bluuebunny/crossref_metadata_2025 huggingface dataset:
The risk of autism spectrum disorder and intellectual disability but not attention deficit/hyperactivity disorder is increased in individuals with esophageal atresia
Authors: Kassa Ann-Marie , Håkanson Cecilia Arana , Lilja Helene Engstrand
Published: December 2022

Knowledge of neurodevelopmental disorders such as attention deficit/hyperactivity disorder (ADHD), autism spectrum disorders (ASD) and intellectual disability (ID) in patients with esophageal atresia (EA) is scarce. The aims of this study were to investigate the prevalence and risk of ADHD, ASD and ID in individuals with EA. Data were obtained from four longitudinal population-based registries in Sweden and analyzed using Cox proportional hazards regression. Patients with EA born in Sweden in 1973–2018 were included together with five controls for each individual with the exposure matched on sex, gestational age at birth, birth year and birth county. Individuals with chromosomal aberrations and syndromes were excluded. In total, 735 individuals with EA and 3675 controls were included. Median age at time of the study was 20 years (3–48). ASD was found in 24 (3.9%), ADHD in 34 (5.5%) and ID in 28 (4.6%) individuals with EA. Patients with EA had a 1.66 times higher risk of ASD (95% confidence interval [CI], 1.05–2.64) and a 3.62 times higher risk of ID (95% CI, 2.23–5.89) compared with controls. The risk of ADHD was not significantly increased. ADHD medication had been prescribed to 88.2% of patients with EA and ADHD and to 84.5% of controls with ADHD. Individuals with EA have a higher risk of ASD and ID than individuals without the exposure. These results are important when establishing follow-up programs for children with EA to allow timely detection and consequentially an earlier treatment and support especially before school start.
Long-term Colectomy Rates of Ulcerative Colitis over 40 Years of Different Therapeutic Eras–Results from a Western Hungarian Population-based Inception Cohort Between 1977 and 2020
Authors: Wetwittayakhlang Panu , Gonczi Lorant , Lakatos Laszlo , Kurti Zsuzsanna , Golovics Petra , Pandur Tunde , David Gyula , Erdelyi Zsuzsanna , Szita Istvan , Lakatos Peter L
Published: December 2022

Background and Aims

Few populaion-based studies have investigated the long-term colectomy rates of ulcerative colitis [UC]. We aimed to assess the colectomy rates over 40 years of different therapeutic eras in a prospective population-based inception cohort from Veszprem Province, Western Hungary.

Methods

Patient inclusion lasted between January1, 1977, and December31, 2018. Patient follow-up ended December 31, 2020. Colectomy rates and disease course were examined in three different eras based on the time of UC diagnosis; cohort A [1977–1995], cohort B [1996–2008], and cohort C [2009–2018].

Results

A total of 1370 incident UC patients were included [male 51.2%, median age at diagnosis 37 years]. Median follow-up was 17 years (interquartile range [IQR] 9–24); 87 patients [6.4%] underwent colectomy. The cumulative probability of colectomy in the total population was 2.6% (95% confidence interval [CI] 2.2-3.0), 4.2% [95% CI 3.6-4.8], 7.0% [95% CI 6.2-7.8], and 10.4% [95% CI 9.1-11.7] after 5, 10, 20, and 30 years, respectively. The proportion of extensive colitis at diagnosis increased over time [24.2%/24.3%/34.9% in cohorts A/B/C, respectively, p = 0.001]. Overall exposure to immunomodulators [11.3%/20.9%/34.4% in cohorts A/B/C, respectively, p <0.001], as well as the probability for biologic therapy initiation increased over time (0%/3.3% [95% CI 2.6-4.0]/13.9% [95% CI 12.1-15.7], p <0.001). There were no statistically significant differences in the cumulative probability of colectomies between cohorts A/B/C: 1.7% [95% CI 1.0-2.4], 2.5% [95% CI 1.9-3.1], and 3.7% [95% CI 2.7-4.7] after 5 years; 3.5% [95% CI 2.5-4.5], 4.2% [95% CI 3.4-5.0], and 4.5% [95% CI 3.3-5.7] after 10 years; and 7.5% [95% CI 6.1-8.9] and 6.3% [95% CI 5.2-7.4] in cohorts A/B after 20 years [log-rank = 0.588]. Extensive colitis (hazard ratio [HR] 2.24, 95% CI 1.55-3.23) and continuous active disease activity [HR 6.36, 95% CI 3.46-11.67] were independent predictors for colectomy.

