bluuebunny/crossref_metadata_2025 huggingface dataset:
Birds suppress pests in corn but release them in soybean crops within a mixed prairie/agriculture system
Authors: Garfinkel Megan B , Minor Emily S , Whelan Christopher J
Published: January 2020

Birds provide ecosystem services (pest control) in many agroecosystems and have neutral or negative ecological effects (disservices) in others. Large-scale, conventional row crop agriculture is extremely widespread globally, yet few studies of bird effects take place in these agroecosystems. We studied indirect effects of insectivorous birds on corn and soybean crops in fields adjacent to a prairie in Illinois (USA). We hypothesized that prairie birds would forage for arthropods in adjacent crop fields and that the magnitude of services or disservices would decrease with distance from the prairie. We used bird-excluding cages over crops to examine the net effect of birds on corn and soybean grain yield. We also conducted DNA metabarcoding to identify arthropod prey in fecal samples from captured birds. Our exclosure experiments revealed that birds provided net services in corn and net disservices in soybeans. Distance from prairie was not a significant predictor of exclosure treatment effect in either crop. Many bird fecal samples contained DNA from both beneficial arthropods and known economically significant pests of corn, but few economically significant pests of soybeans. Song Sparrows (Melospiza melodia), one of our most captured species, most commonly consumed corn rootworms, an economically significant pest of corn crops. We estimated that birds in this system provided a service worth approximately US $275 ha−1 in corn yield gain, and a disservice valued at approximately $348 ha−1 in soybean yield loss. Our study is the first to demonstrate that birds can provide substantial and economically valuable services in field corn, and disservices in soybean crops. The contrasting findings in the 2 crop systems suggest a range of bird impacts within widespread agroecosystems and demonstrate the importance of quantifying net trophic effects.
The Psychology of International Law: An Introduction
Authors: van Aaken Anne , Broude Tomer
Published: January 2020

Public international law scholarship opens evermore to social science theories and methodologies, but the implications of cognitive research and behavioural economics have not been systematically explored, even though they have been successfully applied to domestic legal issues and are increasingly used in public policy and regulation. In this symposium, we aim to fill two research gaps: first, international law and economics and international political economy rarely use behavioural insights, while behavioural law and economics lacks international dimensions, and, second, international political psychology sidesteps the importance of international norms. This introduction surveys the main psychological angles employed in the articles of the symposium as well as the difficulties envisioned in this research agenda of applying psychology to international law and using experiments for the study of international law. These difficulties notwithstanding, behavioural studies have generated many insights that have the potential to greatly enrich our understanding of international law.
Taurodontism in the first permanent molars in Van der Woude syndrome compared to isolated cleft palate
Authors: Awadh Wael , Pegelow Marie , Heliövaara Arja , Rice David P
Published: January 2020

Objectives

To analyse prevalence, pattern, and severity of taurodontism in individuals with Van der Woude syndrome (VWS) exhibiting cleft palate and compare with aged-matched non-syndromic cleft palate (NSCP) and non-cleft controls.

Materials and methods

One hundred and seventy-eight dental panoramic tomographs (DPTs) (105 girls and 73 boys) consisting of 42 VWS patients (x¯=8.55±1.02 years), 42 NSCP patients (x¯=8.59±1.02 years), and 94 normative non-cleft children (x¯=8.79±1.16 years) were assessed and their first permanent molars evaluated. Measurement 3 of the taurodontism index developed by Shifman and Chanannel with the Tulensalo modification was used. Prevalence, pattern, and severity were compared between groups. Statistical differences were determined by one-way analysis of variance and Fisher test. Repeatability was calculated by Cohens Kappa test.

Results

The prevalence of taurodontic molars was 59.5% in VWS, 45.2% in NSCP, and 26.6% in non-cleft controls. The prevalence and severity of taurodontism in VWS and NSCP were significantly higher than in non-cleft children in all first permanent molars. There was no significant difference in prevalence and severity between VWS and NSCP. The odds for having taurodontism in the VWS group was approximately double compared to the NSCP group. Most of the taurodontic molars showed hypotaurodontism and taurodontism occurred bilaterally more frequently than unilaterally.

Conclusion

This study shows a higher prevalence of taurodontism in VWS and NSCP. Most taurodontic molars are hypotaurodontic and most occur bilaterally.
Selection-Driven Gene Inactivation in Salmonella
Authors: Cherry Joshua L
Published: January 2020

Bacterial genes are sometimes found to be inactivated by mutation. This inactivation may be observable simply because selection for function is intermittent or too weak to eliminate inactive alleles quickly. Here, I investigate cases in Salmonella enterica where inactivation is instead positively selected. These are identified by a rate of introduction of premature stop codons to a gene that is higher than expected under selective neutrality, as assessed by comparison to the rate of synonymous changes. I identify 84 genes that meet this criterion at a 10% false discovery rate. Many of these genes are involved in virulence, motility and chemotaxis, biofilm formation, and resistance to antibiotics or other toxic substances. It is hypothesized that most of these genes are subject to an ongoing process in which inactivation is favored under rare conditions, but the inactivated allele is deleterious under most other conditions and is subsequently driven to extinction by purifying selection.
Bacterial Origin and Reductive Evolution of the CPR Group
Authors: Bokhari Rijja Hussain , Amirjan Nooreen , Jeong Hyeonsoo , Kim Kyung Mo , Caetano-Anollés Gustavo , Nasir Arshan
Published: January 2020

