bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution mapping reveals hotspots and sex-biased recombination inPopulus trichocarpa
Authors: Abeyratne Chanaka Roshan , Macaya-Sanz David , Zhou Ran , Barry Kerrie W , Daum Christopher , Haiby Kathy , Lipzen Anna , Stanton Brian , Yoshinaga Yuko , Zane Matthew , Tuskan Gerald A , DiFazio Stephen P 
Published: October 2022

AbstractFine-scale meiotic recombination is fundamental to the outcome of natural and artificial selection. Here, dense genetic mapping and haplotype reconstruction were used to estimate recombination for a full factorial Populus trichocarpa cross of 7 males and 7 females. Genomes of the resulting 49 full-sib families (N = 829 offspring) were resequenced, and high-fidelity biallelic SNP/INDELs and pedigree information were used to ascertain allelic phase and impute progeny genotypes to recover gametic haplotypes. The 14 parental genetic maps contained 1,820 SNP/INDELs on average that covered 376.7 Mb of physical length across 19 chromosomes. Comparison of parental and progeny haplotypes allowed fine-scale demarcation of cross-over regions, where 38,846 cross-over events in 1,658 gametes were observed. Cross-over events were positively associated with gene density and negatively associated with GC content and long-terminal repeats. One of the most striking findings was higher rates of cross-overs in males in 8 out of 19 chromosomes. Regions with elevated male cross-over rates had lower gene density and GC content than windows showing no sex bias. High-resolution analysis identified 67 candidate cross-over hotspots spread throughout the genome. DNA sequence motifs enriched in these regions showed striking similarity to those of maize, Arabidopsis, and wheat. These findings, and recombination estimates, will be useful for ongoing efforts to accelerate domestication of this and other biomass feedstocks, as well as future studies investigating broader questions related to evolutionary history, perennial development, phenology, wood formation, vegetative propagation, and dioecy that cannot be studied using annual plant model systems.
The fly homolog ofSUPT16H, a gene associated with neurodevelopmental disorders, is required in a cell-autonomous fashion for cell survival
Authors: Ma Mengqi , Zhang Xi , Zheng Yiming , Lu Shenzhao , Pan Xueyang , Mao Xiao , Pan Hongling , Chung Hyung-lok , Wang Hua , Guo Hong , Bellen Hugo J 
Published: October 2022

AbstractSUPT16H encodes the large subunit of the FAcilitate Chromatin Transcription (FACT) complex, which functions as a nucleosome organizer during transcription. We identified two individuals from unrelated families carrying de novo missense variants in SUPT16H. The probands exhibit global developmental delay, intellectual disability, epilepsy, facial dysmorphism and brain structural abnormalities. We used Drosophila to characterize two variants: p.T171I and p.G808R. Loss of the fly ortholog, dre4, causes lethality at an early developmental stage. RNAi-mediated knockdown of dre4 in either glia or neurons causes severely reduced eclosion and longevity. Tissue-specific knockdown of dre4 in the eye or wing leads to the loss of these tissues, whereas overexpression of SUPT16H has no dominant effect. Moreover, expression of the reference SUPT16H significantly rescues the loss-of-function phenotypes in the nervous system as well as wing and eye. In contrast, expression of SUPT16H p.T171I or p.G808R rescues the phenotypes poorly, indicating that the variants are partial loss-of-function alleles. While previous studies argued that the developmental arrest caused by loss of dre4 is due to impaired ecdysone production in the prothoracic gland, our data show that dre4 is required for proper cell growth and survival in multiple tissues in a cell-autonomous manner. Altogether, our data indicate that the de novo loss-of-function variants in SUPT16H are indeed associated with developmental and neurological defects observed in the probands.
Impact of Crohn’s Disease Therapies on Histology in Randomized Controlled Trials: Systematic Review With Meta-analysis
Authors: Roseira Joana , Santiago Mafalda , Estevinho Maria Manuela , Moreira Paula , Alves Catarina , Danese Silvio , Peyrin-Biroulet Laurent , Dignass Axel , Feakins Roger , Magro Fernando 
Published: October 2022