Conclusion

No differences in colectomy rates have been observed in the incident UC patients over 40 years despite increasing use of immunomodulators and biologic therapies.
Helicoverpa zea (Lepidoptera: Noctuidae) In-Season and Overwintering Pupation Response to Soil Type
Authors: Dillard DeShae , Reisig Dominic D , Reay-Jones Francis P F
Published: December 2022

Heliothinae soil pupation is understudied despite the key role this life stage plays in their development. Many Heliothinae are important agricultural pests and understanding the interplay of environment and pupation is important to optimize pest management tactics oriented toward pupae. We studied the impact of three soil types (coarse sand, high organic muck, and fine-textured clay) on Helicoverpa zea (Boddie) in-season and overwintering pupal survivorship, diapause, depth, and weight in at two locations (North and South Carolina). We introduced wild-collected (in-season) and laboratory-reared (over the winter) infestations of H. zea larvae to each of the three soils and later excavated pupae. In-season and over the winter pupal survivorship was lower in fine-textured clay soils than in coarse sand or high organic muck. In addition, pupal depth and weight, in-season and over the winter, varied significantly by soil type. In general, depth was the shallowest, and pupae weight was lower when recovered from fine-textured clay soils. Finally, diapausing characteristics varied significantly by location and year, likely impacted by differing environmental conditions. Our results suggest that fine-textured clay soils negatively impact Heliothinae pupation and may be suppressing populations in areas with these soil types.
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

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

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

Forests 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

Understanding 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

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

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

Camelina 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

We 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

Fruit 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

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

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

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.
Effects of thermal conditions on gestating sows’ behaviors and energy requirements
Authors: Abarnou Justine , Durand Maëva , Dourmad Jean-Yves , Gaillard Charlotte
Published: December 2022

Room temperature and individual behavior may influence the energy requirements of gestating sows. These factors are not yet integrated on a daily and individual basis in the calculation of these requirements. The objective of this study was to quantify the effect of temperatures on the sows’ behaviors, especially on the level of physical activity, and on the energy requirements of gestating sows. Over four consecutive weeks, the temperature of two gestation rooms was maintained at medium temperatures (16.7 °C and 18.5 °C, respectively, for room 1 and room 2) for the first and third week, at low temperatures (14.4 °C and 15.3 °C) for the second week, and at high temperatures (31.6 °C and 31.9 °C) for the fourth week. Individual behavior was manually recorded based on videos and the data used to estimate the physical activity and social interactions of 37 gestating sows separated into two groups. The videos were analyzed over two periods of 5 h (“Feeding period” from 2300 to 0400 hours, “Resting period” from 1330 to 1830 hours). The energy requirements were calculated by the InraPorc model, modified for gestating sows, on the basis of a thermo-neutral situation and an average activity of 4 h standing per day for all the sows. The sows of one group were less active in high than low temperatures (83 vs. 103 min standing or walking over 5 h, P < 0.001). Isolation for high temperatures or huddling for low temperatures could be observed when sows were lying down. The sows spent more time lying laterally with high temperatures than low temperatures (66% vs. 52% of time spent lying, respectively, P < 0.001). Both groups reacted differently to high temperatures, in one the sows changed their activity (lying more) whereas in the other they drank more water compared to medium temperatures (11 vs. 8.5 L/d, P = 0.01). In one group, with high temperatures the sows were fed above their requirements (they should have received 110 g of feed per day per sow less, P < 0.001) and with low temperatures the same group should have received 50 g/d per sow more to fulfill their requirements. For the second group of sows, the temperatures did not significantly affect the feed requirements. In conclusion, daily ambient temperature and individual physical activity seem to be relevant information to add in nutritional models to improve precision feeding.
eCry3.1Ab-resistant Western Corn Rootworm Larval Midgut Epithelia Respond Minimally to Bt Intoxication
Authors: Paddock Kyle J , Dellamano Kyle , Hibbard Bruce E , Shelby Kent S
Published: December 2022

Insect resistance to toxins derived from Bacillus thuringiensis (Bt) is a major issue in agriculture. Resistance to Bt has been linked to the loss of toxin binding sites within the insect, changes within the gut microbiota, and midgut tissue regeneration. Histopathological documentation of intoxication and resistance to Bt is lacking for rootworms in the genus Diabrotica (Coleoptera: Chrysomelidae), a major target of Bt corn. Here, we document the morphological response of both Bt-resistant and Bt-susceptible larval western corn rootworm, Diabrotica virgifera virgifera LeConte, to intoxication with eCry3.1Ab. Gut lumen structural differences are subtle between the two colonies when feeding on non-Bt corn. However, upon ingestion of Bt-corn roots, susceptible larvae develop symptoms indicative of gut disruption by Bt, whereas resistant larvae incur milder effects. Mild disruption of the peritrophic matrix and gut lumen is accompanied by stem cell proliferation that may lead to midgut tissue regeneration. These results help contextualize the multifaceted nature of Bt-resistance in western corn rootworm for the first time from a histopathological perspective.
The Strategic Logic of Large Militant Alliance Networks
Authors: Blair Christopher W , Potter Philip B K
Published: December 2022

