bluuebunny/crossref_metadata_2025 huggingface dataset:
The impact of intellectual property rights on labor productivity: do constitutions matter?
Authors: Carbonara Emanuela , Gianfreda Giuseppina , Santarelli Enrico , Vallanti Giovanna
Published: January 2021

Focusing on a sample of 22 industries and 22 OECD countries and controlling for a full set of year-, industry-, and country fixed effects (and their interactions), we first show that intellectual property rights (IPRs) protection, by means of both constitutional provisions and ordinary laws, is positively associated with the dynamics industry-level labor productivity. Disentangling the impact of constitutional provisions from that of ordinary laws, we then show that constitutional provisions protecting IPRs positively affect the differential in labor productivity between high and low R&D intensive industries. This effect is driven by the mutually reinforcing impact of constitutional IPRs protection and R&D investment in the high R&D intensive industries. Furthermore, the impact of constitutions appears to be stronger in those countries where IPRs protection by ordinary laws is weaker.
Characterizing a two-pronged epidemic in Mexico of non-communicable diseases and SARS-Cov-2: factors associated with increased case-fatality rates
Authors: Monterrubio-Flores Eric , Ramírez-Villalobos María D , Espinosa-Montero Juan , Hernandez Bernardo , Barquera Simón , Villalobos-Daniel Victor E , Campos-Nonato Ismael
Published: January 2021

Background

People with a previous diagnosis of non-communicable diseases (NCDs) are more likely to develop serious forms of COVID-19 or die. Mexico is the country with the fourth highest fatality rate from SARS-Cov-2, with high mortality in younger adults.

Objectives

To describe and characterize the association of NCDs with the case-fatality rate (CFR) adjusted by age and sex in Mexican adults with a positive diagnosis for SARS-Cov-2.

Methods

We studied Mexican adults aged ≥20 years who tested positive for SARS-Cov-2 during the period from 28 February to 31 July 2020. The CFR was calculated and associations with history of NCDs (number of diseases and combinations), severity indicators and type of institution that treated the patient were explored. The relative risk (RR) of death was estimated using Poisson models and CFR was adjusted using logistic models.

Results

We analysed 406 966 SARS-Cov-2-positive adults. The CFR was 11.2% (13.7% in men and 8.4% in women). The CFR was positively associated with age and number of NCDs (p trend <0.001). The number of NCDs increased the risk of death in younger adults when they presented three or more NCDs compared with those who did not have any NCDs [RR, 46.6; 95% confidence interval (CI), 28.2, 76.9 for women; RR, 16.5; 95% CI, 9.9, 27.3 for men]. Lastly, there was great heterogeneity in the CFR by institution, from 4.6% in private institutions to 18.9% in public institutions.

Conclusion

In younger adults, higher CFRs were associated with the total number of NCDs and some combinations of type 2 diabetes, chronic kidney disease, chronic obstructive pulmonary disease and cardiovascular disease.
Floating PV; an assessment of water quality and evaporation reduction in semi-arid regions
Authors: Abdelal Qasem
Published: January 2021

This work addresses the potential impact on water quality and quantifies the benefit of the low carbon power source of floating solar panels in evaporation reduction when using them on an open water body, such as an agricultural irrigation pond in semi-arid regions. By utilizing agricultural ponds for low carbon energy conversion, and saving precious water through evaporation reduction, the highly vulnerable agricultural sector will be empowered. A pilot size setup is prepared, key water quality parameters were monitored and evaporation quantities in a PV-covered pond are compared to those from an adjacent open water pond used as a control. Several inclination angles for the panels were tested. Results showed no adverse impact on the water quality; on the contrary, there is evidence of improvement particularly in nitrate and chlorophyll concentrations. Moreover, a reduction of ~60% in evaporation was observed; power generation from the floating panels, on the other hand, was statistically similar to that from ground-mounted panels.
Transferable Acinetobacter baumannii plasmid pDETAB2 encodes OXA-58 and NDM-1 and represents a new class of antibiotic resistance plasmids
Authors: Liu Haiyang , Moran Robert A , Chen Ying , Doughty Emma L , Hua Xiaoting , Jiang Yan , Xu Qingye , Zhang Linghong , Blair Jessica M A , McNally Alan , van Schaik Willem , Yu Yunsong
Published: January 2021

Objectives

To characterize a blaOXA-58- and blaNDM-1-containing MDR plasmid from a rare Acinetobacter baumannii lineage and compare it with related plasmids to explore the distribution and evolution of a new plasmid group.

Methods

A. baumannii DETAB-P2 was isolated from a rectal swab of an intensive care patient. Antibiotic susceptibility was determined using broth microdilution. DETAB-P2 was mated with A. baumannii ATCC 17978 and putative transconjugants were characterized by S1/PFGE and Southern hybridization. WGS was performed on the Illumina and Oxford Nanopore platforms. MLST was performed with the Pasteur and Oxford schemes. Antibiotic resistance genes were identified with ABRicate. Plasmid sequence annotation was performed manually. Complete plasmids in GenBank with the same rep gene were used for comparative analyses.

