bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell Expression Atlas Reveals Cell Heterogeneity in the Creeping Fat of Crohn’s Disease
Authors: Shu Weigang , Wang Yongheng , Li Chuanding , Zhang Lei , Zhuoma Deji , Yang Pengyu , Yan Guorong , Chen Chunqiu , Ba Yongbing , Du Peng , Wang Xiaolei 
Published: January 2023

Abstract

Background
Creeping fat (CrF) has been recognized to play a positive role in Crohn’s disease (CD) progression, yet the cellular compositions within mesenteric adipose tissue (MAT) and their potential mechanism in CrF formation are poorly understood.

Methods
Analysis of 10X single-cell RNA sequencing was performed on 67 064 cells from 3 pairs of surgically resected samples of CrF and their uninvolved MAT. The results were validated in another cohort with 6 paired MAT samples by immunofluorescence.

Results
All samples manifested excellent consistency and repeatability in our study, and 10 cell types from the transcriptome atlas, including 20 clusters, were identified. In CrF, a specific vascular endothelial cell subpopulation highly expressing lipoprotein lipase was first identified, with a significantly increased proportion. This vascular endothelial cell subpopulation manifested robust peroxisome proliferator-activated receptor γ (PPARγ) transcription activity and an upregulated PPAR signaling pathway and was involved in lipid metabolism and the antibacterial response. A novel fibroblast subpopulation (FC3) with remarkable GREM1 and RFLNB expression was identified and validated to predominantly accumulate in the CrF. The FC3 was annotated as inflammation-associated fibroblasts, which are characterized by inflammatory responses and the regulation of Smad phosphorylation related to intestinal fibrosis. The trajectory of fibroblasts revealed their pro-inflammatory and profibrotic conversion tendency during CrF formation with corresponding gene dynamics. Additionally, we unprecedently dissected the different origins and functions of 6 macrophage subclusters within the myeloid compartment.

Conclusions
Our results uncover the cellular heterogeneity in the MAT of CD and the role of these various cellular compositions in CrF development. This comprehensive understanding of CrF provides future directions for in-depth research on and potential targets for MAT-based treatment.
Delays in Therapy Associated With Current Prior Authorization Process for the Treatment of Inflammatory Bowel Disease
Authors: Choi David K , Cohen Nathaniel A , Choden Tenzin , Cohen Russell D , Rubin David T 
Published: January 2023

Lay Summary
Despite a high approval rate, there were unnecessary delays in therapy due to prior authorizations. This study identified the impact of type of IBD, FDA-labeled indication, and dose escalations on approvals.
The challenges of selective fertility and carryover effects in within-sibship analyses: the effect of assisted reproductive technology on perinatal mortality as an example
Authors: Westvik-Johari Kjersti , Håberg Siri E , Lawlor Deborah A , Romundstad Liv Bente , Bergh Christina , Wennerholm Ulla-Britt , Gissler Mika , Henningsen Anna-Karina A , Tiitinen Aila , Pinborg Anja , Opdahl Signe 
Published: January 2023

Abstract

Background
Within-sibship analyses show lower perinatal mortality after assisted reproductive technology (ART) compared with natural conception (NC), a finding that appears biologically unlikely. We investigated whether this may be attributed to bias from selective fertility and carryover effects.

Methods
Using data from national registries in Denmark (1994–2014), Finland (1990–2014) and Norway and Sweden (1988–2015), we studied 5 722 826 singleton pregnancies, including 119 900 ART-conceived and 37 590 exposure-discordant sibships. Perinatal mortality at the population level and within sibships was compared using multilevel logistic regression with random and fixed intercepts, respectively. We estimated selective fertility as the proportion of primiparous women with and without perinatal loss who had a second delivery, and carryover effects through bidirectional and crosswise associations.

Results
Population analysis showed higher perinatal mortality among ART conception compared with NC (odds ratio 1.21, 95% CI 1.13 to 1.30), whereas within-sibship analysis showed the opposite (OR 0.36, 95% CI 0.31 to 0.43). Primiparous women with perinatal loss were more likely to give birth again (selective fertility) and to use ART in this subsequent pregnancy (carryover effects), resulting in strong selection of double-discordant sibships with death of the naturally conceived and survival of the ART-conceived sibling. After controlling for conception method and outcome in the first pregnancy, ART was not consistently associated with perinatal mortality in the second pregnancy.

