bluuebunny/crossref_metadata_2025_split huggingface dataset:
Terminology and equivalence
Authors: León-Araúz Pilar 
Published: June 2022

Abstract
Equivalence has not attracted as much interest as other issues in Terminology. Nevertheless, terminological equivalence can be understood from different perspectives: (1) equivalence at the concept, term or textual level; (2) degree of equivalence (from full to zero equivalence); (3) interlinguistic or intralinguistic equivalence; (4) equivalence based on the syntactic structure of terminological correspondences; (5) equivalence depending on the solution found for each equivalence-related problem; or (6) discovered or created equivalence. This chapter addresses equivalence from different theoretical approaches and their impact on the practice of terminography by analyzing different equivalence-related problems, terminographic methods and products.
On dynamical behavior for optical solitons sustained by the perturbed Chen–Lee–Liu model
Authors: Tarla Sibel , Ali Karmina K , Yilmazer Resat , Osman M S 
Published: June 2022

Abstract
This study investigates the perturbed Chen–Lee–Liu model that represents the propagation of an optical pulse in plasma and optical fiber. The generalized exponential rational function method is used for this purpose. As a result, we obtain some non-trivial solutions such as the optical singular, periodic, hyperbolic, exponential, trigonometric soliton solutions. We aim to express the pulse propagation of the generated solutions, by taking specific values for the free parameters existed in the obtained solutions. The obtained results show that the generalized exponential rational function technique is applicable, simple and effective to get the solutions of nonlinear engineering and physical problems. Moreover, the acquired solutions display rich dynamical evolutions that are important in practical applications.
New reasons for biologists to write with a formal language
Authors: Rodriguez-Esteban Raul 
Published: June 2022

Abstract
Current biological writing is afflicted by the use of ambiguous names, convoluted sentences, vague statements and narrative-fitted storylines. This represents a challenge for biological research in general and in particular for fields such as biological database curation and text mining, which have been tasked to cope with exponentially growing content. Improving the quality of biological writing by encouraging unambiguity and precision would foster expository discipline and machine reasoning. More specifically, the routine inclusion of formal languages in biological writing would improve our ability to describe, compile and model biology.
Smooth sailing: market integration, agglomeration, and productivity growth in interwar Brazil
Authors: Badia-Miró Marc , Carreras-MarÍn Anna , Huberman Michael 
Published: June 2022

Abstract
Leveraging an original dataset on coastal shipping and invoking a new economic geography framework, we study the effects of domestic and international trade costs on industrial concentration and productivity growth in interwar Brazil. In the great wave of globalization before 1914, international trade costs were low and domestic costs high. Economic activity was dispersed along the coastline. The interwar period saw a reversal: international costs surged and domestic costs declined. Economic activity was increasingly concentrated in São Paulo. Agglomeration economies enabled productivity growth in the 1930s, mostly in durable and capital goods.
Two-dimensional variational mode decomposition for seismic record denoising
Authors: Zhang Xingli , Chen Yan , Jia Ruisheng , Lu Xinming 
Published: June 2022

Abstract
Seismic signal denoising is the main task of seismic data processing. This study proposes a novel method for the denoising seismic record on the basis of a two-dimensional variational mode decomposition (2D-VMD) algorithm and permutation entropy (PE). 2D-VMD is a recently introduced adaptive signal decomposition method in which $K$ and $\alpha $ are important decomposing parameters to determine the number of modes, and have a predictable effect on the nature of detected modes. We present a novel method to address the problems of selecting appropriate $K$ and $\alpha $ values and apply these values to the proposed method. First, for a 2D seismic signal, the 2D-VMD method can decompose it into $K$ modes with specific direction and vibration characteristics. Next, the PE value of each mode is calculated. Random noise components are eliminated according to the PE value. Finally, the signal components are reconstructed to acquire the denoised seismic signal. Experimental and simulation results indicate that the proposed method has remarkable denoising effect on synthetic and real seismic signals. We hope that this new method can inspire and help evaluate new ideas in this field.
A Unique Mitochondrial Gene Block Inversion in Antarctic Trematomin Fishes: A Cautionary Tale
Authors: Patel Selina , Evans Clive W , Stuckey Alex , Matzke Nicholas J , Millar Craig D 
Published: June 2022

