bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repurposing of waste PET by microbial biotransformation to functionalized materials for additive manufacturing
Authors: Kolitha Bhagya S , Jayasekara Sandhya K , Tannenbaum Rina , Jasiuk Iwona M , Jayakody Lahiru N 
Published: May 2023

Abstract

Plastic waste is an outstanding environmental thread. Poly(ethylene terephthalate) (PET) is one of the most abundantly produced single-use plastics worldwide, but its recycling rates are low. In parallel, additive manufacturing is a rapidly evolving technology with wide-ranging applications. Thus, there is a need for a broad spectrum of polymers to meet the demands of this growing industry and address post-use waste materials. This perspective article highlights the potential of designing microbial cell factories to upcycle PET into functionalized chemical building blocks for additive manufacturing. We present the leveraging of PET hydrolyzing enzymes and rewiring the bacterial C2 and aromatic catabolic pathways to obtain high-value chemicals and polymers. Since PET mechanical recycling back to original materials is cost-prohibitive, the biochemical technology is a viable alternative to upcycle PET into novel 3D printing materials, such as replacements for acrylonitrile butadiene styrene. The presented hybrid chemo-bio approaches potentially enable the manufacturing of environmentally friendly degradable or higher-value high-performance polymers and composites and their reuse for a circular economy.

One-Sentence Summary
Biotransformation of waste PET to high-value platform chemicals for additive manufacturing.
Glomus tumor mimicking digital adenocarcinoma
Authors: Ascio Noelani-Mei , Tchienga Dimitri , Qureshi Abid , Liu David , Asarian Armand , Genato Romulo , Xiao Philip 
Published: May 2023

Abstract
Glomus tumors are uncommon, benign lesions commonly located on the digits of the hands and are diagnostically challenging. This is because hemangiomas or ganglion cysts are more commonly identified in those locations. Our case report underlines the diagnostic challenge of a glomus tumor and the importance of immunohistochemical staining.
Vermiform appendix torsion complicated by postoperative venous pylephlebitis: a case report and review of literature
Authors: Nyssen Marie , Marliere Camille , Fobe Didier , Kothonidis Konstantinos 
Published: May 2023

Abstract
Vermiform appendix torsion is a rare condition that mimics acute appendicitis and is diagnosed during surgery. On the other hand, pylephlebitis (or septic thrombophlebitis) is a complication that occurs due to occlusive thrombosis of mesenteric venous system branches secondary to intra-abdominal infections. Although rare since the antibiotic era, it must be considered in the differential diagnosis of postoperative fever. We report the case of a 63-year-old man who was diagnosed with acute appendicitis. During laparoscopy, an anti-clockwise vermiform appendix torsion (360°) was identified. On postoperative day 3, the patient developed recurrent pyrexia related to ileocolic vein pylephlebitis, requiring specific management. Vermiform appendix torsion is a rare condition that is indistinguishable from acute appendicitis until an appendicectomy is performed. Whereas previous studies have reported an uneventful postoperative period in cases of vermiform appendix torsion, we present the first case of pylephlebitis as a rare complication and discuss adequate treatment.
Cauliflower mosaic virus disease spectrum uncovers novel susceptibility factorNCED9inArabidopsis thaliana
Authors: Hoffmann Gesa , Shukla Aayushi , López-González Silvia , Hafrén Anders 
Published: May 2023

