bluuebunny/crossref_metadata_2025 huggingface dataset:
Inflammatory Bowel Diseases-related Disability: Risk Factors, Outcomes, and Interventions
Authors: Tse Chung Sang , Hunt Melissa G , Brown Lily A , Lewis James D
Published: August 2023

The diagnosis of inflammatory bowel disease (IBD) is a life-changing moment for most adults. Biomedical advances over the past 2 decades have resulted in unprecedented growth of therapeutic options for IBD. However, due to the incurable nature of IBD, medical and surgical intervention alone may not be adequate to completely normalize health status and prevent long-term disability. In the biopsychosocial model of health and disease, a person’s health and function result from complex physical, psychosocial, and environmental interactions. Adapting the World Health Organization definition, IBD-related disability encompasses limitations in educational and employment opportunities, exclusions in economic and social activities, and impairments in physical and psychosocial function. Although the concept of IBD-related disability is a long-term treatment end point in the updated Selecting Therapeutic Targets in Inflammatory Bowel Disease (STRIDE-II) treatment guideline, it has received limited attention in the literature. This review article explores an etiological framework of the physical and psychosocial aspects that contribute to IBD-related disability. We also explore the impact of IBD-related disability on the direct and indirect costs of IBD. Lastly, we present the available evidence for interventions with the potential to improve function and reduce IBD-related disability.
The architecture of global knowledge production – do low-income countries get more involved?
Authors: Cantner Uwe , Grebel Thomas , Zhang Xijie
Published: August 2023

In this paper, we analyze the extent to which low-income countries integrate into the global knowledge production network. We develop an (undirected) research collaboration model based on which we identify the drivers of global research collaboration using publication data of the field Business and Economics from the Web of Science and macroeconomic data from the United Nations Educational, Scientific and Cultural Organization Institute for Statistics. Network and dynamic panel regression techniques are employed. Our results show that (i) reciprocal preferential attachment and the homophily between countries reinforce scientific collaboration, (ii) there is no evidence that low-income countries are becoming better integrated into the global knowledge production over the years, despite their active participation in international reserach collaboration, while (iii) high-income countries show a basic willingness to cooperate with them, which, in turn, promotes the integration of low-income countries, although this willingness seems to decline; and (iv) as to low-income countries, they have little choice but to invest more in education and R&D in order to advance in the global knowledge production network.
Applications of machine learning to identify and characterize the sounds produced by fish
Authors: Barroso V R , Xavier F C , Ferreira C E L
Published: August 2023

Aquatic ecosystems are constantly changing due to anthropic stressors, which can lead to biodiversity loss. Ocean sound is considered an essential ocean variable, with the potential to improve our understanding of its impact on marine life. Fish produce a variety of sounds and their choruses often dominate underwater soundscapes. These sounds have been used to assess communication, behaviour, spawning location, and biodiversity. Artificial intelligence can provide a robust solution to detect and classify fish sounds. However, the main challenge in applying artificial intelligence to recognize fish sounds is the lack of validated sound data for individual species. This review provides an overview of recent publications on the use of machine learning, including deep learning, for fish sound detection, classification, and identification. Key challenges and limitations are discussed, and some points to guide future studies are also provided.
Bridging photosynthesis and crop yield formation with a mechanistic model of whole-plant carbon–nitrogen interaction
Authors: Chang Tian-Gen , Wei Zhong-Wei , Shi Zai , Xiao Yi , Zhao Honglong , Chang Shuo-Qi , Qu Mingnan , Song Qingfeng , Chen Faming , Miao Fenfen , Zhu Xin-Guang
Published: August 2023

Crop yield is determined by potential harvest organ size, source organ photosynthesis and carbohydrate partitioning. Filling the harvest organ efficiently remains a challenge. Here, we developed a kinetic model of rice grain filling, which scales from the primary biochemical and biophysical processes of photosynthesis to whole-plant carbon and nitrogen dynamics. The model reproduces the rice yield formation process under different environmental and genetic perturbations. In silico screening identified a range of post-anthesis targets—both established and novel—that can be manipulated to enhance rice yield. Remarkably, we pinpointed the stability of grain-filling rate from flowering to harvest as a critical factor for maximizing grain yield. This finding was further validated in two independent super-high-yielding rice cultivars, each yielding approximately 21 t ha−1 of rough rice at 14% moisture content. Furthermore, we revealed that stabilizing the grain-filling rate could lead to a potential yield increase of 30–40% in an elite rice cultivar. Notably, the instantaneous grain-filling rates around 15- and 38-day post-flowering significantly influence grain yield; and we introduced an innovative in situ approach using ear respiratory rates for precise quantification of these rates. We finally derived an equation to predict the maximum dried brown rice yield (Y, t ha−1) of a cultivar based on its potential gross photosynthetic accumulation from flowering to harvest (Apc, t CO2 ha−1): Y = 0.74 × Apc + 1.9. Overall, this work establishes a framework for quantitatively dissecting crop physiology and designing high-yielding ideotypes.
“Globalization and Social Identities at the Individual Level: Populism from Shifting at the Top?”
Authors: Bearce David H , McLeer Andrew , Stallman Ken
Published: August 2023

