bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of knowledge-based clinical decision support system for the management of cardiovascular diseases
Authors: L Canoa J , Pena Gil C , Monserrat L 
Published: December 2022

Abstract

Background
Knowledge-based clinical decision support systems (CDSS) are technological tools that analyze patient information and present justified diagnostic and therapeutic suggestions to the user. They improve adherence to evidence-based medicine and reduce medical errors.

Material and methods
We have developed an advanced CDSS with the following components: 1. Knowledge Management System, which allows the introduction of interoperable clinical variables organized in taxonomies, and the generation, validation and direct maintenance of decision rules by experts doctors. 2. Smart Assistant for Medical Reports Generation, which facilitates user interaction for the introduction of clinical data (natural language and/or data entry forms) and decission making supported by real-time suggestions that are automatically generated by 3. Inference Engine. Rules and variables derived from the most relevant cardiovascular Clinical Practice Guidelines (CPGs) are introduced by cardiologists into the system. The rules undergo a process of peer review and internal and external validation with anonymized clinical cases.

Results
More than 2,000 clinical variables and more than 5,000 rules corresponding to more than 80 CPGs and consensuns papers have been created and validated. An internal and external pilot validation of the system has been successfully carried out for the main cardiovascular problems, such as heart failure, atrial fibrillation, valvulopathies, coronary syndromes, cardiomyopathies, hypertension, diabetes and dyslipidaemias, using more than 400 cases.

Conclusion
Our CDSS is capable of providing real-time diagnostic and therapeutic recommendations for complex scenarios in cardiovascular disease, combining thousands of variables and decision rules in a single system. Prospective evaluation of the system in real clinical environments, certification and integration in Electronic Medical Records for clinical use is required.

Funding Acknowledgement
Type of funding sources: Private company. Main funding source(s): DILEMMA solutions, SL
Developing a Roadmap to Define a Potential Ideotype for Drought Tolerance in Eucalyptus
Authors: Pita-Barbosa Alice , Oliveira Leonardo Araujo , de Barros Nairam Félix , Hodecker Bárbara Elias Reis , Oliveira Franciele S , Araújo Wagner L , Martins Samuel C V 
Published: December 2022

Abstract
Climate change is escalating the water crisis worldwide, leading to unpredictable water availability and water scarcity, which is among the main environmental factors affecting plant growth and yield, severely affecting the productivity of planted forests, most of them composed of Eucalyptus species. The selection of genotypes capable of growing and surviving under water scarcity is required for eucalypt cultivation in areas with seasonal or continuous drought episodes. To achieve this goal, there is the current need for the identification of potential drought tolerance bioindicators, which is a challenging task since plant responses to drought involve numerous genes and strategies. We posit that eco-physiological and morphoanatomical analyses in combination with molecular approaches could help fill the current knowledge gap. In this review, we summarize recent advances in the identification of potential indicators of drought tolerance in Eucalyptus and discuss the typical responses to drought stress, as well as their importance as bioindicators for the development of a drought-tolerant eucalypt ideotype.
Verges Along Forest Roads Promote Wild Bees
Authors: Eckerter Tristan , Erbacher Jörn , Wolf Wanja , Braunisch Veronika , Klein Alexandra-Maria 
Published: December 2022