Results

A. baumannii DETAB-P2 was ST138 by the Pasteur scheme and a novel Oxford type, ST2209. It transferred blaOXA-58 and blaNDM-1 to ATCC 17978 in the 100 072 bp plasmid pDETAB2 that also carried bleMBL, sul2, aacC2d, tet(39), msr(E)-mph(E) and putative mercury resistance and RND efflux system determinants. pDETAB2 represents a new plasmid type, GR34, and contained 16 pdif sites and several novel dif modules. Only a 10 kbp core sequence is shared amongst pDETAB2 and 18 further GR34 plasmids in GenBank, with diverse accessory regions comprised of various dif modules.

Conclusions

GR34 plasmids are found in several Acinetobacter species from diverse environments. They display considerable variation in accessory content owing to the presence of pdif sites and an array of dif modules, some of which contain antibiotic resistance genes.
Cefiderocol: a novel siderophore cephalosporin for multidrug-resistant Gram-negative bacterial infections
Authors: Parsels Katie A , Mastro Keri A , Steele Jeffrey M , Thomas Stephen J , Kufel Wesley D
Published: January 2021

Cefiderocol is a novel siderophore cephalosporin that forms a complex with extracellular free ferric iron, which leads to transportation across the outer cell membrane to exert its bactericidal activity through cell wall synthesis inhibition. This pharmacological property has rendered cefiderocol active against several clinically relevant MDR Gram-negative bacteria as evidenced by several in vitro and in vivo studies. Cefiderocol was first approved by the US FDA on 14 November 2019 for the treatment of complicated urinary tract infections. On 28 September 2020, cefiderocol was approved for the treatment of hospital-acquired bacterial pneumonia and ventilator-associated bacterial pneumonia. The FDA-approved indications are based on clinical data from the APEKS-cUTI, APEKS-NP and CREDIBLE-CR trials. In APEKS-cUTI, cefiderocol demonstrated non-inferiority to imipenem/cilastatin for the treatment of complicated urinary tract infection caused by MDR Gram-negative bacteria. In APEKS-NP, cefiderocol demonstrated non-inferiority to meropenem for treatment of nosocomial pneumonia. However, in CREDIBLE-CR, higher all-cause mortality was observed with cefiderocol compared with best available therapy for the treatment of severe infections caused by Gram-negative bacteria, primarily in the subset of patients with Acinetobacter spp. infections. Several case reports/series have demonstrated clinical success with cefiderocol for a variety of severe infections. The purpose of this article is to review available data on the mechanism of action, in vitro and in vivo data, pharmacokinetics, pharmacodynamics, susceptibility testing, efficacy and safety of cefiderocol to address its role in therapy.
Identification of 16S rRNA mutations in Mycoplasma genitalium potentially associated with tetracycline resistance in vivo but not selected in vitro in M. genitalium and Chlamydia trachomatis
Authors: Le Roy Chloé , Touati Arabella , Balcon Carla , Garraud Justine , Molina Jean-Michel , Berçot Béatrice , de Barbeyrac Bertille , Pereyre Sabine , Peuchant Olivia , Bébéar Cécile
Published: January 2021

Objectives

Tetracyclines are widely used for the treatment of bacterial sexually transmitted infections (STIs) and recently have been used successfully for post-exposure prophylaxis of STIs in MSM. We investigated the in vitro and in vivo development of tetracycline resistance in Chlamydia trachomatis and Mycoplasma genitalium and evaluated 16S rRNA mutations associated with acquired resistance in other bacteria.

Methods

In vitro selection of resistant mutants of reference strains of C. trachomatis and M. genitalium was undertaken by serial passage in medium containing subinhibitory concentrations of tetracycline or doxycycline, respectively. The 16S rRNA gene of the two microorganisms was amplified and sequenced at different passages, as were those of 43 C. trachomatis- and 106 M. genitalium-positive specimens collected in France from 2013 to 2019.

Results

No tetracycline- or doxycycline-resistant strains of C. trachomatis and M. genitalium, respectively, were obtained after 30 serial passages. The tetracycline and doxycycline MICs were unchanged and analysis of the 16S rRNA gene, the molecular target of tetracyclines, of C. trachomatis and M. genitalium revealed no mutation. No mutation in the 16S rRNA gene was detected in C. trachomatis-positive specimens. However, six M. genitalium-positive specimens harboured a mutation potentially associated with tetracycline resistance without known prior tetracycline treatment for patients.

Conclusions

Tetracyclines did not select in vitro-resistant mutants of C. trachomatis or M. genitalium. However, 16S rRNA mutations either responsible for or associated with tetracycline resistance in other bacteria, including mycoplasma species, were identified in several M. genitalium-positive specimens.
Endotracheal tubes coated with a broad-spectrum antibacterial ceragenin reduce bacterial biofilm in an in vitro bench top model
Authors: Latorre María Consuelo , Pérez-Granda María Jesús , Savage Paul B , Alonso Beatriz , Martín-Rabadán Pablo , Samaniego Rafael , Bouza Emilio , Muñoz Patricia , Guembe María
Published: January 2021

Background

Ventilator-associated pneumonia is one of the most common nosocomial infections, caused mainly by bacterial/fungal biofilm. Therefore, it is necessary to develop preventive strategies to avoid biofilm formation based on new compounds.

Objectives

We performed an in vitro study to compare the efficacy of endotracheal tubes (ETTs) coated with the ceragenin CSA-131 and that of uncoated ETTs against the biofilm of clinical strains of Pseudomonas aeruginosa (PA), Escherichia coli (EC) and Staphylococcus aureus (SA).