The candidate phyla radiation (CPR) is a proposed subdivision within the bacterial domain comprising several candidate phyla. CPR organisms are united by small genome and physical sizes, lack several metabolic enzymes, and populate deep branches within the bacterial subtree of life. These features raise intriguing questions regarding their origin and mode of evolution. In this study, we performed a comparative and phylogenomic analysis to investigate CPR origin and evolution. Unlike previous gene/protein sequence-based reports of CPR evolution, we used protein domain superfamilies classified by protein structure databases to resolve the evolutionary relationships of CPR with non-CPR bacteria, Archaea, Eukarya, and viruses. Across all supergroups, CPR shared maximum superfamilies with non-CPR bacteria and were placed as deep branching bacteria in most phylogenomic trees. CPR contributed 1.22% of new superfamilies to bacteria including the ribosomal protein L19e and encoded four core superfamilies that are likely involved in cell-to-cell interaction and establishing episymbiotic lifestyles. Although CPR and non-CPR bacterial proteomes gained common superfamilies over the course of evolution, CPR and Archaea had more common losses. These losses mostly involved metabolic superfamilies. In fact, phylogenies built from only metabolic protein superfamilies separated CPR and non-CPR bacteria. These findings indicate that CPR are bacterial organisms that have probably evolved in an Archaea-like manner via the early loss of metabolic functions. We also discovered that phylogenies built from metabolic and informational superfamilies gave contrasting views of the groupings among Archaea, Bacteria, and Eukarya, which add to the current debate on the evolutionary relationships among superkingdoms.
Does Gender Matter in the Receipt of Informal Care Among Community-Dwelling Older Adults? Evidence from a Cross-National Comparative Study Across the United States, South Korea, and China
Authors: Kwak Minyoung , Kim BoRin , Lee Hyunjoo , Zhang Jiaan
Published: January 2020

Objectives

This study compares patterns of gender difference in the receipt of informal care among community-dwelling older adults across the United States, Korea, and China where family-oriented systems for providing care to older adults are emphasized.

Method

Data came from the 2014 Health and Retirement Study, the 2014 Korea Longitudinal Study of Aging, and the 2015 China Health and Retirement Longitudinal Study. Logistic regression models were used to predict the receipt of informal care by gender. We also examined how the effects of health and living arrangement on the receipt of informal care differ depending on gender.

Results

In the United States and China, older women were more likely to receive informal care than men. However, older Korean women were less likely to receive informal care than men. The effects of health and living arrangement on the use of informal care were moderated by gender in different ways across countries.

Discussion

This study provides evidence that patterns of gender differences in the receipt of informal care vary across the three countries. More attention needs to be paid to the design and implementation of long-term supports and services to address the unique patterns of gender difference in care arrangement in each country.
Volumetric Microsampling of Capillary Blood Spot vs Whole Blood Sampling for Therapeutic Drug Monitoring of Tacrolimus and Cyclosporin A: Accuracy and Patient Satisfaction
Authors: Mbughuni Michael M , Stevens Maria A , Langman Loralie J , Kudva Yogish C , Sanchez William , Dean Patrick G , Jannetto Paul J
Published: January 2020

Background

Immunosuppressant therapeutic drug monitoring (TDM) usually requires outpatient travel to hospitals or phlebotomy sites for venous blood collection; however Mitra® Microsampling Device (MSD) sampling could allow self-collection and shipping of samples to a laboratory for analysis. This study examined the feasibility of using volumetric microsampling by MSD for TDM of tacrolimus (TaC) and cyclosporin A (CsA) in transplant patients, along with their feedback on the process.

Methods

MSD was used to collect TaC and CsA from venous (VB) or capillary (CB) blood. The MSDs were rehydrated, extracted, and analyzed using on-line solid phase extraction coupled to tandem mass spectrometry (SPE-MS/MS). We report an abbreviated method validation of the MSD including: accuracy, precision, linearity, carry-over, and stability using residual venous whole blood (VB) samples. Subsequent clinical validation compared serially collected MSD + CB against VB (200 µL) from transplant patients.

Results

Accuracy comparing VB vs. MSD+VB showed high clinical concordance (TaC = 89% and CsA = 98%). Inter- and intra-precision was ≤11.5 %CV for TaC and CsA. Samples were stable for up to 7 days at room temperature with an average difference of <10%. Clinical validation with MSD+CB correlated well with VB for CsA (slope = 0.95, r2 = 0.88, n = 47) and TaC (slope = 0.98, r2 = 0.82, n = 49). CB vs. VB gave concordance of 94% for CsA and 79% for TaC. A satisfaction survey showed 82% of patients preferred having the capillary collection option.

Conclusion

Transplant patients favored having the ability to collect capillary samples at home for TaC/CsA monitoring. Our results demonstrate good concordance between MSD+CB and VB for TaC and CsA TDM, but additional studies are warranted.
Rates of Fentanyl Positivity in Neonatal Urine Following Maternal Analgesia During Labor and Delivery
Authors: Novikov Natasha , Melanson Stacy E F , Ransohoff Jaime R , Petrides Athena K
Published: January 2020

Background

Fentanyl is commonly given as an analgesic during labor and delivery. The extent of transplacental drug transfer and fetal exposure is not well studied. We analyzed the relationship between neonatal urine fentanyl results and various peripartum factors.

