bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of pararosaniline as a modifier of RNA splicing in Caenorhabditis elegans
Authors: Huynh Dylan , Wu Cheng-Wei 
Published: October 2023

Abstract
Posttranscriptional splicing of premessenger RNA (mRNA) is an evolutionarily conserved eukaryotic process for producing mature mRNA that is translated into proteins. Accurate splicing is necessary for normal growth and development, and aberrant splicing is increasingly evident in various human pathologies. To study environmental factors that influence RNA splicing, we employed a fluorescent Caenorhabditis elegans in vivo splicing reporter as a biomarker for splicing fidelity to screen against the US EPA ToxCast chemical library. We identified pararosaniline hydrochloride as a strong modifier of RNA splicing. Through gene expression analysis, we found that pararosaniline activates the oxidative stress response and alters the expression of key RNA splicing regulator genes. Physiological assays show that pararosaniline is deleterious to C. elegans development, reproduction, and aging. Through a targeted RNAi screen, we found that inhibiting protein translation can reverse pararosaniline's effect on the splicing reporter and provide significant protection against long-term pararosaniline toxicity. Together, this study reveals a new chemical modifier of RNA splicing and describes translation inhibition as a genetic mechanism to provide resistance.
Bivalves as Emerging Model Systems to Study the Mechanisms and Evolution of Sex Determination: A Genomic Point of View
Authors: Nicolini Filippo , Ghiselli Fabrizio , Luchetti Andrea , Milani Liliana 
Published: October 2023

Abstract
Bivalves are a diverse group of molluscs that have recently attained a central role in plenty of biological research fields, thanks to their peculiar life history traits. Here, we propose that bivalves should be considered as emerging model systems also in sex-determination (SD) studies, since they would allow to investigate: 1) the transition between environmental and genetic SD, with respect to different reproductive backgrounds and sexual systems (from species with strict gonochorism to species with various forms of hermaphroditism); 2) the genomic evolution of sex chromosomes (SCs), considering that no heteromorphic SCs are currently known and that homomorphic SCs have been identified only in a few species of scallops; 3) the putative role of mitochondria at some level of the SD signaling pathway, in a mechanism that may resemble the cytoplasmatic male sterility of plants; 4) the evolutionary history of SD-related gene (SRG) families with respect to other animal groups. In particular, we think that this last topic may lay the foundations for expanding our understanding of bivalve SD, as our current knowledge is quite fragmented and limited to a few species. As a matter of fact, tracing the phylogenetic history and diversity of SRG families (such as the Dmrt, Sox, and Fox genes) would allow not only to perform more targeted functional experiments and genomic analyses, but also to foster the possibility of establishing a solid comparative framework.
Stable first-arrival picking through mathematical morphology and edge detection
Authors: Gao Lei , Hong Haolong , Min Fan 
Published: October 2023

SUMMARY
First-arrival picking is a fundamental and challenging task in seismic data processing. Existing algorithms such as the cross-correlation algorithm (CCT) struggle to achieve satisfactory noise immunity while maintaining picking efficiency. In this paper, we propose the first-arrival picking through mathematical morphology and edge detection (FPME) algorithm with three steps. The converting step transforms the original data into a binary image though a filtering technique, where the binary image represents the global energy distribution of high-energy and low-energy samples. The rendering step delimits the signal zone in the binary image through morphological operations, where the signal zone eliminates the noise in the upper part. The picking step detects first arrivals in the signal zone through the edge detection methods, where an evaluation function is designed to select the optimal detection results as first arrivals. Experiments were performed on four field data sets. The results demonstrated that FPME is more stable and reliable than five classic and popular algorithms.
Urban manufacturing and the role of industrial relatedness in sustaining it: the case of the Brussels Capital Region
Authors: Bonaccolto Giovanni , Pedrini Giulio , Talamo Giuseppina 
Published: October 2023

Abstract
This paper revisits the ongoing discussion on the concept of industrial relatedness by applying it to manufacturing industries in urban areas. The analysis uses a sample of firms operating in the Brussels Capital Region area and observed over the period 2009–2015. Based on a two-step quantile regression, results show that industrial relatedness is the agglomeration force that mostly sustains the performance of urban manufacturing, whereas this is not the case for other types of agglomeration externalities. Moreover, among the measures of industrial relatedness, the input–output relationship matters more than product similarity in the perspective of a relocation of manufacturing firms in urban areas.
On the p-Rank of Class Groups of p-Extensions
Authors: Liu Yuan 
Published: October 2023