Conclusions
Whereas population estimates may be biased by residual confounding, within-sibship estimates were biased by selective fertility and carryover effects. It remains unclear whether ART conception contributes to perinatal mortality.
A modified binary version of aphid–ant mutualism for feature selection: a COVID-19 case study
Authors: Eslami N , Yazdani S , Mirzaei M , Hadavandi E 
Published: January 2023

AbstractThe speedy development of intelligent technologies and gadgets has led to a drastic increment of dimensions within the datasets in recent years. Dimension reduction algorithms, such as feature selection methods, are crucial to resolving this obstacle. Currently, metaheuristic algorithms have been extensively used in feature selection tasks due to their acceptable computational cost and performance. In this article, a binary-modified version of aphid–ant mutualism (AAM) called binary aphid–ant mutualism (BAAM) is introduced to solve the feature selection problems. Like AAM, in BAAM, the intensification and diversification mechanisms are modeled via the intercommunication of aphids with other colonies’ members, including aphids and ants. However, unlike AAM, the number of colonies’ members can change in each iteration based on the attraction power of their leaders. Moreover, the second- and third-best individuals can take the place of the ringleader and lead the pioneer colony. Also, to maintain the population diversity, prevent premature convergence, and facilitate information sharing between individuals of colonies including aphids and ants, a random cross-over operator is utilized in BAAM. The proposed BAAM is compared with five other feature selection algorithms using several evaluation metrics. Twelve medical and nine non-medical benchmark datasets with different numbers of features, instances, and classes from the University of California, Irvine and Arizona State University repositories are considered for all the experiments. Moreover, a coronavirus disease (COVID-19) dataset is used to validate the effectiveness of the BAAM in real-world applications. Based on the acquired outcomes, the proposed BAAM outperformed other comparative methods in terms of classification accuracy using various classifiers, including K nearest neighbor, kernel-based extreme learning machine, and multi-class support vector machine, choosing the most informative features, the best and mean fitness values and convergence speed in most cases. As an instance, in the COVID-19 dataset, BAAM achieved 96.53% average accuracy and selected the most informative feature subset.
The WTO’S Contribution to the Challenges of Global Commons
Authors: Okonjo-Iweala Ngozi 
Published: January 2023

ABSTRACT
Global trade can be an important part of the solution to modern global challenges, just as the rule-based multilateral trading system played an instrumental role in fostering peace and prosperity since its creation in 1947. Trade has been a lifeline for producing and accessing critical medical supplies from face masks to vaccines almost since the beginning of the pandemic; trade is also an important means for adapting to climate change as well as cutting emissions; and trade has helped net-food-importing countries faced with food crisis. For trade to be a part of solutions to the range of modern challenges, the role of the World Trade Organization (WTO) is indispensable, and it must be updated for it to remain fit for purpose. The continuing reinvention of the WTO will not be easy, but the outcomes of the 12th Ministerial Conference (MC12) are a good start. In this special contribution to the Journal of International Economic Law, I reflect on the WTO’s role for the twenty-first century and beyond and how the MC12 outcomes will serve as a foundation and a platform for Members to build on to reinvent the WTO.
Pilot study of aerosols visualized and evaluated in a radiotherapy room
Authors: Musha Atsushi , Kubo Nobuteru , Kawamura Hidemasa , Okano Naoko , Yanagisawa Kunio , Sugawara Kazuaki , Okamoto Ryuta , Takahashi Kozo , Kawabata Hideki , Ohno Tatsuya 
Published: January 2023