Methods

A total of 96 neonates with urine toxicology screening between January 2017 and September 2018 were included in the study. Medical record review was used to obtain maternal, neonatal, and anesthesia parameters. A subset of 9 specimens were further tested for levels of fentanyl and norfentanyl by liquid chromatography-tandem mass spectrometry.

Results

In 29% (n = 24) of cases associated with fentanyl-containing labor analgesia, neonatal toxicology screens were positive for the presence of fentanyl. Positive test results strongly correlated with the cumulative dose and duration of labor analgesia (P < 0.001). The odds of positive neonatal fentanyl screen results increased 4-fold for every 5 hours of maternal exposure to labor analgesia. Importantly, however, neonatal outcomes for infants with positive and negative urine fentanyl screens were the same.

Conclusions

Our study establishes that maternal fentanyl analgesia is strongly associated with positive neonatal urine fentanyl screens and suggests that more judicious use of these laboratory tests may be warranted.
The FDA authorization of direct-to-consumer genetic testing for three BRCA1/2 pathogenic variants: a twitter analysis of the public’s response
Authors: Roberts Megan C , Allen Caitlin G , Andersen Brittany L
Published: January 2020

Objectives

In March 2018, the Food and Drug Administration (FDA) announced its authorization of a direct-to-consumer (DTC) genetic test for three pathogenic BRCA1/2 variants. We sought to determine to whether social media discussion increased following the authorization, who was driving social media conversations, and what topics were discussed.

Methods

Using Crimson Hexagon, we described tweets before, during, and after the FDA announcement authorizing 23andMe to return BRCA1/2 results (3/4/18–3/10/18). We conducted qualitative coding of a subset of 605 tweets to better understand Twitter communication.

Results

We identified 11 055 twitter posts across the week of FDA’s announcement. Twitter discourse about 23andMe and the FDA authorization peaked the day following the FDA’s press release. Most tweets (48.6%) were informational and 26.3% were either expressing opinions (about 23andMe and/or FDA authorization, 14.9%) or testimonials (personal experiences with genetic testing, 11.4%). The types of tweets varied over the week-long period (P <  .001).

Discussion

Twitter discussion about the FDA’s authorization of DTC for three pathogenic BRCA1/2 variants increased immediately following the announcement. As more genetic technologies are brought to the DTC market, social media sites, like Twitter, will play a role in disseminating this information, providing a platform for information exchange, consumer testimonials, opinion pieces, and research.
Mass Spectrometry-Based Rapid Quantitative Bioanalysis of Flibanserin: Pharmacokinetic and Brain Tissue Distribution Study in Female Rats
Authors: Sharma Manish Kumar , Rathod Rajeshwari , Sengupta Pinaki
Published: January 2020

Flibanserin (FLB) is the first United States Food and Drug Administration (USFDA) approved serotonin modulator recently marketed to treat acquired generalized women hypoactive sexual desire disorder. The scope of this study was to develop and validate a sensitive, selective and reliable ultra-performance liquid chromatography–mass spectroscopy/mass spectroscopy-based quantification method for FLB in rat plasma as well as brain tissue samples. The method includes a simple liquid–liquid sample extraction procedure. FLB was subjected to chromatographic separation using a poroshell C18 column with the mobile phase comprising a mixture of acetonitrile (ACN), 10 mM ammonium acetate and acetic acid (90:10:0.1, v/v/v). Detection and quantification of FLB after positive electrospray ionization were carried out in selective ion monitoring mode. The fragment ions (m/z) of FLB (parent ion: 391.1741) and IS (parent ion: 448.1550) were monitored at 161.0704 and 285.0917, respectively. A linear response of FLB was observed over a concentration range of 2.5–600 ng/mL in plasma and 5–500 ng/mL in brain tissue homogenate. The intra- and inter-day precision and accuracy of the method met the acceptable limits specified in the USFDA bioanalytical method validation guideline. The analyte was found to be stable in benchtop, freeze-thaw, auto-injector and dry extract stability studies. The developed method was used to quantitate FLB in the plasma and brain tissue of a single-dose oral pharmacokinetic and brain tissue distribution study in female rats. Maximum FLB concentration in plasma and brain was achieved within an hour; however, the total amount of the drug that reached the brain was significantly less than in plasma. Rate of elimination of FLB from brain was also faster resulting in a lesser half-life in brain compared to the plasma.
Comparison of Serum Concentrations of Ustekinumab Obtained by Three Commercial Assays in Patients with Crohn’s Disease
Authors: Verdon Christine , Vande Casteele Niels , Heron Valérie , Germain Pascale , Afif Waqqas
Published: January 2020

Background

Data on the association of ustekinumab (UST) drug concentrations and clinical outcomes are conflicting. We assessed serum UST drug and anti-UST antibody concentrations using three commercially available assays.

Methods

Sixty-one blood samples were analyzed for serum UST drug and anti-UST antibody concentrations using three assays: one homogeneous mobility shift assay (HMSA, Prometheus, Assay A), and two enzyme-linked immunosorbent assays (ELISA; Progenika, Dynacare, Assay B and Theradiag, Assay C).

