bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detailed traveltime tomography and seismic catalogue around the 2019 Mw7.1 Ridgecrest, California, earthquake using dense rapid-response seismic data
Authors: White Malcolm C A , Fang Hongjian , Catchings Rufus D , Goldman Mark R , Steidl Jamison H , Ben-Zion Yehuda 
Published: June 2021

SUMMARY
We derive a detailed earthquake catalogue and Vp, Vs and Vp/Vs models for the region around the 2019 Mw 6.4 and Mw7.1 Ridgecrest, California, earthquake sequence using data recorded by rapid-response, densely deployed sensors following the Ridgecrest main shock and the regional network. The new catalogue spans a 4-month period, starting on 1 June 2019, and it includes nearly 95 000 events detected and located with iterative updates to our velocity models. The final Vp and Vs models correlate well with surface geology in the top 4 km of the crust and spatial seismicity patterns at depth. Joint interpretation of the derived catalogue, velocity models, and surface geology suggests that (i) a compliant low-velocity zone near the Garlock Fault arrested the Mw 7.1 rupture at the southeast end; (ii) a stiff high-velocity zone beneath the Coso Mountains acted as a strong barrier that arrested the rupture at the northwest end and (iii) isolated seismicity on the Garlock Fault accommodated transtensional-stepover strain triggered by the main events. The derived catalogue and velocity models can be useful for multiple future studies, including further analysis of seismicity patterns, derivations of accurate source properties (e.g. focal mechanisms) and simulations of earthquake processes and radiated seismic wavefields.
Germline predisposition to hematopoietic malignancies
Authors: Feurstein Simone , Drazer Michael , Godley Lucy A 
Published: June 2021

Abstract
Once thought to be exceedingly rare, the advent of next-generation sequencing has revealed a plethora of germline predisposition disorders that confer risk for hematopoietic malignancies (HMs). These syndromes are now recognized to be much more common than previously thought. The recognition of a germline susceptibility risk allele in an individual impacts the clinical management and health surveillance strategies in the index patient and relatives who share the causative DNA variant. Challenges to accurate clinical testing include a lack of familiarity in many health care providers, the requirement for DNA samples that reasonably approximate the germline state, and a lack of standardization among diagnostic platforms as to which genes are sequenced and their capabilities in detecting the full range of variant types that confer risk. Current knowledge gaps include a comprehensive understanding of all predisposition genes; whether scenarios exist in which an allogeneic stem cell transplant using donor hematopoietic stem cells with deleterious variants is permissive; and effective means of delivering genetic counseling and results disclosure for these conditions. We are hopeful that comprehensive germline genetic testing, universal germline testing for all patients with an HM, universal germline testing for allogeneic hematopoietic stem cell donors, and the development of preventive strategies to delay or even prevent malignancies will be available in the near future. These factors will likely contribute to improved health outcomes for at-risk individuals and their family members.
What We Talk About When We Talk About Soft Power
Authors: Henne Peter S 
Published: June 2021

AbstractSoft power is a perennial buzzword in policy discussions, but its popularity has not translated into scholarly or policy impact. In this policy article, I argue that this is because many references to soft power are vague and undefined, referring to any use of culture or ideology in a state's foreign policy and leaving unclear soft power's relationship with hard power. Drawing on recent scholarly work on nonmaterial sources of power, I address this issue by arguing that soft power is one among several forms of cultural–symbolic instruments of power that can either complement or substitute for material resources. I also provide a typology to categorize these forms, according to whether they involve direct or diffuse relations, and whether they are intended to integrate or fragment international collective action. This approach can provide more specific language to both analyze and advocate for alternatives to military and economic tools in statecraft. I demonstrate its utility with illustrative case studies on Saudi and Russian foreign policy. This article can contribute to policy debates by allowing for more clarity in discussions on soft power and related forms of power. It can also contribute to scholarship in this area by helping to better connect it to policy discussions.
Executive Power Sharing in the Face of Civil War
Authors: Wucherpfennig Julian 
Published: June 2021

AbstractScholars have debated whether executive power sharing can secure peace in multiethnic states, but concerns about endogeneity due to reverse causation render this a difficult problem for empirical analyses. In the absence of a suitable instrumental variable, I explore an actor-based approach by studying a simple formal model. This highlights the conditions under which governments are likely to share power with a domestic challenger depending on the threat of violence. I then formulate a statistical “strategic selection” model that closely mirrors the theoretical model, thereby directly incorporating endogeneity. Applied to data at the level of ethnic groups, the estimation results indicate that power sharing is indeed enacted strategically by governments in anticipation of the risk of conflict. However, shedding new light on an ongoing debate, I find that the critics have overstated the case against power sharing: rather than spurring it, power sharing robustly reduces civil conflict.
Long-Term Outcomes After Toe-To-Thumb Transfers for Burn Reconstruction in Children
Authors: Yoon Alfred P , Jones Neil F 
Published: June 2021