Ideological and operational credibility are essential to the success of transnational terrorist organizations. We demonstrate that militant groups can leverage large alliance networks to bolster their ideological and operational reputations. Organizations can draw on operational capabilities and successes to build international networks that bolster their ideological credibility. Conversely, organizations with reputations for ideological authority can lend it to affiliates, who offer reach into active conflicts, bolstering claims to operational capacity. This logic of comparative advantage suggests that militant alliances can be a strategic response to underlying material or ideological deficits. We illustrate these dynamics through data-driven case studies of al-Qaeda and the Islamic State's cooperative networks.
Management of imported complicated urogenital schistosomiasis in Europe: a TropNet retrospective study
Authors: Basile Gregorio , Tamarozzi Francesca , Salas-Coronas Joaquín , Soriano-Pérez Manuel Jesús , Luzón-García Pilar , Moro Lucia , Antinori Spinello , Arsuaga Marta , Bartoloni Alessandro , Tomasoni Lina Rachele , Gobbi Federico Giovanni , Köhler Carsten , Salvador Fernando , Bocanegra Cristina , Zammarchi Lorenzo
Published: December 2022

Background

Schistosomiasis is a neglected tropical disease caused by trematodes of the genus Schistosoma. Schistosoma haematobium causes urogenital schistosomiasis (UGS), a chronic disease characterized by pathology of the urogenital tract leading to potentially severe morbidity for which the treatment is poorly standardized. We conducted a survey in TropNet centres on the clinical presentations and management strategies of complicated urogenital schistosomiasis (cUGS).

Methods

We reviewed the clinical records of patients seen at TropNet centres over a 20-year timespan (January 2001–December 2020). Case definition for cUGS included the presence of urogenital cancer, obstructive uropathy, kidney insufficiency of all grades and female or male genital involvement leading to infertility. Collected data included demographic information, patient category (traveller or migrant), imaging data, microbiological data (serology results and presence/absence of eggs in urine), histological features and outcome at last visit recorded.

Results

Eight centres contributed with at least one case. Overall, 31 patients matched the inclusion criteria. Sub-Saharan Africa was the most likely place of infection for included patients. Median age was 30.6 years (range 21–46, interquartile ranges, IQR 27–33). Most patients (28/31, 90.3%) were males. Hydronephrosis was the most frequent complication, being present in 18 (58.1%) patients, followed by cancer, present in 5 patients (16.1%); 27 patients (87.1%) required surgical management of some sort. Use of praziquantel varied across centres, with six different regimens employed.

Discussion

Very few cases of cUGSs were found in our survey, possibly indicating underdiagnosis of this condition. Hydronephrosis was the most frequently observed urogenital complication, and most patients required invasive procedures. Infection by S. haematobium can result in considerable morbidity, resulting in clinically challenging presentations requiring a multidisciplinary approach. As such, development of common protocols for early diagnosis and treatment is urgently needed.
Fractality in Chinese prose
Authors: Liu Jin , Gunn Edward , Youssef Fuad , Tharayil Jacob , Lansford Wyatt , Zeng Ying
Published: December 2022

This study explores long-range correlations in terms of sentence or segment length variation in Chinese narrative texts and nonfiction prose. (Drożdż et al. 2016, Quantifying origin and character of long-range correlations in narrative texts. Information Sciences, 331 32–44) analyzed Western novels and found fractal patterns, defined as self-similar, wavelet recurrence, and alternation. Inspired by this study, our research tries to determine whether similar patterns commonly exist in Chinese literature and compares the similarities and differences with Western literature. We calculated the Hurst exponent, β-values, and Δα values for ninety-five Chinese novels, ranging historically from late Qing to contemporary Internet novels, covering the geopolitical regions from Mainland China to Taiwan and Hong Kong. We also made comparisons with pre-modern vernacular novels, historical texts in classical Chinese, contemporary nonfiction and expository writings, as well as randomly generated texts. We found that Chinese novels exhibit fractal patterns as well. In particular, the texts exhibit a better fractal quality if the sentence lengths are measured by Chinese characters, instead of words. There is no clear correlation between fractality and cultural–political contexts and individual authors, but historically speaking, modern Chinese texts show stronger long-range correlations than pre-modern texts. Moreover, long-range correlations in Chinese literature are weaker than in Western literature, and there is a lower percentage of novels with multifractal structures. Our data also show that the fractality not only exists in literary texts, but also in nonliterary, non-narrative, and expository writings; yet, there is no long-range correlation in randomly generated texts. We further conclude that fractality is a fundamental feature of prose writing and human writing.
The interpretation of topic models for scholarly analysis: An evaluation and critique of current practice
Authors: Gillings Mathew , Hardie Andrew
Published: December 2022

