bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ecological factors related to seed germination and early seedling establishment inUlmus minorMill., an endangered riparian tree species
Authors: López-Almansa Juan Carlos 
Published: April 2023

AbstractNatural populations of Ulmus minor Mill., an outstanding component of European riparian forests, are endangered due to Dutch elm disease, which has led to the development of several breeding programs throughout Europe. However, the reproductive ecology of this species is scarcely known even though sexual regeneration is an essential factor that must be understood before implementing elm stand restoration. In this paper, the main ecological factors affecting seed germination and early seedling establishment in U. minor are studied through a factorial design with five different factors: Light (levels: Full-sun, Shade), Initial water (levels: Initially-flooded, Initially-irrigated), Subsequent water (levels: Semi-submerged, Later-irrigated), Soil cover (levels: Bare-soil, Litter) and Substrate (levels: Silty-clay, Sandy-loam). Seed germination and seedling survival were monitored for 7 weeks. All factors except Initial water and Substrate turned out to be highly significant. Shade increased seed germination and seedling survival. Response to Initial water fluctuated, with an early higher percentage of germinated seeds in Initially-flooded but a higher seedling survival in Initially-irrigated. Subsequent water did not affect seedling establishment and survival, but Semi-submerged treatments increased seed germination. Bare-soilincreased seed germination too, whereas, in the medium term, Litter affected positively seedling survival. Sandy-loam substrates favoured seed germination, but Silty-claysubstrates favoured seedling survival. Together, these results suggest that the most favourable scenario for U. minor sexual regeneration may be a combination of a not-too-severe late-winter or early-spring flood followed by a wet spring and summer, probably with a higher establishment in heavy-textured substrates located in small gaps and forest edges where the overstorey provides some protection against strong sunlight.
quEHRy: a question answering system to query electronic health records
Authors: Soni Sarvesh , Datta Surabhi , Roberts Kirk 
Published: April 2023

Abstract

Objective
We propose a system, quEHRy, to retrieve precise, interpretable answers to natural language questions from structured data in electronic health records (EHRs).

Materials and Methods
We develop/synthesize the main components of quEHRy: concept normalization (MetaMap), time frame classification (new), semantic parsing (existing), visualization with question understanding (new), and query module for FHIR mapping/processing (new). We evaluate quEHRy on 2 clinical question answering (QA) datasets. We evaluate each component separately as well as holistically to gain deeper insights. We also conduct a thorough error analysis for a crucial subcomponent, medical concept normalization.

Results
Using gold concepts, the precision of quEHRy is 98.33% and 90.91% for the 2 datasets, while the overall accuracy was 97.41% and 87.75%. Precision was 94.03% and 87.79% even after employing an automated medical concept extraction system (MetaMap). Most incorrectly predicted medical concepts were broader in nature than gold-annotated concepts (representative of the ones present in EHRs), eg, Diabetes versus Diabetes Mellitus, Non-Insulin-Dependent.

Discussion
The primary performance barrier to deployment of the system is due to errors in medical concept extraction (a component not studied in this article), which affects the downstream generation of correct logical structures. This indicates the need to build QA-specific clinical concept normalizers that understand EHR context to extract the “relevant” medical concepts from questions.

Conclusion
We present an end-to-end QA system that allows information access from EHRs using natural language and returns an exact, verifiable answer. Our proposed system is high-precision and interpretable, checking off the requirements for clinical use.
Weakly supervised spatial relation extraction from radiology reports
Authors: Datta Surabhi , Roberts Kirk 
Published: April 2023

Abstract

Objective
Weak supervision holds significant promise to improve clinical natural language processing by leveraging domain resources and expertise instead of large manually annotated datasets alone. Here, our objective is to evaluate a weak supervision approach to extract spatial information from radiology reports.

Materials and Methods
Our weak supervision approach is based on data programming that uses rules (or labeling functions) relying on domain-specific dictionaries and radiology language characteristics to generate weak labels. The labels correspond to different spatial relations that are critical to understanding radiology reports. These weak labels are then used to fine-tune a pretrained Bidirectional Encoder Representations from Transformers (BERT) model.