AbstractBackgroundThe effectiveness of Crohn’s disease treatments for inducing histological outcomes has not been addressed systematically. We performed a systematic review and meta-analysis of randomized controlled trials in Crohn’s disease to assess the impact of therapies on mucosal histopathology.MethodsDatabases (MEDLINE, CENTRAL, Web of Science, EMBASE) were searched for randomized controlled trials including adult patients and evaluating histological outcomes. Risk of bias was evaluated using the Critical Appraisal Skills Programme. Histological outcomes, pooled frequencies, pooled odds ratios, and standard mean differences of the histological scores were compared between the intervention and placebo groups using a random-effects model.ResultsOut of 2070 records, 10 studies were included. The quality of the studies ranged from moderate to high, but they were clinically and methodologically diverse. All interventions were superior to placebo. Histological response was achieved by 68% of patients, and 38% achieved remission. Pooled odds ratio for histological remission in patients receiving intervention vs placebo was 4.14 (95% CI, 2.28-7.50; I2 0%; P &lt; .01). Heterogeneity in histological response estimates was significant, and subgroup analysis of the odds ratio results was limited by the low number of studies per group. The standard mean difference of histological scores was higher for patients receiving intervention in both induction and maintenance studies (−2.95; 95% CI, −4.17 to −1.74; I2 83% P &lt; .00; and −2.58; 95% CI, −3.89 to −1.27; I2 56% P &lt; .00).ConclusionsCrohn’s disease therapies are effective for achieving histological outcomes. Adherence to recently published consensus on histopathology harmonization assessment in Crohn’s disease would facilitate adequate comparison between studies in the future.
Integrating Radiomics With Clinicoradiological Scoring Can Predict High-Risk Patients Who Need Surgery in Crohn’s Disease: A Pilot Study
Authors: Chirra Prathyush , Sharma Anamay , Bera Kaustav , Cohn H Matthew , Kurowski Jacob A , Amann Katelin , Rivero Marco-Jose , Madabhushi Anant , Lu Cheng , Paspulati Rajmohan , Stein Sharon L , Katz Jeffrey A , Viswanath Satish E , Dave Maneesh 
Published: October 2022

Abstract

Background
Early identification of Crohn’s disease (CD) patients at risk for complications could enable targeted surgical referral, but routine magnetic resonance enterography (MRE) has not been definitively correlated with need for surgery. Our objective was to identify computer-extracted image (radiomic) features from MRE associated with risk of surgery in CD and combine them with clinical and radiological assessments to predict time to intervention.

Methods
This was a retrospective single-center pilot study of CD patients who had an MRE within 3 months prior to initiating medical therapy. Radiomic features were extracted from annotated terminal ileum regions on MRE and combined with clinical variables and radiological assessment (via Simplified Magnetic Resonance Index of Activity scoring for wall thickening, edema, fat stranding, ulcers) in a random forest classifier. The primary endpoint was high- and low-risk groups based on need for surgery within 1 year of MRE. The secondary endpoint was time to surgery after treatment.

Results
Eight radiomic features capturing localized texture heterogeneity within the terminal ileum were significantly associated with risk of surgery within 1 year of treatment (P &lt; .05); yielding a discovery cohort area under the receiver-operating characteristic curve of 0.67 (n = 50) and validation cohort area under the receiver-operating characteristic curve of 0.74 (n = 23). Kaplan-Meier analysis of radiomic features together with clinical variables and Simplified Magnetic Resonance Index of Activity scores yielded the best hazard ratio of 4.13 (P = (7.6 × 10-6) and concordance index of 0.71 in predicting time to surgery after MRE.

Conclusions
Radiomic features on MRE may be associated with risk of surgery in CD, and in combination with clinicoradiological scoring can yield an accurate prognostic model for time to surgery.
Global Bifurcation of Capillary-Gravity Water Waves With Overhanging Profiles and Arbitrary Vorticity
Authors: Wahlén Erik , Weber Jörg 
Published: October 2022