AbstractViruses are intimately linked with their hosts and especially dependent on gene-for-gene interactions to establish successful infections. On the host side, defence mechanisms such as tolerance and resistance can occur within the same species, leading to differing virus accumulation in relation to symptomology and plant fitness. The identification of novel resistance genes against viruses and susceptibility factors is an important part of understanding viral patho­genesis and securing food production. The model plant Arabidopsis thaliana displays a wide symptom spectrum in response to RNA virus infections, and unbiased genome-wide association studies have proven a powerful tool to identify novel disease-genes. In this study we infected natural accessions of A. thaliana with the pararetrovirus cauliflower mosaic virus (CaMV) to study the phenotypic variations between accessions and their correlation with virus accumulation. Through genome-wide association mapping of viral accumulation differences, we identified several susceptibility factors for CaMV, the strongest of which was the abscisic acid synthesis gene NCED9. Further experiments confirmed the importance of abscisic acid homeostasis and its disruption for CaMV disease.
Secondary fibromyalgia: An entity to be remembered—A case series with axial spondyloarthritis
Authors: Yilmaz Ebru 
Published: May 2023

ABSTRACT
Fibromyalgia (FM) is a clinical syndrome characterised by chronic widespread musculoskeletal pain, stiffness, and tenderness in addition to a variety of physical and mental symptoms such as fatigue, sleep disturbances, depression, anxiety, cognitive dysfunction, headaches, and digestive problems. FM can be associated with or coexist with other inflammatory rheumatic diseases such as rheumatoid arthritis, systemic lupus erythematosus, osteoarthritis, and spondyloarthritis. This phenomenon is called secondary FM. Although FM cannot be considered an autoimmune disease, it may in some cases be an early sign of an autoimmune disease. Therefore, clinicians should be cautious in these situations. This case series presents three patients diagnosed with axial spondyloarthritis coexisted with FM symptoms.
Enhanced nonenzymatic RNA copying with in-situ activation of short oligonucleotides
Authors: Ding Dian , Zhang Stephanie J , Szostak Jack W 
Published: May 2023

Abstract
The nonenzymatic copying of RNA is thought to have been necessary for the transition between prebiotic chemistry and ribozyme-catalyzed RNA replication in the RNA World. We have previously shown that a potentially prebiotic nucleotide activation pathway based on phospho-Passerini chemistry can lead to the efficient synthesis of 2-aminoimidazole activated mononucleotides when carried out under freeze-thaw cycling conditions. Such activated nucleotides react with each other to form 5′–5′ 2-aminoimidazolium bridged dinucleotides, enabling template-directed primer extension to occur within the same reaction mixture. However, mononucleotides linked to oligonucleotides by a 5′–5′ 2-aminoimidazolium bridge are superior substrates for nonenzymatic primer extension; their higher intrinsic reactivity and their higher template affinity enable faster template copying at lower substrate concentrations. Here we show that eutectic phase phospho-Passerini chemistry efficiently activates short oligonucleotides and promotes the formation of monomer-bridged-oligonucleotide species during freeze-thaw cycles. We then demonstrate that in-situ generated monomer-bridged-oligonucleotides lead to efficient nonenzymatic template copying in the same reaction mixture. Our demonstration that multiple steps in the pathway from activation chemistry to RNA copying can occur together in a single complex environment simplifies this aspect of the origin of life.
Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation
Authors: Vlasenok Maria , Margasyuk Sergey , Pervouchine Dmitri D 
Published: May 2023

Abstract
Alternative splicing (AS) and alternative polyadenylation (APA) are two crucial steps in the post-transcriptional regulation of eukaryotic gene expression. Protocols capturing and sequencing RNA 3′-ends have uncovered widespread intronic polyadenylation (IPA) in normal and disease conditions, where it is currently attributed to stochastic variations in the pre-mRNA processing. Here, we took advantage of the massive amount of RNA-seq data generated by the Genotype Tissue Expression project (GTEx) to simultaneously identify and match tissue-specific expression of intronic polyadenylation sites with tissue-specific splicing. A combination of computational methods including the analysis of short reads with non-templated adenines revealed that APA events are more abundant in introns than in exons. While the rate of IPA in composite terminal exons and skipped terminal exons expectedly correlates with splicing, we observed a considerable fraction of IPA events that lack AS support and attributed them to spliced polyadenylated introns (SPI). We hypothesize that SPIs represent transient byproducts of a dynamic coupling between APA and AS, in which the spliceosome removes the intron while it is being cleaved and polyadenylated. These findings indicate that cotranscriptional pre-mRNA splicing could serve as a rescue mechanism to suppress premature transcription termination at intronic polyadenylation sites.
Refining the genomic determinants underlying escape from X-chromosome inactivation
Authors: Peeters Samantha , Leung Tiffany , Fornes Oriol , Farkas Rachelle A , Wasserman Wyeth W , Brown Carolyn J 
Published: May 2023