Results

The median (IQR) serum UST concentrations for the three assays were: Assay A 7.50 (5.35 to 12.88) µg/mL, Assay B 4.02 (2.46 to 6.95) µg/mL and Assay C 4.35 (2.62 to 7.50) µg/mL. A Kruskal–Wallis test confirmed a statistically significant difference between the different assays, X2(2) = 30.606, p < 0.001. Linear regression showed near twofold increased difference in the absolute drug concentrations between the HMSA and either ELISA. Linear quantitative correlation was observed for all three assays (r = 0.836 for A versus B, r = 0.792 for A versus C, r = 0.936 for B versus C; p < 0.01). The intraclass correlation coefficient (ICC) between assay A and B was 0.649 (95% confidence interval [CI] −0.208 to 0.874); assay A and C was 0.671 (95% CI −0.165 to 0.878); and assay B and C was 0.958 (95% CI 0.928 to 0.975); p < 0.001. No anti-UST antibodies were detected.

Conclusion

A good correlation was observed for serum UST drug concentrations and a good agreement was observed between the ELISA tests. However, agreement was poor between the HMSA and each ELISA tests. Clinical recommendations regarding drug concentrations should be based on assay type used.
The Common Approach to Article 1: The Scope of Each State’s Obligation to Ensure Respect for the Geneva Conventions
Authors: Robson Verity
Published: January 2020

Common Article 1 of the Geneva Conventions of 1949 is foundational, but not exceptional: the duty to respect and ensure respect for the Conventions must be considered within the framework of public international law as a whole. The Article obliges each High Contracting Party and its organs to respect the Geneva Conventions, and to ensure respect for these Conventions by the population over which it exercises authority and any other persons or groups whose conduct is attributable to it. This scope is demonstrated by the ordinary meaning of the term, subsequent agreements, subsequent practice and other relevant rules of international law, and confirmed by reference to the travaux preparatoires. In particular, erga omnes status does not affect it. As a matter of good faith performance of the Conventions, each High Contracting Party also has a duty not to encourage violations by others. Common Article 1 does not require, as some authors have argued, the prevention or termination of breaches of the Geneva Conventions by other parties to conflict, but High Contracting Parties may choose to take steps toward doing so, as a matter of policy.
Observation and confirmation of nine strong-lensing systems in Dark Energy Survey Year 1 data
Authors: Nord B , Buckley-Geer E , Lin H , Kuropatkin N , Collett T , Tucker D L , Diehl H T , Agnello A , Amara A , Abbott T M C , Allam S , Annis J , Avila S , Bechtol K , Brooks D , Burke D L , Carnero Rosell A , Carrasco Kind M , Carretero J , Cunha C E , da Costa L N , Davis C , De Vicente J , Doel P , Eifler T F , Evrard A E , Fernandez E , Flaugher B , Fosalba P , Frieman J , García-Bellido J , Gaztanaga E , Gruen D , Gruendl R A , Gutierrez G , Hartley W G , Hollowood D L , Honscheid K , Hoyle B , James D J , Kuehn K , Lahav O , Lima M , Maia M A G , March M , Marshall J L , Melchior P , Menanteau F , Miquel R , Plazas A A , Romer A K , Roodman A , Rykoff E S , Sanchez E , Scarpine V , Schindler R , Schubnell M , Sevilla-Noarbe I , Smith M , Soares-Santos M , Sobreira F , Suchyta E , Swanson M E C , Tarle G , Thomas D , Zhang Y ,   (DES Collaboration)
Published: January 2020

We describe the observation and confirmation of nine new strong gravitational lenses discovered in Year 1 data from the Dark Energy Survey (DES). We created candidate lists based on (i) galaxy group and cluster samples, and (ii) photometrically selected galaxy samples. We selected 46 candidates through visual inspection and then used the Gemini Multi-Object Spectrograph(GMOS) at the Gemini South telescope to acquire a spectroscopic follow-up of 21 of these candidates. Through an analysis of these spectroscopic follow-up data, we confirmed nine new lensing systems and rejected two candidates, and the analysis was inconclusive on 10 candidates. For each of the confirmed systems, our report measured spectroscopic properties, estimated source image–lens separations, and estimated enclosed masses as well. The sources that we targeted have an i-band surface brightness range of $i_{\rm SB} \sim 22\!-\!24\, {\rm mag}\,{\rm arcsec}^{-2}$ and a spectroscopic redshift range of zspec ∼ 0.8−2.6. The lens galaxies have a photometric redshift range of zlens ∼ 0.3−0.7. The lensing systems range in source image–lens separation from 2 to 9 arcsec and in enclosed mass from 1012 to 1013 M⊙.
The relationship between X-ray and optical absorbers in active galactic nuclei
Authors: Jaffarian Gunnar W , Gaskell C Martin
Published: January 2020

We present a large compilation of reddening estimates from broad-line Balmer decrements for active galactic nuclei (AGNs) with measured X-ray column densities. The median reddening is E(B − V) ≈ 0.77 ± 0.10 for type-1 to type-1.9 AGNs with reported column densities. This is notably higher than the median reddening of AGNs from the SDSS. We attribute this to the selection bias of the SDSS towards blue AGNs. For other AGNs, we find evidence of a publication bias against reporting low column densities. We find a significant correlation between NH and E(B − V) but with a large scatter of ±1 dex. On average, the X-ray columns are consistent with those predicted from E(B − V) for a solar neighbourhood dust-to-gas ratio. We argue that the large scatter of column densities and reddenings can be explained by X-ray column density variability. For AGNs with detectable broad-line regions (BLRs) that have undergone significant changes of Seyfert type (‘changing-look’ AGNs), we do not find any statistically significant differences in NH or E(B − V) compared to standard type-1 to type-1.9 AGNs. There is no evidence for any type-1 AGNs being Compton thick. We also analyse type-2 AGNs and find no significant correlation between NH and narrow-line region reddening. We find no evidence for a previously claimed anticorrelation. The median column density of LINERs is 22.68 ± 0.75 compared to a column density of 22.90 ± 0.28 for type-2 AGNs. We find the majority of low column density type-2 AGNs are LINERs, but NH is probably underestimated because of scattered light.
Effects of opacity temperature dependence on radiatively accelerated clouds
Authors: Dyda Sergei , Proga Daniel , Reynolds Christopher S
Published: January 2020