Abstract
We study two-dimensional periodic capillary-gravity water waves propagating at the free surface of water in a flow with arbitrary, prescribed vorticity over a flat bed. Using conformal mappings and a new reformulation of Bernoulli’s equation, the problem is equivalently cast into the form “identity plus compact”, which is amenable to Rabinowitz’s global bifurcation theorem, while no restrictions on the geometry of the surface profile and no assumptions regarding the absence of stagnation points in the flow have to be made. Within the scope of this new formulation, local curves and global families of solutions, bifurcating from laminar flows with a flat surface, are constructed.
The acquisition of transferable extrachromosomal fec operon is associated with a cefiderocol MIC increase in Enterobacterales
Authors: Kocer Kaan , Boutin Sébastien , Heeg Klaus , Nurjadi Dennis 
Published: October 2022

Abstract

Background
Cefiderocol is a novel siderophore cephalosporin active against MDR Gram-negative bacilli, including MBL-harbouring Enterobacterales. The detection of multiple cefiderocol-resistant blaVIM-carrying Enterobacterales isolates (MIC = 4 mg/L) from a single patient suggested an additional, potentially transferable, resistance determinant as blaVIM typically does not elevate cefiderocol MIC above the resistance threshold.

Methods
Transfer of a mobile genetic element was performed in liquid mating experiments. All donor isolates and transconjugants were characterized by short-read WGS to identify potential resistance determinants. mRNA expression of siderophore receptors was determined by quantitative RT–PCR. Validation was performed by transformation. Antibiotic susceptibility was determined by broth microdilution.

Results
Liquid mating experiments indicated the presence of transferable resistance determinants. Comparative genomic analysis of the clinical isolates and their respective transconjugants revealed the transfer of an accessory fec operon (fecABCDEIR). Transformation of the fec operon-containing vector into a TOP10 Escherichia coli led to an elevation of the cefiderocol MIC by at least 16-fold. Higher expression of fecA as a proxy for the fec operon mRNA expression was associated with phenotypic cefiderocol resistance. Both VIM and the accessory fec operon contribute to the elevation of cefiderocol MIC beyond the resistance threshold. The acquisition of an accessory fec operon via liquid mating confers phenotypic cefiderocol resistance in both E. coli J53 and Pseudomonas aeruginosa PAO1, indicating a broad-host-range nature of this mobile resistance determinant.

Conclusions
The emergence of a transferable cefiderocol resistance determinant without prior exposure to the substance is worrisome and should be monitored closely.
A survey of pregnant patients’ perspectives on the implementation of artificial intelligence in clinical care
Authors: Armero William , Gray Kathryn J , Fields Kara G , Cole Naida M , Bates David W , Kovacheva Vesela P 
Published: October 2022

Abstract

Objective
To evaluate and understand pregnant patients’ perspectives on the implementation of artificial intelligence (AI) in clinical care with a focus on opportunities to improve healthcare technologies and healthcare delivery.

Materials and Methods
We developed an anonymous survey and enrolled patients presenting to the labor and delivery unit at a tertiary care center September 2019–June 2020. We investigated the role and interplay of patient demographic factors, healthcare literacy, understanding of AI, comfort levels with various AI scenarios, and preferences for AI use in clinical care.

Results
Of the 349 parturients, 57.6% were between the ages of 25–34 years, 90.1% reported college or graduate education and 69.2% believed the benefits of AI use in clinical care outweighed the risks. Cluster analysis revealed 2 distinct groups: patients more comfortable with clinical AI use (Pro-AI) and those who preferred physician presence (AI-Cautious). Pro-AI patients had a higher degree of education, were more knowledgeable about AI use in their daily lives and saw AI use as a significant advancement in medicine. AI-Cautious patients reported a lack of human qualities and low trust in the technology as detriments to AI use.

Discussion
Patient trust and the preservation of the human physician-patient relationship are critical in moving forward with AI implementation in healthcare. Pregnant individuals are cautiously optimistic about AI use in their care.