This paper reconsiders the proposition that globalization leads to more transnational and less national identities. Providing an argument specifying how these various international processes could shift identities at the individual level, it hypothesizes that globalization should be associated with more transnational/less national identities for people toward the top of society based on their experience with and information about globalization, but not for those at the bottom. Based on the identity shift happening at the top but not at the bottom, globalization should also be associated with a larger identity difference between the elite and the mass public. Using data from the sixth wave of the World Values Survey conducted across fifty-six countries from 2010 to 2014 and the seventh wave across forty-four countries from 2017 to 2020, it presents results consistent with these hypotheses. These results help explain the current “anti-global” backlash, providing evidence consistent with populist theories but inconsistent with rising nationalism.
Climate, Women, and Conflict: Rebel Groups’ Armed Activities after Major Disasters
Authors: Ide Tobias
Published: August 2023

This study builds long-anticipated bridges between the literature on (i) climate/disaster security, (ii) women, peace, and security, and (iii) rebel group behavior. Specifically, I analyze how rebel groups react to disasters (like droughts, earthquakes, floods, or storms) by intensifying or reducing their armed activities. This addresses a crucial knowledge gap: While a large literature is dealing with the impacts of climate change and disasters on armed conflict onset or incidence, knowledge on how environmental factors shape the behavior of particular conflict actors remains scarce. I argue that rebel groups escalate fighting when disaster-related opportunities occur (e.g., easier recruitment) but scale back their armed activities if adversely affected by the disasters (e.g., loss of resources). However, this relationship is contingent of the rebels’ inclusion of female combatants. Empirically, this study draws on a unique sample of thirty-six cases of disasters striking armed conflict zones and integrates quantitative and qualitative data via a qualitative comparative analysis. The results suggest that rebel groups intensify their armed activities to exploit disaster-related opportunities but can only do so when female combatants provide them with sufficient capabilities. Conversely, rebels have to reduce fighting when adversely affected by disasters unless they can draw on female members to cope with disaster impacts.
The cross-reactivity of cannabinoid analogs (delta-8-THC, delta-10-THC and CBD), their metabolites and chiral carboxy HHC metabolites in urine of six commercially available homogeneous immunoassays
Authors: Wolf Carl E , Pokhai Ashley A , Poklis Justin L , Williams Grace R
Published: August 2023

There has been an exponential surge in the presence and use of cannabinoids since the federal legalization of hemp (Agricultural Improvement Act of 2018). This growth is attributed to delta-9-tetrahydrocannabinol (delta-9-THC) and cannabidiol (CBD), the most abundant phytocannabinoid components of cannabis and hemp, respectively, but with many other emerging THC analogs. Structurally, these analogs are similar to delta-9-THC, yet very little information is available about their potency and even less information is available regarding their detectability using commercially available cannabinoid screening kits. Due to their structural similarity, current cannabinoid homogeneous immunoassay screening methods may be able to detect these emerging cannabinoid analogs and their metabolites. Six urine immunoassay kits (Abbott Cannabinoids—Abbott Diagnostics, LZI Cannabinoids (cTHC) Enzyme Immunoassay—Lin-Zhi International, DRI® Cannabinoid Assay and CEDIA™ THC—Thermo Fisher Scientific, ONLINE DAT Cannabinoid II—Roche Diagnostics and Syva EMIT®II Plus—Siemens Healthineers) were evaluated at two different cutoff concentrations: 50 ng/mL and 20 or 25 ng/mL, assay dependent. The analysis was performed on an Abbott Architect Plus c4000 (Abbott Diagnostics). Delta-8-THC, CBD, olivetol and their major metabolites, and delta-10-THC and HHC carboxylic acid chiral analogs were evaluated. The cross-reactivity was evaluated by preparing each analyte at 20, 50, 100 and 1,000 ng/mL in urine. Analytes that did not cross-react at 1,000 ng/mL for a cutoff were considered not detectable. If detected, the lowest concentration was used as the decision point to determine the precision at the immunoassay’s cutoff. The six commercially available urine cannabinoid homogeneous immunoassay screening kits cross reacted with the following analogs: delta-8-THC, 11-OH-delta-8-THC, 11-COOH-delta-8-THC, 6-OH-CBD, 7-OH-CBD, all delta-10-THC and HHC carboxylic acid chiral analogs and olivetol with varying selectivity depending on the screening kit and cutoff concentration. The kits did not cross-react with the following analogs: CBD, 7-COOH-CBD, Abnormal CBD, CBDA-A and olivetolic acid.
Null models to explain highly diverse community of intertidal decapods on a temperate rocky coast in Antofagasta, northern Chile (23º27ʹS)
Authors: De los Ríos-Escalante Patricio , Ibáñez-Arancibia Eliana , Esse Carlos , Zúñiga Oscar , Fajardo Maritza , Ghory Farhana S
Published: August 2023