AbstractHealth care institutions provide prevention strategies for coronavirus disease 2019 and non-infectious disease care. We investigated the characteristics of patient contamination in a radiotherapy room by examining the trajectory and number of airborne particles in the air when talking and coughing occurred and clarified the actual state of contamination in this closed space. Aerosols were visualized and evaluated in the vertical height and head-to-tail width directions when the participant was lying on the radiotherapy tabletop. Aerosol reach was significantly greater for loud voice and coughing both at vertical height and the head-to-tail width direction. The size and number of particles around the radiotherapy tabletop were also visualized and evaluated in the radiotherapy room. The radiotherapy staff who were in the presence of the participant sometimes had many particles adhering to their facial area; particle adhesion to the staff was dominated by small size particles. Particle adherence to the irradiation device surface near the ceiling had particles larger than 1 mm. Tabletop particles tended to have a wider size range, including bigger sizes and a larger count compared to the surrounding floor. The 0.7-m radius distance from the participant's mouth tended to be highly contaminated, and the smaller the particle size, the farther it reached. The capacity to estimate areas prone to contamination can be used to predict infection of other patients and medical staff in a radiotherapy room.
Argumentation Frameworks with Attack Classification
Authors: Vassiliades Alexandros , Flouris Giorgos , Patkos Theodore , Bikakis Antonis , Bassiliades Nick , Plexousakis Dimitris 
Published: January 2023

Abstract
Abstract argumentation frameworks (AAFs), introduced by Dung (1995, Artif. Intell., 228, 321–357), enabled a new way of reasoning with arguments, which does not take into account the internal structure of arguments but only how they are related to each other. The only form of relation considered in AAFs is a binary attack relation on the set of arguments. From the definitions of acceptability semantics of AAFs, it is obvious that attacks actually have a dual role: on the one hand, they generate conflicts; on the other hand, they can defend other arguments from attacks. In this paper, we propose a framework, where the modeller can explicitly specify the role of each attack. For this purpose, we define a set of conflict-generating attacks ${\mathcal {R}_{C}}$ and a set of defending attacks ${\mathcal {R}_{d}}$, as well as a family of semantics that considers the role of each attack while determining which arguments are attacked, which are defended and which will be included in each extension. We study the formal properties of the proposed framework and semantics, show that our framework is a generalization of AAFs and assess its semantics against a set of principles. Finally, we present a web application that provides an interface for creating custom argumentation frameworks and uses ASP to compute their extensions.
Kink oscillations of magnetic flux tubes in presence of resistivity
Authors: Ebrahimi Zanyar , Javaherian Mohsen 
Published: January 2023

ABSTRACTKink oscillations in the solar coronal flux tubes are among the best seismological tools for estimating the unknown parameters of the solar corona. Here, we study the effect of resistivity on the linear evolution of magnetohydrodynamic (MHD) kink waves in magnetic flux tubes with transverse inhomogeneity in the plasma density. In thin tube thin boundary approximation, we obtain the well-known resistive spectrum of Alfvén continuum modes with a semi-analytical method and study the relative importance of the eigenmodes in the spectrum. As shown in previous studies, the quasi-mode solution of ideal MHD appears in the spectrum. Results show that while the internal and external homogeneous regions of the flux tube oscillate dominantly in quasi-mode in the inhomogeneous region in each magnetic surface a different combination of resistive eigenmodes contributes to the perturbations. Comparing the results obtained here with those obtained previously in the same configuration for a viscous plasma shows that resistivity is less efficient than viscosity in transforming the energy of the wave to heat.
Validation of new ACR/EULAR 2022 classification criteria for anti-neutrophil cytoplasmic antibody–associated vasculitis
Authors: Sada Ken-ei , Kaname Shinya , Higuchi Tomoaki , Furuta Shunsuke , Nagasaka Kenji , Nanki Toshihiro , Tsuboi Naotake , Amano Koichi , Dobashi Hiroaki , Hiromura Keiju , Bando Masashi , Wada Takashi , Arimura Yoshihiro , Makino Hirofumi , Harigai Masayoshi 
Published: January 2023

ABSTRACT

Objective
The objective of this study was to compare the American College of Rheumatology/European Alliance of Associations for Rheumatology 2022 criteria with the previous classification algorithm for anti-neutrophil cytoplasmic antibody–associated vasculitis.

Methods
We used data from two nationwide, prospective, inception cohort studies. The enrolled patients were classified as having eosinophilic granulomatosis with polyangiitis (EGPA), granulomatosis with polyangiitis (GPA), or microscopic polyangiitis (MPA) according to the new criteria; these criteria were compared with Watts’ algorithm.