Abstract
Children are one of the most vulnerable populations to burns, and hands are frequently burned anatomical structures. Restoring function in a severely burned pediatric hand is challenging. We present our experience with pediatric toe-to-thumb transfers for burn reconstruction. A retrospective review was conducted of all pediatric toe-to-thumb transfer patients between 2009 and 2014. Children younger than the age of 18 who underwent secondary reconstruction after electrical or thermal burn injuries with at least a 5-year follow-up were included. Functional outcomes were measured with the modified Kapandji score. Complications of the reconstructed hand as well as the donor foot were recorded. Four children with 10 toe-to-hand transfers (four great toes, two second toes, and two combined second–third toes) met the inclusion criteria. The average follow-up length was 104 months (range 60–144 months). Two children sustained thermal burn injuries and two sustained electrical burn injuries. Three children achieved opposition of the reconstructed toe-to-thumb transfer to the small finger (Kapandji score 5), and one child achieved opposition of the reconstructed toe-to-thumb transfer to the proximal phalanx of the middle finger, the only remaining finger (Kapandji score 3). No donor foot morbidities were noted postoperatively. Toe-to-thumb transfers should be considered the standard of care for thumb reconstruction in children with severe burn injuries of their hands to provide restoration of sensation, pinch, grasp, and opposition with minimal morbidity of the donor foot.
Evaluating and Comparing the Natural Cell Structure and Dimensions of Honey Bee Comb Cells of Chinese Bee, Apis cerana cerana (Hymenoptera: Apidae) and Italian Bee, Apis mellifera ligustica (Hymenoptera: Apidae)
Authors: Yang Shunhua , Deng Shangkao , Kuang Haiou , Zhou Danyin , Gong Xueyang , Dong Kun 
Published: June 2021

Abstract
The hexagonal structure of the honey bee comb cell has been the source of many studies attempting to understand its structure and function. In the storage area of the comb, only honey is stored and no brood is reared. We predicted that honey bees may construct different hexagonal cells for brood rearing and honey storage. We used quantitative analyses to evaluate the structure and function of the natural comb cell in the Chinese bee, Apis cerana cerana and the Italian bee, A. mellifera ligustica. We made cell molds using a crystal glue solution and measured the structure and inclination of cells. We found that the comb cells of A. c. cerana had both upward-sloping and downward-sloping cells; while the A. m. ligustica cells all tilted upwards. Interestingly, the cells did not conform to the regular hexagonal prism structure and showed irregular diameter sizes. In both species, comb cells also were differentiated into worker, drone and honey cells, differing in their diameter and depth. This study revealed unique differences in the structure and function of comb cells and showed that honey bees design their cells with precise engineering to increase storage capacity, and to create adequate growing room for their brood.
Root stem cell niche networks: it’s complexed! Insights from Arabidopsis
Authors: Pardal Renan , Heidstra Renze 
Published: June 2021

Abstract
The presence of two meristematic cell populations in the root and shoot apex allows plants to grow indefinitely. Due to its simple and predictable tissue organization, the Arabidopsis root apical meristem remains an ideal model to study mechanisms such as stem cell specification, asymmetric cell division, and differentiation in plants. The root stem cell niche consists of a quiescent organizing centre surrounded by mitotically active stem cells, which originate all root tissues. The transcription factors PLETHORA, SCARECROW, and WOX5 form signalling hubs that integrate multiple inputs from an increasing number of proteins implicated in the regulation of stem cell niche function. Recently, locally produced auxin was added to the list of important mobile factors in the stem cell niche. In addition, protein–protein interaction data elegantly demonstrate how parallel pathways can meet in a common objective. Here we discuss how multiple networks converge to specify and maintain the root stem cell niche.
A precise photometric ratio via laser excitation of the sodium layer – II. Two-photon excitation using lasers detuned from 589.16 and 819.71 nm resonances
Authors: Albert Justin E , Budker Dmitry , Chance Kelly , Gordon Iouli E , Bustos Felipe Pedreros , Pospelov Maxim , Rochester Simon M , Sadeghpour H R 
Published: June 2021