Methods

We applied an in vitro bench top model using coated and uncoated ETTs that were treated with three different clinical strains of PA, EC and SA for 5 days. After exposure to biofilm, ETTs were analysed for cfu count by culture of sonicate and total number of cells by confocal laser scanning microscopy.

Results

The median (IQR) cfu/mL counts of PA, EC and SA in coated and uncoated ETTs were, respectively, as follows: 1.00 × 101 (0.0–3.3 × 102) versus 3.32 × 109 (6.6 × 108–3.8 × 109), P < 0.001; 0.0 (0.0–5.4 × 103) versus 1.32 × 106 (2.3 × 103–5.0 × 107), P < 0.001; and 8.1 × 105 (8.5 × 101–1.4 × 109) versus 2.7 × 108 (8.6 × 106–1.6 × 1011), P = 0.058. The median (IQR) total number of cells of PA, EC and SA in coated and non-coated ETTs were, respectively, as follows: 11.0 [5.5–not applicable (NA)] versus 87.9 (60.5–NA), P = 0.05; 9.1 (6.7–NA) versus 62.6 (42.0–NA), P = 0.05; and 97.7 (94.6–NA) versus 187.3 (43.9–NA), P = 0.827.

Conclusions

We demonstrated significantly reduced biofilm formation in coated ETTs. However, the difference for SA was not statistically significant. Future clinical studies are needed to support our findings.
Income Shocks and Conflict: Evidence from Nigeria
Authors: Abidoye Babatunde , Calì Massimiliano
Published: January 2021

This paper examines the relationship between income shocks and conflict across Nigerian states over the 2000s. By matching consumption, production, commodity prices and conflict data, the analysis captures two opposite channels linking agricultural price changes to conflict. Consistently with the opportunity cost mechanism of conflict, price increases of commodities produced by the households have a conflict-reducing effect, while the opposite is true for prices of consumed commodities. The net impact turns out to be conflict inducing in contrast with most of the related literature that focuses on the production side of agricultural price shocks. These results underscore the importance of modelling both production and consumption effects to get consistent estimates of the impact of price changes on conflict.
Confirming the Presence ofLegionella pneumophilain Your Water System: A Review of CurrentLegionellaTesting Methods
Authors: Walker James T , McDermott Paul J
Published: January 2021

Legionnaires’ disease has been recognized since 1976 and Legionella pneumophila still accounts for more than 95% of cases. Approaches in countries, including France, suggest that focusing risk reduction specifically on L. pneumophila is an effective strategy, as detecting L. pneumophila has advantages over targeting multiple species of Legionella. In terms of assays, the historically accepted plate culture method takes 10 days for confirmed Legionella spp. results, has variabilities which affect trending and comparisons, requires highly trained personnel to identify colonies on a plate in specialist laboratories, and does not recover viable-but-non-culturable bacteria. PCR is sensitive, specific, provides results in less than 24 h, and determines the presence/absence of Legionella spp. and/or L. pneumophila DNA. Whilst specialist personnel and laboratories are generally required, there are now on-site PCR options, but there is no agreement on comparing genome units to colony forming units and action limits. Immunomagnetic separation assays are culture-independent, detect multiple Legionella species, and results are available in 24 h, with automated processing options. Field-use lateral flow devices provide presence/absence determination of L. pneumophila serogroup 1 where sufficient cells are present, but testing potable waters is problematic. Liquid culture most probable number (MPN) assays provide confirmed L. pneumophila results in 7 days that are equivalent to or exceed plate culture, are robust and reproducible, and can be performed in a variety of laboratory settings. MPN isolates can be obtained for epidemiological investigations. This accessible, non-technical review will be of particular interest to building owners, operators, risk managers, and water safety groups and will enable them to make informed decisions to reduce the risk of L. pneumophila.
Enzymolysis–Microwave-Assisted Hydrodistillation for Extraction of Volatile Oil from Atractylodes Chinensis and Its Hypoglycemic Activity in vitro
Authors: Wang Yitong , Yan Meixing , Qin Ruiqing , Gong Yanling
Published: January 2021

Background

Atractylodes chinensis (family Asteraceae) is a perennial herb with many pharmacological effects.

Objective

Extraction of volatile oil from Atractylodes chinensis was optimized and its hypoglycemic activities were studied.

Methods

Enzymolysis–microwave-assisted hydrodistillation (EMAHD) was adopted to extract the volatile oil, and the technology was optimized using a single-factor experiment that incorporated response surface methodology (RSM). The extraction rates of volatile oil by EMAHD, microwave-assisted hydrodistillation (MAHD), and hydrodistillation (HD) methods were compared at different times. The ingredients of Atractylodes chinensis volatile oil were analyzed by gas chromatography–mass spectrometry. Scanning electron microscopy (SEM) were used to analyze the microstructural changes in Atractylodes chinensis residue before and after extraction. The inhibition of α-amylase activity was determined.

Results

The obtained optimal extraction conditions for EMAHD were as follows: enzyme concentration 1.6%, pH 7, enzymolysis time 20 min, enzymolysis temperature 50°C, liquid–solid ratio 30:1, microwave power 455 W, and microwave time 40 min. The levels of the main ingredients and the in vitro inhibition of α-amylase activities were higher for Atractylodes chinensis volatile oil extracted by EMAHD than by HD or MAHD. The powder residue of Atractylodes chinensis remaining after EMAHD showed a ruptured and collapsed cell structure, indicating accelerated dissolution of the volatile oil.