Abstract
We prove a local–global principle for the embedding problems of global fields with restricted ramification. By this local–global principle, for a global field $k$, we use only the local information to give a presentation of the maximal pro-$p$ Galois group of $k$ with restricted ramification, when some Galois cohomological conditions are satisfied. For a Galois $p$-extension $K/k$, we use our presentation result for $k$ to study the structure of pro-$p$ Galois groups of $K$. Then for $k={{\mathbb{Q}}}$ and $k={{\mathbb{F}}}_{q}(t)$ with $p\nmid q$, we give upper and lower bounds for the rank of $p$-torsion subgroup of the class group of $K$, and these bounds depend on the structure of the Galois group and the inertia subgroups of $K/k$. Finally, we study the $p$-rank of class groups of cyclic $p$-extensions of ${{\mathbb{Q}}}$ and the $2$-rank of class groups of multiquadratic extensions of ${{\mathbb{Q}}}$, for a fixed ramification type.
Medical Informatics Operating Room Vitals and Events Repository (MOVER): a public-access operating room database
Authors: Samad Muntaha , Angel Mirana , Rinehart Joseph , Kanomata Yuzo , Baldi Pierre , Cannesson Maxime 
Published: October 2023

Abstract

Objectives
Artificial intelligence (AI) holds great promise for transforming the healthcare industry. However, despite its potential, AI is yet to see widespread deployment in clinical settings in significant part due to the lack of publicly available clinical data and the lack of transparency in the published AI algorithms. There are few clinical data repositories publicly accessible to researchers to train and test AI algorithms, and even fewer that contain specialized data from the perioperative setting. To address this gap, we present and release the Medical Informatics Operating Room Vitals and Events Repository (MOVER).

Materials and Methods
This first release of MOVER includes adult patients who underwent surgery at the University of California, Irvine Medical Center from 2015 to 2022. Data for patients who underwent surgery were captured from 2 different sources: High-fidelity physiological waveforms from all of the operating rooms were captured in real time and matched with electronic medical record data.

Results
MOVER includes data from 58 799 unique patients and 83 468 surgeries. MOVER is available for download at https://doi.org/10.24432/C5VS5G, it can be downloaded by anyone who signs a data usage agreement (DUA), to restrict traffic to legitimate researchers.

Discussion
To the best of our knowledge MOVER is the only freely available public data repository that contains electronic health record and high-fidelity physiological waveforms data for patients undergoing surgery.

Conclusion
MOVER is freely available to all researchers who sign a DUA, and we hope that it will accelerate the integration of AI into healthcare settings, ultimately leading to improved patient outcomes.
Hypermedia-based software architecture enables Test-Driven Development
Authors: Post Andrew R , Ho Nancy , Rasmussen Erik , Post Ivan , Cho Aika , Hofer John , Maness Arthur T , Parnell Timothy , Nix David A 
Published: October 2023

Abstract

Objectives
Using agile software development practices, develop and evaluate an architecture and implementation for reliable and user-friendly self-service management of bioinformatic data stored in the cloud.

Materials and methods
Comprehensive Oncology Research Environment (CORE) Browser is a new open-source web application for cancer researchers to manage sequencing data organized in a flexible format in Amazon Simple Storage Service (S3) buckets. It has a microservices- and hypermedia-based architecture, which we integrated with Test-Driven Development (TDD), the iterative writing of computable specifications for how software should work prior to development. Relying on repeating patterns found in hypermedia-based architectures, we hypothesized that hypermedia would permit developing test “templates” that can be parameterized and executed for each microservice, maximizing code coverage while minimizing effort.

Results
After one-and-a-half years of development, the CORE Browser backend had 121 test templates and 875 custom tests that were parameterized and executed 3031 times, providing 78% code coverage.

Discussion
Architecting to permit test reuse through a hypermedia approach was a key success factor for our testing efforts. CORE Browser’s application of hypermedia and TDD illustrates one way to integrate software engineering methods into data-intensive networked applications. Separating bioinformatic data management from analysis distinguishes this platform from others in bioinformatics and may provide stable data management while permitting analysis methods to advance more rapidly.