ABSTRACTThis paper is the second in a pair of papers on the topic of the generation of a two-colour artificial star [which we term a laser photometric ratio star (LPRS)] of de-excitation light from neutral sodium atoms in the mesosphere, for use in precision telescopic measurements in astronomy and atmospheric physics, and more specifically for the calibration of measurements of dark energy using type Ia supernovae. The two techniques, respectively, described in both this and the previous paper would each generate an LPRS with a precisely 1:1 ratio of yellow (589/590 nm) photons to near-infrared (819/820 nm) photons produced in the mesosphere. Both techniques would provide novel mechanisms for establishing a spectrophotometric calibration ratio of unprecedented precision, from above most of Earth’s atmosphere, for upcoming telescopic observations across astronomy and atmospheric physics; thus greatly improving the performance of upcoming measurements of dark energy parameters using type Ia supernovae. The technique described in this paper has the advantage of producing a much brighter (specifically, brighter by approximately a factor of 103) LPRS, using lower power (≤30 W average power) lasers, than the technique using a single 500 W average power laser described in the first paper of this pair. However, the technique described here would require polarization filters to be installed into the telescope camera in order to sufficiently remove laser atmospheric Rayleigh backscatter from telescope images, whereas the technique described in the first paper would only require more typical wavelength filters in order to sufficiently remove laser Rayleigh backscatter.
Patterns and Causes of Signed Linkage Disequilibria in Flies and Plants
Authors: Sandler George , Wright Stephen I , Agrawal Aneil F 
Published: June 2021

Abstract
Most empirical studies of linkage disequilibrium (LD) study its magnitude, ignoring its sign. Here, we examine patterns of signed LD in two population genomic data sets, one from Capsella grandiflora and one from Drosophila melanogaster. We consider how processes such as drift, admixture, Hill–Robertson interference, and epistasis may contribute to these patterns. We report that most types of mutations exhibit positive LD, particularly, if they are predicted to be less deleterious. We show with simulations that this pattern arises easily in a model of admixture or distance-biased mating, and that genome-wide differences across site types are generally expected due to differences in the strength of purifying selection even in the absence of epistasis. We further explore how signed LD decays on a finer scale, showing that loss of function mutations exhibit particularly positive LD across short distances, a pattern consistent with intragenic antagonistic epistasis. Controlling for genomic distance, signed LD in C. grandiflora decays faster within genes, compared with between genes, likely a by-product of frequent recombination in gene promoters known to occur in plant genomes. Finally, we use information from published biological networks to explore whether there is evidence for negative synergistic epistasis between interacting radical missense mutations. In D. melanogaster networks, we find a modest but significant enrichment of negative LD, consistent with the possibility of intranetwork negative synergistic epistasis.
Determining subpopulation methylation profiles from bisulfite sequencing data of heterogeneous samples using DXM
Authors: Fong Jerry , Gardner Jacob R , Andrews Jared M , Cashen Amanda F , Payton Jacqueline E , Weinberger Kilian Q , Edwards John R 
Published: June 2021

Abstract
Epigenetic changes, such as aberrant DNA methylation, contribute to cancer clonal expansion and disease progression. However, identifying subpopulation-level changes in a heterogeneous sample remains challenging. Thus, we have developed a computational approach, DXM, to deconvolve the methylation profiles of major allelic subpopulations from the bisulfite sequencing data of a heterogeneous sample. DXM does not require prior knowledge of the number of subpopulations or types of cells to expect. We benchmark DXM’s performance and demonstrate improvement over existing methods. We further experimentally validate DXM predicted allelic subpopulation-methylation profiles in four Diffuse Large B-Cell Lymphomas (DLBCLs). Lastly, as proof-of-concept, we apply DXM to a cohort of 31 DLBCLs and relate allelic subpopulation methylation profiles to relapse. We thus demonstrate that DXM can robustly find allelic subpopulation methylation profiles that may contribute to disease progression using bisulfite sequencing data of any heterogeneous sample.
A transferrable and integrative type I-F Cascade for heterologous genome editing and transcription modulation
Authors: Xu Zeling , Li Yanran , Cao Huiluo , Si Meiru , Zhang Guangming , Woo Patrick C Y , Yan Aixin 
Published: June 2021

AbstractThe Class 1 type I CRISPR–Cas systems represent the most abundant and diverse CRISPR systems in nature. However, their applications for generic genome editing have been hindered due to difficulties of introducing the class-specific, multi-component effectors (Cascade) in heterologous hosts for functioning. Here we established a transferrable Cascade system that enables stable integration and expression of a highly active type I-F Cascade in heterologous bacterial hosts for various genetic exploitations. Using the genetically recalcitrant Pseudomonas species as a paradigm, we show that the transferred Cascade displayed substantially higher DNA interference activity and greater editing capacity than both the integrative and plasmid-borne Cas9 systems, and enabled deletion of large fragments such as the 21-kb integrated cassette with efficiency and simplicity. An advanced I-F-λred system was further developed to enable editing in genotypes with poor homologous recombination capacity, clinical isolates lacking sequence information, and cells containing anti-CRISPR elements Acrs. Lastly, an ‘all-in-one’ I-F Cascade-mediated CRISPRi platform was developed for transcription modulation by simultaneous introduction of the Cascade and the programmed mini-CRISPR array in one-step. This study provides a framework for expanding the diverse type I Cascades for widespread, heterologous genome editing and establishment of editing techniques in ‘non-model’ bacterial species.
Food insecurity and nutritional status among older adults: a systematic review
Authors: Pereira Marlus H Q , Pereira Maria L A S , Campos Glaucia C , Molina Maria C B 
Published: June 2021

Abstract

Context
Food insecurity (FI), characterized by difficulty or inability to access adequate food, has become a public health problem.