Results
Among 477 patients, 10.7%, 9.9%, and 75.6% were classified as having EGPA, GPA, and MPA, respectively; 6.1% were unclassifiable. Three patients met both the EGPA and MPA criteria, and eight patients met both the GPA and MPA criteria. Of 78 patients with GPA classified using Watts’ algorithm, 27 (34.6%) patients were reclassified as having MPA. Ear, nose, and throat involvement was significantly less frequent in patients reclassified as having MPA than in those reclassified as having GPA. Of 73 patients unclassifiable using Watts’ algorithm, 62 were reclassified as having MPA. All patients reclassified as having MPA were myeloperoxidase-anti-neutrophil cytoplasmic antibody positive, and 46 had interstitial lung disease.

Conclusion
Although the American College of Rheumatology/European Alliance of Associations for Rheumatology 2022 criteria cause overlapping multiple criteria fulfilments in some patients, those items contribute to classifying unclassifiable patients using Watts’ algorithm into MPA.
Fatal cerebral venous sinus thrombosis with preceding thrombocytopenia in a patient with new-onset eosinophilic granulomatosis with polyangiitis
Authors: Tanomogi Naoki , Ota Takahiro , Sato Daisuke , Itagaki Shingo , Shimada Kota 
Published: January 2023

ABSTRACT
A previously healthy, 44-year-old, female patient was hospitalised for acute abdominal pain and bilateral pneumonia. Eosinophilic granulomatosis with polyangiitis (EGPA) was diagnosed on the basis of eosinophilia, eosinophilic tissue inflammation, polyneuropathy, and bilateral pneumonia. She had a fatal cerebral venous sinus thrombosis following thrombocytopenia, which was apparently caused by platelet consumption. It may have been possible to prevent the deterioration of the venous thrombosis by starting immunosuppressive or anticoagulant therapy earlier. If a patient with EGPA presents with unexplained thrombocytopenia, the physician should assess for physical findings or laboratory abnormalities suggestive of thrombosis. Additionally, if the patient complains of headache or nausea with normal head computed tomography findings, magnetic resonance imaging or magnetic resonance venography should be performed to assess for cerebral venous sinus thrombosis.
Giant cell arteritis with myeloperoxidase anti-neutrophil cytoplasmic antibody seropositivity in a patient with systemic sclerosis
Authors: Kitahara Yoshihiro , Nakamura Rie , Kawai Makiko , Hirakawa Tetsu , Hamada Arisa , Mito Mineyo , Nakano Kikuo 
Published: January 2023

ABSTRACT
To the best of our knowledge, systemic sclerosis with overlapping characteristics of both microscopic polyangiitis and giant cell arteritis (i.e. microscopic polyangiitis involving the superficial temporal artery or giant cell arteritis with myeloperoxidase anti-neutrophil cytoplasmic antibody seropositivity) has not been reported previously. An 82-year-old woman with diffuse cutaneous systemic sclerosis experienced dyspnoea on exertion and fever. No signs of infection were observed on computed tomography. Her fever persisted despite antibiotic treatment for occult bacterial infection and secondary Clostridioides difficile–associated diarrhoea. Microscopic polyangiitis was suspected because of myeloperoxidase anti-neutrophil cytoplasmic antibody seropositivity, and giant cell arteritis was suspected as a differential diagnosis due to swelling of the superficial temporal artery. Arterial biopsy revealed inflammatory cell infiltration with granuloma formation. Based on the presence of granulomatous inflammation in the superficial temporal artery, we concluded that giant cell arteritis with myeloperoxidase anti-neutrophil cytoplasmic antibody seropositivity occurred as a complication. After glucocorticoid therapy, her fever and dyspnoea on exertion improved with a gradual decline in the serum myeloperoxidase anti-neutrophil cytoplasmic antibody levels. It is possible that vasculitis occurs as a complication in patients with systemic sclerosis in cases where the fever persists and cannot be explained by systemic sclerosis itself, infectious disease, or malignancy. Clinicians must be careful not to prematurely diagnose microscopic polyangiitis based on myeloperoxidase anti-neutrophil cytoplasmic antibody seropositivity or giant cell arteritis based on the swelling of the superficial temporal artery. Careful evaluation of the presence of granulomatous inflammation in an arterial biopsy specimen is essential to differentiate between microscopic polyangiitis and giant cell arteritis.
Enhancement of protein translation by CRISPR/dCasRx coupled with SINEB2 repeat of noncoding RNAs
Authors: Cao Congcong , Li Aolin , Xu Chaojie , Wu Baorui , Liu Jun , Liu Yuchen 
Published: January 2023

