bluuebunny/crossref_metadata_2025 huggingface dataset:
Expectation pooling: an effective and interpretable pooling method for predicting DNA–protein binding
Authors: Luo Xiao , Tu Xinming , Ding Yang , Gao Ge , Deng Minghua
Published: October 2019

Motivation

Convolutional neural networks (CNNs) have outperformed conventional methods in modeling the sequence specificity of DNA–protein binding. While previous studies have built a connection between CNNs and probabilistic models, simple models of CNNs cannot achieve sufficient accuracy on this problem. Recently, some methods of neural networks have increased performance using complex neural networks whose results cannot be directly interpreted. However, it is difficult to combine probabilistic models and CNNs effectively to improve DNA–protein binding predictions.

Results

In this article, we present a novel global pooling method: expectation pooling for predicting DNA–protein binding. Our pooling method stems naturally from the expectation maximization algorithm, and its benefits can be interpreted both statistically and via deep learning theory. Through experiments, we demonstrate that our pooling method improves the prediction performance DNA–protein binding. Our interpretable pooling method combines probabilistic ideas with global pooling by taking the expectations of inputs without increasing the number of parameters. We also analyze the hyperparameters in our method and propose optional structures to help fit different datasets. We explore how to effectively utilize these novel pooling methods and show that combining statistical methods with deep learning is highly beneficial, which is promising and meaningful for future studies in this field.

Availability and implementation

All code is public in https://github.com/gao-lab/ePooling.

Supplementary information

Supplementary data are available at Bioinformatics online.
MIRUReader: MIRU-VNTR typing directly from long sequencing reads
Authors: Tang Cheng Yee , Ong Rick Twee-Hee
Published: October 2019

Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is widely used to genotype Mycobacterium tuberculosis complex in epidemiological studies for tracking tuberculosis transmission. Recent long-read sequencing technologies from Pacific Biosciences and Oxford Nanopore Technologies can produce reads that are long enough to cover the entire repeat regions in each MIRU-VNTR locus which was previously not possible using the short reads from Illumina high-throughput sequencing technologies. We thus developed MIRUReader for MIRU-VNTR typing directly from long sequence reads.

Availability and implementation

Source code and documentation for MIRUReader program is freely available at https://github.com/phglab/MIRUReader.

Supplementary information

Supplementary data are available at Bioinformatics online.
Domain-invariant features for mechanism of action prediction in a multi-cell-line drug screen
Authors: Boyd Joseph C , Pinheiro Alice , Del Nery Elaine , Reyal Fabien , Walter Thomas
Published: October 2019

Motivation

High-content screening is an important tool in drug discovery and characterization. Often, high-content drug screens are performed on one single-cell line. Yet, a single-cell line cannot be thought of as a perfect disease model. Many diseases feature an important molecular heterogeneity. Consequently, a drug may be effective against one molecular subtype of a disease, but less so against another. To characterize drugs with respect to their effect not only on one cell line but on a panel of cell lines is therefore a promising strategy to streamline the drug discovery process.

Results

The contribution of this article is 2-fold. First, we investigate whether we can predict drug mechanism of action (MOA) at the molecular level without optimization of the MOA classes to the screen specificities. To this end, we benchmark a set of algorithms within a conventional pipeline, and evaluate their MOA prediction performance according to a statistically rigorous framework. Second, we extend this conventional pipeline to the simultaneous analysis of multiple cell lines, each manifesting potentially different morphological baselines. For this, we propose multi-task autoencoders, including a domain-adaptive model used to construct domain-invariant feature representations across cell lines. We apply these methods to a pilot screen of two triple negative breast cancer cell lines as models for two different molecular subtypes of the disease.

Availability and implementation

https://github.com/jcboyd/multi-cell-line or https://zenodo.org/record/2677923.

Supplementary information

Supplementary data are available at Bioinformatics online.
Revision and Update of the Consensus Definitions of Invasive Fungal Disease From the European Organization for Research and Treatment of Cancer and the Mycoses Study Group Education and Research Consortium
Authors: Donnelly J Peter , Chen Sharon C , Kauffman Carol A , Steinbach William J , Baddley John W , Verweij Paul E , Clancy Cornelius J , Wingard John R , Lockhart Shawn R , Groll Andreas H , Sorrell Tania C , Bassetti Matteo , Akan Hamdi , Alexander Barbara D , Andes David , Azoulay Elie , Bialek Ralf , Bradsher Robert W , Bretagne Stephane , Calandra Thierry , Caliendo Angela M , Castagnola Elio , Cruciani Mario , Cuenca-Estrella Manuel , Decker Catherine F , Desai Sujal R , Fisher Brian , Harrison Thomas , Heussel Claus Peter , Jensen Henrik E , Kibbler Christopher C , Kontoyiannis Dimitrios P , Kullberg Bart-Jan , Lagrou Katrien , Lamoth Frédéric , Lehrnbecher Thomas , Loeffler Jurgen , Lortholary Olivier , Maertens Johan , Marchetti Oscar , Marr Kieren A , Masur Henry , Meis Jacques F , Morrisey C Orla , Nucci Marcio , Ostrosky-Zeichner Luis , Pagano Livio , Patterson Thomas F , Perfect John R , Racil Zdenek , Roilides Emmanuel , Ruhnke Marcus , Prokop Cornelia Schaefer , Shoham Shmuel , Slavin Monica A , Stevens David A , Thompson George R , Vazquez Jose A , Viscoli Claudio , Walsh Thomas J , Warris Adilia , Wheat L Joseph , White P Lewis , Zaoutis Theoklis E , Pappas Peter G
Published: October 2019

Background

Invasive fungal diseases (IFDs) remain important causes of morbidity and mortality. The consensus definitions of the Infectious Diseases Group of the European Organization for Research and Treatment of Cancer and the Mycoses Study Group have been of immense value to researchers who conduct clinical trials of antifungals, assess diagnostic tests, and undertake epidemiologic studies. However, their utility has not extended beyond patients with cancer or recipients of stem cell or solid organ transplants. With newer diagnostic techniques available, it was clear that an update of these definitions was essential.