The decapod fauna on intertidal shores in northern Chile is characterized by its relatively high diversity and abundance due to the presence of continuous upwelling by the Humboldt Current, which results in a high productivity. The decapod fauna on intertidal rocky shores is characterized by coexisting species that inhabits in natural shelters such as cracks and eroded rocks, as well as among macroalgae. We aimed to monitor the brachyuran and anomuran (porcellanid) crabs in three intertidal sites during two periods of time in September-December 2019 in the Antofagasta region, one site without human intervention and two sites in the city of Antofagasta, for which we applied null models in ecology. We assumed that the communities are random, a viewpoint that is more robust because it reduces the risk of error type I. The results of the application of null models on the co-occurrence species revealed that species associations are mainly structured for all sites, whereas the niche-sharing null model revealed that the reported species did not share ecological niches and in consequence there is not interspecific competition. The results would probably indicate that the species of intertidal decapods have a micro-specific ecological-niche differentiation, which would explain the existence of structured pattern in species associations. The results were compared with information for other sites along the continental Chilean coast.
Roadblocks to Disarmament in the Nuclear Non-Proliferation Treaty System
Authors: Hood Anna
Published: August 2023

For the last five decades, the states parties to the Nuclear Non-Proliferation Treaty (NPT) have come together every 5 years at Review Conferences to explore how they can advance the Treaty’s goals, including the pursuit of nuclear disarmament. Despite lengthy negotiations, the Review Conferences have failed to reach a consensus final document as many times as they have succeeded and even when a final document has been agreed it has contained few tangible gains for those working towards a nuclear weapon free world. This state of affairs played out again in 2022 when the NPT’s 10th Review Conference ended without agreement and with many states decrying the weakness of the disarmament provisions that had been under discussion. It has been common in the aftermath of Review Conferences for academics to consider the contemporary political issues that stymied progress. While such studies are important, it is also necessary to consider what deeper structural issues may be at play in preventing the goal of nuclear disarmament from being advanced in the NPT context. To this end, this article identifies and analyses three key structural issues with the NPT and NPT Review Conferences that create difficulties for those pursuing a nuclear disarmament agenda. First, it explores issues with the scope and content of Article VI and how it has been interpreted by the nuclear weapon states. Secondly, it looks at the difficulties that arise from the commitment to achieving consensus outcomes at the Review Conferences and, thirdly, it considers the limitations of who actually attends and contributes to Review Conferences.
Recent trends in radiotherapy use for major cancers in Korea
Authors: Yang Kyungmi , Lee Jeong Eun , Park Won , Ahn Yong Chan , Huh Seung Jae
Published: August 2023

Background

Although the trend in radiotherapy in all cancer patients has been studied, changes in radiotherapy modalities for specific cancer types have not been reported. This study aimed to analyze radiotherapy patterns for major cancers in Korea in recent years.

Materials and Methods

We collected data from claims and reimbursement records of the Health and Insurance Review and Assessment Service from 2017 to 2020, according to initial diagnostic codes. The radiotherapy modalities for major cancers, such as lung, stomach, colorectal, breast and liver cancer, were analyzed. The radiotherapy modalities consisted of two-dimensional radiotherapy, three-dimensional conformal radiotherapy, intensity-modulated radiotherapy, proton radiotherapy and stereotactic body radiotherapy.

Results

Overall, from 2017 to 2020, the use of two-dimensional radiotherapy and three-dimensional conformal radiotherapy decreased, and intensity-modulated radiotherapy increased. In 2017, three-dimensional conformal radiotherapy accounted for approximately half of the radiotherapy in patients for lung and colorectal cancer, which was replaced by intensity-modulated radiotherapy in 2020. In 2020, stereotactic body radiotherapy also accounted for a large proportion of radiotherapy used in liver cancer cases. Intensity-modulated radiotherapy was most used, followed by three-dimensional conformal radiotherapy and two-dimensional radiotherapy for breast cancer in 2020. Among major cancers, radiotherapy utilization for breast cancer is the highest. Compared with other cancers, the number of patients receiving radiotherapy for stomach cancer was low.

Conclusion

The number of patients receiving radiotherapy for major cancers has increased. The use of advanced forms of radiotherapy, such as intensity-modulated radiotherapy, is rapidly increasing for major cancers. The rate of radiotherapy utilization was higher in major cancer patients than in all cancer patients.
Laparoscopic minor liver resection for hepatocellular carcinoma
Authors: Kokudo Takashi , Takemura Nobuyuki , Inagaki Fuyuki , Yoshizaki Yuhi , Mihara Fuminori , Edamoto Yoshihiro , Yamada Kazuhiko , Kokudo Norihiro
Published: August 2023

Background

Previous studies have suggested that laparoscopic liver resection for hepatocellular carcinoma is associated with lower postoperative complications compared with open liver resection.

Methods

We conducted a retrospective analysis of 109 hepatocellular carcinoma patients who underwent minor liver resection at a Japanese tertiary care hospital from November 2010 to December 2022.