We study how different opacity–temperature scalings affect the dynamical evolution of irradiated gas clouds using time-dependent radiation-hydrodynamics simulations. When clouds are optically thick, the bright side heats up and expands, accelerating the cloud via the rocket effect. Clouds that become more optically thick as they heat accelerate $\sim\! 35{{\ \rm per\ cent}}$ faster than clouds that become optically thin. An enhancement of $\sim\! 85{{\ \rm per\ cent}}$ in the acceleration can be achieved by having a broken power-law opacity profile, which allows the evaporating gas driving the cloud to become optically thin and not attenuate the driving radiation flux. We find that up to $\sim\! 2{{\ \rm per\ cent}}$ of incident radiation is re-emitted by accelerating clouds, which we estimate as the contribution of a single accelerating cloud to an emission or absorption line. Re-emission is suppressed by ‘bumps’ in the opacity–temperature relation since these decrease the opacity of the hot, evaporating gas, primarily responsible for the reradiation. If clouds are optically thin, they heat nearly uniformly, expand and form shocks. This triggers the Richtmyer–Meshkov instability, leading to cloud disruption and dissipation on thermal time-scales. Our work shows that, for some parameters, the rocket effect due to radiation-ablated matter leaving the back of the cloud is important for cloud acceleration. We suggest that this rocket effect can be at work in active galactic nuclei outflows.
RNU6-1 in circulating exosomes differentiates GBM from non-neoplastic brain lesions and PCNSL but not from brain metastases
Authors: Puigdelloses Montserrat , González-Huárriz Marisol , García-Moure Marc , Martínez-Vélez Naiara , Esparragosa Vázquez Inés , Bruna Jordi , Zandio Beatriz , Agirre Amaia , Marigil Miguel , Petrirena Gregorio , Nuñez-Córdoba Jorge M , Tejada-Solís Sonia , Díez-Valle Ricardo , Gállego-Culleré Jaime , Martínez-Vila Eduardo , Patiño-García Ana , Alonso Marta M , Gállego Pérez-Larraya Jaime
Published: January 2020

Background

Glioblastoma (GBM) is the most common malignant primary brain tumor in adults. Circulating biomarkers may assist in the processes of differential diagnosis and response assessment. GBM cells release extracellular vesicles containing a subset of proteins and nucleic acids. We previously demonstrated that exosomes isolated from the serum of GBM patients had an increased expression of RNU6-1 compared to healthy subjects. In this exploratory study, we investigated the role of this small noncoding RNA as a diagnostic biomarker for GBM versus other brain lesions with some potential radiological similarities.

Methods

We analyzed the expression of RNU6-1 in circulating exosomes of GBM patients (n = 18), healthy controls (n = 30), and patients with subacute stroke (n = 30), acute/subacute hemorrhage (n = 30), acute demyelinating lesions (n = 18), brain metastases (n = 21), and primary central nervous system lymphoma (PCNSL; n = 12) using digital droplet PCR.

Results

Expression of RNU6-1 was significantly higher in GBM patients than in healthy controls (P = .002). RNU6-1 levels were also significantly higher in exosomes from GBM patients than from patients with non-neoplastic lesions (stroke [P = .05], hemorrhage [P = .01], demyelinating lesions [P = .019]) and PCNSL (P = .004). In contrast, no significant differences were found between patients with GBM and brain metastases (P = .573). Receiver operator characteristic curve analyses supported the role of this biomarker in differentiating GBM from subacute stroke, acute/subacute hemorrhage, acute demyelinating lesions, and PCNSL (P < .05), but again not from brain metastases (P = .575).

Conclusions

Our data suggest that the expression of RNU6-1 in circulating exosomes could be useful for the differentiation of GBM from non-neoplastic brain lesions and PCNSL, but not from brain metastases.
The state as owner—China’s experience
Authors: Milhaupt Curtis J
Published: January 2020

This essay explores China’s experience with state ownership of business enterprise. After a short historical survey of the rise, fall, and re-emergence of the state-owned enterprise (SOE) as a form of business organization, the essay examines the creation, ownership structure, and role of SOEs under Chinese state capitalism. It further discusses the government’s ongoing efforts to reform its SOEs. These efforts are illuminating because they highlight the serious tension inherent in the party-state’s dual goals of maintaining SOEs as a tool for advancing non-financial social and industrial policy objectives, and addressing the corporate governance challenges of these enterprises. The essay concludes by examining implications from the preceding analysis—for China’s domestic economy, for policy-makers outside China, and for the corporate form itself.
Asset Price Bubbles and Systemic Risk
Authors: Brunnermeier Markus , Rother Simon , Schnabel Isabel
Published: January 2020

We analyze the relationship between asset price bubbles and systemic risk, using bank-level data covering almost 30 years. Banks’ systemic risk already rises during a bubble’s buildup and even more so during its bust. The increase in risk strongly differs across banks and by bubble. It depends on bank characteristics (especially bank size) and bubble characteristics and can become very large: in a median real estate bust, systemic risk increases by almost 70% of the median for banks with unfavorable characteristics. These results emphasize the importance of bank-level factors in the buildup of financial fragility during bubble episodes.

Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online.
The Multispecies Coalescent Model Outperforms Concatenation Across Diverse Phylogenomic Data Sets
Authors: Jiang Xiaodong , Edwards Scott V , Liu Liang
Published: January 2020

A statistical framework of model comparison and model validation is essential to resolving the debates over concatenation and coalescent models in phylogenomic data analysis. A set of statistical tests are here applied and developed to evaluate and compare the adequacy of substitution, concatenation, and multispecies coalescent (MSC) models across 47 phylogenomic data sets collected across tree of life. Tests for substitution models and the concatenation assumption of topologically congruent gene trees suggest that a poor fit of substitution models, rejected by 44% of loci, and concatenation models, rejected by 38% of loci, is widespread. Logistic regression shows that the proportions of GC content and informative sites are both negatively correlated with the fit of substitution models across loci. Moreover, a substantial violation of the concatenation assumption of congruent gene trees is consistently observed across six major groups (birds, mammals, fish, insects, reptiles, and others, including other invertebrates). In contrast, among those loci adequately described by a given substitution model, the proportion of loci rejecting the MSC model is 11%, significantly lower than those rejecting the substitution and concatenation models. Although conducted on reduced data sets due to computational constraints, Bayesian model validation and comparison both strongly favor the MSC over concatenation across all data sets; the concatenation assumption of congruent gene trees rarely holds for phylogenomic data sets with more than 10 loci. Thus, for large phylogenomic data sets, model comparisons are expected to consistently and more strongly favor the coalescent model over the concatenation model. We also found that loci rejecting the MSC have little effect on species tree estimation. Our study reveals the value of model validation and comparison in phylogenomic data analysis, as well as the need for further improvements of multilocus models and computational tools for phylogenetic inference. [Bayes factor; Bayesian model validation; coalescent prior; congruent gene trees; independent prior; Metazoa; posterior predictive simulation.]
Genome Sequence of Micromonospora terminaliae TMS7T, a New Endophytic Actinobacterium Isolated from the Medicinal Plant Terminalia mucronata
Authors: Cui Yongtao , Lv Yang , Song Mengqiu , Wang Sai , Hu Haitao , Jahan Noushin , Zhu Bo , Guo Longbiao
Published: January 2020

Micromonospora terminaliae sp. nov., type strain TMS7T, is a gram-positive nonmotile aerobic actinobacterium that was recently isolated from a surface-sterilized stem of the medicinal plant Terminalia mucronata. This strain was described as a novel species in the Micromonospora genus. To elucidate the application potential of this species, its genome was completely sequenced, using the PacBio SMRT cell platform, and was compared with selected complete genome sequences of other Micromonospora species. Genomic analysis revealed that the genome of TMS7T consists of one circular DNA chromosome of 6,717,200 bp with a GC content of 73.35% and one plasmid of 24,912 bp with a GC content of 65.39%. The entire genome contains 6,311 predicted coding genes, 57 transfer RNAs, and nine ribosomal RNA genes. The genome contains a type III polyketide biosynthesis gene cluster, which encodes enzymes that catalyze the production of alkyl-O-dihydrogeranyl-methoxyhydroquinone. This information combined with the previous report that this strain can grow well on pH 10 medium with 4% NaCl (wt/vol) indicates that this strain may have potential biocontrol applications for economic plants cultivated on alkaline soil.
Translating Workforce Development Policy Interventions for Community Health Workers: Application of a Policy Research Continuum
Authors: Fulmer Erika B. , Barbero Colleen , Gilchrist Siobhan , Shantharam Sharada S. , Bhuiya Aunima R. , Taylor Lauren N. , Jones Christopher D.
Published: January 2020

Context:

There is a need for knowledge translation to advance health equity in the prevention and control of cardiovascular disease and type 2 diabetes. One recommended strategy is engaging community health workers (CHWs) to have a central role in related interventions. Despite strong evidence of effectiveness for CHWs, there is limited information examining the impact of state CHW policy interventions. This article describes the application of a policy research continuum to enhance knowledge translation of CHW workforce development policy in the United States.

Methods:

During 2016-2019, a team of public health researchers and practitioners applied the policy research continuum, a multiphased systematic assessment approach that incorporates legal epidemiology to enhance knowledge translation of CHW workforce development policy interventions in the United States. The continuum consists of 5 discrete, yet interconnected, phases including early evidence assessments, policy surveillance, implementation studies, policy ratings, and impact studies.

Results:

Application of the first 3 phases of the continuum demonstrated (1) how CHW workforce development policy interventions are linked to strong evidence bases, (2) whether existing state CHW laws are evidence-informed, and (3) how different state approaches were implemented.