Methods

To achieve this, 10 working groups looked closely at imaging, laboratory diagnosis, and special populations at risk of IFD. A final version of the manuscript was agreed upon after the groups’ findings were presented at a scientific symposium and after a 3-month period for public comment. There were several rounds of discussion before a final version of the manuscript was approved.

Results

There is no change in the classifications of “proven,” “probable,” and “possible” IFD, although the definition of “probable” has been expanded and the scope of the category “possible” has been diminished. The category of proven IFD can apply to any patient, regardless of whether the patient is immunocompromised. The probable and possible categories are proposed for immunocompromised patients only, except for endemic mycoses.

Conclusions

These updated definitions of IFDs should prove applicable in clinical, diagnostic, and epidemiologic research of a broader range of patients at high-risk.
Occult Adenocarcinoma Arising in Crohn’s-Related Strictures: A Case Series
Authors: Singh Kevin , Singh Amandeep , Philpott Jessica , Liska David , Lai Keith
Published: October 2019

Strictures are frequent complications of Crohn’s disease, but malignant small bowel strictures are uncommon and their diagnosis is often challenging. In this case series, we present 3 patients with underlying Crohn’s disease and symptomatic strictures who were found to have adenocarcinomas arising within the strictures at time of operation or after histopathological examination. Given the critical need to identify such malignancies early and the diagnostic difficulty, we use this opportunity to review the presentation, diagnosis, and management of strictures and adenocarcinomas arising in the ileum to raise awareness of this entity so that optimal outcomes can be achieved, if identified early in the disease course.
PCIR: a database of Plant Chloroplast Inverted Repeats
Authors: Zhang Rui , Ge Fangfang , Li Huayang , Chen Yudong , Zhao Ying , Gao Ying , Liu Zhiguo , Yang Long
Published: October 2019

Inverted repeats (IRs) serve as potential biomarkers for genomic instability, DNA replication and other genetic processes. However, little information can be found in databases to help researchers recognize potential IR nucleotides, explore junction sites and annotate related functional genes. Plant Chloroplast Inverted Repeats (PCIR) is an interactive, web-based platform containing various sequenced chloroplast genomes that enables detection, searching and visualization of large-scale detailed information on IRs. PCIR contains many datasets, including 21 433 IRs, 113 plants chloroplast genomes, 16 948 functional genes and 21 659 visual maps. This database offers an online prediction tool for detecting IRs based on DNA sequences. PCIR can also analyze phylogenetic relationships using IR information among different species and provide users with high-quality marker maps. This database will be a valuable resource for IR distribution patterns, related genes and architectural features.
Wolbachia Infection in Two Species: Novel Views on the Colonization Ability of Wolbachia in Aphids
Authors: Chen Rui , Su Xiaomin , Chen Jing , Jiang Liyun , Qiao Ge-Xia
Published: October 2019

Wolbachia pipientis (Rickettsiales: Anaplasmataceae) is an intracellular symbiont residing in arthropods and filarial nematodes. Sixteen supergroups have been described from different host taxa. Four supergroups A, B, M, and N were found in aphids according to prior studies. The cotton aphid, Aphis gossypii, and the green peach aphid, Myzus persicae, are typical polyphagous species with global distributions. We conducted an extensive and systematic survey of Wolbachia infections in these aphids from China. High incidences of Wolbachia infection were detected. The total infection incidence was 60% in A. gossypii and 88% in M. persicae. Both aphid species were infected with supergroups A, B and M. Different incidences of infection were observed among the seven geographical regions in China, which suggested a positive relationship between Wolbachia infections and the geographical distribution of aphid species. Furthermore, multiple infection patterns (M, B, A&M, B&M, and A&B&M) were observed. Infection patterns M and B&M were detected in almost all populations. Patterns A&B&M and B showed geographical restriction in North China. Three factors can possibly influence the Wolbachia infection incidences and patterns: the geographical distribution, aphid species, and different supergroup types.
Associations of recreational and non-recreational physical activity with coronary artery calcium density vs. volume and cardiovascular disease events: the Multi-Ethnic Study of Atherosclerosis
Authors: Thomas Isac C , Takemoto Michelle L , Forbang Nketi I , Larsen Britta A , Michos Erin D , McClelland Robyn L , Allison Matthew A , Budoff Matthew J , Criqui Michael H
Published: October 2019

Aims 

The benefits of physical activity (PA) on cardiovascular disease (CVD) are well known. However, studies suggest PA is associated with coronary artery calcium (CAC), a subclinical marker of CVD. In this study, we evaluated the associations of self-reported recreational and non-recreational PA with CAC composition and incident CVD events. Prior studies suggest high CAC density may be protective for CVD events.