AbstractForests in Germany are occupied with roads, paths, and trails with a density of 5.03 km/km². Their construction and maintenance create a network of verges promoting flowering plants. Whether these verges are visited by bees, which factors are determining their abundance, diversity, and composition, and which flowering resources are used is unknown. We selected 13 verges in the Black Forest (Germany), sweep-netted wild bees along transects, calculated the flowering area of all herbs, and measured the area (hectares) of grassland within 1 km around the transects. To evaluate the resource use of a common bumblebee species, we analyzed the pollen load of common carder bees (Bombus pascuorum) using microscopes. The abundance and diversity of wild bees was positively related to flowering area. With an increasing area of grassland, the abundance of ubiquitous species increased. Wild bee community composition was driven by flowering area. Common carder bees collected pollen from several flower resources but mainly used few species, such as the common hemp nettle (Galeopsis tetrahit L.). As the flowering area influenced wild bee abundance, diversity, and composition, we suggest creating road verges that favor the occurrence of native flowering plants to support wild bees in forest ecosystems.Study Implications: Forest road verges generally have higher light availability than the forest interior and therefore have higher availability of flowering plants. Although the importance of verges for wild bee conservation in agricultural landscapes is known, forest road verges are understudied. Our study demonstrates that forest road verges are important habitats for many ubiquitous bees and that the flowering area on these verges is the key determinant for the abundance and diversity of wild bees. Therefore, creating road verges that favor the occurrence of native flowering plants is key to support bees on these verges.
Whole-genome Analysis Reveals Contrasting Relationships Among Nuclear and Mitochondrial Genomes Between Three Sympatric Bat Species
Authors: Laine Veronika N , Sävilammi Tiina , Wahlberg Niklas , Meramo Katarina , Ossa Gonzalo , Johnson Joseph S , Blomberg Anna S , Yeszhanov Aidyn B , Yung Veronica , Paterson Steve , Lilley Thomas M 
Published: December 2022

AbstractUnderstanding mechanisms involved in speciation can be challenging, especially when hybridization or introgression blurs species boundaries. In bats, resolving relationships of some closely related groups has proved difficult due subtle interspecific variation both in morphometrics and molecular data sets. The endemic South American Histiotus bats, currently considered a subgenus of Eptesicus, harbor unresolved phylogenetic relationships and of those is a trio consisting of two closely related species: Eptesicus (Histiotus) macrotus and Eptesicus (Histiotus) montanus, and their relationship with a third, Eptesicus (Histiotus) magellanicus. The three sympatric species bear marked resemblance to each other, but can be differentiated morphologically. Furthermore, previous studies have been unable to differentiate the species from each other at a molecular level. In order to disentangle the phylogenetic relationships of these species, we examined the differentiation patterns and evolutionary history of the three Eptesicus (H.) species at the whole-genome level. The nuclear DNA statistics between the species suggest strong gene flow and recent hybridization between E. (H.) montanus and E. (H.) macrotus, whereas E. (H.) magellanicus shows a higher degree of isolation. In contrast, mitochondrial DNA shows a closer relationship between E. (H.) magellanicus and E. (H.) montanus. Opposing patterns in mtDNA and nuclear markers are often due to differences in dispersal, and here it could be both as a result of isolation in refugia during the last glacial maximum and female philopatry and male-biased dispersal. In conclusion, this study shows the importance of both the nuclear and mitochondrial DNA in resolving phylogenetic relationships and species histories.
Genome Reference Assembly for Bottlenecked Southern Australian Koalas
Authors: Blanchard Adam Mark , Emes Richard David , Greenwood Alex David , Holmes Nadine , Loose Matthew William , McEwen Gail Katherine , Meers Joanne , Speight Natasha , Tarlinton Rachael Eugenie 
Published: December 2022

Abstract
Koala populations show marked differences in inbreeding levels and in the presence or absence of the endogenous Koala retrovirus (KoRV). These genetic differences among populations may lead to severe disease impacts threatening koala population viability. In addition, the recent colonization of the koala genome by KoRV provides a unique opportunity to study the process of retroviral adaptation to vertebrate genomes and the impact this has on speciation, genome structure, and function. The genome build described here is from an animal from the bottlenecked Southern population free of endogenous and exogenous KoRV. It provides a more contiguous genome build than the previous koala reference derived from an animal from a more outbred Northern population and is the first koala genome from a KoRV polymerase–free animal.
Global Pain and Aging: A Cross-Sectional Study on Age Differences in the Intensity of Chronic Pain Among Middle-Aged and Older Adults in 20 Countries
Authors: Calvo Esteban , Córdova Cynthia , Shura Robin , Allel Kasim , Alvaro Castillo-Carniglia , Keyes Katherine M , Mauro Christine , Mauro Pia M , Medina José T , Mielenz Thelma , Taramasco Carla , Martins Silvia S 
Published: December 2022

Abstract

Objectives
This study aims to examine age differences in the intensity of chronic pain among middle-aged and older adults, where intensity is measured on a scale differentiating between chronic pain that is often troubling and likely requires intervention versus more endurable sensations. We aim to explore whether individual health and national gross domestic product (GDP) explain these differences as well.