Conclusions and Highlights

EMAHD is deemed a method with many advantages for extraction of volatile oil from Atractylodes chinensis. The volatile oil of Atractylodes chinensis is a promising component for treating hyperglycemia.
Frequency of Pathogenic Germline Variants in Cancer-Susceptibility
Genes in the Childhood Cancer Survivor Study
Authors: Kim Jung , Gianferante Matthew , Karyadi Danielle M , Hartley Stephen W , Frone Megan N , Luo Wen , Robison Leslie L , Armstrong Gregory T , Bhatia Smita , Dean Michael , Yeager Meredith , Zhu Bin , Song Lei , Sampson Joshua N , Yasui Yutaka , Leisenring Wendy M , Brodie Seth A , de Andrade Kelvin C , Fortes Fernanda P , Goldstein Alisa M , Khincha Payal P , Machiela Mitchell J , McMaster Mary L , Nickerson Michael L , Oba Leatrisse , Pemov Alexander , Pinheiro Maisa , Rotunno Melissa , Santiago Karina , Wegman-Ostrosky Talia , Diver W Ryan , Teras Lauren , Freedman Neal D , Hicks Belynda D , Zhu Bin , Wang Mingyi , Jones Kristine , Hutchinson Amy A , Dagnall Casey , Savage Sharon A , Tucker Margaret A , Chanock Stephen J , Morton Lindsay M , Stewart Douglas R , Mirabello Lisa
Published: January 2021

Background

Pediatric cancers are the leading cause of death by disease in children despite improved survival rates overall. The contribution of germline genetic susceptibility to pediatric cancer survivors has not been extensively characterized. We assessed the frequency of pathogenic or likely pathogenic (P/LP) variants in 5451 long-term pediatric cancer survivors from the Childhood Cancer Survivor Study.

Methods

Exome sequencing was conducted on germline DNA from 5451 pediatric cancer survivors (cases who survived ≥5 years from diagnosis; n = 5105 European) and 597 European cancer-free adults (controls). Analyses focused on comparing the frequency of rare P/LP variants in 237 cancer-susceptibility genes and a subset of 60 autosomal dominant high-to-moderate penetrance genes, for both case-case and case-control comparisons.

Results

Of European cases, 4.1% harbored a P/LP variant in high-to-moderate penetrance autosomal dominant genes compared with 1.3% in controls (2-sided P = 3 × 10-4). The highest frequency of P/LP variants was in genes typically associated with adult onset rather than pediatric cancers, including BRCA1/2, FH, PALB2, PMS2, and CDKN2A. A statistically significant excess of P/LP variants, after correction for multiple tests, was detected in patients with central nervous system cancers (NF1, SUFU, TSC1, PTCH2), Wilms tumor (WT1, REST), non-Hodgkin lymphoma (PMS2), and soft tissue sarcomas (SDHB, DICER1, TP53, ERCC4, FGFR3) compared with other pediatric cancers.

Conclusion

In long-term pediatric cancer survivors, we identified P/LP variants in cancer-susceptibility genes not previously associated with pediatric cancer as well as confirmed known associations. Further characterization of variants in these genes in pediatric cancer will be important to provide optimal genetic counseling for patients and their families.
Distress Trajectories for Parents of Children With DSD: A Growth Mixture Model
Authors: Perez Megan N , Clawson Ashley H , Baudino Marissa N , Austin Paul F , Baskin Laurence S , Chan Yee-Ming , Cheng Earl Y , Coplen Douglas , Diamond David A , Fried Allyson J , Kolon Thomas , Kropp Bradley , Lakshmanan Yegappan , Meyer Theresa , Nokoff Natalie J , Palmer Blake W , Paradis Alethea , Poppas Dix P , Reyes Kristy J. Scott , Williot Pierre , Wolfe-Christensen Cortney , Yerkes Elizabeth B , Wisniewski Amy B , Mullins Larry L
Published: January 2021

Objective

This study identifies trajectories of parent depressive symptoms after having a child born with genital atypia due to a disorder/difference of sex development (DSD) or congenital adrenal hyperplasia (CAH) and across the first year postgenitoplasty (for parents who opted for surgery) or postbaseline (for parents who elected against surgery for their child). Hypotheses for four trajectory classes were guided by parent distress patterns previously identified among other medical conditions.

Methods

Participants included 70 mothers and 50 fathers of 71 children diagnosed with a DSD or CAH with reported moderate to high genital atypia. Parents were recruited from 11 US DSD specialty clinics within 2 years of the child’s birth and prior to genitoplasty. A growth mixture model (GMM) was conducted to identify classes of parent depressive symptoms over time.

Results

The best fitting model was a five-class linear GMM with freely estimated intercept variance. The classes identified were termed “Resilient,” “Recovery,” “Chronic,” “Escalating,” and “Elevated Partial Recovery.” Four classes have previously been identified for other pediatric illnesses; however, a fifth class was also identified. The majority of parents were classified in the “Resilient” class (67.6%).