Discussion:

As a knowledge translation tool, the continuum enhances dissemination of timely, useful information to inform decision making and supports the effective implementation and scale-up of science-based policy interventions. When fully implemented, it assists public health practitioners in examining the utility of different policy intervention approaches, the effects of adaptation, and the linkages between policy interventions and more distal public health outcomes.
Laparoscopic Hyperthermic Intraperitoneal Perfusion Chemotherapy for Patients With Malignant Ascites Secondary to Unresectable Gastric Cancer: Retracted
Authors: Ba Ming-Chen , Long Hui , Zhang Xiang-Liang , Gong Yuan-Feng , Tang Yun-Qiang , Wu Yin-Bing , Yu Fei-Hong , Cui Shu-Zhong
Published: January 2020

Background:

To compare the efficacy of 3 chemotherapeutic combinations for laparoscopic hyperthermic intraperitoneal perfusion chemotherapy (HIPPC) in the treatment of malignant ascites secondary to unresectable gastric cancer (GC).

Materials and Methods:

From January 2010 to December 2013, 38 GC patients were randomly divided into 3 groups and treated by laparoscopic HIPPC with 1 of the 3 following chemotherapy combinations: raltitrexed (Ra) with oxaliplatin (L-OHP), Ra with cisplatin (DDP), and Ra with mitomycin C (MMC). Perioperative complications, patients’ quality of life, and survival were recorded and compared among the 3 groups.

Results:

The intraoperative course was successful in all patients, and no perioperative death or complication related to laparoscopic HIPPC was documented. The median follow-up period was 9 months and the median survival was 7.5 months for all patients. Patients in the Ra/L-OHP group had a median survival of 8.7 months, the Ra/DDP group had a median survival of 5.6 months, and the Ra/MMC group had a median survival of 7.5 months. Patients’ median survival in the Ra/L-OHP group and Ra/MMC group is significantly longer than Ra/DDP group (P<0.05). No significant difference was found in total remission rate of ascites, increase in the Karnofsky performance scale, and incidence rate of port-site metastases among the 3 groups.

Conclusions:

Laparoscopy-assisted HIPPC provide modest yet encouraging efficacy for malignant ascites secondary to disseminated GC. Our preliminary data indicate that the chemotherapeutical combination of Ra/L-OHP and Ra/MMC might be more beneficial compared with Ra/DDP in terms of patients’ survival.
Pharmacological modulation of the autophagy pathway enhances Mtb killing
Authors: Quaid Kate Mc , Keane Joseph , Kornfeld Hardy , O'Sullivan Mary , O'leary Seonadh
Published: January 2020

Mycobacterium tuberculosis (Mtb) is the causative agent for tuberculosis which remains a serious health concern globally. The emergence of multi-drug resistant strains and the failure of BCG vaccine to control the epidemic highlight the need to achieve a better understanding of the host immune response and develop new therapies. Autophagy has been identified as an important element in both innate and adaptive immunity against tuberculosis. However Mtb employs an array of immune modulators to invade and thrive in macrophages including by inhibiting autophagosome fusion with lysosomes. Our aim is to identify novel modulators of the autophagy pathway. To do this we have screened a number of FDA approved autophagy-enhancing drugs to reverse the Mtb-induced block of autophagic flux and boost host immune responses.

Murine BMDMs expressing EGFP-LC3 were infected with H37Ra and treated with or without autophagy-enhancing drugs. The number of GFP-LC3-positive puncta per cell was quantified by high content analysis to assess autophagic induction and flux, thereby identifying compounds capable of overcoming the Mtb-induced block in autophagy. We identified three compounds, Sorafenib, Valproic Acid and Carbamazepine, which promote autophagic flux in Mtb-infected cells. Human MDMs were infected with H37Ra and treated with or without these drugs to determine their ability to promote intracellular killing of Mtb and boost the innate immune response. Our data show that Sorafenib, Valproic Acid and Carbamazepine are capable of overcoming the Mtb-induced block in autophagy and reducing bacterial burden in MDMs. This work highlights the potential for autophagy-enhancing drugs as adjunctive treatment for tuberculosis.
Antimicrobial resistance in bacteria associated with childhood pneumonia in Malawi
Authors: Moody Mitchell
Published: January 2020

Community acquired pneumonia (CAP) is a disease caused by an infection (by bacteria, viruses or fungi) that in cases of chronic infection lead to high mortality rates particularly in children. Pneumonia is the leading cause of death in children under the age of five worldwide with over 2 million deaths reported in 2016 by the World Health Organisation. Developing countries in sub Saharan Africa such as Malawi see some of the highest rates of the disease. CAP infections are responsible for 20% of deaths of new-borns in Malawi. Antibiotic resistance in disease causing organisms is of growing concern in countries like Malawi.

We obtained bacterial isolates from blood samples taken from Malawian children, aged 18 -60 months, diagnosed with CAP. Streptococcus pneumonia is the primary pathogen in CAP but associated ESKAPE pathogens like Pseudomonas and Staphylococci spp. and Escherichia coli are of growing importance. These were the most common bacteria purified, isolated and characterised from these samples resulting in a unique culture collection. These pathogens have been screened for antimicrobial resistance with a variety of antibiotics to generate a resistance profile based on the minimal inhibitory concentrations of selected isolates using antibiotic susceptibility disks and by broth dilution method. Initial assessment shows current front-line therapies used by the Malawian ministry of health are ineffective in treating CAP.