Conclusion
Our findings provide insights into the status of AI use in perinatal care and provide a platform for driving patient-centered innovations.
Analysis of singular values in a 3D joint inversion problem of MMT and MCSEM data
Authors: da Silva Pinheiro Jéssica Larissa , Correa Silva Marcos Welby , Rao Ying 
Published: October 2022

Abstract
Single value decomposition (SVD) is a mathematical method of decomposing a matrix into three other matrices that have very important properties of the original matrix. One of these matrices provides us with the singular values of the original matrix. By analysing these singular values, we can determine whether an inverse problem has an ambiguous solution or whether the solution is stable. With this analysis we can also check whether the estimated solution gives an exact fit to the data, find out which combinations of parameters can be determined by observations and which cannot, and more. In this work, SVD was applied to assess the feasibility of a joint 3D inversion of marine magnetotelluric method (MMT) and marine controlled source electromagnetic method (MCSEM) data, as these methods should theoretically provide complementary information. The singular values were generated from the Hessian matrix of each method and from the joint implementation, and we compared them by considering the null space of each method. The analysis of the singular values proved to be an important step before the iterative inversion process, indicating the feasibility of the inversion without spending much time. However, we still need to spend the time to calculate the Jacobian and Hessian matrices.
Graph-based pan-genomes: increased opportunities in plant genomics
Authors: Wang Shuo , Qian Yong-Qing , Zhao Ru-Peng , Chen Ling-Ling , Song Jia-Ming 
Published: October 2022

AbstractDue to the development of sequencing technology and the great reduction in sequencing costs, an increasing number of plant genomes have been assembled, and numerous genomes have revealed large amounts of variations. However, a single reference genome does not allow the exploration of species diversity, and therefore the concept of pan-genome was developed. A pan-genome is a collection of all sequences available for a species, including a large number of consensus sequences, large structural variations, and small variations including single nucleotide polymorphisms and insertions/deletions. A simple linear pan-genome does not allow these structural variations to be intuitively characterized, so graph-based pan-genomes have been developed. These pan-genomes store sequence and structural variation information in the form of nodes and paths to store and display species variation information in a more intuitive manner. The key role of graph-based pan-genomes is to expand the coordinate system of the linear reference genome to accommodate more regions of genetic diversity. Here, we review the origin and development of graph-based pan-genomes, explore their application in plant research, and further highlight the application of graph-based pan-genomes for future plant breeding.
Explaining migrant integration policies: A comparative study across 56 countries
Authors: Solano Giacomo , De Coninck David 
Published: October 2022

AbstractThis article provides novel insights into the main factors associated with integration policies at the national level. Existing literature has analysed specific factors in Western countries, while a comprehensive, theoretically informed, and up-to-date overview is missing, especially regarding non-Western countries. This article fills this gap by combining 2014 and 2019 Migrant Integration Policy Index data on integration policies in 56 countries—including non-Western countries—with publicly available international data on migration and asylum trends, economic conditions, and public opinion on migration. Building upon existing literature, we introduce three perspectives: evidence-based, institutionalist, and partisan perspectives. The evidence-based perspective assumes that policy-makers act based on objective factors related to the policy issue (e.g. the number of migrants). The institutionalist perspective points to the relevance of institutional conditions, such as labour markets and welfare institutions. The partisan perspective refers to the role of political ideologies and attitudes in public opinion and in the media. Results suggest that factors related to the institutionalist perspective play the most critical role, alongside factors linked to the partisan perspective. However, the results provide evidence for all three perspectives. Migrant integration policies are associated with several factors: the number of asylum applications and the number of refugees (evidence-based perspective); GDP (per capita) and welfare expenditure (institutionalist perspective); political ideology; and public opinion (partisan perspective).
Magnetic braking saturates: evidence from the orbital period distribution of low-mass detached eclipsing binaries from ZTF
Authors: El-Badry Kareem , Conroy Charlie , Fuller Jim , Kiman Rocio , van Roestel Jan , Rodriguez Antonio C , Burdge Kevin B 
Published: October 2022