Conclusions

This study provides new knowledge about the trajectories of depressive symptoms for parents of children with DSD. Future studies are needed to identify developmental, medical, or familial predictors of these trajectories.
Overconstrained models of time delay lenses redux: how the angular tail wags the radial dog
Authors: Kochanek C S
Published: January 2021

The two properties of the radial mass distribution of a gravitational lens that are well constrained by Einstein rings are the Einstein radius RE and ξ2 = REα″(RE)/(1 − κE), where α″(RE) and κE are the second derivative of the deflection profile and the convergence at RE, respectively. However, if there is a tight mathematical relationship between the radial mass profile and the angular structure, as is true of ellipsoids, an Einstein ring can appear to strongly distinguish radial mass distributions with the same ξ2. This problem is beautifully illustrated by the ellipsoidal models in Millon et al. When using Einstein rings to constrain the radial mass distribution, the angular structure of the models must contain all the degrees of freedom expected in nature (e.g. external shear, different ellipticities for the stars and the dark matter, modest deviations from elliptical structure, modest twists of the axes, modest ellipticity gradients, etc.) that work to decouple the radial and angular structures of the gravity. Models of Einstein rings with too few angular degrees of freedom will lead to strongly biased likelihood distinctions between radial mass distributions and very precise but inaccurate estimates of H0 based on gravitational lens time delays.
The formation of isolated ultradiffuse galaxies in romulus25
Authors: Wright Anna C , Tremmel Michael , Brooks Alyson M , Munshi Ferah , Nagai Daisuke , Sharma Ray S , Quinn Thomas R
Published: January 2021

We use the romulus25 cosmological simulation volume to identify the largest-ever simulated sample of field ultradiffuse galaxies (UDGs). At z = 0, we find that isolated UDGs have average star formation rates (SFRs), colours, and virial masses for their stellar masses and environment. UDGs have moderately elevated H i masses, being 70 per cent (300 per cent) more H i rich than typical isolated dwarf galaxies at luminosities brighter (fainter) than MB = −14. However, UDGs are consistent with the general isolated dwarf galaxy population and make up ∼20 per cent of all field galaxies with 107 < M⋆/M⊙ < 109. The H i masses, effective radii, and overall appearances of our UDGs are consistent with existing observations of field UDGs, but we predict that many isolated UDGs have been missed by current surveys. Despite their isolation at z = 0, the UDGs in our sample are the products of major mergers. Mergers are no more common in UDG than non-UDG progenitors, but mergers that create UDGs tend to happen earlier – almost never occurring after z = 1, produce a temporary boost in spin, and cause star formation to be redistributed to the outskirts of galaxies, resulting in lower central SFRs. The centres of the galaxies fade as their central stellar populations age, but their global SFRs are maintained through bursts of star formation at larger radii, producing steeper negative g −r colour gradients. This formation channel is unique relative to other proposals for UDG formation in isolated galaxies, demonstrating that UDGs can potentially be formed through multiple mechanisms.
The IRX–β relation of high-redshift galaxies
Authors: Liang Lichen , Feldmann Robert , Hayward Christopher C , Narayanan Desika , Çatmabacak Onur , Kereš Dušan , Faucher-Giguère Claude-André , Hopkins Philip F
Published: January 2021

The relation between infrared excess (IRX) and UV spectral slope (βUV) is an empirical probe of dust properties of galaxies. The shape, scatter, and redshift evolution of this relation are not well understood, however, leading to uncertainties in estimating the dust content and star formation rates (SFRs) of galaxies at high redshift. In this study, we explore the nature and properties of the IRX–βUV relation with a sample of z = 2–6 galaxies ($M_*\approx 10^9\!-\!10^{12}\, \mathrm{M}_\odot$) extracted from high-resolution cosmological simulations (MassiveFIRE) of the Feedback in Realistic Environments (FIRE) project. The galaxies in our sample show an IRX–βUV relation that is in good agreement with the observed relation in nearby galaxies. IRX is tightly coupled to the UV optical depth, and is mainly determined by the dust-to-star geometry instead of total dust mass, while βUV is set both by stellar properties, UV optical depth, and the dust extinction law. Overall, much of the scatter in the IRX–βUV relation of our sample is found to be driven by variations of the intrinsic UV spectral slope. We further assess how the IRX–βUV relation depends on viewing direction, dust-to-metal ratio, birth-cloud structures, and the dust extinction law and we present a simple model that encapsulates most of the found dependencies. Consequently, we argue that the reported ‘deficit’ of the infrared/sub-millimetre bright objects at z ≳ 5 does not necessarily imply a non-standard dust extinction law at those epochs.
Dissecting and modelling galaxy assembly bias
Authors: Xu Xiaoju , Zehavi Idit , Contreras Sergio
Published: January 2021

Understanding the galaxy-halo connection is fundamental for contemporary models of galaxy clustering. The extent to which the haloes’ assembly history and environment impact galaxy clustering (a.k.a. galaxy assembly bias; GAB), remains a complex and challenging problem. Using a semi-analytic galaxy formation model, we study the individual contributions of different secondary halo properties to the GAB signal. These are obtained by comparing the clustering of stellar-mass selected samples to that of shuffled samples where the galaxies are randomly reassigned to haloes of fixed mass and a specified secondary halo property. We explore a large range of internal halo properties and environmental measures. We find that commonly used properties like halo age or concentration amount to only 20–30 per cent of the signal, while the smoothed matter density or the tidal anisotropy can account for the full level of GAB (though care should be given to the specific definition). For the ‘successful’ measures, we examine the occupancy variations and the associated changes in the halo occupation function parameters. These are used to create mock catalogues that reproduce the full level of GAB. Finally, we propose a practical modification of the standard halo occupation distribution model, which can be tuned to any level of assembly bias. Fitting the parameters to our semi-analytic model, we demonstrate that the corresponding mock catalogue recovers the target level of GAB as well as the occupancy variations. Our results enable producing realistic mock catalogues and directly inform theoretical modelling of assembly bias and attempts to detect it in the Universe.
SurVirus: a repeat-aware virus integration caller
Authors: Rajaby Ramesh , Zhou Yi , Meng Yifan , Zeng Xi , Li Guoliang , Wu Peng , Sung Wing-Kin
Published: January 2021