Methods and results 

We evaluated 3393 participants of the Multi-Ethnic Study of Atherosclerosis with prevalent CAC. After adjusting for demographics, the highest quintile of recreational PA was associated with 0.07 (95% confidence interval 0.01–0.13) units greater CAC density but was not associated with CAC volume. In contrast, the highest quintile of non-recreational PA was associated with 0.08 (0.02–0.14) units lower CAC density and a trend toward 0.13 (−0.01 to 0.27) log-units higher CAC volume. There were 520 CVD events over a 13.7-year median follow-up. Recreational PA was associated with lower CVD risk (hazard ratio 0.88, 0.79–0.98, per standard deviation), with an effect size that was not changed with adjustment for CAC composition or across levels of prevalent CAC.

Conclusion 

Recreational PA may be associated with a higher density but not a higher volume of CAC. Non-recreational PA may be associated with lower CAC density, suggesting these forms of PA may not have equivalent associations with this subclinical marker of CVD. While PA may affect the composition of CAC, the associations of PA with CVD risk appear to be independent of CAC.
Personalized antiplatelet therapy guided by a novel detection of platelet aggregation function in stable coronary artery disease patients undergoing percutaneous coronary intervention: a randomized controlled clinical trial
Authors: Zheng Ying-Ying , Wu Ting-Ting , Yang Yi , Hou Xian-Geng , Gao Ying , Chen You , Yang Yi-Ning , Li Xiao-Mei , Ma Xiang , Ma Yi-Tong , Xie Xiang
Published: October 2019

Aims

A number of studies have attempted to demonstrate the benefits associated with personalized antiplatelet therapy guided by platelet function testing, which has led to disappointing findings. In this study, we used a new platelet function test to guide antiplatelet therapy in stable coronary artery disease (CAD) patients after percutaneous coronary intervention (PCI).

Methods and results

In the present randomized controlled trial, a total of 2237 patients with stable CAD undergoing PCI were randomly chosen to be administered personalized antiplatelet therapy (personalized group; n = 1123) or standard antiplatelet treatment (standard group; n = 1114). The patients in the standard therapy group, without detecting the platelet aggregation rate, were administered a 75 mg/day clopidogrel maintenance dosage plus 100 mg/day of aspirin for at least 6 months after the procedure. For the patients in the personalized therapy group, the antiplatelet strategy was performed according to the maximum aggregation rate (MAR), determined using a novel platelet analyser, PL-12. If MAR > 55%, 90 mg ticagrelor was administered twice daily plus 100 mg/day of aspirin after PCI. If MAR ≤55%, 75 mg/day clopidogrel plus 100 mg/day of aspirin was administered after PCI. The primary endpoint was net clinical adverse events, which were a composite of cardiac death, myocardial infarction, stroke, stent thrombosis, urgent revascularization, and bleeding [Bleeding Academic Research Consortium (BARC) definitions, Type 2, 3, or 5], in the 180-day period after randomization. The primary endpoint was reached in 58 patients in the personalized group, compared with 85 patients in the standard group [5.1% vs. 7.5%, hazard ratio (HR) 0.678, 95% confidence interval (CI) 0.486–0.947, P = 0.023], on intention-to-treat analysis. We also found that the net clinical adverse events (including ischaemic and bleeding events) were significantly reduced in the personalized group at 30 days after PCI compared to the standard group (1.5% vs. 3.0%, HR 0.510, 95% CI 0.284–0.915, P = 0.020). We did not find a significant difference in major bleeding events at either the 30-day (0.5% vs. 0.3%, P = 0.322) or the 180-day follow-up (2.1% vs. 1.6%, P = 0.364) between the two groups.

Conclusion

The present study suggests that personalized antiplatelet therapy according to MAR can significantly improve the net clinical benefit 180 days after PCI.
Surgical ablation for atrial fibrillation during isolated coronary artery bypass surgery
Authors: Suwalski Piotr , Kowalewski Mariusz , Jasiński Marek , Staromłyński Jakub , Zembala Marian , Widenka Kazimierz , Brykczyński Mirosław , Skiba Jacek , Zembala Michał Oskar , Bartuś Krzysztof , Hirnle Tomasz , Dziembowska Inga , Deja Marek , Tobota Zdzisław , Maruszewski Bohdan J
Published: October 2019

OBJECTIVES

Our goal was to evaluate early sequelae and long-term survival in patients undergoing isolated coronary artery bypass grafting (CABG) with concomitant surgical ablation for atrial fibrillation (AF).

METHODS

Procedural data from KROK (Polish National Registry of Cardiac Surgery Procedures) were collected. A total of 7879 patients with underlying AF underwent isolated CABG between 2006 and 2018 in 37 reference centres across Poland. The mean follow-up was 4.7 ± 3.5 years [median (interquartile range) 4.3 (1.7–7.4)]. Propensity score matching and Cox proportional hazards models were used to compare isolated CABG + ablation with isolated CABG.