Results

The laparoscopic liver resection group experienced significantly lower median intraoperative blood loss compared with the open liver resection group (P = 0.0001). Furthermore, the laparoscopic liver resection group had a significantly shorter median hospital stay compared with the open liver resection group (P = 0.0002). However, there was no significant difference in median postoperative survival between the laparoscopic liver resection group and the open liver resection group (P = 0.717).

Conclusions

Laparoscopic minor liver resection for hepatocellular carcinoma resulted in reduced blood loss and hospital stay without compromising long-term survival outcomes.
Algorithmic Harm in Consumer Markets
Authors: Bar-Gill Oren , Sunstein Cass R , Talgam-Cohen Inbal
Published: August 2023

Machine learning algorithms are increasingly able to predict what goods and services particular people will buy, and at what price. It is possible to imagine a situation in which relatively uniform, or coarsely set, prices and product characteristics are replaced by far more in the way of individualization. Companies might, for example, offer people shirts and shoes that are particularly suited to their situations, that fit with their particular tastes, and that have prices that fit their personal valuations. In many cases, the use of algorithms promises to increase efficiency and to promote social welfare; it might also promote fair distribution. But when consumers suffer from an absence of information or from behavioral biases, algorithms can cause serious harm. Companies might, for example, exploit such biases in order to lead people to purchase products that have little or no value for them or to pay too much for products that do have value for them. Algorithmic harm, understood as the exploitation of an absence of information or of behavioral biases, can disproportionately affect members of identifiable groups, including women and people of color. Since algorithms exacerbate the harm caused to imperfectly informed and imperfectly rational consumers, their increasing use provides fresh support for existing efforts to reduce information and rationality deficits, especially through optimally designed disclosure mandates. In addition, there is a more particular need for algorithm-centered policy responses. Specifically, algorithmic transparency—transparency about the nature, uses, and consequences of algorithms—is both crucial and challenging; novel methods designed to open the algorithmic “black box” and “interpret” the algorithm’s decision-making process should play a key role. In appropriate cases, regulators should also police the design and implementation of algorithms, with a particular emphasis on the exploitation of an absence of information or of behavioral biases.
Do economic incentives promote physical activity? Evidence from the London Congestion Charge
Authors: Nakamura Ryota , Albanese Andrea , Coombes Emma , Suhrcke Marc
Published: August 2023

This study investigates the impact of economic incentives on travel-related physical activity, leveraging the London Congestion Charge’s disincentivising of sedentary travel modes via increasing the cost of private car use within Central London. The scheme imposes charges on most types of cars entering, exiting, and operating within the Central London area, while individuals living inside the charging zone are eligible for a 90% reduction in congestion charges. Geographical location information provides the full-digit postcode data necessary to precisely identify the eligibility for the discount of participants in the London Travel Demand Survey for the period 2005–2011. Using a boundary regression-discontinuity design reveals a statistically significantly positive impact on active commuting (i.e. cycling and walking) around the border of the charging zone. The effect is larger for lower-income households and car owners. The findings are robust against multiple specifications and validation tests.
Bearded or smooth? Awns improve yield when wheat experiences heat stress during grain fill in the southeastern United States
Authors: DeWitt Noah , Lyerly Jeanette , Guedira Mohammed , Holland James B , Murphy J Paul , Ward Brian P , Boyles Richard E , Mergoum Mohamed , Babar Md Ali , Shakiba Ehsan , Sutton Russel , Ibrahim Amir , Tiwari Vijay , Santantonio Nicholas , Van Sanford David A , Howell Kimberly , Smith Jared H , Harrison Stephen A , Brown-Guedira Gina
Published: August 2023

The presence or absence of awns—whether wheat heads are ‘bearded’ or ‘smooth’ – is the most visible phenotype distinguishing wheat cultivars. Previous studies suggest that awns may improve yields in heat or water-stressed environments, but the exact contribution of awns to yield differences remains unclear. Here we leverage historical phenotypic, genotypic, and climate data for wheat (Triticum aestivum) to estimate the yield effects of awns under different environmental conditions over a 12-year period in the southeastern USA. Lines were classified as awned or awnless based on sequence data, and observed heading dates were used to associate grain fill periods of each line in each environment with climatic data and grain yield. In most environments, awn suppression was associated with higher yields, but awns were associated with better performance in heat-stressed environments more common at southern locations. Wheat breeders in environments where awns are only beneficial in some years may consider selection for awned lines to reduce year-to-year yield variability, and with an eye towards future climates.
Hierarchical contribution of Argonaute proteins to antiviral protection
Authors: Ludman Márta , Szalai Gabriella , Janda Tibor , Fátyol Károly
Published: August 2023