Methods
Cross-nationally harmonized data from 20 countries on self-reported intensity of chronic pain (0 = no, 1 = mild, 2 = moderate, 3 = severe) in 104,826 individuals aged 50+ observed in 2012–2013. Two-level hierarchical ordinal linear models with individuals nested within countries were used to isolate estimations from heterogeneity explained by methodological differences across single-country studies.

Results
Overall, mean participant age was 66.9 (SD = 9.9), 56.1% were women, and 41.9% of respondents reported any chronic pain. Chronic pain intensity rose sharply with age in some countries (e.g., Korea and Slovenia), but this association waned or reversed in other countries (e.g., the United States and Denmark). Cross-country variation and age differences in chronic pain were partly explained (85.5% and 35.8%, respectively) by individual-level health (especially arthritis), country-level wealth (as indicated by GDP per capita), and demographics.

Discussion
Chronic pain intensity is not an inevitable consequence of chronological age, but the consequence of potential selection effects and lower activity levels combined with individual-level health and country-level wealth. Our findings suggest further investigation of health conditions and country affluence settings as potential targets of medical and policy interventions aiming to prevent, reduce, or manage chronic pain among older patients and aging populations.
Engineered Cleistogamy inCamelina sativafor bioconfinement
Authors: Huang Debao , Gao Liwei , McAdams Jeremy , Zhao Fangzhou , Lu Hongyan , Wu Yonghui , Martin Jeremy , Sherif Sherif M , Subramanian Jayasankar , Duan Hui , Liu Wusheng 
Published: December 2022

AbstractCamelina sativa is a self-pollinating and facultative outcrossing oilseed crop. Genetic engineering has been used to improve camelina yield potential for altered fatty acid composition, modified protein profiles, improved seed and oil yield, and enhanced drought resistance. The deployment of transgenic camelina in the field posits high risks related to the introgression of transgenes into non-transgenic camelina and wild relatives. Thus, effective bioconfinement strategies need to be developed to prevent pollen-mediated gene flow (PMGF) from transgenic camelina. In the present study, we overexpressed the cleistogamy (i.e. floral petal non-openness)-inducing PpJAZ1 gene from peach in transgenic camelina. Transgenic camelina overexpressing PpJAZ1 showed three levels of cleistogamy, affected pollen germination rates after anthesis but not during anthesis, and caused a minor silicle abortion only on the main branches. We also conducted field trials to examine the effects of the overexpressed PpJAZ1 on PMGF in the field, and found that the overexpressed PpJAZ1 dramatically inhibited PMGF from transgenic camelina to non-transgenic camelina under the field conditions. Thus, the engineered cleistogamy using the overexpressed PpJAZ1 is a highly effective bioconfinement strategy to limit PMGF from transgenic camelina, and could be used for bioconfinement in other dicot species.
An improved assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and refines time of divergence estimates for the Cannabaceae family
Authors: Padgitt-Cobb Lillian K , Pitra Nicholi J , Matthews Paul D , Henning John A , Hendrix David A 
Published: December 2022