RESULTS

Of the included patients, 346 (4.39%) underwent surgical ablation. Patients in this group were significantly younger (66.4 ± 7.5 vs 69.2 ± 8.2; P < 0.001) but had a non-significant, different baseline surgical risk (EuroSCORE: 2.11 vs 2.50; P = 0.088). After a rigorous 1:3 propensity matching (LOGIT model: 306 cases of isolated CABG + ablation vs 918 of isolated CABG alone), surgical ablation was associated with a lower 30-day risk of death [risk ratio 0.37, 95% confidence interval (CI) 0.15–0.91; P = 0.032] and multiorgan failure (risk ratio 0.29, 95% CI 0.10–0.94; P = 0.029). In the long term, surgical ablation was associated with a significant 33% improved overall survival rate: hazard ratio 0.67, 95% CI 0.49–0.90; P = 0.008. The benefit of ablation was sustained in the subgroups but was most pronounced in lower risk older patients (age >70 years, P = 0.020; elective status, P = 0.011) with 3-vessel disease (P = 0.036), history of a cerebrovascular accident (P = 0.018) and preserved left ventricular function [left ventricular ejection fraction >50%; P = 0.017; no signs of heart failure (per New York Heart Association functional class); P = 0.001] and those undergoing on-pump CABG (P < 0.001).

CONCLUSION

Surgical ablation for AF in patients undergoing isolated CABG is safe and associated with significantly improved long-term survival.
Purcell performances in Palestine under the British Mandate
Authors: Schab Alon
Published: October 2019

Palestine, from the end of World War I to the foundation of the state of Israel, had a vibrant concert scene led partly by local musicians (and from 1933 onwards, by an elite of leading performers and composers who fled from Europe), and partly by the cultural institutions of the British Mandate, including the Palestine Broadcasting Service. While the collaborations between these two forces often yielded inspired musical results, each had its own agendas and priorities. The music of Henry Purcell was perceived as a cultural asset of the British and, as such, its performance became the platform for tacit negotiation of local musical identity, as well as a means to communicate with the British administration. The present study examines how Purcell’s music was treated in Palestine, which works by Purcell were performed, which scores and editions were available to local musicians, how the 250th anniversary of his death (1945) was commemorated, what motivated musicians to perform Purcell in concert, and what happened to the performance of Purcell’s music in Israel after Britain withdrew its forces from Palestine in 1948.
How does socioeconomic status affect the incidence of hospital-treated poisonings? A retrospective study
Authors: Koskela Lauri O , Raatiniemi Lasse V , Liisanantti Janne H
Published: October 2019

Background

Hospital-treated poisonings have a good outcome in general. The role of regional differences and socioeconomic status has been established in intensive care admissions and various causes of death, but not yet in hospital-treated poisonings. We set out to determine whether the incidence of hospital-treated poisonings is affected by the annual income of the residential area.

Methods

All poisonings in Northern Ostrobothnia region of Finland treated in Oulu University Hospital during 2013–2016 were studied. Oulu University Hospital is the primary hospital in the area. Postal code areas of the county were categorized on the basis of their median annual net income as low-, middle- and high-income areas.

Results

A total of 2142 poisoning cases were studied. The number of individual patients was 1525. In the low-income areas, the crude incidence of poisonings was more than 2-fold when compared with the middle- and high-income areas. In adolescents aged 13 to 17 years, the incidence in the low-income areas was almost 3-fold compared with the other two categories at 335/100 000/year (95% CI, 236–463). Four patients (0.2%) died during the hospital stay and 50 patients (2.3%) died within 6 months from the last admission.

Conclusions

The incidence of hospital-treated poisoning was at least 2-fold in low-income areas when compared with middle- or high-income areas. For adolescent population from 13 to 17 years, the incidence in low-income areas was almost 3-fold when compared with other areas.
The contribution of obesity to the population burden of high metabolic cardiovascular risk among different ethnic groups. The HELIUS study
Authors: Perini Wilco , van Valkengoed Irene G M , Snijder Marieke B , Peters Ron J G , Kunst Anton E
Published: October 2019

Background

The burden of cardiovascular risk is distributed unequally between ethnic groups. It is uncertain to what extent this is attributable to ethnic differences in general and abdominal obesity. Therefore, we studied the contribution of general and abdominal obesity to metabolic cardiovascular risk among different ethnic groups.

Methods

We used data of 21 411 participants of Dutch, South-Asian Surinamese, African-Surinamese, Ghanaian, Turkish or Moroccan origin in Healthy Life in an Urban Setting (Amsterdam, the Netherlands). Obesity was defined using body-mass-index (general) or waist-to-height-ratio (abdominal). High metabolic risk was defined as having at least two of the following: triglycerides ≥1.7 mmol/l, fasting glucose ≥5.6 mmol/l, blood pressure ≥130 mmHg systolic and/or ≥85 mmHg diastolic and high-density lipoprotein cholesterol <1.03 mmol/l (men) or <1.29 mmol/l (women).

Results

Among ethnic minority men, age-adjusted prevalence rates of high metabolic risk ranged from 32 to 59% vs. 33% among Dutch men. Contributions of general obesity to high metabolic risk ranged from 7.1 to 17.8%, vs. 10.1% among Dutch men, whereas contributions of abdominal obesity ranged from 52.1 to 92.3%, vs. 53.9% among Dutch men. Among ethnic minority women, age-adjusted prevalence rates of high metabolic risk ranged from 24 to 35% vs. 12% among Dutch women. Contributions of general obesity ranged from 14.6 to 41.8%, vs. 20% among Dutch women, whereas contributions of abdominal obesity ranged from 68.0 to 92.8%, vs. 72.1% among Dutch women.