Antiviral RNAi is the main protective measure employed by plants in the fight against viruses. The main steps of this process have been clarified in recent years, primarily relying on the extensive genetic resources of Arabidopsis thaliana. Our knowledge of viral diseases of crops, however, is still limited, mainly due to the fact that A. thaliana is a non-host for many agriculturally important viruses. In contrast, Nicotiana benthamiana has an unparalleled susceptibility to viruses and, since it belongs to the Solanaceae family, it is considered an adequate system for modeling infectious diseases of crops such as tomatoes. We used a series of N. benthamiana mutants created by genome editing to analyze the RNAi response elicited by the emerging tomato pathogen, pepino mosaic virus (PepMV). We uncovered hierarchical roles of several Argonaute proteins (AGOs) in anti-PepMV defense, with the predominant contribution of AGO2. Interestingly, the anti-PepMV activities of AGO1A, AGO5, and AGO10 only become apparent when AGO2 is mutated. Taken together, our results prove that hierarchical actions of several AGOs are needed for the plant to build effective anti-PepMV resistance. The genetic resources created here will be valuable assets for analyzing RNAi responses triggered by other agriculturally important pathogenic viruses.
TeloBase: a community-curated database of telomere sequences across the tree of life
Authors: Lyčka Martin , Bubeník Michal , Závodník Michal , Peska Vratislav , Fajkus Petr , Demko Martin , Fajkus Jiří , Fojtová Miloslava
Published: August 2023

Discoveries over the recent decade have demonstrated the unexpected diversity of telomere DNA motifs in nature. However, currently available resources, ‘Telomerase database’ and ‘Plant rDNA database’, contain just fragments of all relevant literature published over decades of telomere research as they have a different primary focus and limited updates. To fill this gap, we gathered data about telomere DNA sequences from a thorough literature screen as well as by analysing publicly available NGS data, and we created TeloBase (http://cfb.ceitec.muni.cz/telobase/) as a comprehensive database of information about telomere motif diversity. TeloBase is supplemented by internal taxonomy utilizing popular on-line taxonomic resources that enables in-house data filtration and graphical visualisation of telomere DNA evolutionary dynamics in the form of heat tree plots. TeloBase avoids overreliance on administrators for future data updates by having a simple form and community-curation system for application and approval, respectively, of new telomere sequences by users, which should ensure timeliness of the database and topicality. To demonstrate TeloBase utility, we examined telomere motif diversity in species from the fungal genus Aspergillus, and discovered (TTTATTAGGG)n sequence as a putative telomere motif in the plant family Chrysobalanaceae. This was bioinformatically confirmed by analysing template regions of identified telomerase RNAs.
spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes
Authors: Hacker William C , Elcock Adrian H
Published: August 2023

Stochastic simulation models have played an important role in efforts to understand the mechanistic basis of prokaryotic transcription and translation. Despite the fundamental linkage of these processes in bacterial cells, however, most simulation models have been limited to representations of either transcription or translation. In addition, the available simulation models typically either attempt to recapitulate data from single-molecule experiments without considering cellular-scale high-throughput sequencing data or, conversely, seek to reproduce cellular-scale data without paying close attention to many of the mechanistic details. To address these limitations, we here present spotter (Simulation of Prokaryotic Operon Transcription & Translation Elongation Reactions), a flexible, user-friendly simulation model that offers highly-detailed combined representations of prokaryotic transcription, translation, and DNA supercoiling. In incorporating nascent transcript and ribosomal profiling sequencing data, spotter provides a critical bridge between data collected in single-molecule experiments and data collected at the cellular scale. Importantly, in addition to rapidly generating output that can be aggregated for comparison with next-generation sequencing and proteomics data, spotter produces residue-level positional information that can be used to visualize individual simulation trajectories in detail. We anticipate that spotter will be a useful tool in exploring the interplay of processes that are crucially linked in prokaryotes.
Increased levels of eIF2A inhibit translation by sequestering 40S ribosomal subunits
Authors: Grove Daisy J , Levine Daniel J , Kearse Michael G
Published: August 2023

eIF2A was the first eukaryotic initiator tRNA carrier discovered but its exact function has remained enigmatic. Uncharacteristic of translation initiation factors, eIF2A is reported to be non-cytosolic in multiple human cancer cell lines. Attempts to study eIF2A mechanistically have been limited by the inability to achieve high yield of soluble recombinant protein. Here, we developed a purification paradigm that yields ∼360-fold and ∼6000-fold more recombinant human eIF2A from Escherichia coli and insect cells, respectively, than previous reports. Using a mammalian in vitro translation system, we found that increased levels of recombinant human eIF2A inhibit translation of multiple reporter mRNAs, including those that are translated by cognate and near-cognate start codons, and does so prior to start codon recognition. eIF2A also inhibited translation directed by all four types of cap-independent viral IRESs, including the CrPV IGR IRES that does not require initiation factors or initiator tRNA, suggesting excess eIF2A sequesters 40S subunits. Supplementation with additional 40S subunits prevented eIF2A-mediated inhibition and pull-down assays demonstrated direct binding between recombinant eIF2A and purified 40S subunits. These data support a model that eIF2A must be kept away from the translation machinery to avoid sequestering 40S ribosomal subunits.
A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences
Authors: Ordóñez Carlos D , Mayoral-Campos Carmen , Egas Conceição , Redrejo-Rodríguez Modesto
Published: August 2023