AbstractWe present a chromosome-level assembly of the Cascade hop (Humulus lupulus L. var. lupulus) genome. The hop genome is large (2.8 Gb) and complex, and early attempts at assembly were fragmented. Recent advances have made assembly of the hop genome more tractable, transforming the extent of investigation that can occur. The chromosome-level assembly of Cascade was developed by scaffolding the previously reported Cascade assembly generated with PacBio long-read sequencing and polishing with Illumina short-read DNA sequencing. We developed gene models and repeat annotations and used a controlled bi-parental mapping population to identify significant sex-associated markers. We assessed molecular evolution in gene sequences, gene family expansion and contraction, and time of divergence from Cannabis sativa and other closely related plant species using Bayesian inference. We identified the putative sex chromosome in the female genome based on significant sex-associated markers from the bi-parental mapping population. While the estimate of repeat content (~64%) is similar to the estimate for the hemp genome, syntenic blocks in hop contain a greater percentage of LTRs. Hop is enriched for disease resistance-associated genes in syntenic gene blocks and expanded gene families. The Cascade chromosome-level assembly will inform cultivation strategies and serve to deepen our understanding of the hop genomic landscape, benefiting hop researchers and the Cannabaceae genomics community.
SlMYB1regulates the accumulation of lycopene, fruit shape, and resistance toBotrytis cinereain tomato
Authors: Yin Ziyi , Liu Jiazong , Zhao Haipeng , Chu Xiaomeng , Liu Haoqi , Ding Xiangyu , Lu Chongchong , Wang Xinyu , Zhao Xiangyu , Li Yang , Ding Xinhua 
Published: December 2022

AbstractFruit lycopene, shape, and resistance are essential traits in vegetables whose final product is fruit, and they are also closely related to and strictly regulated by multiple transcription factors. Lycopene, which cannot be synthesized by the human body and can only be ingested from the outside, was important in maintaining human health. During fruit ripening and post-harvest, tomato plants face a variety of biotic or abiotic stresses, which might inflict great damage to fruit quality due to its flat shape and pointed tip during storage and transportation. Therefore, there is an urgent need for key molecular switches to simultaneously improve fruit lycopene and resistance to biotic stress during ripening. Here, we identified the MYB transcription factor SlMYB1 in tomato plants which could bind to the promoters of lycopene synthesis-related genes, SlLCY1, SlPSY2, and the pathogen-related gene SlPR5 directly, to regulate the fruit lycopene and resistance to Botrytis cinerea in tomato. In addition to regulating lycopene synthesis, SlMYB1 also regulates the content of soluble sugar, soluble protein and flavonoid in tomato. What’s more, SlMYB1 could regulate the tomato fruit shape, making it smoother or flatter to prevent skin damage caused by vibration on fruits. RNA sequencing (RNA-seq) further showed that SlMYB1 fruit-specific expression lines had multiple differentially expressed genes compared with those from wild-type plants, suggesting that SlMYB1 might have multiple roles in fruit nutritional quality control and resistance to stresses, which is a rare occurrence in previous studies. In summary, our results revealed that SlMYB1 was an essential multi-functional transcription factor that could regulate the lycopene and resistance to Botrytis cinerea, and change the shape of fruit in tomato plants.
Deep Dive Into MicroRNAs in Inflammatory Bowel Disease
Authors: Alfaifi Jaber , Germain Adeline , Heba Anne-Charlotte , Arnone Djésia , Gailly Laura , Ndiaye Ndeye Coumba , Viennois Emilie , Caron Bénédicte , Peyrin-Biroulet Laurent , Dreumont Natacha 
Published: December 2022

Abstract
Inflammatory bowel disease (IBD), which includes ulcerative colitis and Crohn’s disease, is thought to develop in genetically predisposed individuals as a consequence of complex interactions between dysregulated inflammatory stimuli, immunological responses, and environmental factors. The pathogenesis of IBD has yet to be fully understood. The global increase in the incidence of IBD suggests a gap in the current understanding of the disease. The development of a new diagnostic tool for inflammatory bowel disease that is both less invasive and more cost-effective would allow for better management of this condition. MicroRNAs (miRNAs) are a class of noncoding RNAs with important roles as posttranscriptional regulators of gene expression, which has led to new insights into understanding IBD. Using techniques such as microarrays and real-time polymerase chain reactions, researchers have investigated the patterns in which patients with Crohn’s disease and ulcerative colitis show alterations in the expression of miRNA in tissue, blood, and feces. These miRNAs are found to be differentially expressed in IBD and implicated in its pathogenesis through alterations in autophagy, intestinal barrier, and immune homeostasis. In this review, we discuss the miRNA expression profiles associated with IBD in tissue, peripheral blood, and feces and provide an overview of the miRNA mechanisms involved in IBD.
Evidence of Residual Ongoing Viral Replication in Chronic Hepatitis B Patients Successfully Treated With Nucleos(t)ide Analogues
Authors: Yu Tong , Zhang Miaoqu , Zhang Hanyue , Zheng Jianming , Shen Chuan , Jiang Ning , Zou Lei , Wang Jing , Yu Yiqi , Zhang Qiran , Yu Shuili , Huang Yanfang , Huang Yuxian , Zhang Jiming , Qiu Chao , Zhang Wenhong , Meng Zhefeng 
Published: December 2022