Abstract
X-chromosome inactivation (XCI) epigenetically silences one X chromosome in every cell in female mammals. Although the majority of X-linked genes are silenced, in humans 20% or more are able to escape inactivation and continue to be expressed. Such escape genes are important contributors to sex differences in gene expression, and may impact the phenotypes of X aneuploidies; yet the mechanisms regulating escape from XCI are not understood. We have performed an enrichment analysis of transcription factor binding on the X chromosome, providing new evidence for enriched factors at the transcription start sites of escape genes. The top escape-enriched transcription factors were detected at the RPS4X promoter, a well-described human escape gene previously demonstrated to escape from XCI in a transgenic mouse model. Using a cell line model system that allows for targeted integration and inactivation of transgenes on the mouse X chromosome, we further assessed combinations of RPS4X promoter and genic elements for their ability to drive escape from XCI. We identified a small transgenic construct of only 6 kb capable of robust escape from XCI, establishing that gene-proximal elements are sufficient to permit escape, and highlighting the additive effect of multiple elements that work together in a context-specific fashion.
Arena3Dweb: interactive 3D visualization of multilayered networks supporting multiple directional information channels, clustering analysis and application integration
Authors: Kokoli Maria , Karatzas Evangelos , Baltoumas Fotis A , Schneider Reinhard , Pafilis Evangelos , Paragkamian Savvas , Doncheva Nadezhda T , Jensen Lars Juhl , Pavlopoulos Georgios A 
Published: May 2023

Abstract
Arena3Dweb is an interactive web tool that visualizes multi-layered networks in 3D space. In this update, Arena3Dweb supports directed networks as well as up to nine different types of connections between pairs of nodes with the use of Bézier curves. It comes with different color schemes (light/gray/dark mode), custom channel coloring, four node clustering algorithms which one can run on-the-fly, visualization in VR mode and predefined layer layouts (zig-zag, star and cube). This update also includes enhanced navigation controls (mouse orbit controls, layer dragging and layer/node selection), while its newly developed API allows integration with external applications as well as saving and loading of sessions in JSON format. Finally, a dedicated Cytoscape app has been developed, through which users can automatically send their 2D networks from Cytoscape to Arena3Dweb for 3D multi-layer visualization. Arena3Dweb is accessible at http://arena3d.pavlopouloslab.info or http://arena3d.org
Prognostic evaluation of re-resection for recurrent glioblastoma using the novel RANO classification for extent of resection: A report of the RANO resect group
Authors: Karschnia Philipp , Dono Antonio , Young Jacob S , Juenger Stephanie T , Teske Nico , Häni Levin , Sciortino Tommaso , Mau Christine Y , Bruno Francesco , Nunez Luis , Morshed Ramin A , Haddad Alexander F , Weller Michael , van den Bent Martin , Beck Juergen , Hervey-Jumper Shawn , Molinaro Annette M , Tandon Nitin , Rudà Roberta , Vogelbaum Michael A , Bello Lorenzo , Schnell Oliver , Grau Stefan J , Chang Susan M , Berger Mitchel S , Esquenazi Yoshua , Tonn Joerg-Christian 
Published: May 2023

Abstract

Background
The value of re-resection in recurrent glioblastoma remains controversial as a randomized trial that specifies intentional incomplete resection cannot be justified ethically. Here, we aimed to (1) explore the prognostic role of extent of re-resection using the previously proposed Response Assessment in Neuro-Oncology (RANO) classification (based upon residual contrast-enhancing (CE) and non-CE tumor), and to (2) define factors consolidating the surgical effects on outcome.

