey prior to and immediately after their procedure. Level of anxiety as well as anticipated and actual levels of pain prior to and following the procedure were assessed using a 0–10-point Likert scale. Correlation, bivariate, and regression analyses were performed.

Results

Regarding the biopsy experience, 133/163 (81.6%) of patients reported it as better than expected. Anxiety decreased significantly from a prebiopsy mean score of 5.52 to a postbiopsy mean score of 2.25 (P < 0.001). Average and greatest pain experienced during the procedure had mean scores of 2.03 and 2.77, respectively, both significantly lower compared to preprocedural expectation (mean 4.53) (P < 0.001). Lower pain scores were reported in US-guided procedures compared to stereotactic- and MRI-guided biopsies (P < 0.001). No significant differences in pain scores were seen in those undergoing single versus multiple biopsies, or when benign, elevated-risk, or malignant lesions were sampled. Positive correlations were seen with prebiopsy anxiety levels and procedural pain as well as with anticipated pain and actual procedural pain.

Conclusion

Image-guided biopsies are often better tolerated by patients than anticipated. We stress the benefit of conveying this information to patients prior to biopsy, as decreased anxiety correlates with lower levels of pain experienced during the procedure.
Reevaluating Agricultural Productivity Gaps with Longitudinal Microdata
Authors: Hamory Joan , Kleemans Marieke , Li Nicholas Y , Miguel Edward
Published: September 2020

Recent research has pointed to large gaps in labor productivity between the agricultural and non-agricultural sectors in low-income countries, as well as between workers in rural and urban areas. Most estimates are based on national accounts or repeated cross-sections of microsurvey data, and as a result typically struggle to account for individual selection between sectors. This paper uses long-run individual-level panel data from two low-income countries (Indonesia and Kenya) to explore these gaps. Accounting for individual fixed effects leads to much smaller estimated productivity gains from moving into the non-agricultural sector (or urban areas), reducing estimated gaps by roughly 67%–92%. Furthermore, gaps do not emerge up to 5 years after a move between sectors. We evaluate whether these findings imply a re-assessment of the conventional wisdom regarding sectoral gaps, discuss how to reconcile them with existing cross-sectional estimates, and consider implications for the desirability of sectoral reallocation of labor.
Taxonomic and phylogenetic beta diversity of cricetid rodents in Oaxaca, southern Mexico
Authors: Cornejo-Latorre Cristian , Moreno Claudia E , Martín-Regalado Cintia Natalia , Briones-Salas Miguel
Published: September 2020

Understanding the ecological and historical causes and processes that shape biodiversity distribution patterns remains a challenging and fundamental task in biogeography, ecology, and evolution. To address this issue, taxonomic and phylogenetic β diversity can help us to assess the importance of ecological and historical factors that structure these biotic patterns. To make inferences about the processes underlying current spatial patterns in communities of Cricetidae across the state of Oaxaca, Mexico, their taxonomic and phylogenetic β diversity were assessed jointly. Our aims were: 1) to examine taxonomic and phylogenetic β diversity and their turnover and nestedness components among physiographic subprovinces; 2) to test for statistical significance of observed phylogenetic β diversity against the expected values of a null model; and 3) to evaluate if these metrics were correlated with geographical distance. We obtained the species composition for 12 subprovinces based on distribution models for 49 cricetid species present in Oaxaca, then carried out a maximum likelihood analysis to estimate their phylogenetic relationships. Our results show that the taxonomic and phylogenetic dissimilarities mainly were explained by the turnover component of species and lineages. In almost all pairwise comparisons, the null model approach revealed random patterns for phylogenetic β diversity values and its components. Mantel correlation models showed that the values of total taxonomic and phylogenetic diversity and their components are correlated with the geographical distances between subprovinces. Our results suggest that both taxonomic and phylogenetic β diversity are explained by the interplay between biogeographical history from southern Mexico, and the recent speciation processes in cricetid rodents. Given that speciation processes are allopatric for most cricetid taxa, the high values of spatial turnover can be explained by the small ranges of species, coupled with current abiotic conditions that act as filters, promoting specialization of species on particular conditions. Our results show the importance of the phylogenetic approach to unravel the multidimensional spatial patterns of biodiversity.
Unusual localizations of hydatid cysts: a rare case report from Syria
Authors: Douba Zain , Sinno Judy A , Jawish Haya , Hakim Nour , Mouselli Abdullah , Shihade Mohamad B , Abdullah Mohamed A , Alhames Samer
Published: September 2020