Conclusion
Software engineering practices are underutilized in informatics. Similar informatics projects will more likely succeed through application of good architecture and automated testing. Our approach is broadly applicable to data management tools involving cloud data storage.
Postoperative weight-bearing restrictions and rehabilitation protocols after hip arthroscopy for femoroacetabular impingement: a systematic review
Authors: Hemstock Riley , Mulhall Drew , Didyk Janine , Ogborn Dan , Lemmex Devin 
Published: October 2023

ABSTRACT
Despite recent increased interest in hip arthroscopy for the management of femoroacetabular impingement (FAI), there is little evidence to guide weight-bearing recommendations and rehabilitation postoperatively. The primary objective of this study was to determine if sufficient evidence exists to recommend specific weight-bearing restrictions postoperatively. This study was registered with PROSPERO (CRD42021247741). PubMed, MEDLINE and Embase were searched on 3 March 2023 for Level I–IV studies including patients over the age of 18 years, with a minimum 1-year follow-up and reporting of a weight-bearing status, a patient-reported outcome measure (PROM) and a clinical outcome. Meta-analysis was precluded due to heterogeneity in the included studies, and a descriptive analysis was undertaken. Methodological quality and risk of bias were assessed with the methodological index for non-randomized studies (MINORS). Twenty-four studies including 2231 patients who underwent hip arthroscopy for treatment of FAI were included (follow-up interval 33.2 ± 24.7 months). Most articles (62.5%) were case series. There were seven terms describing weight-bearing recommendations, with 83% being some variation of ‘partial weight-bearing’. Eight PROMs were reported, with 83% using the modified Harris Hip Score and 87.5% of studies reporting reoperation rates. Only 75% of studies reported rehabilitation protocols. The average MINORS score was 11.07 ± 1.10 out of 16 for non-comparative studies and 18.22 ± 1.48 out of 24 for comparative studies. The reporting of weight-bearing status, clinical outcomes, PROMs and rehabilitation parameters remains poor. At present, sufficient comparative evidence does not exist to make specific weight-bearing recommendation postoperatively.
Completion pneumonectomy via sternotomy and complete intrathoracic liver migration in metastatic osteosarcoma
Authors: Chang Shantel , Kirk Frazer , Fuller Robert , Provenzano Sylvio 
Published: October 2023

Abstract
Pulmonary metastasectomy is the well-accepted surgical management for recurrent osteosarcoma in the lung. A pneumonectomy is seldom performed, even more so via a sternotomy. We report an unusual case of a pneumonectomy via median sternotomy for a pulmonary metastasis with complete migration of the liver into the intrathoracic space, a complication rarely observed. The patient remains disease-free on follow-up, 21 years following the initial diagnosis. Aggressive approaches for metastasectomy, despite clinician hesitation in the age of minimally invasive surgery, can yield excellent outcomes for a cancer with otherwise poor prognosis.
Berber Influence on Arabic Form IX in North Africa
Authors: Souag Lameen 
Published: October 2023

Abstract
Arabic dialects west of Libya stand out within Arabic and Semitic languages more generally for using a fairly productive verb pattern FʕāL for change-of-state quality verbs, since before the 12th century. This has long been identified with Classical Arabic’s Form IX (iFʕaLLa) or XI (iFʕāLLa), but does not regularly correspond to either, and shows a rather different lexical distribution. This article proposes a new explanation for its unexpected form, greater productivity, and uniquely Western distribution, based on contact with Berber. Across most Berber varieties, a verb pattern whose perfective stem may be reconstructed as *ăFSāL &gt; *əFSāL is regularly used for change-of-state verbs. The originally accidental similarity in form and function would have allowed first-language Berber speakers learning Arabic in the Umayyad period to identify this with Arabic Form IX/XI, and therefore to extend its use to their Arabic.
Nucleoporin 50 proteins affect longevity and salinity stress tolerance in seeds
Authors: Oishi Ayumi , Nakagawa Shitomi , Tamura Kentaro 
Published: October 2023