Results
Our weakly supervised BERT model provided satisfactory results in extracting spatial relations without manual annotations for training (spatial trigger F1: 72.89, relation F1: 52.47). When this model is further fine-tuned on manual annotations (relation F1: 68.76), performance surpasses the fully supervised state-of-the-art.

Discussion
To our knowledge, this is the first work to automatically create detailed weak labels corresponding to radiological information of clinical significance. Our data programming approach is (1) adaptable as the labeling functions can be updated with relatively little manual effort to incorporate more variations in radiology language reporting formats and (2) generalizable as these functions can be applied across multiple radiology subdomains in most cases.

Conclusions
We demonstrate a weakly supervision model performs sufficiently well in identifying a variety of relations from radiology text without manual annotations, while exceeding state-of-the-art results when annotated data are available.
Metrics in action: how social media metrics shape news production on Facebook
Authors: Mukerjee Subhayan , Yang Tian , Peng Yilang 
Published: April 2023

Abstract
Social media metrics allow media outlets to get a granular, real-time understanding of audience preferences, and may therefore be used to decide what content to prioritize in the future. We test this mechanism in the context of Facebook, by using topic modeling and longitudinal data analysis on a large dataset comprising all posts published by major media outlets used by American citizens (N≈2.23M, 2015–2019). We find that while the overall effect of audience engagement on future news coverage is significant, there is substantial heterogeneity in how individual outlets respond to different kinds of topics. A handful of right-wing media outlets are more likely to respond to audience engagement metrics than other outlets, but with partisan politics topics and not with entertainment-oriented content. Our research sheds new light on how social media platforms have shaped journalistic practices and has implications for the future health of journalism in the United States.
Families of choice with no choice: remarks concerning the situation of families of choice in Polish law
Authors: Drapalska-Grochowicz Marlena 
Published: April 2023

Abstract
This article focuses on the situation of families of choice in Polish law. The first research objective was to determine whether and how parenting in families of choice is regulated by law. To achieve this goal, the author analysed appropriate statute and case law, taking into account the sociological and psychological background of family relationships. The second objective was to find legal and non-legal factors affecting the current situation of families of choice in Polish law. Then it was assessed whether it is possible to provide court protection to the families of choice in the process of applying current regulations. This article shows that although the Polish legislator considers family life an important value, it is restricted to a specific understanding of family. Neither the Polish legislator nor the legal discourse recognize the needs of the families of choice, and the chances of changing the current situation are small.
A new approach for the construction of historical databases—NoSQL Document-oriented databases: the example ofAtlantoCracies
Authors: Diaz-Ordoñez Manuel , Rodríguez Baena Domingo Savio , Yun-Casalilla Bartolomé 
Published: April 2023

AbstractThis article proposes, and justifies, the use of the Document-oriented databases as a flexible, easy to use, and powerful digital tool in the field of historical research. First, the reasons that have made relational databases the predominant instrument among historians are studied, while detailing the problems involved in their use. Next, the way in which historians have tried to face these problems by using other digital tools is explained, as well as the limitations that such use entails. Through a case study—that of European aristocratic networks in early modern times—it is shown, however, that Document-oriented databases, present notable advantages and have greater explanatory power for the historian’s work. Thanks to their flexibility, they are better adapted to the often-unpredictable nature of historical sources without diminishing their ease of use or their analytical potential.
Proverbs as indicators of proficiency for art-generating AI
Authors: Tosina Fernández Luis J 
Published: April 2023

Abstract
Art generated by Artificial Intelligence (AI) is currently having great repercussion online. The reason for this is the fact that it allows people without creative talent to produce outstanding works by just typing in the description of what they want to illustrate. However, the appearance of this technology has also caused some discomfort among artists and graphic designers, who see their craft threatened by a service that is available to anyone free of charge. In this article, the capability of some of these platforms to process figurative language will be assessed with the help of five well-known proverbs found in almost identical terms across a number of Western languages. These proverbs were used as the prompts on five of the most popular AI art generators accessible at present. After analyzing the results, our experiment concludes that AI evidences significant deficiencies in the processing of proverbs and, therefore, of figurative language. Consequently, AI does not seem able to substitute human agency completely in artistic creation yet. This exposes an aspect that needs improvement not just for the creative applications of AI but for other applications that it may have in the future. To achieve this, disciplines such as psycholinguistics should be integrated into the teams that develop AI.
Structural adjustment and the political economy of capital flight
Authors: Nosrati Elias , Kern Andreas , Reinsberg Bernhard , Sevinc Dilek 
Published: April 2023