Our research aims to fully characterise these strains at the genetic level to better understand the mechanisms behind how antibiotic resistance develops to aid in combating this growing issue in countries like Malawi.
Vorinostat (SAHA) promotes innate and adaptive immunity to Mycobacterium tuberculosis
Authors: Cox Donal , Coleman Amy , Gogan Karl , Dunne Padraic , Basdeo Sharee , Keane Joseph
Published: January 2020

Mycobacterium tuberculosis (Mtb) is increasingly resistant to antibiotics. Therefore, it is paramount to develop host-directed therapies (HDT) aimed at activating the host immune response to promote bacterial killing. Mtb is phagocytosed by alveolar macrophages (AM) and infiltrating monocyte-derived macrophages (MDM) in the lung which upregulate effector functions by epigenetic modifications to enable transcription. Suberanilohydroxamic acid (Vorinostat; SAHA), an FDA-approved histone deacetylase inhibitor, can modulate these changes and support immunity.

Human AM were purified from bronchoalveolar lavage. MDM were obtained from blood of healthy donors and patients with TB. Macrophages were infected with Mtb in the presence of SAHA. After 24 hours, cytokine secretion was quantified. Macrophages were washed and co-cultured with CFSE-labelled PBMC from IGRA positive donors. T-cell responses were analysed by flow cytometry and ELISA. Macrophages were lysed and colony forming units were enumerated.

SAHA increased IL-1β and decreased IL-10 in human AM and MDM infected with Mtb. Proliferating T-helper cells co-cultured with Mtb-infected, SAHA-treated AM or MDM exhibited enhanced IFN-γ and GMCSF co-production. SAHA promotes proinflammatory immune responses to Mtb infection in human AM and MDM, with a subsequent effect on T cell responses. SAHA may therefore be beneficial as a host-directed therapy or vaccine adjunct against TB.
Saezia sanguinis gen. nov., sp. nov., a Betaproteobacteria member of order Burkholderiales, isolated from human blood
Authors: Medina-Pascual María J. , Monzón Sara , Villalón Pilar , Cuesta Isabel , González-Romo Fernando , Valdezate Sylvia
Published: January 2020

The taxonomic position of an unknown bacterial strain designated CNM695-12, isolated from the blood of an immunocompromised subject, was investigated via phenotypic, chemotaxonomic, genotypic and genomic analyses. Bacterial cells were determined to be Gram-stain-negative bacilli, aerobic, non-motile and non-spore-forming. The strain showed catalase activity but no oxidase activity. Optimal growth occurred at 37 °C, pH 7 and with 0–1 % NaCl. C16 : 0, summed feature 8 (comprising C18 : 1ω7c /﻿C18:1 ω6c), and C18 : 1ω9c were the most abundant fatty acids, and ubiquinone 8 was the major respiratory quinone. The polar lipids present included phosphatidylglycerol, phosphatidylethanolamine and other aminophospholipids. The 16S rRNA gene sequence showed approximately 93.5 % similarity to those of different species with validly published names within the order

Burkholderiales

(e.g.

Leptothrix mobilis

Feox-1T,

Aquabacterium commune

B8T
, Aquabacterium citratiphilum B4T and

Schlegelella thermodepolymerans

K14T). Phylogenetic analyses based on 16S rRNA gene sequences and concatenated alignments including the sequences for 107 essential proteins, revealed the strain to form a novel lineage close to members of the family

Comamonadaceae

. The highest average nucleotide identity and average amino acid identity values were obtained with

Schlegelella thermodepolymerans

K14T (69.6 and 55.7 % respectively). The genome, with a size of 3.35 Mb, had a DNA G+C content of 52.4 mol% and encoded 3056 predicted genes, 3 rRNA, 1 transfer–messengerRNA and 51 tRNA. Strain CNM695-12 thus represents a novel species belonging to a novel genus within the order

Burkholderiales

, for which the name Saezia sanguinis gen. nov., sp. nov. is proposed. The type strain is CNM695-12T (=DSM 104959T=CECT 9208T).
Oligonucleotides can act as superscaffolds that enhance liquid-liquid phase separation of intracellular mixtures
Authors: Joseph Jerelle A. , Espinosa Jorge R. , Sanchez-Burgos Ignacio , Garaizar Adiran , Frenkel Daan , Collepardo-Guevara Rosana
Published: January 2020

Intracellular liquid-liquid phase separation (LLPS) enables the formation of biomolecular condensates, which play a crucial role in the spatiotemporal organisation of biomolecules (proteins, oligonucleotides). While LLPS of biopolymers has been demonstrated in both experiments and computer simulations, the physical determinants governing phase separation of protein-oligonucleotide systems are not fully understood. Here, we introduce a minimal coarse-grained model to investigate concentration-dependent features of protein-oligonucleotide mixtures. We demonstrate that adding oligonucleotides to biomolecular condensates composed of oligonucleotide-binding scaffold proteins enhances LLPS; since oligonucleotides act as ultra-high-valency molecules (termed ‘superscaffolds’) that increase the molecular connectivity among scaffold proteins. Importantly, we find that oligonucleotides promote protein LLPS via a seeding-type mechanism; recruiting numerous protein molecules and reducing the thermodynamic and kinetic barriers for nucleation and phase separation. By probing the conformational properties of oligonucleotides within droplets, we show that these biopolymers can undergo phase separation-driven compaction, which may be entropic in nature. Finally, we provide a quantitative comparison between mixture composition, protein valency, and protein-oligonucleotide interaction strengths. We find that superscaffolds preferentially recruit higher valency proteins to condensates, and that multiphase immiscibility within condensates can be achieved by modulating the relative protein-oligonucleotide binding strengths. These results shed light on the roles of oligonucleotides in ribonu-cleoprotein granule formation, heterochromatin compaction, and internal structuring of the nucleolus and stress granules.