A significant portion of human cancers are due to viruses integrating into human genomes. Therefore, accurately predicting virus integrations can help uncover the mechanisms that lead to many devastating diseases. Virus integrations can be called by analysing second generation high-throughput sequencing datasets. Unfortunately, existing methods fail to report a significant portion of integrations, while predicting a large number of false positives. We observe that the inaccuracy is caused by incorrect alignment of reads in repetitive regions. False alignments create false positives, while missing alignments create false negatives. This paper proposes SurVirus, an improved virus integration caller that corrects the alignment of reads which are crucial for the discovery of integrations. We use publicly available datasets to show that existing methods predict hundreds of thousands of false positives; SurVirus, on the other hand, is significantly more precise while it also detects many novel integrations previously missed by other tools, most of which are in repetitive regions. We validate a subset of these novel integrations, and find that the majority are correct. Using SurVirus, we find that HPV and HBV integrations are enriched in LINE and Satellite regions which had been overlooked, as well as discover recurrent HBV and HPV breakpoints in human genome-virus fusion transcripts.
Identifying Content-Based Engagement Patterns in a Smoking Cessation Website and Associations With User Characteristics and Cessation Outcomes: A Sequence and Cluster Analysis
Authors: Perski Olga , Watson Noreen L , Mull Kristin E , Bricker Jonathan B
Published: January 2021

Introduction

Using WebQuit as a case study, a smoking cessation website grounded in Acceptance and Commitment Therapy, we aimed to identify sequence clusters of content usage and examine their associations with baseline characteristics, change to a key mechanism of action, and smoking cessation.

Methods

Participants were adult smokers allocated to the WebQuit arm in a randomized controlled trial (n = 1,313). WebQuit contains theory-informed content including goal setting, self-monitoring and feedback, and values- and acceptance-based exercises. Sequence analysis was used to temporally order 30-s website usage segments for each participant. Similarities between sequences were assessed with the optimal matching distance algorithm and used as input in an agglomerative hierarchical clustering analysis. Associations between sequence clusters and baseline characteristics, acceptance of cravings at 3 months and self-reported 30-day point prevalence abstinence at 12 months were examined with linear and logistic regression.

Results

Three qualitatively different sequence clusters were identified. “Disengagers” (576/1,313) almost exclusively used the goal-setting feature. “Tryers” (375/1,313) used goal setting and two of the values- and acceptance-based components (“Be Aware,” “Be Willing”). “Committers” (362/1,313) primarily used two of the values- and acceptance-based components (“Be Willing,” “Be Inspired”), goal setting, and self-monitoring and feedback. Compared with Disengagers, Committers demonstrated greater increases in acceptance of cravings (p = .01) and 64% greater odds of quit success (ORadj = 1.64, 95% CI = 1.18, 2.29, p = .003).

Discussion

WebQuit users were categorized into Disengagers, Tryers, and Committers based on their qualitatively different content usage patterns. Committers saw increases in a key mechanism of action and greater odds of quit success.

Implications

This case study demonstrates how employing sequence and cluster analysis of usage data can help researchers and practitioners gain a better understanding of how users engage with a given eHealth intervention over time and use findings to test theory and/or to improve future iterations to the intervention. Future WebQuit users may benefit from being directed to the values- and acceptance-based and the self-monitoring and feedback components via reminders over the course of the program.
Immigration and Poverty
Authors: Rigzin Tsewang , Kaushal Neeraj
Published: January 2021

Immigration impacts two distinct dimensions of poverty: poverty among immigrants and global poverty. Emigration generally involves moving to better opportunities, and the process lowers poverty among emigrants. Immigration also impacts global poverty through multiple channels including remittances, the proliferation of economic activities, and exchange of ideas between immigrant-sending countries that are generally low income and receiving countries that are often rich. Finally, immigrants improve productivity in the host country through innovation and new economic activities, in turn creating employment and lowering poverty. Immigrants generally have higher poverty when they first arrive in the host country on account of multiple disadvantages they experience, including lack of host-country-specific skills, discrimination on account of their immigration status, and limited access to safety net programs and services that reduce poverty. But their poverty levels decline with increases in the duration of residency in the host country and across generations.
Anselm of Canterbury
Authors: Williams Thomas
Published: January 2021

Anselm of Canterbury (b. 1033–d. 1109) is the most enduringly influential philosopher-theologian of the Latin West between Augustine and the thirteenth century. Best known among philosophers for his “ontological” argument for the existence of God in the Proslogion and among theologians for his account of the Atonement in Cur Deus Homo, he is regarded as the quintessential “classical theist,” and his accounts of the divine nature and attributes, of freedom and the fall, and of human redemption continue to attract attention. This article provides an annotated list of Anselm’s complete works as well as selected English translations and secondary literature.
Agroforestry: The North American Perspective
Authors: Lovell Sarah T. , Garrett Harold E. "Gene"
Published: January 2021