Conclusions

Obesity, especially abdominal obesity, contributes significantly to the prevalence of high metabolic cardiovascular risk. Results suggest that this contribution varies substantially between ethnic groups, which helps explain ethnic differences in cardiovascular risk.
Differential regulation of physiological activities by RcsB and OmpR in Yersinia enterocolitica
Authors: Meng Jiao , Bai Jiaqi , Xu Junhong , Huang Can , Chen Jingyu
Published: October 2019

A thorough understanding of the mechanisms of Rcs and EnvZ/OmpR phosphorelay systems that allow Yersinia enterocolitica to thrive in various environments is crucial to prevent and control Y. enterocolitica infections. In this study, we showed that RcsB and OmpR have the ability to function differently in modulating a diverse array of physiological processes in Y. enterocolitica. The rcsB mutant stimulated flagella biosynthesis and increased motility, biofilm formation and c-di-GMP production by upregulating flhDC, hmsHFRS and hmsT. However, mutation in ompR exhibited a non-motile phenotype due to the lack of flagella. Biofilm formation was reduced and less c-di-GMP was produced through the downregulation of flhDC, hmsHFRS and hmsT expression when Y. enterocolitica was exposed to low osmolarity conditions. Furthermore, OmpR was identified to be important for Y. enterocolitica to grow in extreme temperature conditions. Importantly, ompR mutations in Y. enterocolitica were more sensitive to polymyxin B and sodium dodecyl sulfate than rcsB mutations. Since motility, biofilm formation and environmental tolerance are critical for bacterial colonization of the host, these findings indicated that OmpR is more critical than RcsB in shaping the pathogenic phenotype of Y. enterocolitica.
Soil bacteria and protists show different sensitivity to polycyclic aromatic hydrocarbons at controlled chemical activity
Authors: Winding Anne , Modrzyński Jakub Jan , Christensen Jan H , Brandt Kristian K , Mayer Philipp
Published: October 2019

This study linked growth inhibition of soil bacteria and protists to the chemical activity (a) of polycyclic aromatic hydrocarbons (PAHs) and compared the sensitivities of bacteria and protists. Passive dosing from pre-loaded silicone provided well-defined and constant a of PAHs in independent tests. Single-species growth inhibition with two bacterial (Pseuodomonas fluorescens DR54 and Sinorhizobium meliloti) and two protist (Cercomonas longicauda and Acanthamoeba castellanii) strains at maximum a (amax) of nine and four PAHs, respectively, showed no inhibition of PAHs with amax below 0.1 (pyrene and anthracene), while growth inhibition was observed for PAHs with amax above 0.1 (e.g. fluorene, fluoranthene and naphthalene). The bacteria were less sensitive than the protists. Soil bacterial community-level growth inhibition by naphthalene was in good agreement with single-species data, but also indicated the presence of sensitive bacteria that were inhibited by a below 0.05 and increasing pre-exposure time giving higher inhibition. The a of 50% inhibition (Ea50) was 0.434 and 0.329 for 0.5 and 4 h pre-exposure time, respectively. Invertebrates tended to be more sensitive than single-celled organisms tested here. This suggests that PAH exposure leads to differential toxicity in soil biota, which may affect soil food web structure and cycling of organic matter.
Production of long-chain hydroxy fatty acids by Starmerella bombicola
Authors: De Graeve Marilyn , Van de Velde Isabelle , Saey Lien , Chys Maarten , Oorts Hanne , Kahriman Hümeyra , Mincke Stein , Stevens Christian , De Maeseneire Sofie L , Roelants Sophie L K W , Soetaert Wim K G
Published: October 2019

To decrease our dependency for the diminishing source of fossils resources, bio-based alternatives are being explored for the synthesis of commodity and high-value molecules. One example in this ecological initiative is the microbial production of the biosurfactant sophorolipids by the yeast Starmerella bombicola. Sophorolipids are surface-active molecules mainly used as household and laundry detergents. Because S. bombicola is able to produce high titers of sophorolipids, the yeast is also used to increase the portfolio of lipophilic compounds through strain engineering. Here, the one-step microbial production of hydroxy fatty acids by S. bombicola was accomplished by the selective blockage of three catabolic pathways through metabolic engineering. Successful production of 17.39 g/l (ω-1) linked hydroxy fatty acids was obtained by the successive blockage of the sophorolipid biosynthesis, the β-oxidation and the ω-oxidation pathways. Minor contamination of dicarboxylic acids and fatty aldehydes were successfully removed using flash chromatography. This way, S. bombicola was further expanded into a flexible production platform of economical relevant compounds in the chemical, food and cosmetic industries.
Genome Assembly of the A-Group Wolbachia in Nasonia oneida Using Linked-Reads Technology
Authors: Wang Xiaozhu , Xiong Xiao , Cao Wenqi , Zhang Chao , Werren John H , Wang Xu
Published: October 2019

Wolbachia are obligate intracellular bacteria which commonly infect various nematode and arthropod species. Genome sequences have been generated from arthropod samples following enrichment for the intracellular bacteria, and genomes have also been assembled from arthropod whole-genome sequencing projects. However, these methods remain challenging for infections that occur at low titers in hosts. Here we report the first Wolbachia genome assembled from host sequences using 10× Genomics linked-reads technology. The high read depth attainable by this method allows for recovery of intracellular bacteria that are at low concentrations. Based on the depth differences (714× for the insect and 59× for the bacterium), we assembled the genome of a Wolbachia in the parasitoid jewel wasp species Nasonia oneida. The final draft assembly consists of 1,293, 06 bp in 47 scaffolds with 1,114 coding genes and 97.01% genome completeness assessed by checkM. Comparisons of the five Multi Locus Sequence Typing genes revealed that the sequenced Wolbachia genome is the A1 strain (henceforth wOneA1) previously reported in N. oneida. Pyrosequencing confirms that the wasp strain lacks A2 and B types previously detected in this insect, which were likely lost during laboratory culturing. Assembling bacterial genomes from host genome projects can provide an effective method for sequencing bacterial genomes, even when the infections occur at low density in sampled tissues.
Two-sensor microtremor SPAC method: potential utility of imaginary spectrum components
Authors: Cho Ikuo
Published: October 2019