Abstract
The financial haemorrhaging of lower income countries in the form of capital flight is a leading cause of global economic inequality. On an annual basis, trillions of dollars bypass the already starved fiscal spaces of nations mired in poverty, making their way instead to lucrative offshore bank accounts governed by secrecy jurisdictions. The present article relates this phenomenon to the institutional architecture of the global financial system and provides causal evidence that structural adjustment programmes implemented at the behest of international financial organizations amplify such capital flight. In particular, by isolating exogenous variation in policy conditionalities through the use of instrumental variables, we find that trade liberalization, financial sector reforms and privatization measures mandated by the International Monetary Fund in developing contexts substantially increase financial outflows occurring via current and capital account transactions. Our findings thus document the contribution that structural adjustment makes to an underappreciated facet of contemporary global inequality.
Molecular subtypes of respiratory Adenovirus infection outbreak in children in Northern Vietnam and risk factors of more severe cases
Authors: Nguyen Dinh-Dung , Phung Lan Tuyet , Thanh Tran Huyen Thi , Thanh Ly Ha Thi , Mai Vo Anh Hang , Dinh Nhung Phuong , Doan Phuong Mai , Nguyen Anh Thi , Dang Luc Danh , Doan Thia Thi , Pham Khuong Thi , Pham Huong Lan , Xuan Dai Hoang , Nguyen Thao Phuong , Tran Bao Thai , Thuc Tran Trang Thi , Minh Le Huong Thi , Pham An Nhat , Antoniou Antony , Ho Nhan Thi 
Published: April 2023

AbstractBackgroundUnder the pressure of the outbreak of respiratory Human Adenovirus (HAdV) infections in children in Northern Vietnam in the end of 2022, this study was initiated to identify the HAdV subtype(s) responsible for the outbreak in relation to the clinical features of the patients and examine the risk factors of more severe cases.MethodsThe study was conducted on pediatric patients tested positive with HAdV using multiplex real- time PCR between October and November 2022. Nasal swab samples were used for sequencing to identify HAdV subtypes and clinical data were collected retrospectively.ResultsAmong 97 successfully sequenced samples, the predominant subtypes were HAdV-B3 (83%), HAdV-B7 (16%) and HAdV-C2 (1%). Lower respiratory manifestations were found in 25% of patients (5% with severe pneumonia). There was no significant association between HAdV type and clinical features except that those infected with HAdV type 3 exhibited higher WBC and neutrophil % (p<0.001). Co- infection of HAdV with ≥1 other respiratory viruses or bacteria was found in 70.8% of those with lower respiratory illnesses (OR (95%CI); p-value vs. those without =5.21 (1.60, 19.36); 0.0084 after adjusting for age at hospital visit, sex, birth delivery method, day of disease at hospital visit), and in 100% of those with severe pneumonia vs. 33% of those without (p=0.005).ConclusionHAdV-B3 and HAdV-B7 were predominant in the outbreak. Co-infection of HAdV together with other respiratory viruses or bacteria was a strong risk factor for lower respiratory tract illnesses and severe pneumonia. The findings advocate the advantages of multi-factor microbial panels for the diagnosis and prognosis of respiratory infections in children.
Transgenic female mice producingtrans10,cis12-conjugated linoleic acid present excessive prostaglandin E2, adrenaline, corticosterone, glucagon, and FGF21
Authors: Rao Yu , Liang Lu-Wen , Li Mei-Juan , Wang Yang-Yang , Wang Bao-Zhu , Gou Ke-Mian 
Published: April 2023