AbstractThe use of new long noncoding RNAs (lncRNAs) as biotechnological or therapeutic tools is still in its infancy, despite recent efforts to uncover their involvement in various biological processes including mRNA translation. An important question is whether lncRNA functional elements can be used to target translation of mRNAs of interest by incorporating the RNA-targeting CRISPR tools. The CRISPR/dCasRx-SINEB2 technology was developed in this research by coupling the sgRNA of a catalytically inactive Type VI-D Cas13 enzyme (CasRx) to an integrated SINEB2 domain of uchl1 lncRNA that promotes the translation of targeted mRNA. It has been demonstrated to be effective and adaptable in selectively increasing the expression of a variety of exogenous and endogenous proteins with a variety of functions with minimal off-target effects. dCasRx-SINEB2 is currently the sole CRISPR-related technique for translational control of gene expression, and works just as well or even better than the traditional RNAe tool under comparable conditions. Additionally, human cancer cells can be prevented from proliferating and migrating both in vitro and in vivo by dCasRx-SINEB2-targeted mRNA translation of transcripts encoding for antitumor proteins, including PTEN and P53. The present study provides an innovative protein enhancement method that will have several applications in biopharmaceuticals production and cancer research.
Structural predictions of protein–DNA binding: MELD-DNA
Authors: Esmaeeli Reza , Bauzá Antonio , Perez Alberto 
Published: January 2023

AbstractStructural, regulatory and enzymatic proteins interact with DNA to maintain a healthy and functional genome. Yet, our structural understanding of how proteins interact with DNA is limited. We present MELD-DNA, a novel computational approach to predict the structures of protein–DNA complexes. The method combines molecular dynamics simulations with general knowledge or experimental information through Bayesian inference. The physical model is sensitive to sequence-dependent properties and conformational changes required for binding, while information accelerates sampling of bound conformations. MELD-DNA can: (i) sample multiple binding modes; (ii) identify the preferred binding mode from the ensembles; and (iii) provide qualitative binding preferences between DNA sequences. We first assess performance on a dataset of 15 protein–DNA complexes and compare it with state-of-the-art methodologies. Furthermore, for three selected complexes, we show sequence dependence effects of binding in MELD predictions. We expect that the results presented herein, together with the freely available software, will impact structural biology (by complementing DNA structural databases) and molecular recognition (by bringing new insights into aspects governing protein–DNA interactions).
Structure of a 28.5 kDa duplex-embedded G-quadruplex system resolved to 7.4 Å resolution with cryo-EM
Authors: Monsen Robert C , Chua Eugene Y D , Hopkins Jesse B , Chaires Jonathan B , Trent John O 
Published: January 2023

AbstractGenomic regions with high guanine content can fold into non-B form DNA four-stranded structures known as G-quadruplexes (G4s). Extensive in vivo investigations have revealed that promoter G4s are transcriptional regulators. Little structural information exists for these G4s embedded within duplexes, their presumed genomic environment. Here, we report the 7.4 Å resolution structure and dynamics of a 28.5 kDa duplex-G4-duplex (DGD) model system using cryo-EM, molecular dynamics, and small-angle X-ray scattering (SAXS) studies. The DGD cryo-EM refined model features a 53° bend induced by a stacked duplex-G4 interaction at the 5’ G-tetrad interface with a persistently unstacked 3’ duplex. The surrogate complement poly dT loop preferably stacks onto the 3’ G-tetrad interface resulting in occlusion of both 5’ and 3’ tetrad interfaces. Structural analysis shows that the DGD model is quantifiably more druggable than the monomeric G4 structure alone and represents a new structural drug target. Our results illustrate how the integration of cryo-EM, MD, and SAXS can reveal complementary detailed static and dynamic structural information on DNA G4 systems.