Abstract

Background
Chronic hepatitis B is usually treated with nucleos(t)ide analogues (NAs). However, a cure is rarely achieved, even with years of treatment. Here, we investigated whether viral replication is completely halted and how long covalently closed circular DNA (cccDNA) persists in patients successfully treated with NAs.

Methods
A series of longitudinal serum samples and a collection of cross-sectional liver biopsies were obtained from patients successfully treated with NAs. Viral variants in serum HBV RNA were enumerated by deep sequencing. Viral replication intermediates in hepatocytes were directly visualized by in situ hybridization. The apparent half-life of each cccDNA was estimated.

Results
Three of 6 successfully treated patients demonstrated clear evidence of a small proportion of virus evolution, although the overwhelming proportion of variants were identical or possessed a similar degree of divergence through time. The apparent half-life of variants was estimated to be from approximately 7.42 weeks to infinite. Hepatocytes remained positive for cytoplasmic nucleocapsids-associated relaxed circular DNA in 4 of 7 liver needle biopsies.

Conclusions
We conclude that even after prolonged treatment, a small proportion of the cccDNA reservoir is constantly replenished by continued low-level HBV replication, whereas a large proportion of the cccDNA reservoir persists over time.
Modeling net energy partition patterns of growing–finishing pigs using nonlinear regression and artificial neural networks
Authors: Wang Li , Shi Huangwei , Hu Qile , Gao Wenjun , Wang Lu , Lai Changhua , Zhang Shuai 
Published: December 2022

Abstract
The objectives of this study were to evaluate the net energy (NE) partition patterns of growing–finishing pigs at different growing stages and to develop the corresponding prediction models using nonlinear regression (NLR) and artificial neural networks (ANN). Twenty-four pigs with an initial body weight (BW) of ~30 kg were kept in metabolic cages and fed ad libitum and were moved into six respiration chambers in turns until ~90 kg. The NE partition patterns, i.e., NE for maintenance (NEm), NE retained as protein (NEp), and NE retained as lipid (NEl), were calculated based on indirect calorimetry and nitrogen balance techniques. The energy balance data collected through the animal trial was then randomly split into a training data set containing 75% of the samples and a testing data set containing the remaining 25% of the samples. The NLR models and a series of ANN models were established on the training data set to predict the metabolizable energy intake, NE intake, NEm, NEp, and NEl of pigs. The best-fitted ANN models were selected by 5-fold cross-validation in the training data set. The prediction performance of the best-fitted NLR and ANN models were compared on the testing data set. The results showed that the average NE intakes of pigs were 17.71, 23.25, 24.56, and 28.96 MJ/d in 30 to 45 kg, 45 to 60 kg, 60 to 75 kg, and 75 to 90 kg, respectively. The NEm and NEl (MJ/d) kept increasing as BW increased from 30 kg to 90 kg, while the NEp increased to its maximum value and then kept in a certain range of 4.64 to 4.88 MJ/d. The proportion of NEm for pigs at 30 to 90 kg stayed within the range of 42.0% to 48.6%, while the proportion of NEl kept increasing. For the prediction models built based on the animal trial, ANN models exhibited better performance than NLR models for all the target outputs. In conclusion, NE partition patterns changed in different growth stages of pigs, and ANN models are more flexible and powerful than NLR models in predicting the NE partition patterns of growing–finishing pigs.