Multiple displacement amplification (MDA) has proven to be a useful technique for obtaining large amounts of DNA from tiny samples in genomics and metagenomics. However, MDA has limitations, such as amplification artifacts and biases that can interfere with subsequent quantitative analysis. To overcome these challenges, alternative methods and engineered DNA polymerase variants have been developed. Here, we present new MDA protocols based on the primer-independent DNA polymerase (piPolB), a replicative-like DNA polymerase endowed with DNA priming and proofreading capacities. These new methods were tested on a genomes mixture containing diverse sequences with high-GC content, followed by deep sequencing. Protocols relying on piPolB as a single enzyme cannot achieve competent amplification due to its limited processivity and the presence of ab initio DNA synthesis. However, an alternative method called piMDA, which combines piPolB with Φ29 DNA polymerase, allows proficient and faithful amplification of the genomes. In addition, the prior denaturation step commonly performed in MDA protocols is dispensable, resulting in a more straightforward protocol. In summary, piMDA outperforms commercial methods in the amplification of genomes and metagenomes containing high GC sequences and exhibits similar profiling, error rate and variant determination as the non-amplified samples.
ZENBU-Reports: a graphical web-portal builder for interactive visualization and dissemination of genome-scale data
Authors: Severin Jessica , Agrawal Saumya , Ramilowski Jordan A , Deviatiiarov Ruslan , Shin Jay W , Carninci Piero , de Hoon Michiel
Published: August 2023

In the genomic era, data dissemination and visualization is an integral part of scientific publications and research projects involving international consortia producing massive genome-wide data sets, intra-organizational collaborations, or individual labs. However, creating custom supporting websites is oftentimes impractical due to the required programming effort, web server infrastructure, and data storage facilities, as well as the long-term maintenance burden. ZENBU-Reports (https://fantom.gsc.riken.jp/zenbu/reports) is a web application to create interactive scientific web portals by using graphical interfaces while providing storage and secured collaborative sharing for data uploaded by users. ZENBU-Reports provides the scientific visualization elements commonly used in supplementary websites, publications and presentations, presenting a complete solution for the interactive display and dissemination of data and analysis results during the full lifespan of a scientific project both during the active research phase and after publication of the results.
Machine learning based lineage tree reconstruction improved with knowledge of higher level relationships between cells and genomic barcodes
Authors: Prusokiene Alisa , Prusokas Augustinas , Retkute Renata
Published: August 2023

Tracking cells as they divide and progress through differentiation is a fundamental step in understanding many biological processes, such as the development of organisms and progression of diseases. In this study, we investigate a machine learning approach to reconstruct lineage trees in experimental systems based on mutating synthetic genomic barcodes. We refine previously proposed methodology by embedding information of higher level relationships between cells and single-cell barcode values into a feature space. We test performance of the algorithm on shallow trees (up to 100 cells) and deep trees (up to 10 000 cells). Our proposed algorithm can improve tree reconstruction accuracy in comparison to reconstructions based on a maximum parsimony method, but this comes at a higher computational time requirement.
Combined inhibition of topoisomerase I and poly(ADP-ribose) polymerase: A synergistic therapeutic strategy for glioblastoma with phosphatase and tensin homolog deficiency
Authors: Kim Olga , Butler Madison , Sergi Zach , Robey Robert W , Zhang Meili , Chari Raj , Pang Ying , Yu Guangyang , Zhang Wei , Song Hua , Davis Dionne , Hawley Robert G , Wen Xinyu , Wang Herui , Quezado Martha , Tran Bao , Merchant Mythili , Ranjan Alice , Furnari Frank B , Khan Javed , Gilbert Mark R , Ryan Miller Christopher , Gottesman Michael M , Pommier Yves , Wu Jing
Published: August 2023

Background

Deletions or loss-of-function mutations in phosphatase and tensin homolog (PTEN) are common in glioblastoma (GBM) and have been associated with defective DNA damage repair. Here we investigated whether PTEN deficiency presents a vulnerability to a simultaneous induction of DNA damage and suppression of repair mechanisms by combining topoisomerase I (TOP1) and PARP inhibitors.

Methods

Patient-derived GBM cells and isogenic PTEN-null and PTEN-WT glioma cells were treated with LMP400 (Indotecan), a novel non-camptothecin TOP1 inhibitor alone and in combination with a PARP inhibitor, Olaparib or Niraparib. RNAseq analysis was performed to identify treatment-induced dysregulated pathways.

Results

We found that GBM cells lacking PTEN expression are highly sensitive to LMP400; however, rescue of the PTEN expression reduces sensitivity to the treatment. Combining LMP400 with Niraparib leads to synergistic cytotoxicity by inducing G2/M arrest, DNA damage, suppression of homologous recombination-related proteins, and activation of caspase 3/7 activity significantly more in PTEN-null cells compared to PTEN-WT cells. LMP400 and Niraparib are not affected by ABCB1 and ABCG2, the major ATP-Binding Cassette (ABC) drug efflux transporters expressed at the blood-brain barrier (BBB), thus suggesting BBB penetration which is a prerequisite for potential brain tumor treatment. Animal studies confirmed both an anti-glioma effect and sufficient BBB penetration to prolong survival of mice treated with the drug combination.