Topic modelling is a method of statistical data mining of a corpus of documents, popular in the digital humanities and, increasingly, in social sciences. A critical methodological issue is how ‘topics’ (groups of co-selected word types) can be interpreted in analytically meaningful terms. In the current literature, this is typically done by ‘eyeballing’; that is, cursory and largely unsystematic examination of the ‘top’ words in each algorithmically identified word group. We critically evaluate this approach in a dual analysis, comparing the ‘eyeballing’ approach with an alternative using sample close reading across the corpus. We used MALLET to extract two topic models from a test corpus: one with stopwords included, another with stopwords excluded. We then used the aforementioned methods to assign labels to these topics. The results suggest that a close-reading approach is more effective not only in level of detail but even in terms of accuracy. In particular, we found that: assigning labels via eyeballing yields incomplete or incorrect topic labels; removing stopwords drastically affects the analysis outcome; topic labelling and interpretation depend considerably on the analysts’ specialist knowledge; and differences of perspective or construal are unlikely to be captured through a topic model. We conclude that an interpretive paradigm founded in close reading may make topic modelling more appealing to humanities researchers.
Creating specialized corpora from digitized historical newspaper archives
Authors: Wilson Black Joshua
Published: December 2022

The availability of large digital archives of historical newspaper content has transformed the historical sciences. However, the scale of these archives can limit the direct application of advanced text processing methods. Even if it is computationally feasible to apply sophisticated language processing to an entire digital archive, if the material of interest is a small fraction of the archive, the results are unlikely to be useful. Methods for generating smaller specialized corpora from large archives are required to solve this problem. This article presents such a method for historical newspaper archives digitized using the METS/ALTO XML standard (Veridian Software, n.d.). The method is an ‘iterative bootstrapping’ approach in which candidate corpora are evaluated using text mining techniques, items are manually labelled, and Naïve Bayes text classifiers are trained and applied in order to produce new candidate corpora. The method is illustrated by a case study that investigates philosophical content, broadly construed, in pre-1900 English-language New Zealand newspapers. Extensive code is provided in Supplementary Materials.
The origin of stars in the inner 500 parsecs in TNG50 galaxies
Authors: Boecker Alina , Neumayer Nadine , Pillepich Annalisa , Frankel Neige , Ramesh Rahul , Leaman Ryan , Hernquist Lars
Published: December 2022

We investigate the origin of stars in the innermost 500 pc of galaxies spanning stellar masses of $5\times 10^{8-12}\, \mathrm{M}_{\odot }$ at z = 0 using the cosmological magnetohydrodynamical TNG50 simulation. Three different origins of stars comprise galactic centres: (1) in situ (born in the centre), (2) migrated (born elsewhere in the galaxy and ultimately moved to the centre), (3) ex situ (accreted from other galaxies). In situ and migrated stars dominate the central stellar mass budget on average with 73 and 23 per cent, respectively. The ex situ fraction rises above 1 per cent for galaxies $\gtrsim 10^{11}\, \mathrm{M}_{\odot }$. Yet, only 9 per cent of all galaxies exhibit no ex situ stars in their centres and the scatter of ex situ mass is significant ($4\!-\!6\, \mathrm{dex}$). Migrated stars predominantly originate closely from the centre ($1\!-\!2\, \mathrm{kpc}$), but if they travelled together in clumps distances reach $\sim \! 10\, \mathrm{kpc}$. Central and satellite galaxies possess similar amounts and origins of central stars. Star-forming galaxies ($\gtrsim 10^{10}\, \mathrm{M}_{\odot }$) have on average more ex situ mass in their centres than quenched ones. We predict readily observable stellar population and dynamical properties: (1) migrated stars are distinctly young ($\sim \! 2\, \mathrm{Gyr}$) and rotationally supported, especially for Milky Way-mass galaxies, (2) in situ stars are most metal-rich and older than migrated stars, (3) ex situ stars are on random motion dominated orbits and typically the oldest, most metal-poor and α-enhanced population. We demonstrate that the interaction history with other galaxies leads to diverse pathways of building up galaxy centres in a Lambda cold dak matter universe. Our work highlights the necessity for cosmological context in formation scenarios of central galactic components and the potential to use galaxy centres as tracers of overall galaxy assembly.
Interfering with nucleotide excision by the coronavirus 3′-to-5′ exoribonuclease
Authors: Chinthapatla Rukesh , Sotoudegan Mohamad , Srivastava Pankaj , Anderson Thomas K , Moustafa Ibrahim M , Passow Kellan T , Kennelly Samantha A , Moorthy Ramkumar , Dulin David , Feng Joy Y , Harki Daniel A , Kirchdoerfer Robert N , Cameron Craig E , Arnold Jamie J
Published: December 2022

Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3′-to-5′ proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3′-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3′-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
Telomerase RNA in Hymenoptera (Insecta) switched to plant/ciliate-like biogenesis
Authors: Fajkus Petr , Adámik Matej , Nelson Andrew D L , Kilar Agata M , Franek Michal , Bubeník Michal , Frydrychová Radmila Čapková , Votavová Alena , Sýkorová Eva , Fajkus Jiří , Peška Vratislav
Published: December 2022

In contrast to the catalytic subunit of telomerase, its RNA subunit (TR) is highly divergent in size, sequence and biogenesis pathways across eukaryotes. Current views on TR evolution assume a common origin of TRs transcribed with RNA polymerase II in Opisthokonta (the supergroup including Animalia and Fungi) and Trypanosomida on one hand, and TRs transcribed with RNA polymerase III under the control of type 3 promoter, found in TSAR and Archaeplastida supergroups (including e.g. ciliates and Viridiplantae taxa, respectively). Here, we focus on unknown TRs in one of the largest Animalia order - Hymenoptera (Arthropoda) with more than 300 available representative genomes. Using a combination of bioinformatic and experimental approaches, we identify their TRs. In contrast to the presumed type of TRs (H/ACA box snoRNAs transcribed with RNA Polymerase II) corresponding to their phylogenetic position, we find here short TRs of the snRNA type, likely transcribed with RNA polymerase III under the control of the type 3 promoter. The newly described insect TRs thus question the hitherto assumed monophyletic origin of TRs across Animalia and point to an evolutionary switch in TR type and biogenesis that was associated with the divergence of Arthropods.
Malignancy risk in kidney transplant recipients exposed to immunosuppression pre-transplant for the treatment of glomerulonephritis
Authors: Massicotte-Azarniouch David , Detwiler Randal K , Hu Yichun , Falk Ronald J , Saha Manish K , Hogan Susan L , Derebail Vimal K
Published: December 2022

Background

Kidney transplant patients with glomerulonephritis (GN) as their native disease may receive significant amounts of pre-transplant immunosuppression (PTI), which could increase the risk for development of malignancy post-transplant.

Methods

We conducted a single-center, retrospective study of kidney transplant recipients from January 2005 until May 2020. Patients with GN as their native kidney disease who received PTI for treatment of GN (n = 184) were compared with a control cohort (n = 579) of non-diabetic, non-PTI-receiving kidney transplant patients. We calculated hazard ratios (HR) with 95% confidence intervals (95% CI) for outcomes of first occurrence of solid or hematologic malignancy, non-melanoma skin cancer (NMSC) and post-transplant lymphoproliferative disorder (PTLD).

Results

Over a median follow-up of 5.7 years, PTI for GN was associated with significantly increased risk for malignancy compared with controls [13.0%  vs 9.7%, respectively; adjusted HR 1.82 (95% CI 1.10–3.00)], but not for NMSC [10.3% vs 11.4%, respectively; adjusted HR 1.09 (95% CI 0.64–1.83)] or PTLD [3.3% vs 3.1%, respectively; adjusted HR 1.02 (95% CI 0.40–2.61)]. The risk for malignancy was significantly increased in those who received cyclophosphamide [HR 2.59 (95% CI 1.48–4.55)] or rituximab [HR 3.82 (95% CI 1.69–8.65)] pre-transplant, and particularly in those who received both cyclophosphamide and rituximab, but not for calcineurin inhibitors or mycophenolate.

Conclusion

The use of PTI for treatment of GN, especially cyclophosphamide or even with rituximab, is associated with increased risk for development of solid or hematologic malignancy post-transplant. These data highlight potential risks with treatment of GN and underscore the importance of post-transplant malignancy surveillance in this patient population.