Objective
To analyze studies relating FI with nutritional status (NS) among older adults and the associated factors.

Data search
Articles published up to June 2020 were investigated in 5 databases: PubMed, Embase, Scopus, LILACS, and Web of Science. The search, selection, extraction, and quality evaluation were carried out by 2 reviewers.

Data extraction
The authors identified characteristics of the studies and the main data regarding the relationship of interest.

Results
Twenty-two studies were included in the review and their characteristics are summarized and presented using narrative synthesis. In 10 studies (45.4%), a relationship was observed between FI and malnutrition; in another 6 (27.3%), a relationship was observed between FI and being overweight.

Conclusion
A relationship was identified between FI, especially severe forms, and malnutrition, as well as between FI, especially mild forms, and people being overweight. Thus, FI among older adults relates to a 2-fold burden of nutritional outcomes, depending on the level.

Systematic Review Registration
PROSPERO registration no. CRD42020185086.
Downsizing in plants—UV light induces pronounced morphological changes in the absence of stress
Authors: Qian Minjie , Rosenqvist Eva , Prinsen Els , Pescheck Frauke , Flygare Ann-Marie , Kalbina Irina , Jansen Marcel A.K. , Strid Åke 
Published: June 2021

Abstract
Ultraviolet (UV) light induces a stocky phenotype in many plant species. In this study, we investigate this effect with regard to specific UV wavebands (UV-A or UV-B) and the cause for this dwarfing. UV-A- or UV-B-enrichment of growth light both resulted in a smaller cucumber (Cucumis sativus L.) phenotype, exhibiting decreased stem and petiole lengths and leaf area (LA). Effects were larger in plants grown in UV-B- than in UV-A-enriched light. In plants grown in UV-A-enriched light, decreases in stem and petiole lengths were similar independent of tissue age. In the presence of UV-B radiation, stems and petioles were progressively shorter the younger the tissue. Also, plants grown under UV-A-enriched light significantly reallocated photosynthates from shoot to root and also had thicker leaves with decreased specific LA. Our data therefore imply different morphological plant regulatory mechanisms under UV-A and UV-B radiation. There was no evidence of stress in the UV-exposed plants, neither in photosynthetic parameters, total chlorophyll content, or in accumulation of damaged DNA (cyclobutane pyrimidine dimers). The abscisic acid content of the plants also was consistent with non-stress conditions. Parameters such as total leaf antioxidant activity, leaf adaxial epidermal flavonol content and foliar total UV-absorbing pigment levels revealed successful UV acclimation of the plants. Thus, the UV-induced dwarfing, which displayed different phenotypes depending on UV wavelengths, occurred in healthy cucumber plants, implying a regulatory adjustment as part of the UV acclimation processes involving UV-A and/or UV-B photoreceptors.
Genome- and transcriptome-wide off-target analyses of an improved cytosine base editor
Authors: Randall Linnell Bentley , Sretenovic Simon , Wu Yuechao , Yin Desuo , Zhang Tao , Eck Joyce Van , Qi Yiping 
Published: June 2021

Abstract
Cytosine base editors (CBEs) are the promising tools for precise genome editing in plants. It is important to investigate potential off-target effects of an efficient CBE at the genome and transcriptome levels in a major crop. Based on comparison of five cytidine deaminases and two different promoters for expressing single-guide RNAs (sgRNAs), we tested a highly efficient A3A/Y130F-BE3 system for efficient C-to-T base editing in tomato (Solanum lycopersicum). We then conducted whole-genome sequencing of four base-edited tomato plants, three Green fluorescent protein (GFP)-expressing control plants, and two wild-type plants. The sequencing depths ranged from 25× to 49× with read mapping rates &gt;97%. No sgRNA-dependent off-target mutations were detected. Our data show an average of approximately 1,000 single-nucleotide variations (SNVs) and approximately 100 insertions and deletions (indels) per GFP control plant. Base-edited plants had on average elevated levels of SNVs (approximately 1,250) and indels (approximately 300) per plant. On average, about 200 more C-to-T (G-to-A) mutations were found in a base-edited plant than a GFP control plant, suggesting some level of sgRNA-independent off-target effects, though the difference is not statistically significant. We also conducted RNA sequencing of the same four base-edited plants and three GFP control plants. An average of approximately 200 RNA SNVs was discovered per plant for either base-edited or GFP control plants. Furthermore, no specific enrichment of C-to-U mutations can be found in the base-edited plants. Hence, we cannot find any evidence for bona fide off-target mutations by A3A/Y130F-BE3 at the transcriptome level.