Conclusions

Our findings provide a proof of concept for the combined treatment with LMP400 and Niraparib in a subset of GBM patients with PTEN deficiency.
Postsecondary Education Experiences and Attainment Among Youth With Foster Care Backgrounds
Authors: Okpych Nathanael J. , Geiger Jennifer M. , Johnson Royel M.
Published: August 2023

This article focuses on postsecondary education among young people who currently are or were in foster care (i.e., out-of-home care settings, including relative and nonrelative foster homes, group care, and other institutional settings). While there are numerous terms and labels used to refer to this group, we will use person-first language to avoid the risk of implying that “being in foster care system is related to internal characteristics of the individual” (Geiger and Gross 2019, p. 3, cited under Overview of Policies), rather than a function of the conditions in which they are placed. In the United States, as in many other countries, young people with foster care experience are among the most underserved student groups. Although most of these youth aspire to go to college, the reality is that few realize that dream. Most studies show that about 50 percent or less of young people in US foster care enroll in college, and about 2–10 percent earn a college degree. While research on postsecondary education among youth with foster care experience has increased in several countries, growth has been particularly rapid and expansive in the United States. Federal US child welfare policies began to address the difficult transition of youth aging out of foster care, broadly, in the mid-1980s. Since the turn of the millennium, several key policies have explicitly targeted education of youth in foster care by reducing unnecessary school changes, funding educational support services, providing grants and tuition waivers for postsecondary education expenses, and extending the age limit until which youth can remain in foster care. Internationally, countries are in various stages of policy development, with some beginning to study and raise awareness about the educational journeys of youth aging out of care, while others have well-developed national policies for this population. Research on programs designed to promote college success includes studies focused on pre-college programming to increase readiness and skills for navigating college, campus support programs (CSPs) that provide comprehensive support to students enrolled in college, publications that describe and evaluate CSPs, and the role of programs in student enrollment and attainment. This article begins by reviewing US-based studies on educational aspirations and outcomes (and disparities by race and gender), as well as barriers and promoters of postsecondary attainment. This is followed by studies on policies and programs designed to promote postsecondary access and completion. The article concludes with two sections on literature outside of the United States on postsecondary education among youth with out-of-home care experience.
Ancrene Wisse
Authors: Milne Krista A.
Published: August 2023

Judging from the significant number of copies that have survived, Ancrene Wisse (c. 1220–1230) was one of the most popular English works of the thirteenth century. The work was designed as a guide for religious recluses known as anchorites. Since it stands as an early example of Middle English from the West Midlands, Ancrene Wisse was of interest to early-20th-century philologists, including J. R. R. Tolkien. The work has attracted much attention as an early example of vernacular pastoralia—works designed to guide members of the Church through their religious lives. As one of the earliest surviving works of English literature addressed to women, Ancrene Wisse has also been the subject of feminist literary and historical analysis. As this brief survey suggests, the scholarship on Ancrene Wisse is vast, and this guide is intended to highlight some of the most influential and recent scholarship on the work.
Factors Influencing Popular Support for War
Authors: Lizotte Mary-Kate
Published: August 2023

Starting with perception of the widespread discontent with the United States war in Vietnam, scholars and politicians have presumed that war and military action are not maintainable without citizen support. Accordingly, scholars have devoted extensive effort to uncover what factors influence popular support for war. Thus there is a large literature studying both major and minor wars as well as other types of military interventions. These studies of attitudes toward war fit into two categories. The first addresses the aggregate, national level of support for wars or military interventions. These studies focus on specific characteristics of wars and interventions, including the purpose for which they are fought, the types of military actions or tactics that are planned or executed, the number of casualties anticipated or actually suffered, and the anticipated or actual success or failure of the war. Many of these studies focus on popular support for actions taken by the United States, but there are also studies of opinion in Canada, Western Europe, Japan, and elsewhere. A second category of scholarship addresses the correlates of individuals’ support for wars and military interventions. Much of this research begins with the hypothesis that individuals’ ideology and partisanship are important correlates of support for war, but additional studies have investigated the importance of gender, race, and the impact of the media on citizen support. In addition to the research summarized here, readers should consult the Oxford Bibliographies in Political Science article, “Public Opinion and Foreign Policy” by Joshua D. Kertzer, especially the section on “Public Opinion and the Use of Force.”
Small Cities
Authors: Kosta Ervin
Published: August 2023