We build a model of discretization errors, known as directional aliasing, to theoretically evaluate how biases in the microtremor spatial autocorrelation (SPAC) coefficient, or the real part of the SPAC spectrum of microtremor analysis, are related to the magnitudes of the imaginary part when a seismic array of only two sensors is used. By using this model, we investigate the potential utility of the imaginary spectrum component as an indicator of applicability of the two-sensor SPAC method to the field of microtremors generated at an observation site. Field data of microtremors from compact seismic arrays (1–15 m) are used to test the model. It is found that, when the imaginary components are very large in magnitude (where the threshold depends on the rk, the array radius times the wavenumber), the field of microtremors is dominated by waves arriving from a single direction parallel to the array axis and the SPAC coefficients tend to be underestimated in small rk ranges (i.e. rk < 3.8; the range considered throughout this study). In the present study, which is based on the observations of 400 microtremor arrays, the underestimates seldom exceeded 30 per cent. The SPAC coefficient estimates could be corrected in that case by using information on the imaginary part. When the imaginary components are very modest in magnitude, by contrast, there are two possible scenarios: either (i) the waves are arriving predominantly from a single direction perpendicular to the array axis and the SPAC coefficients are wildly overestimated (i.e. there was a small percentage of low-quality data, with relative errors exceeding +50 per cent, based on the observed data analyses), or (ii) the wavefield is close to isotropic and the SPAC coefficients are unbiased (i.e. 70–90 per cent of all observed data fell within the relative error range of ±20 per cent). It is difficult in that case to have SPAC coefficient estimates corrected by using information on the imaginary part alone.
Shear wave structure of a transect of the Los Angeles basin from multimode surface waves and H/V spectral ratio analysis
Authors: Perton Mathieu , Spica Zack J , Clayton Robert W , Beroza Gregory C
Published: October 2019

We use broad-band stations of the ‘Los Angeles Syncline Seismic Interferometry Experiment’ (LASSIE) to perform a joint inversion of the Horizontal to Vertical spectral ratios (H/V) and multimode dispersion curves (phase and group velocity) for both Rayleigh and Love waves at each station of a dense line of sensors. The H/V of the autocorrelated signal at a seismic station is proportional to the ratio of the imaginary parts of the Green’s function. The presence of low-frequency peaks (∼0.2 Hz) in H/V allows us to constrain the structure of the basin with high confidence to a depth of 6 km. The velocity models we obtain are broadly consistent with the SCEC CVM-H community model and agree well with known geological features. Because our approach differs substantially from previous modelling of crustal velocities in southern California, this research validates both the utility of the diffuse field H/V measurements for deep structural characterization and the predictive value of the CVM-H community velocity model in the Los Angeles region. We also analyse a lower frequency peak (∼0.03 Hz) in H/V and suggest it could be the signature of the Moho. Finally, we show that the independent comparison of the H and V components with their corresponding theoretical counterparts gives information about the degree of diffusivity of the ambient seismic field.
Physiological and pathological roles of LRRK2 in the nuclear envelope integrity
Authors: Shani Vered , Safory Hazem , Szargel Raymonde , Wang Ninghan , Cohen Tsipora , Elghani Fatimah Abd , Hamza Haya , Savyon Mor , Radzishevsky Inna , Shaulov Lihi , Rott Ruth , Lim Kah-Leong , Ross Christopher A , Bandopadhyay Rina , Zhang Hui , Engelender Simone
Published: October 2019

Mutations in LRRK2 cause autosomal dominant and sporadic Parkinson’s disease, but the mechanisms involved in LRRK2 toxicity in PD are yet to be fully understood. We found that LRRK2 translocates to the nucleus by binding to seven in absentia homolog (SIAH-1), and in the nucleus it directly interacts with lamin A/C, independent of its kinase activity. LRRK2 knockdown caused nuclear lamina abnormalities and nuclear disruption. LRRK2 disease mutations mostly abolish the interaction with lamin A/C and, similar to LRRK2 knockdown, cause disorganization of lamin A/C and leakage of nuclear proteins. Dopaminergic neurons of LRRK2 G2019S transgenic and LRRK2 −/− mice display decreased circularity of the nuclear lamina and leakage of the nuclear protein 53BP1 to the cytosol. Dopaminergic nigral and cortical neurons of both LRRK2 G2019S and idiopathic PD patients exhibit abnormalities of the nuclear lamina. Our data indicate that LRRK2 plays an essential role in maintaining nuclear envelope integrity. Disruption of this function by disease mutations suggests a novel phosphorylation-independent loss-of-function mechanism that may synergize with other neurotoxic effects caused by LRRK2 mutations.
Graph clustering in industrial networks
Authors: Bouet V , Klimenko A Y
Published: October 2019