Agroforestry has a long, rich history that is rooted in activities practiced by indigenous communities around the world. Native peoples were known to gather fruits, nuts, and understory herbs from the forest, based on their deep ecological knowledge of the natural system, and they often cultivated preferred species. For modern applications, agroforestry can be defined as the intentional integration of trees and shrubs with crops or livestock to create a multifunctional system with a wide range of benefits. In temperate regions, agroforestry is characterized by six key practices: (1) alley cropping—planting rows of trees with a companion crop grown between the rows; (2) forest farming—growing high-value specialty crops in the shaded forest understory; (3) riparian buffers—protecting water resources such as streams with a zone of trees, shrubs, and herbaceous plants; (4) silvopasture—combining trees, forage, and livestock for multiple products; (5) windbreaks—planting rows of trees and shrubs to protect crops or livestock from wind and to reduce soil erosion; and (6) urban food forests—integrating trees, shrubs, and herbaceous plants that provide edible products for the good of the community. The environmental benefits of agroforestry have been widely studied and continue to be a source of great interest. Most recently, the potential for agroforestry to contribute to climate change adaption and mitigation is being explored. While the science of agroforestry has been influenced to a great extent by the field of ecology and related disciplines, social science dimensions are increasingly captured through the study of adoption behaviors, preferences, and cultural benefits. The investigation of the role of economic and policy drivers is critical to understanding strategies to motivate landowners to adopt these practices at a level that would expand agroforestry into the mainstream. Landscape-level planning and design could provide a vision and a pathway for a broader transformation to a system that encourages perennial habitats including specialty crops that supply edible products. Such a strategy could place agroforestry more directly into the growing call to support regional food systems and positive human health outcomes. This article focuses on the trends and directions in agroforestry research primarily in North America, with emphasis on developments in the early 21st century.
Hunger and Food Shortages
Authors: Sharp Kelly Kean
Published: January 2021

Woven into the fabric of history, hunger and food shortage experienced by individuals, communities, or large-scale societies are important historical markers, often used to chronicle significant points in time. As such, the histories of hunger and food shortage in various places and times in the Atlantic world serve as a productive lens with which to study the political, social, cultural, economic, and environmental parameters of Atlantic world history from pre-contact to present day. Within Atlantic history, just as in the early 21st century, hunger and food shortage can be a result of environmental conditions or natural disaster, such as the severe winters and wet summers which caused Europe’s Great Famine (1315–1322). Hunger and food shortage was and is also the result of intentionally orchestrated conditions including any combination of warfare, politics, poverty, and power. In the early decades of cross-Atlantic contact, food shortage and hunger was a common experience for both immunocompromised indigenous populations as well as inexperienced European explorers and early settlers. Control over food as well as limiting access to it came to serve as an important tool in white control over the land and people of the New World, both indigenous and those forcibly migrated from Africa. While food shortage was a common experience in European history due to mercantilist practices and harvest failures, food shortage and hunger in contemporary history largely is focused on western Africa. Despite the enormous expansion of agricultural productivity, extensive networks of transport infrastructure, and the interlinked global economy, hunger and food shortages still persist in all parts of the world, and indeed thrive, in all parts of the world.
William Dwight Whitney
Authors: Alter Stephen G.
Published: January 2021

The American Sanskritist and linguist William Dwight Whitney (b. 1827–d. 1894) was his country’s most important professional language scholar and linguistic theorist of the 19th century. Whitney grew up in Northampton, Massachusetts, attended Williams College in that state, and for nearly three years did advanced study of “Oriental” languages in Germany at the universities of Berlin and Tübingen. In 1854 he began a long career at Yale College in Connecticut, teaching Sanskrit Language and Literature as well as modern languages, chiefly French and German. Whitney was a pillar of the American Oriental Society (established 1842), and a founder and the first president of the American Philological Association (established 1869). His research specialty was Indology: he was an expert in Sanskrit grammar. The focus of the present article, however, will be Whitney’s general linguistic thought, beginning with an overview of his ideas about language as a whole and about language prescriptivism. Then follows a description of the 18th-century sources of Whitney’s views, as well as of Whitney’s long debate with Friedrich Max Müller, who embodied all of the worst tendencies (as Whitney regarded them) of romanticist language theory. Responding to such tendencies made up a large portion of Whitney’s own theoretical output. Our discussion then considers Whitney’s legacy in three areas: (1) his influence on and critique of Neogrammarian doctrine, (2) the inspiration (both positive and negative) Whitney gave to Ferdinand de Saussure, and (3) the impetus he gave to aspects of 20th–21st-century sociolinguistic investigation, particularly by calling attention to the phenomenon of lexical diffusion. Whitney’s career as a language theorist began in 1864, with a lecture series on “The Principles of Linguistic Science” presented at the Smithsonian Institution in Washington, DC, and, in an expanded version, at Boston’s Lowell Institute. These lectures became the basis of his book Language and the Study of Language (1867), a number of short pieces gathered and republished in Volume 1 of his Oriental and Linguistic Studies (1873), and his book The Life and Growth of Language (1875). All of these writings expressed Whitney’s quintessentially Anglo-American Common-Sense realist language philosophy. His 1867 and 1875 books were translated into the major European languages, the latter work being more successful in terms of the international attention it received and its impact, particularly on the German Neogrammarians, but also due to its long use as a linguistics textbook at institutions in the United States.
Post-Collective Agriculture
Authors: Ho Peter , Zaratin Francesco
Published: January 2021