Methods
The RANO resect group retrospectively compiled an 8-center cohort of patients with first recurrence from previously resected glioblastomas. The associations of re-resection and other clinical factors with outcome were analyzed. Propensity score-matched analyses were constructed to minimize confounding effects when comparing the different RANO classes.

Results
We studied 681 patients with first recurrence of Isocitrate Dehydrogenase (IDH) wild-type glioblastomas, including 310 patients who underwent re-resection. Re-resection was associated with prolonged survival even when stratifying for molecular and clinical confounders on multivariate analysis; ≤1 cm3 residual CE tumor was associated with longer survival than non-surgical management. Accordingly, “maximal resection” (class 2) had superior survival compared to “submaximal resection” (class 3). Administration of (radio-)chemotherapy in the absence of postoperative deficits augmented the survival associations of smaller residual CE tumors. Conversely, “supramaximal resection” of non-CE tumor (class 1) was not associated with prolonged survival but was frequently accompanied by postoperative deficits. The prognostic role of residual CE tumor was confirmed in propensity score analyses.

Conclusions
The RANO resect classification serves to stratify patients with re-resection of glioblastoma. Complete resection according to RANO resect classes 1 and 2 is prognostic.
Radio-chemotherapy feasibility for biopsy-only unresectable IDH wild-type glioblastomas (BO-GBM)
Authors: Harlay Vincent , Appay Romain , Bequet Céline , Petrirena Gregorio , Campello Chantal , Barrié Maryline , Autran Didier , Graillon Thomas , Boissonneau Sébastien , Dufour Henry , Figarella-Branger Dominique , Padovani Laetitia , Barlier Anne , Nanni Isabelle , Tabouret Emeline , Chinot Olivier 
Published: May 2023

Abstract

Background
“Biopsy-only” glioblastoma (BO-GBM) is a heterogeneous, understudied group of patients associated with a poor outcome. Our objective was to explore the pattern of care and prognosis associated with BO-GBM in our center.

Methods
Patients with IDH wild-type BO-GBM included in a prospective regional cohort initiated in 2014 and closed in 2017 were retrospectively reviewed for patient characteristics, MRI findings, treatment allocation, and delivery.

Results
Of 535 patients included in the cohort, 137 patients were included in the present analysis. The median age was 66 years old and the median KPS was 70. Forty-six patients (33.6%) were referred to radiotherapy and chemotherapy (RT–TMZ) regimen, 75 (54.7%), considered unfitted for RT, received chemotherapy upfront (CT) and 16 (11.7%) were referred to palliative care (PC). Regarding the first group, 91% of patients completed the RT–TMZ. In the CT group, 11 of 75 patients (14.7%) underwent radiotherapy after chemotherapy upfront. Median overall survival was 12.3 months (95% CI, 15.30–24.16), 5.7 months (95% CI, 6.22–9.20), and 1.9 months (95% CI, 1.43–5.08) in RT–TMZ, CT, and PC groups, respectively. In multivariate analyses, progression-free survival was impacted by baseline KPS (P &lt; .001) and MGMT status (P = .004). Overall survival was impacted by baseline KPS (P &lt; .001) and age (P = .030).