ABSTRACT
We constrain the orbital period (Porb) distribution of low-mass detached main-sequence eclipsing binaries (EBs) with light-curves from the Zwicky Transient Facility (ZTF), which provides a well-understood selection function and sensitivity to faint stars. At short periods (Porb ≲ 2 d), binaries are predicted to evolve significantly due to magnetic braking (MB), which shrinks orbits and ultimately brings detached binaries into contact. The period distribution is thus a sensitive probe of MB. We find that the intrinsic period distribution of low-mass (0.1 ≲ M1/M⊙ &lt; 0.9) binaries is basically flat (${\rm d}N/{\rm d}P_{\rm orb} \propto P_{\rm orb}^0$) from Porb = 10 d down to the contact limit. This is strongly inconsistent with predictions of classical MB models based on the Skumanich relation, which are widely used in binary evolution calculations and predict ${\rm d}N/{\rm d}P_{\rm orb} \propto P_{\rm orb}^{7/3}$ at short periods. The observed distributions are best reproduced by models in which the magnetic field saturates at short periods with a MB torque that scales roughly as $\dot{J}\propto P_{\rm orb}^{-1}$, as opposed to $\dot{J} \propto P_{\rm orb}^{-3}$ in the standard Skumanich law. We also find no significant difference between the period distributions of binaries containing fully and partially convective stars. Our results confirm that a saturated MB law, which was previously found to describe the spin-down of rapidly rotating isolated M dwarfs, also operates in tidally locked binaries. We advocate using saturated MB models in binary evolution calculations. Our work supports previous suggestions that MB in cataclysmic variables (CVs) is much weaker than assumed in the standard evolutionary model, unless mass transfer leads to significant additional angular momentum loss in CVs.
Launch of a sounding balloon for horizontal and vertical modelling of ALAN propagation in the atmosphere
Authors: Cavazzani S , Fiorentin P , Bettanini C , Bartolomei M , Bertolin C , Ortolani S , Bertolo A , Binotto R , Olivieri L , Aboudan A , Colombatti G 
Published: October 2022

ABSTRACT
The propagation of light radiation in the atmosphere is a topic that needs to be properly analysed to mitigate its negative influence on astronomical observations. This work describes a novel approach for evaluating atmospheric propagation of artificial light at night (ALAN), emphasizing the dependence on altitude and aerosols. It is based on an innovative experiment using a sounding balloon equipped with two sky-quality meters (SQM): one vertically pointed at 30° (SQM-V) and the other horizontally at 90° (SQM-H) from the zenith. The system was launched during astronomical night conditions from an area of the Italian Apennines with low ground light emission and crossed the Tuscan sky, observing the vertical and horizontal ALAN propagation. The data analysis of the two SQMs and their georeferentiation through altitude and trajectory reconstruction allows us to model the propagation of light in the experimental field of view from a few hundred metres up to an altitude of about 30 km. In this work, the main focus is given to the tropospheric part of the atmosphere up to 12 500 m: the processed data are used to validate a theoretical model taking into account the altitude, course of the balloon, atmospheric composition, and population of the cities overflown by the balloon, obtaining a correlation of 0.85 with SQM-H and 0.91 with SQM-V. The magnitude values of close to 21.5 $\mathrm{mag\, arcsec}^{-2}$ measured by SQM-V at 2000 m are an important experimental result for evaluating the influence of aerosols and altitude on ALAN propagation.
A case of glucocorticoid-resistant adult Still’s disease complicated by pulmonary hypertension and interstitial lung disease
Authors: Kusaka Katsuhide , Miyagawa Ippei , Kosaka Shunpei , Matsunaga Satsuki , Nakayamada Shingo , Tanaka Yoshiya 
Published: October 2022

ABSTRACT
Adult Still’s disease (ASD) is rarely complicated by pulmonary hypertension (PH). A 76-year-old woman experienced ASD relapse with repeated exacerbation of PH and interstitial lung disease. Although she had been treated with immunosuppressive agents and pulmonary vasodilators, the ASD relapsed with fever, rash, increased inflammatory responses and exacerbated interstitial lung disease, and PH. The pathology of PH appeared to encompass groups 1 [pulmonary arterial hypertension (PAH)], 1ʹ [pulmonary veno-occlusive disease (PVOD)], and 3. Remission induction therapy with high-dose glucocorticoid and tocilizumab was administered, and switching or adding pulmonary vasodilators was also attempted. As the disease activity of ASD decreased, the mean pulmonary arterial pressure and pulmonary vascular resistance improved. PH is an extremely rare form of organ dysfunction in individuals with ASD. Like other systemic autoimmune diseases, PH (PAH or PVOD) can determine the prognosis of ASD. Because of PH’s rarity, it is important to sufficiently evaluate its pathology, considering the possibility that PH is not clinically classified as PAH (group 1), and to administer immunosuppressive therapy and vasodilators according to the pathology.