While cities have existed for millennia, it wasn’t until the advent of industrialization in the late eighteenth century that the world entered a process of mass urbanization. Sociology has been preoccupied with understanding the nature of urban life since then. Yet since the turn of the twenty-first century, sociologists, geographers, and urban studies scholars have begun noting that the voluminous literature on cities and urban life produced over a century of research and theorizing is almost exclusively based on the metropolitan experience of big cities in the Global North. Emerging literature on small cities has identified several trends that have rendered them nearly invisible to urban sociology. In their search for generalizable knowledge, sociologists have prioritized big cities as the best indicators of urbanity, creating seemingly universal categories of urban analysis that often hide, instead of illuminate, the urban dynamics of small cities. This focus has also created a false sense that most urban dwellers live in the metropolis. In the United States, the majority of the urban population lives in cities with less than 250,000 inhabitants, making them the modal form of urban life, while big cities like NYC, LA, and Chicago are the exception. That said, while drawing attention to small cities as a distinct category of urban research, sociologists have nonetheless struggled to define what constitutes a “small city.” One difficulty stems from sizeism, or the inability to draw clear boundaries based on population size. While “incorporated areas with less than 100,000 residents” is often used as a shorthand, urban characteristics do not suddenly change once such an arbitrary population number is surpassed. Another difficulty is the relativeness of “small” in global context: a Chinese city of 700,000 could be considered small in that context, but not elsewhere. Despite these definitional challenges, this scholarship maintains that renewed attention to small cities should bring tangible benefits to urban sociology at large. Small cities do not represent a lack of, deviant, or antagonistic forms of urbanity; they constitute an important node within the diverse modes of urbanity. Their urban problems may be recognizable to big cities, but often operate through a different set of variables within the small city context. This encyclopedia entry summarizes this corrective turn to the big city bias, outlines existing research on small(er) cities, and underscores growing calls for giving small cities their due attention.
Representation and Processing of Multi-Word Expressions in First and Second Language Speakers
Authors: Siyanova Anna
Published: August 2023

Multi-word expressions (henceforth, MWEs) are familiar, conventional sequences of two or more words in length. Common examples of MWEs include collocations (e.g., provide service, helping hand), binomials (e.g., bride and groom, research and development), lexical bundles (e.g., in line with, contrary to), idioms (e.g., tie the knot, spill the beans), proverbs (e.g., better late than never, early bird catches the worm), and other phrasal elements. MWEs vary vastly in their properties, but what they have in common is that proficient language users recognize them as familiar, conventional sequences. Because MWEs are familiar, established, and predictable ways of expressing thoughts and ideas, they render our discourse natural, idiomatic, and easily comprehensible. As has been shown in the literature, it is easier and more efficient to acquire and use language in chunks rather than having to create word combinations anew. Chunking has been recognized as an important strategy in linguistic processing, necessary for smooth and efficient language comprehension and production. MWEs have been of interest to scholars from a range of related disciplines—theoretical and applied linguistics, computational and corpus linguistics, psycholinguistics and cognitive science, neurolinguistics, and clinical linguistics. As a result, MWEs have been studied from a variety of distinct yet complementary perspectives that probed their acquisition, on-line processing (comprehension and production), and use by first (L1) and second (L2) language speakers, adults and children, as well as individuals with language disorders. These complementary approaches have painted an extremely detailed picture of MWEs as a complex linguistic phenomenon. The perspective covered in the present article will largely center on the cognitive and psycholinguistic properties and realities of MWEs, with a particular focus on MWE representation and on-line processing (that is, processing happening in real time).
Lexical Ambiguity
Authors: Boland Julie E.
Published: August 2023

A lexical ambiguity, or homonym, is a string of sounds (in spoken language) or a string of characters (in written language) that corresponds to more than one word and/or meaning. Homophones sound the same, but may be spelled differently (e.g., I, eye, aye). Homographs are spelled the same, but may be pronounced differently (e.g., tear: as in tear in my eye or tear the paper). Many words are both homophonous and homographic (e.g., bank, bark). The word bat is both semantically ambiguous (it can refer to a flying animal or a piece of sports equipment) and syntactically ambiguous (it can be either a noun or a verb, as in bat her eyes). If the lexical alternatives differ in frequency, the most frequent one is called the dominant meaning and less frequent alternatives are called subordinate meanings. In order to understand a sentence containing an ambiguous word (e.g., The bat flew through the air), one must resolve both the meaning and syntactic form of the word, relying on some combination of context and frequency. In this example, the preceding determiner the rules out a verb meaning of bat, but two noun meanings are possible. In the absence of any richer context, a reader could choose the most frequent meaning or rely on the relative plausibility of the two types of bats flying through the air. Ambiguous words often appear in sentences that either disambiguate the word fully or strongly bias one particular meaning, but even in these cases, the word is considered lexically ambiguous. Researchers usually make a distinction between words with unrelated meanings, as in the examples above, and words with two or more related meanings (e.g., newspaper: as in work at the newspaper or read the newspaper.) The latter type are considered polysemous rather than lexically ambiguous. This distinction has proven useful, but is somewhat fraught because the distinction between related and unrelated meanings is ill-defined. Finally, most research on lexical ambiguity focuses on ambiguities within a language, but interlingual homographs can also be found, in which words with the same spelling, but different meanings, occur across languages. For example, coin occurs in both English and French, but means “corner” in French.