Abstract
Many Antarctic notothenioid fishes have major rearrangements in their mitochondrial (mt) genomes. Here, we report the complete mt genomes of 3 trematomin notothenioids: the bald notothen (Trematomus (Pagothenia) borchgrevinki), the spotted notothen (T. nicolai), and the emerald notothen (T. bernacchii). The 3 mt genomes were sequenced using next-generation Illumina technology, and the assemblies verified by Sanger sequencing. When compared with the canonical mt gene order of the Antarctic silverfish (Pleuragramma antarctica), we found a large gene inversion in the 3 trematomin mt genomes that included tRNAIle, ND1, tRNALeu2, 16S, tRNAVal, 12S, tRNAPhe, and the control region. The trematomin mt genomes contained 3 intergenic spacers, which are thought to be the remnants of previous gene and control region duplications. All control regions included the characteristic conserved regulatory sequence motifs. Although short-read next-generation DNA sequencing technology has allowed the rapid and cost-effective sequencing of a large number of complete mt genomes, it is essential in all cases to verify the assembly in order to prevent the publication and use of erroneous data.
Process intensification at the expression system level for the production of 1-phosphate aldolase in antibiotic-free E. coli fed-batch cultures
Authors: Pasini Martina , Fernández-Castané Alfred , Caminal Gloria , Overton Tim W , Ferrer Pau 
Published: June 2022

Abstract
To successfully design expression systems for industrial biotechnology and biopharmaceutical applications; plasmid stability, efficient synthesis of the desired product and the use of selection markers acceptable to regulatory bodies are of utmost importance. In this work we demonstrate the application of a set of IPTG-inducible protein expression systems -- harboring different features namely, antibiotic vs auxotrophy marker; two-plasmids vs single plasmid expression system; expression levels of the repressor protein (LacI) and the auxotrophic marker (glyA) -- in high-cell density cultures to evaluate their suitability in bioprocess conditions that resemble industrial settings. Results revealed that the first generation of engineered strain showed a 50% reduction in the production of the model recombinant protein fuculose-1-phosphate aldolase (FucA) compared to the reference system from QIAGEN. The over-transcription of glyA was found to be a major factor responsible for the metabolic burden. The second- and third-generation of expression systems presented an increase in FucA production and advantageous features. In particular, the third-generation expression system is antibiotic-free, autotrophy-selection based and single-plasmid and, is capable to produce FucA at similar levels compared to the original commercial expression system. These new tools open new avenues for high-yield and robust expression of recombinant proteins in E. coli.
Of Two-Tailed Lizards: Spells, Folk-Knowledge, and Navigating Manila, 1620–1650
Authors: Findley David Max 
Published: June 2022

Abstract
Although seventeenth-century Manila has been anointed the birthplace of global trade and its diversity is well-established, how individuals navigated that milieu is only recently coming to light. To elucidate how various persons experienced Manila, this article assembles and analyzes nearly one hundred denunciations of sorcery (hechicería) made to the Philippine branch of the Inquisition between ca. 1620 and 1650. The hexes and spells sold in this period promised material and physical benefits. Individuals purchased or learned about spells primarily from Indigenous Philippine peoples, but also from Manila’s Moluccan, Indian, and Japanese residents who either imitated Philippine hexes or marketed their own, distinct spells. This exchange took place outside Manila’s city walls, in the sprawling city of Extramuros, where frequent interactions between diverse peoples facilitated exchange and even contributed to the emergence of novel, hybridized hexes mixing Catholic invocations and Philippine rituals. Cumulatively, what these denunciations of a minor crime capture is the everyday interactions between diverse peoples that defined Manila. In the process, they establish how residents experienced and navigated the world’s first global city.
The role of magnetic fields in the stability and fragmentation of filamentary molecular clouds: two case studies at OMC-3 and OMC-4
Authors: Li Pak Shing , Lopez-Rodriguez Enrique , Soam Archana , Klein Richard I 
Published: June 2022