ABSTRACTDietarytrans10,cis12-conjugated linoleic acid (t10c12-CLA) is a potential candidate in anti-obesity trials. A transgenic mouse was previously successfully established to determine the anti-obesity properties of t10c12-CLA in male mice that could produce endogenous t10c12-CLA. To test whether there is a different impact of t10c12-CLA on lipid metabolism in both sexes, this study investigated the adiposity and metabolic profiles of female Pai mice that exhibited a dose-dependent expression of foreign Pai gene and a shift of t10c12-CLA content in tested tissues. Compared to their gender-match wild-type littermates, Pai mice had no fat reduction but exhibited enhanced lipolysis and thermogenesis by phosphorylated hormone-sensitive lipase and up-regulating uncoupling proteins in brown adipose tissue. Simultaneously, Pai mice showed hepatic steatosis and hypertriglyceridemia by decreasing gene expression involved in lipid and glucose metabolism. Further investigations revealed that t10c10-CLA induced excessive prostaglandin E2, adrenaline, corticosterone, glucagon and inflammatory factors in a dose-dependent manner, resulting in less heat release and oxygen consumption in Pai mice. Moreover, fibroblast growth factor 21 overproduction only in monoallelic Pai/wt mice indicates that it was sensitive to low doses of t10c12-CLA. These results suggest that chronic t10c12-CLA has system-wide effects on female health via synergistic actions of various hormones.
Interplay of two small RNAs fine-tunes hierarchical flagellar gene expression in the foodborne pathogenCampylobacter jejuni
Authors: König Fabian , Svensson Sarah L. , Sharma Cynthia M. 
Published: April 2023

AbstractLike for many enteric bacteria, flagella are a crucial virulence factor for the foodborne pathogenCampylobacter jejuni, allowing the bacteria to move through the viscous mucus of the human intestine. Assembly of the complex flagellar machinery and filament requires hierarchical regulation via transcriptional control of each component. InC. jejuni, class I genes are transcribed from σ70-dependent promoters and class II/III genes with the help of the alternative sigma factors RpoN (σ54) and FliA (σ28). In contrast to transcriptional control, less is known about post-transcriptional regulation of flagellar biosynthesis cascades via small regulatory RNAs (sRNAs). Here, we characterized two sRNAs with opposing effects on the cascade that fine-tuneC. jejuniflagellar filament assembly and thereby impact motility. We demonstrate that the highly conservedCampylobactersRNA CJnc230 (FlmE, flagellar length andmotilityenhancer), encoded downstream of the flagellar hook structural protein FlgE, is dependent on RpoN and that RNase III processes CJnc230 from theflgEmRNA, while RNase Y and PNPase mature its 3’ end. We identify mRNAs encoding a regulator of flagella-flagella interactions and the anti-σ28factor FlgM as direct targets of CJnc230 repression. Overexpression of CJnc230 de-represses FliA activity and upregulates class III flagellar genes, such as the major flagellinflaA, culminating in longer flagella and increased motility. In contrast, overexpression of the FliA-dependent sRNA CJnc170 (FlmR, flagellar length andmotilityrepressor) reduces flagellar length and motility. Overall, our study demonstrates sRNA-mediated post-transcriptional regulation fine-tunesC. jejuniflagellar biosynthesis through balancing of the hierarchically expressed components.
A mobile CRISPRi collection enables genetic interaction studies for the essential genes ofEscherichia coli
Authors: Rachwalski Kenneth , Tu Megan M , Madden Sean J , Hansen Drew M , Brown Eric D 
Published: April 2023