Hydatid disease (HD) is an infection with the metacestode stage of the tapeworm Echinococcus. It is commonly seen in South America, The Middle East, Eastern Mediterranean, Africa and China. Hydatid cysts usually affect the liver followed by the lungs. Involvement in other organs has been reported. However, in the majority of the cases, cysts are localized in one organ or one region. We report a rare case of a 36-year-old woman who presented to the hospital in Syria with long-standing history of non-specific abdominal pain. Computerized tomography showed several hydatid cysts in the liver, spleen, left lung, mediastinum (adjacent to the aortic arch), both breasts and above the right gluteal muscles.
Novel assessment of intestinal anastomotic perfusion using ICG SPY in a continuous flow LVAD patient
Authors: Kaufman Daniel , Sherwinter Danny , Kaleya Ron , Saunders Paul C
Published: September 2020

HeartMate II left ventricular assist device (LVAD) assists heart failure patients by generating continuous flow via axial flow pump placed in the left ventricle. Little is known of the effect of continuous flow on intestinal anastomoses. This is the first case visually documenting altered perfusion patterns in patients with LVADs using indocyanine green (ICG). A 72-year-old male required a colon resection, for adenocarcinoma, following implantation of an LVAD. Perfusion of the anastomosis was evaluated using indocyanine. During the assessment, an unusual perfusion pattern was noticed. Normally, flow as measured by SPY is seen as an initial blush of contrast followed by a gradual, pulsatile increase in the progression of the indocyanine through the tissues. In this patient, instead of the usual initial blush, a continuous beam of ICG was seen to flow though the blood vessels. This novel perfusion pattern is consistent with flow generated from LVAD.
Non-Gaussianity in the weak lensing correlation function likelihood – implications for cosmological parameter biases
Authors: Lin Chien-Hao , Harnois-Déraps Joachim , Eifler Tim , Pospisil Taylor , Mandelbaum Rachel , Lee Ann B , Singh Sukhdeep ,   (The LSST Dark Energy Science Collaboration)
Published: September 2020

We study the significance of non-Gaussianity in the likelihood of weak lensing shear two-point correlation functions, detecting significantly non-zero skewness and kurtosis in 1D marginal distributions of shear two-point correlation functions in simulated weak lensing data. We examine the implications in the context of future surveys, in particular LSST, with derivations of how the non-Gaussianity scales with survey area. We show that there is no significant bias in 1D posteriors of Ωm and σ8 due to the non-Gaussian likelihood distributions of shear correlations functions using the mock data (100 deg2). We also present a systematic approach to constructing approximate multivariate likelihoods with 1D parametric functions by assuming independence or more flexible non-parametric multivariate methods after decorrelating the data points using principal component analysis (PCA). While the use of PCA does not modify the non-Gaussianity of the multivariate likelihood, we find empirically that the 1D marginal sampling distributions of the PCA components exhibit less skewness and kurtosis than the original shear correlation functions. Modelling the likelihood with marginal parametric functions based on the assumption of independence between PCA components thus gives a lower limit for the biases. We further demonstrate that the difference in cosmological parameter constraints between the multivariate Gaussian likelihood model and more complex non-Gaussian likelihood models would be even smaller for an LSST-like survey. In addition, the PCA approach automatically serves as a data compression method, enabling the retention of the majority of the cosmological information while reducing the dimensionality of the data vector by a factor of ∼5.
Separate Universe calibration of the dependence of halo bias on cosmic web anisotropy
Authors: Ramakrishnan Sujatha , Paranjape Aseem
Published: September 2020

We use the Separate Universe technique to calibrate the dependence of linear and quadratic halo bias b1 and b2 on the local cosmic web environment of dark matter haloes. We do this by measuring the response of halo abundances at fixed mass and cosmic web tidal anisotropy α to an infinite wavelength initial perturbation. We augment our measurements with an analytical framework developed in earlier work that exploits the near-lognormal shape of the distribution of α and results in very high precision calibrations. We present convenient fitting functions for the dependence of b1 and b2 on α over a wide range of halo mass for redshifts 0 ≤ z ≤ 1. Our calibration of b2(α) is the first demonstration to date of the dependence of non-linear bias on the local web environment. Motivated by previous results that showed that α is the primary indicator of halo assembly bias for a number of halo properties beyond halo mass, we then extend our analytical framework to accommodate the dependence of b1 and b2 on any such secondary property that has, or can be monotonically transformed to have, a Gaussian distribution. We demonstrate this technique for the specific case of halo concentration, finding good agreement with previous results. Our calibrations will be useful for a variety of halo model analyses focusing on galaxy assembly bias, as well as analytical forecasts of the potential for using α as a segregating variable in multitracer analyses.
Square Kilometre Array Science Data Challenge 1: analysis and results
Authors: Bonaldi A , An T , Brüggen M , Burkutean S , Coelho B , Goodarzi H , Hartley P , Sandhu P K , Wu C , Yu L , Zhoolideh Haghighi M H , Antón S , Bagheri Z , Barbosa D , Barraca J P , Bartashevich D , Bergano M , Bonato M , Brand J , de Gasperin F , Giannetti A , Dodson R , Jain P , Jaiswal S , Lao B , Liu B , Liuzzo E , Lu Y , Lukic V , Maia D , Marchili N , Massardi M , Mohan P , Morgado J B , Panwar M , Prabhakar P , Ribeiro V A R M , Rygl K L J , Sabz Ali V , Saremi E , Schisano E , Sheikhnezami S , Vafaei Sadr A , Wong A , Wong O I
Published: September 2020