ABSTRACTWe present the stability analysis of two regions, OMC-3 and OMC-4, in the massive and long molecular cloud complex of Orion A. We obtained 214 $\mu$m HAWC + /SOFIA polarization data, and we make use of archival data for the column density and C18O (1–0) emission line. We find clear depolarization in both observed regions and that the polarization fraction is anticorrelated with the column density and the polarization-angle dispersion function. We find that the filamentary cloud and dense clumps in OMC-3 are magnetically supercritical and strongly subvirial. This region should be in the gravitational collapse phase and is consistent with many young stellar objects (YSOs) forming in the region. Our histogram of relative orientation (HRO) analysis shows that the magnetic field is dynamically sub-dominant in the dense gas structures of OMC-3. We present the first polarization map of OMC-4. We find that the observed region is generally magnetically subcritical except for an elongated dense core, which could be a result of projection effect of a filamentary structure aligned close to the line of sight. The relative large velocity dispersion and the unusual positive shape parameters at high column densities in the HROs analysis suggest that our viewing angle may be close to axes of filamentary substructures in OMC-4. The dominating strong magnetic field in OMC-4 is unfavourable for star formation and is consistent with much fewer YSOs than in OMC-3.
Jets from main sequence and white dwarf companions during common envelope evolution
Authors: Zou Yangyuxin , Chamandy Luke , Carroll-Nellenback Jonathan , Blackman Eric G , Frank Adam 
Published: June 2022

ABSTRACT
It has long been speculated that jet feedback from accretion on to the companion during a common envelope (CE) event could affect the orbital evolution and envelope unbinding process. We present global 3D hydrodynamical simulations of CE evolution (CEE) that include a jet subgrid model and compare them with an otherwise identical model without a jet. Our binary consists of a 2-M⊙ red giant branch primary and a 1- or 0.5-M⊙ main sequence (MS) or white dwarf (WD) secondary companion modelled as a point particle. We run the simulations for 10 orbits (40 d). Our jet model adds mass at a constant rate $\dot{M}_\mathrm{j}$ of the order of the Eddington rate, with maximum velocity vj of the order of the escape speed, to two spherical sectors with the jet axis perpendicular to the orbital plane. We explore the influence of the jet on orbital evolution, envelope morphology and envelope unbinding, and assess the dependence of the results on the jet mass-loss rate, launch speed, companion mass, opening angle, and accretion rate. In line with our theoretical estimates, jets are choked around the time of first periastron passage and remain choked thereafter. Subsequent to choking, but not before, jets efficiently transfer energy to bound envelope material. This leads to increases in unbound mass of up to $\sim 10{{\ \rm per\ cent}}$, as compared to the simulations without jets. We also estimate the cumulative effects of jets over a full CE phase, finding that jets launched by MS and WD companions are unlikely to dominate envelope unbinding.
Web-based platform for analysis of RNA folding from high throughput chemical probing data
Authors: Jurich Christopher P , Brivanlou Amir , Rouskin Silvi , Yesselman Joseph D 
Published: June 2022

Abstract
RNA structures play critical roles in regulating gene expression across all domains of life and viruses. Chemical probing methods coupled with massively parallel sequencing have revolutionized the RNA structure field by enabling the assessment of many structures in their native, physiological context. Previously, we developed Dimethyl-Sulfate-based Mutational Profiling and Sequencing (DMS-MaPseq), which uses DMS to label the Watson-Crick face of open and accessible adenine and cytosine bases in the RNA. We used this approach to determine the genome-wide structures of HIV-1 and SARS-CoV-2 in infected cells, which permitted uncovering new biology and identifying therapeutic targets. Due to the simplicity and ease of the experimental procedure, DMS-MaPseq has been adopted by labs worldwide. However, bioinformatic analysis remains a substantial hurdle for labs that often lack the necessary infrastructure and computational expertise. Here we present a modern web-based interface that automates the analysis of chemical probing profiles from raw sequencing files (http://rnadreem.org). The availability of a simple web-based platform for DMS-MaPseq analysis will dramatically expand studies of RNA structure and aid in the design of structure-based therapeutics.
Chemoenzymatic labeling of DNA methylation patterns for single-molecule epigenetic mapping
Authors: Gabrieli Tslil , Michaeli Yael , Avraham Sigal , Torchinsky Dmitry , Margalit Sapir , Schütz Leonie , Juhasz Matyas , Coruh Ceyda , Arbib Nissim , Zhou Zhaohui Sunny , Law Julie A , Weinhold Elmar , Ebenstein Yuval 
Published: June 2022