The present work investigates clustering of a graph-based representation of industrial connections derived from international trade data by Hidalgo et al. (2007, The product space conditions the development of nations. Science, 317) and confirms the existence of nine industrial clusters that are reasonably consistent with expected historical patterns of diffusion of innovation and technology. This supports the notion that technological development occurs in sequential waves of innovation. The clustering method developed in this work follows conceptual ideas introduced by Pons and Latapy (2006, Computing communities in large networks using random walks. J. Graph Alg. Appl., 10, 191–218), Lambiotte and Barahona (2009, Laplacian dynamics and multiscale modular structure in networks. arXiv.org.) and other researchers—random walks can be used to assess hierarchical structures of network communities. We, however, implement these ideas differently in order to match the physics of the problem under consideration and introduce a hierarchical clustering procedure that is progressive in time and is combined with concurrent reordering of the elements. An equivalent spectral interpretation of the clustering procedure is also given and discussed in the paper.
Rise of Machine Agency: A Framework for Studying the Psychology of Human–AI Interaction (HAII)
Authors: Sundar S Shyam
Published: October 2019

Advances in personalization algorithms and other applications of machine learning have vastly enhanced the ease and convenience of our media and communication experiences, but they have also raised significant concerns about privacy, transparency of technologies and human control over their operations. Going forth, reconciling such tensions between machine agency and human agency will be important in the era of artificial intelligence (AI), as machines get more agentic and media experiences become increasingly determined by algorithms. Theory and research should be geared toward a deeper understanding of the human experience of algorithms in general and the psychology of Human–AI interaction (HAII) in particular. This article proposes some directions by applying the dual-process framework of the Theory of Interactive Media Effects (TIME) for studying the symbolic and enabling effects of the affordances of AI-driven media on user perceptions and experiences.
Forced Technology Transfer and the US–China Trade War: Implications for International Economic Law
Authors: Qin Julia Ya
Published: October 2019

Forced technology transfer has emerged from the US–China trade war as a new issue of systemic importance. The USA, the European Union, and Japan have jointly condemned forced technology transfer as a practice undermining the proper function of international trade and called for new WTO rules to discipline the practice. This article examines the issue in the broad context of international economic law. It seeks to address the following questions: What does ‘forced technology transfer’ mean? Where did this practice come from? Why is there insufficient international regulation on the issue? What exactly are the problems inherent in such practice? And what can be done to improve the relevant international regulation?
A prophylaxis study of acute exacerbation of interstitial pneumonia after lung cancer surgery
Authors: Ito Hiroyuki , Nakayama Haruhiko , Yokose Tomoyuki , Nagashima Takuya , Morohoshi Takao , Tajiri Michihiko , Maehara Takamitsu , Watanabe Katsuya , Arai Hiromasa , Yamamoto Taketsugu , Woo Tekkan , Nishii Teppei , Ishikawa Yoshihiro , Morita Satoshi , Masuda Munetaka
Published: October 2019

Introduction

Acute exacerbation of interstitial pneumonia (AE-IP) is a lethal complication after lung surgery. We conducted a prospective, multi-institutional phase II trial to assess the efficacy and safety of prophylactic measures.

Method

Patients with lung cancer with dorsal subpleural fibrotic changes occupying three or more segments of both lower lobes and planned anatomical lung resection were enrolled. Prior to surgery, patients received a 125-mg bolus injection of methylprednisolone and continuous intravenous infusion of sivelestat sodium hydrate (sivelestat) for 2 days.

Results

Sixty-nine patients were analysed. Preoperative high-resolution computed tomography (HRCT) showed 37 (53.6%) cases presented with usual interstitial pneumonia (UIP) and possible UIP pattern. There were 60 lobectomies and 9 segmentectomies. Thirty-eight cases were in clinical stage I. No adverse events associated with prophylaxis were observed. There were four cases of AE-IP (5.8%), higher than the expected 2.0%. Three of the four cases showed inconsistencies with the UIP pattern in preoperative HRCT and were pathologically diagnosed as UIP. All patients died of respiratory failure. Overall, 89.9% were diagnosed as idiopathic interstitial pneumonias; UIP was found in 48 patients (69.6%). Severe post-operative complications occurred in 11.6% of the cases. There were 35 deaths, 17 cases of lung cancer and 11 cases related to interstitial pneumonias. The overall survival rate at 3 years was 41.8% of the total and 47.2% of cases with clinical stage I.

Conclusions

Perioperative use of sivelestat and low-dose methylprednisolone in patients with anatomical lung resection was safe but did not prove to be a prophylactic effect for AE-IP.
Visualization of different carrier concentrations in n-type-GaN semiconductors by phase-shifting electron holography with multiple electron biprisms
Authors: Yamamoto Kazuo , Nakano Kiyotaka , Tanaka Atsushi , Honda Yoshio , Ando Yuto , Ogura Masaya , Matsumoto Miko , Anada Satoshi , Ishikawa Yukari , Amano Hiroshi , Hirayama Tsukasa
Published: October 2019