As the largest radio telescope in the world, the Square Kilometre Array (SKA) will lead the next generation of radio astronomy. The feats of engineering required to construct the telescope array will be matched only by the techniques developed to exploit the rich scientific value of the data. To drive forward the development of efficient and accurate analysis methods, we are designing a series of data challenges that will provide the scientific community with high-quality data sets for testing and evaluating new techniques. In this paper, we present a description and results from the first such Science Data Challenge 1 (SDC1). Based on SKA MID continuum simulated observations and covering three frequencies (560, 1400, and 9200 MHz) at three depths (8, 100, and 1000 h), SDC1 asked participants to apply source detection, characterization, and classification methods to simulated data. The challenge opened in 2018 November, with nine teams submitting results by the deadline of 2019 April. In this work, we analyse the results for eight of those teams, showcasing the variety of approaches that can be successfully used to find, characterize, and classify sources in a deep, crowded field. The results also demonstrate the importance of building domain knowledge and expertise on this kind of analysis to obtain the best performance. As high-resolution observations begin revealing the true complexity of the sky, one of the outstanding challenges emerging from this analysis is the ability to deal with highly resolved and complex sources as effectively as the unresolved source population.
Structured, relativistic jets driven by radiation
Authors: Coughlin Eric R , Begelman Mitchell C
Published: September 2020

Relativistic jets, or highly collimated and fast-moving outflows, are endemic to many astrophysical phenomena. The jets produced by gamma-ray bursts (GRBs) and tidal disruption events (TDEs) are accompanied by the accretion of material on to a black hole or neutron star, with the accretion rate exceeding the Eddington limit of the compact object by orders of magnitude. In such systems, radiation dominates the energy–momentum budget of the outflow, and the dynamical evolution of the jet is governed by the equations of radiation hydrodynamics. Here, we show that there are analytical solutions to the equations of radiation hydrodynamics in the viscous (i.e. diffusive) regime that describe structured, relativistic jets, which consist of a fast-moving, highly relativistic core surrounded by a slower moving, less relativistic sheath. In these solutions, the slower moving, outer sheath contains most of the mass, and the jet structure is mediated by local anisotropies in the radiation field. We show that, depending on the pressure and density profile of the ambient medium, the angular profile of the jet Lorentz factor is Gaussian or falls off even more steeply with angle. These solutions have implications for the nature of jet production and evolution in hyperaccreting systems, and demonstrate that such jets – and the corresponding jet structure – can be sustained entirely by radiative processes. We discuss the implications of these findings in the context of jetted TDEs and short and long GRBs.
NIHAO – XXV. Convergence in the cusp-core transformation of cold dark matter haloes at high star formation thresholds
Authors: Dutton Aaron A , Buck Tobias , Macciò Andrea V , Dixon Keri L , Blank Marvin , Obreja Aura
Published: September 2020

We use cosmological hydrodynamical galaxy formation simulations from the NIHAO project to investigate the response of cold dark matter (CDM) haloes to baryonic processes. Previous work has shown that the halo response is primarily a function of the ratio between galaxy stellar mass and total virial mass, and the density threshold above which gas is eligible to form stars, n[cm−3]. At low n all simulations in the literature agree that dwarf galaxy haloes are cuspy, but at high n ≳ 100 there is no consensus. We trace halo contraction in dwarf galaxies with n ≳ 100 reported in some previous simulations to insufficient spatial resolution. Provided the adopted star formation threshold is appropriate for the resolution of the simulation, we show that the halo response is remarkably stable for n ≳ 5, up to the highest star formation threshold that we test, n = 500. This free parameter can be calibrated using the observed clustering of young stars. Simulations with low thresholds n ≤ 1 predict clustering that is too weak, while simulations with high star formation thresholds n ≳ 5, are consistent with the observed clustering. Finally, we test the CDM predictions against the circular velocities of nearby dwarf galaxies. Low thresholds predict velocities that are too high, while simulations with n ∼ 10 provide a good match to the observations. We thus conclude that the CDM model provides a good description of the structure of galaxies on kpc scales provided the effects of baryons are properly captured.
tsRBase: a comprehensive database for expression and function of tsRNAs in multiple species
Authors: Zuo Yuanli , Zhu Lei , Guo Zhixin , Liu Wenrong , Zhang Jiting , Zeng Zhen , Wu Qingbin , Cheng Jian , Fu Xin , Jin Yang , Zhao Yun , Peng Yong
Published: September 2020