SummaryOrdered collections of precise gene deletions inE. coliand other model microbes have proven to be invaluable resources to study the dispensability of the non-essential genome in different environmental and genetic contexts. The dispensability of canonically essential genes, however, has been largely unstudied in such contexts. Advances in gene editing, in particular CRISPR interference (CRISPRi), have enabled depletion of essential cellular machinery to study the downstream effects on bacterial physiology. Here, we describe the construction of an orderedE. coliCRISPRi collection, designed to knock down the expression of 356 essential genes with the induction of a catalytically inactive Cas9, harbored on the conjugative plasmid pFD152, that also encodes for expression of specific guide RNA scaffolds. This mobile CRISPRi library can be conjugated into other ordered genetic libraries, to assess combined effects of essential gene knockdowns with non-essential gene deletions. As proof of concept, we probed cell envelope synthesis with two crosses. First, we crossed a deletion in the genelppwith the entire CRISPRi library. Similarly, we crossed the CRISPRi knockdown oflolAwith ∼4,000 deletion strains of the Keio collection. These experiments revealed a number of notable genetic interactions for the essential phenotype probed and, in particular, showed supressing interactions for the loci in question.
Chemical stimuli override a temperature-dependent morphological program by reprogramming the transcriptome of a fungal pathogen
Authors: Assa Dror , Voorhies Mark , Sil Anita 
Published: April 2023

AbstractThe human fungal pathogenHistoplasmachanges its morphology in response to temperature. At 37°C it grows as a budding yeast whereas at room temperature it transitions to hyphal growth. Prior work has demonstrated that 15-20% of transcripts are temperature-regulated, and that transcription factors Ryp1-4 are necessary to establish yeast growth. However, little is known about transcriptional regulators of the hyphal program. To identify TFs that regulate filamentation, we utilize chemical inducers of hyphal growth. We show that addition of cAMP analogs or an inhibitor of cAMP breakdown overrides yeast morphology, yielding inappropriate hyphal growth at 37°C. Additionally, butyrate supplementation triggers hyphal growth at 37°C. Transcriptional profiling of cultures filamenting in response to cAMP or butyrate reveals that a limited set of genes respond to cAMP while butyrate dysregulates a larger set. Comparison of these profiles to previous temperature- or morphology-regulated gene sets identifies a small set of morphology-specific transcripts. This set contains 9 TFs of which we characterized three,STU1,FBC1, andPAC2, whose orthologs regulate development in other fungi. We found that each of these TFs is individually dispensable for room-temperature (RT) induced filamentation but each is required for other aspects of RT development.FBC1andPAC2, but notSTU1, are necessary for filamentation in response to cAMP at 37°C. Ectopic expression of each of these TFs is sufficient to induce filamentation at 37°C. Finally,PAC2induction of filamentation at 37°C is dependent onSTU1, suggesting these TFs form a regulatory circuit that, when activated at RT, promotes the hyphal program.ImportanceFungal illnesses pose a significant disease burden. However, the regulatory circuits that govern the development and virulence of fungi remain largely unknown. This study utilizes chemicals that can override the normal growth morphology of the human pathogenHistoplasma. Using transcriptomic approaches, we identify novel regulators of hyphal morphology and refine our understanding of the transcriptional circuits governing morphology inHistoplasma.
Transcriptional dissection of symptomatic profiles across the brain of men and women with depression
Authors: Mansouri Samaneh , Pessoni André M , Rivera Arturo M , Tamminga Carol A. , Parise Eric , Turecki Gustavo , Nestler Eric J. , Chen Ting-Huei , Labonté Benoit 
Published: April 2023

AbstractMajor depressive disorder (MDD) is one of the most important causes of disability worldwide. While recent work provides insights into the molecular alterations in the brain of patients with MDD, whether these molecular signatures can be associated with the expression of specific symptom domains in males and females remains unclear. Here, we identified sex-specific gene modules associated with the expression of MDD, combining differential gene expression and co-expression network analyses in six cortical and subcortical brain regions. Our results show varying levels of network homology between males and females across brain regions, although the association between these structures and the expression of MDD remains highly sex-specific. We refined these associations to several symptom domains and identified transcriptional signatures associated with distinct functional pathways, including GABAergic and glutamatergic neurotransmission, metabolic processes, and intracellular signal transduction, across brain regions associated with distinct symptomatic profiles in a sex-specific fashion. In most cases, these associations were specific to males or to females with MDD, although a subset of gene modules associated with common symptomatic features in both sexes was also identified. Together, our findings suggest that the expression of distinct MDD symptom domains is associated with sex-specific transcriptional structures across brain regions.