Since the start of the economic reforms in 1978, China has developed today into one of the world’s leading producers of agricultural produce—particularly pork, poultry, fruits, vegetables, wheat, corn, and rice. The transition of China’s collectivist Soviet-style agricultural production toward a modernized, mechanized, and market-based agriculture has taken many decades to take effect. A major breakthrough that marked the start of China’s agricultural transition was the nationwide adoption of the Household Contract Responsibility System in the mid-1980s. In addition to these managerial and structural changes, the Chinese government engaged in the liberalization of agricultural prices and supply and marketing systems, as well as the stimulation of agricultural diversification, mechanization, and economies of scale. As agriculture continued to develop, millions of farmers were lifted out of poverty and migrated to the cities to find employment in the industries and services. At the same time, however, China encountered significant problems as a result. For one, how to ensure food security and feed close to one-fifth of the earth’s population with less than one-tenth of its farmland? On top of that, over time vast tracts of fertile, arable land were lost due to its (legal and illegal) conversion into urban construction land. Raising agricultural production was also severely constrained by the small and fragmented nature of Chinese farms. Well into the 2010s, over 90 percent of these were smaller than 2.5 acres, while cropland was scattered over numerous different plots. Furthermore, ensuring adequate social welfare, education, and health care for the rural populace had become a daunting challenge in the face of the growing divide between urban citizens and the peasant population. Last but not least, rapid rural industrialization through township and village enterprises (TVEs), once hailed as a miracle of China’s reforms, had taken a heavy toll in the form of soil, air, and water pollution, giving rise to “cancer villages”, “black rivers,” and heavily degraded natural resources. At the time of this writing, Chinese agriculture is caught in between two worlds: on the one hand, one may find smallholders tilling scattered agricultural plots, on the other hand, there are high-tech food-processing factories and the peri-urban, sometimes ecologically guided industrial farms. The stark contrast between a highly modernized sector versus a traditional one will continue to explain the paradoxical dynamics of Chinese post-collective agriculture for the foreseeable future.
Activist and Socially Engaged Art
Authors: Kester Grant
Published: January 2021

The terms “activist” or “socially engaged” art (used interchangeably throughout this article) refer to artistic practices that are integrated with, or responsive to, forms of political protest and resistance. This typically entails some connection to a social or political movement, community, or group that is seeking to challenge an authoritarian regime or contest hegemonic forms of domination, often associated with differences of class, race, ethnicity, or sexuality. The form taken by activist art can range from relatively abbreviated performative gestures to extended engagements with institutional power structures, to modes of symbolic or discursive production circulating in the public sphere (murals, graphic art, etc.). In each case, however, we can observe a reciprocal relationship between artistic production and mechanisms of social and political transformation oriented toward human emancipation. Between the mid-19th and mid-20th centuries there were significant interconnections between the concept of an activist art practice and the modern avant-garde. I’ll provide a brief outline of some of these navigational points in the section Historical Studies. It’s not possible, however, to provide a comprehensive account of sources across this broader historical range. For the purposes of this article, I will focus primarily on work since the 1960s, when we can observe the initial expression of a recognizably contemporary set of referents for activist or engaged art practice. Even within this limited time frame, the range of possible material far exceeds the space necessary to acknowledge relevant sources. Activist art practices, by their very nature, tend to overlap with, and ramify into, a range of adjacent forms of cultural production. We can find meaningful connections to activist theater (Augusto Boal), radical pedagogy (Paolo Freire), the Art and Labor movement, the traditions of community and street art, digital activism, tactical media, activist filmmaking, and urban murals, among many other relevant sources. Moreover, there are distinctive manifestations of activist or engaged art in every region of the globe. Argentine activist practice has its own unique traditions and concerns, as does art produced in Eastern Europe, South Africa, India, Japan, and Mexico. Rather than attempting to fully address each of these areas, I will offer a series of chronological divisions that chart some of the shifts that have occurred in the production of activist art since the mid-20th century.
RhoA and Cdc42 in T cells: Are they targetable for T cell-mediated inflammatory diseases?
Authors: Guo Fukun
Published: January 2021

Many inflammatory diseases are not curable, necessitating a better understanding of their pathobiology that may help identify novel biological targets. RhoA and Cdc42 of Rho family small GTPases regulate a variety of cellular functions such as actin cytoskeletal organization, cell adhesion, migration, proliferation, and survival. Recent characterization of mouse models of conditional gene knockout of RhoA and Cdc42 has revealed their physiological and cell type-specific roles in a number of cell types. In T lymphocytes, which play an important role in the pathogenesis of most, if not all, of the inflammatory diseases, we and others have investigated the effects of T cell-specific knockout of RhoA and Cdc42 on T cell development in the thymus, peripheral T cell homeostasis, activation, and differentiation to effector and regulatory T cells, and on T cell-mediated allergic airway inflammation and colitis. Here we highlight the phenotypes resulting from RhoA and Cdc42 deletion in T cells and discuss whether pharmacological targeting of RhoA and Cdc42 is feasible in treating asthma that is driven by allergic airway inflammation and colitis.