tRNA-derived small RNAs (tsRNAs) are a class of novel small RNAs, ubiquitously present in prokaryotes and eukaryotes. It has been reported that tsRNAs exhibit spatiotemporal expression patterns and can function as regulatory molecules in many biological processes. Current tsRNA databases only cover limited organisms and ignore tsRNA functional characteristics. Thus, integrating more relevant tsRNA information is helpful for further exploration. Here, we present a tsRNA database, named tsRBase, which integrates the expression pattern and functional information of tsRNAs in multiple species. In tsRBase, we identified 121 942 tsRNAs by analyzing more than 14 000 publicly available small RNA-seq data covering 20 species. This database collects samples from different tissues/cell-lines, or under different treatments and genetic backgrounds, thus helps depict specific expression patterns of tsRNAs under different conditions. Importantly, to enrich our understanding of biological significance, we collected tsRNAs experimentally validated from published literatures, obtained protein-binding tsRNAs from CLIP/RIP-seq data, and identified targets of tsRNAs from CLASH and CLEAR-CLIP data. Taken together, tsRBase is the most comprehensive and systematic tsRNA repository, exhibiting all-inclusive information of tsRNAs from diverse data sources of multiple species. tsRBase is freely available at http://www.tsrbase.org.
Functional hydrogel coatings
Authors: Liu Junjie , Qu Shaoxing , Suo Zhigang , Yang Wei
Published: September 2020

Hydrogels—natural or synthetic polymer networks that swell in water—can be made mechanically, chemically and electrically compatible with living tissues. There has been intense research and development of hydrogels for medical applications since the invention of hydrogel contact lenses in 1960. More recently, functional hydrogel coatings with controlled thickness and tough adhesion have been achieved on various substrates. Hydrogel-coated substrates combine the advantages of hydrogels, such as lubricity, biocompatibility and anti-biofouling properties, with the advantages of substrates, such as stiffness, toughness and strength. In this review, we focus on three aspects of functional hydrogel coatings: (i) applications and functions enabled by hydrogel coatings, (ii) methods of coating various substrates with different functional hydrogels with tough adhesion, and (iii) tests to evaluate the adhesion between functional hydrogel coatings and substrates. Conclusions and outlook are given at the end of this review.
The Ethics of Tobacco Harm Reduction: An Analysis of E-Cigarette Availability From the Perspectives of Utilitarianism, Bioethics, and Public Health Ethics
Authors: Thomas Rebecca , Parker Lisa S , Shiffman Saul
Published: September 2020

Much evidence suggests e-cigarettes are substantially less harmful than combustible cigarettes. Assuming this is true, we analyze the ethical case for a policy of e-cigarette availability (ECA) as a tobacco harm reduction strategy. ECA involves making e-cigarettes available to allow smokers to switch to them, and informing smokers of the lower risks of e-cigarettes vis-à-vis smoking. After suggesting that utilitarian/consequentialist considerations do not provide an adequate ethical analysis, we analyze ECA using two other ethical frameworks. First, ECA is supported by a public health ethics framework. ECA is a population-level intervention consistent with respecting individual autonomy by using the least restrictive means to accomplish public health goals, and it supports equity and justice. Second, ECA is supported by four principles that form a biomedical ethics framework. By reducing smokers’ health risks and not harming them, ECA fulfills principles of beneficence and non-maleficence. Because ECA allows smokers to make informed health decisions for themselves, it fulfills the principle requiring respect for persons and their autonomy. Here, we consider whether nicotine addiction and thus ECA undermine autonomy, and also discuss the ethical warrant for special protections for youth. Finally, ECA can also advance justice by providing a harm reduction alternative for disadvantaged groups that disproportionately bear the devastating consequences of smoking. Policies of differential taxation of cigarettes and e-cigarettes can facilitate adoption of less harmful alternatives by those economically disadvantaged. We conclude that public health and biomedical ethics frameworks are mutually reinforcing and supportive of ECA as a tobacco harm reduction strategy.

Implications: Making e-cigarettes and information about them available is supported as ethical from multiple ethical perspectives.