Phase-shifting electron holography (PS-EH) using a transmission electron microscope (TEM) was applied to visualize layers with different concentrations of carriers activated by Si (at dopant levels of 1019, 1018, 1017 and 1016 atoms cm−3) in n-type GaN semiconductors. To precisely measure the reconstructed phase profiles in the GaN sample, three electron biprisms were used to obtain a series of high-contrast holograms without Fresnel fringes generated by a biprism filament, and a cryo-focused-ion-beam (cryo-FIB) was used to prepare a uniform TEM sample with less distortion in the wide field of view. All layers in a 350-nm-thick TEM sample were distinguished with 1.8-nm spatial resolution and 0.02-rad phase-resolution, and variations of step width in the phase profile (corresponding to depletion width) at the interfaces between the layers were also measured. Thicknesses of the active and inactive layers at each dopant level were estimated from the observed phase profile and the simulation of theoretical band structure. Ratio of active-layer thickness to total thickness of the TEM sample significantly decreased as dopant concentration decreased; thus, a thicker TEM sample is necessary to visualize lower carrier concentrations; for example, to distinguish layers with dopant concentrations of 1016 and 1015 atoms cm−3. It was estimated that sample thickness must be more than 700 nm to make it be possible to detect sub-layers by the combination of PS-EH and cryo-FIB.
Race, Socioeconomic Status, and Health-Care Access Disparities in Ovarian Cancer Treatment and Mortality: Systematic Review and Meta-Analysis
Authors: Karanth Shama , Fowler Mackenzie E , Mao XiHua , Wilson Lauren E , Huang Bin , Pisu Maria , Potosky Arnold , Tucker Tom , Akinyemiju Tomi
Published: October 2019

Background

Ovarian cancer remains a leading cause of death from gynecological malignancies. Race, socioeconomic status (SES), and access to health care are important predictors of quality treatment and survival. We provide a systematic review and meta-analysis on the role of these predictors on disparities in ovarian cancer treatment and mortality.

Methods

Using the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines, we searched PubMed, EMBASE, and Scopus for relevant articles published between January 2000 and March 2017. We selected studies published in the United States that evaluated the role of race, SES, or health-care access on disparities in ovarian cancer treatment or survival. Pooled relative risk (RR) and 95% confidence intervals (CIs) were calculated for each outcome using a random-effects model.

Results

A total of 41 studies met the inclusion criteria for systematic review. In meta-analysis, there was a 25% decrease (RR = 0.75, 95% CI = 0.66 to 0.84) in receipt of adherent ovarian cancer treatment and 18% increased risk (RR = 1.18, 95% CI = 1.11 to 1.26) of mortality for blacks compared to whites. Receipt of adherent ovarian cancer treatment was 15% lower (RR = 0.85, 95% CI = 0.77 to 0.94) in the lowest vs highest SES group and 30% lower (RR = 0.70, 95% CI = 0.58 to 0.85) among patients at lower vs higher hospital volumes.

Conclusion

We found consistent and strong evidence for continued lack of quality ovarian cancer treatment and higher mortality among ovarian cancer patients who are black, are of low SES, and/or have poor access to care. Interventions focused on these groups targeting specific barriers to care are needed to reduce disparities in ovarian cancer treatment and mortality.
Building Resilience by Becoming a Circus Artist
Authors: VAN ES VERA , ROMMES ELS , De Kwaadsteniet Leontien
Published: October 2019

Due to the traumatic events they may have experienced, refugee youth are vulnerable to mental health problems. Social Circus is a psycho-social intervention that aims to enhance resilience by promoting self-esteem, interpersonal trust and social support through classes in circus arts. To explore these effects on refugee youth, a qualitative study was conducted in south-east Turkey. Semi-structured interviews and participative observations revealed that circus classes offered participants structure and a new purpose in life. Participating youth became more active, while impulsive behaviour decreased. Experiencing success through visible progress and holding the positively valued position of a circus artist seemed to contribute to the children’s self-esteem. In addition, the mental and physical support received during circus classes could increase interpersonal trust. By creating opportunities for social interaction and building relationships, Social Circus may also promote social support. This study provides preliminary evidence that Social Circus may enhance resilience in refugee youth.
Higher Education in the Context of Mass Displacement: Towards Sustainable Solutions for Refugees
Authors: Pherali Tejendra , Abu Moghli Mai
Published: October 2019

This article provides a theoretical review of higher-education (HE) access for refugees in humanitarian situations. Drawing upon the case of Syrian refugees in Lebanon, we discuss challenges and opportunities around developing new HE modalities to enhance its role in the humanitarian response as well as reconfiguring refugees’ ‘unknowable future’. We also examine opportunities for HE access and the process of multidimensional partnerships, engaging with emerging practices and experiments in this sector from the perspective of future education and highlighting the opportunities that investment in HE can serve for solidarity and peace in contexts of mass displacement. Finally, we reflect upon possible ways forward and offer insights into potential sustainable solutions not only for Syrian refugees in Lebanon, but also for young displaced populations globally.
Acculturation, Social Support and Mental Health Outcomes among Syrian Refugees in Germany
Authors: Green Molly , King Elizabeth , Fischer Florian
Published: October 2019

Syrian refugees in Germany number around 700,000 and they are managing acculturation and mental health issues. In May–July 2018, we conducted a cross-sectional survey among 97 Syrian refugees in Germany using measures of acculturation, social support, depressive symptoms and wellbeing. We ran linear-regression models and created an interaction term of two aspects of acculturation, focused on the outcomes of depressive symptoms and wellbeing, along with the possible moderation of social support. Affiliation with German culture was positively associated with wellbeing. More acculturation to German culture may promote positive mental health. Higher levels of social support were associated with lower levels of wellbeing and higher levels of depressive symptoms; this could reflect reverse causality or more connections with those back home. This study provides insight into acculturation and mental health among a significant refugee population in Germany.