Conclusion
BO-GBM constitute a large and heterogeneous population in which one-third of patients is amenable to the standard of care, with survival outcome close to one of the patients who underwent surgery. Reliable criteria are needed to help select patients for adequate treatment while new strategies are warranted for BO-GBM unfit for RT.
Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae
Authors: Chen Yongming , Guo Yiwen , Xie Xiaoming , Wang Zihao , Miao Lingfeng , Yang Zhengzhao , Jiao Yuannian , Xie Chaojie , Liu Jie , Hu Zhaorong , Xin Mingming , Yao Yingyin , Ni Zhongfu , Sun Qixin , Peng Huiru , Guo Weilong 
Published: May 2023

Abstract
Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.
Natural allelic variation in GRAIN SIZE AND WEIGHT 3 of wild rice regulates the grain size and weight
Authors: Bai Feng , Ma Huijin , Cai Yichang , Shahid Muhammad Qasim , Zheng Yuebin , Lang Chuan , Chen Zhixiong , Wu Jinwen , Liu Xiangdong , Wang Lan 
Published: May 2023

Abstract
Grain size is important for yield in rice (Oryza sativa L.). Although many genes involved in grain size have been isolated, few can be used in breeding due to their interactions and phenotypic effects. Here, we describe natural variation in the granule-type quantitative trait locus GRAIN SIZE AND WEIGHT 3 (GSW3) located on chromosome 3 in wild rice (Oryza rufipogon Griff.) that encodes a GTPase-regulated protein and negatively regulates grain length, grain width, and 1,000-grain weight. The insertion of a 232-bp fragment of the genomic sequence in the wild rice, a natural allelic variant gene (GSW3), increased the expression levels and reduced the grain length and width and 1,000-grain weight. Knockout of GSW3 in the wild rice inbred line Huaye 3 increased the grain length and width and 1,000-grain weight. Introducing GSW3Huaye3 into cultivated rice line KJ01 and overexpressing GSW3Huaye3 in Huaye 3 resulted in reduced grain length and width and 1,000-grain weight, and grain size and 1,000-grain weight changes were closely related to GSW3 expression levels. GSW3 regulated the grain length and width simultaneously by promoting grain glume cell division and longitudinal and transverse cell growth. GSW3 was also involved in regulating the gibberellic acid signaling pathway and negatively regulated plant growth. Furthermore, a critical SNP in the GSW3 coding region was obviously correlated with grain size variation in a core collection of cultivated rice. This SNP resulted in an amino acid substitution from Gln to Arg at position 161 in GSW3, which reduced the grain size. Our study shows that GSW3 negatively regulates the grain shape, which could explain different grain shapes in modern cultivars and wild rice. GSW3 may also be used for breeding rice varieties with improved grain shapes and higher yield.
Mortality in patients with incident rheumatoid arthritis and depression: a Danish cohort study of 11 071 patients and 55 355 comparators
Authors: Pedersen Jens K , Wang Lei , Risbo Nickolaj , Pedersen Alma B , Andersen Kjeld , Ellingsen Torkell 
Published: May 2023

Abstract

Objectives
In patients with RA, the association between mortality and depression has been investigated only in patients with prevalent RA. In this study, we estimated the mortality risk associated with depression, defined as the first filling of a prescription for antidepressants, in patients with incident RA and background population comparators.

Methods
From 2008 to 2018, we identified patients with incident RA in the nationwide Danish rheumatologic database, DANBIO. For each patient, we randomly selected five comparators. Participants were not treated with antidepressants or diagnosed with depression 3 years prior to the index date. From other registers we collected data on socioeconomic status, mortality and cause of death using unique personal identifiers. Using Cox models, we calculated hazard rate ratios (HRR) with 95% CI.

Results
In depressed patients with RA vs patients without depression, adjusted HRR for all-cause mortality was 5.34 (95% CI 3.02, 9.45) during 0–2 years and 3.15 (95% CI 2.62, 3.79) during the total follow-up period, and highest in patients &lt;55 years with HRR 8.13 (95% CI 3.89, 17.02). In comparators with depression vs comparators without depression, the association with mortality was similar to that in patients with RA. There were no unnatural causes of death among depressed patients with RA. The most frequent natural causes of death were cancer, cardiovascular disease, stroke and pneumonia.

Conclusion
In patients with RA, depression was a predictor of death but with a strength similar to that in matched comparators.