Abstract
DNA methylation, specifically, methylation of cytosine (C) nucleotides at the 5-carbon position (5-mC), is the most studied and significant epigenetic modification. Here we developed a chemoenzymatic procedure to fluorescently label non-methylated cytosines in CpG context, allowing epigenetic profiling of single DNA molecules spanning hundreds of thousands of base pairs. We used a CpG methyltransferase with a synthetic S-adenosyl-l-methionine cofactor analog to transfer an azide to cytosines instead of the natural methyl group. A fluorophore was then clicked onto the DNA, reporting on the amount and position of non-methylated CpGs. We found that labeling efficiency was increased up to 2-fold by the addition of a nucleosidase, presumably by degrading the inactive by-product of the cofactor after labeling, preventing its inhibitory effect. We used the method to determine the decline in global DNA methylation in a chronic lymphocytic leukemia patient and then performed whole-genome methylation mapping of the model plant Arabidopsis thaliana. Our genome maps show high concordance with published bisulfite sequencing methylation maps. Although mapping resolution is limited by optical detection to 500–1000 bp, the labeled DNA molecules produced by this approach are hundreds of thousands of base pairs long, allowing access to long repetitive and structurally variable genomic regions.
The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets
Authors: Deschamps-Francoeur Gabrielle , Couture Sonia , Abou-Elela Sherif , Scott Michelle S 
Published: June 2022

Abstract
Box C/D small nucleolar RNAs (snoRNAs) are a conserved class of RNA known for their role in guiding ribosomal RNA 2′-O-ribose methylation. Recently, C/D snoRNAs were also implicated in regulating the expression of non-ribosomal genes through different modes of binding. Large scale RNA–RNA interaction datasets detect many snoRNAs binding messenger RNA, but are limited by specific experimental conditions. To enable a more comprehensive study of C/D snoRNA interactions, we created snoGloBe, a human C/D snoRNA interaction predictor based on a gradient boosting classifier. SnoGloBe considers the target type, position and sequence of the interactions, enabling it to outperform existing predictors. Interestingly, for specific snoRNAs, snoGloBe identifies strong enrichment of interactions near gene expression regulatory elements including splice sites. Abundance and splicing of predicted targets were altered upon the knockdown of their associated snoRNA. Strikingly, the predicted snoRNA interactions often overlap with the binding sites of functionally related RNA binding proteins, reinforcing their role in gene expression regulation. SnoGloBe is also an excellent tool for discovering viral RNA targets, as shown by its capacity to identify snoRNAs targeting the heavily methylated SARS-CoV-2 RNA. Overall, snoGloBe is capable of identifying experimentally validated binding sites and predicting novel sites with shared regulatory function.
ATRT-04. Clinical and (epi)genetic characterisation of patients with atypical teratoid/rhabdoid tumor (ATRT) and extracranial malignant rhabdoid tumor conceived following assisted reproduction technologies (ART)
Authors: Nemes Karolina , Benesch Martin , Kolerova Julia , Johann Pascal , Hasselblatt Martin , Thomas Christian , Bens Susanne , Liaugaudiene Olga , Sadeghipour Alireza , von der Weid Nicolas , Schmid Irene , Gidding Corrie , Erdreich-Epstein Anat , Khurana Claudia , Ebetsberger-Dachs Georg , Lemmer Andreas , Marqués Carmen Hernández , Khatib Ziad , Pears Jane , Quehenberger Franz , Biegel Jaclyn A , Siebert Reiner , Frühwald Michael C 
Published: June 2022

Abstract
INTRODUCTION: Anecdotal case reports suggest an association between assisted reproduction technologies (ART) and malignant rhabdoid tumors (MRT). We performed a multi-institutional retrospective analysis of the EU-RHAB database, complemented by additional cases outside of EU-RHAB to compile clinical, (epi)genetic characteristics and outcome data of children with MRT following ART. METHODS: Data of 14 patients (from 311 patients with MRT) from 9 countries were analyzed (2010-2018). Tumors and matching blood samples were examined for SMARCB1 mutations using FISH, MLPA and sequencing. Molecular subgroups were determined using DNA methylation arrays and correlated with a validation cohort (n=22, tumor samples of MRT; n=39 blood samples of patients small for gestational age). RESULTS: The median age at diagnosis of the 13 girls and 1 boy was 9 months (0 – 66). 8 patients with ATRT, 3 with extracranial, extrarenal-, 1 with renal rhabdoid tumor and 2 with synchronous tumors were identified. Distant metastases at diagnosis were present in 6 patients. A germline mutation (GLM) was detected in 5 patients. In 11 tumors complete data on SMARCB1 mutational status were available. DNA methylation subgrouping was available in 10 tumors and 6 blood samples. A female predominance was noted as compared to the EU-RHAB cohort with MRT born without ART (n=213, p=0.009). A total of 8 patients received gross total resection, n=12 patients received conventional chemotherapy (EU-RHAB=9, Head Start II=2, IRS III=1). Radiotherapy was applied to 6 patients. 10 patients achieved CR, and 5 remain in continuing CR. Significant genome-wide DNA methylation differences (including imprinted genes) between patients born after ART and patients born without ART could not be demonstrated. CONCLUSIONS: Long-term survival is achievable in patients who develop MRT after ART, even in cases with GLM, metastatic disease at diagnosis, or relapse. Larger epidemiological studies are needed to confirm a potential association between MRT and ART.
ATRT-12. LIN28A expression correlates with poor prognosis and the MYC subgroup in AT/RTs
Authors: Dottermusch Matthias , Brakopp Sina , Struve Nina , Frühwald Michael C , Merk Daniel J , Tabatabai Ghazaleh , Schüller Ulrich , Hasselblatt Martin , Neumann Julia E 
Published: June 2022

Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are malignant embryonal tumors of the central nervous system, which mainly affect young children. These tumors are defined by loss of SMARCB1 (or SMARCA4 in rare cases) and can be categorized into three main DNA methylation subgroups (i.e. –MYC, -SHH, -TYR). AT/RTs commonly display heterogeneous expression of LIN28A, an RNA-binding protein, which regulates pluripotency and plays critical roles during embryonic development. The biological impact and clinical significance of LIN28A expression in AT/RTs remains unknown. In this study, we investigated 80 samples of molecularly and clinically characterized AT/RTs for LIN28A expression using immunohistochemistry. Staining signal of tumor tissue was assessed and scored via semi-automated digital image analysis. Global LIN28A expression intensity and heterogeneity were tested for correlation with DNA methylation subtype, tumor localization, as well as patient age, gender and overall survival. LIN28A was found with strongly varying staining patterns and intensities across our cohort of AT/RTs, with significantly elevated expression in the MYC subgroup. Moreover, we identified strong global and focal LIN28A expression as an independent negative prognostic factor in AT/RTs. In summary, we show that AT/RT-MYC tumors display significantly increased LIN28A expression in comparison to the other DNA methylation subgroups, suggesting a subgroup-specific intratumoral role of LIN28A. Furthermore, we demonstrate an impact of LIN28A expression on survival in AT/RTs. Further investigations on the functions of LIN28A in AT/RTs in vitro and in vivo are ongoing and aim to uncover potential therapeutic implications in these tumors.
ATRT-23. SIRT2 cooperates with SMARCB1 to induce a differentiation block in ATRT
Authors: Alimova Irina , Wang Dong , Pierce Angela , Lakshmanachetty Senthilnath , Prince Eric , Danis Etienne , Serkova Natalie , Madhavan Krishna , Balakrishnan Ilango , Yang Min , Lin Henning , Foreman Nicholas , Venkataraman Sujatha , Vibhakar Rajeev 
Published: June 2022

Abstract
Atypical Teratoid Rhabdoid Tumor is a highly aggressive pediatric brain tumor with poor prognosis driven by loss of the chromatin remodeling factor SMARCB1 that is responsible for determining cellular pluripotency and lineage commitment. The mechanisms by which SMARCB1 deletion results in tumorigenesis remain unclear. We investigated the effect of SIRT2 inhibition in ATRT which was identified as a primary dependency in ATRT. SIRT2 inhibition with shRNA or Thiomyristoyl (TM) decreased ATRT cell growth, inhibited clonogenic potential and leaded to the cell cycle arrest. SIRT2 inhibition effectively suppresses pluripotency-associated genomic programs, significantly changed stem cell frequency, decreased tumor-sphere formation of ATRT cells and attenuated tumor cell self-renewal. In vivo SIRT2 inhibition decreased oncogenic markers and increased accumulation neuronal differentiation markers. Furthermore, SIRT2 induced apoptosis, decreased tumor growth and prolonged survival in orthotopic xenograft models. Single-cell RNA transcriptome analysis of xenoftaft tumors reveals elimination of tumor cells expressing stem cell genes and expansion of tumor cells expressing differentiated genes following TM treatment in ATRT. We demonstrated that SIRT2 inhibition is a molecular vulnerability in SMARCB1-deleted ATRT.