Abstract
Nucleoporin 50 (Nup50) is an evolutionarily conserved protein that is a constituent of the nuclear pore complex (NPC); however, its physiological role in plants is unclear. Arabidopsis has two Nup50 proteins, Nup50a and Nup50b, which are highly expressed in developing seeds. Green fluoresceent protein (GFP)-fused Nup50a and Nup50b are localized exclusively in the nucleopolasm, implying an additional function beyond the NPC in the nuclear envelope. To investigate the function of Nup50s, we employed the CRISPR/Cas9 [clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9] system to generate a nup50a nup50b double mutant, which exhibited premature translation termination of both Nup50 proteins. While the mutant showed no significant abnormal phenotype during vegetative growth, the nup50a nup50b seeds had an abnormal shape compared with the wild type. Comparative transcriptomics using immature seeds revealed that Nup50s regulate the expression of various genes, including cell wall-related genes. The nup50a nup50b seeds exhibited reduced seed longevity and salinity stress tolerance. Tetrazolium uptake and mucilage release assays implied that the nup50a nup50b seeds had greater water permeability than the wild type. Taken together, our results imply that Nup50s play a critical role in seed formation by regulating gene expression.
PubHubs identity management
Authors: Jacobs Bart , Westerbaana Bram , Javed Omar , van Stekelenburg Harm , Vervoort Lian , den Besten Jan 
Published: October 2023

Abstract
Finding a combination between privacy and accountability in the online world is a challenge. Too little accountability supports problematic behaviour. Too little privacy undermines individual freedom and has a chilling effect. This paper describes the identity infrastructure of a new open source community platform called PubHubs. It combines local group conversations, via its own adaptation of Matrix, with proportional authentication of users, in local identity spaces. PubHubs thus achieves a combination of privacy and accountability. The technical core of the paper describes the cryptographic protocols for managing digital identities, via both personal attributes and local pseudonyms. Around this core, the roles of digital identities within the PubHubs platform are explained in functional terms, giving participants for instance more certainty about others in a conversation, or giving moderators new tools.
The composition and thermal properties of a cool core lacking a brightest cluster galaxy
Authors: Su Yuanyuan , Combes Francoise , Olivares Valeria , Castignani Gianluca , Torne Pablo , van Weeren Reinout 
Published: October 2023

ABSTRACT
We present a multiwavelength observation of a cool core that does not appear to be associated with any galaxy, in a nearby cluster, Abell 1142. Its X-ray surface brightness peak of ≲2 keV is cooler than the ambient intracluster gas of ≳3 keV, and is offset from its brightest cluster galaxy (BCG) by 80 kpc in projection, representing the largest known cool core – BCG separation. This BCG-less cool core allows us to measure the metallicity of a cluster centre with a much-reduced contribution from the interstellar medium (ISM) of the BCG. XMM–Newton observation reveals a prominent Fe abundance peak of $1.07^{+0.16}_{-0.15}$ Z⊙ and an α/Fe abundance ratio close to the solar ratio, fully consistent with those found at the centres of typical cool core clusters. This finding hints that BCGs play a limited role in enriching the cluster centres. However, the discussion remains open, given that the α/Fe abundance ratios of the orphan cool core and the BCG ISM are not significantly different. Abell 1142 may have experienced a major merger more than 100 Myr ago, which has dissociated its cool core from the BCG. This implies that the Fe abundance peak in cool core clusters can be resilient to cluster mergers. Our recent Institut de Radio Astronomie Millimétrique 30-m observation did not detect any CO emission at its X-ray peak and we find no evidence for massive runaway cooling in the absence of recent active galactic nucleus feedback. The lack of a galaxy may contribute to an inefficient conversion of the ionized warm gas to the cold molecular gas.
Thallium hyperaccumulation status of the violets of the Allchar arsenic–thallium deposit (North Macedonia) confirmed through synchrotron µXRF imaging
Authors: Jakovljević Ksenija , Mišljenović Tomica , Bačeva Andonovska Katerina , Echevarria Guillaume , Baker Alan J M , Brueckner Dennis , van der Ent Antony 
Published: October 2023

Abstract
The abandoned Allchar Mine in the Republic of North Macedonia is a globally unique deposit with the highest known grades of thallium (Tl) and arsenic (As) mineralization. We aimed to determine the distribution of As and Tl in whole dehydrated shoots of the three Viola taxa using synchrotron micro-X-ray fluorescence analysis. Additionally, soil and plant organ samples were collected from all three Viola taxa at the Allchar site and analysed using inductively coupled plasma–atomic emission spectrometry. Concentrations of Tl were extremely high in all three Viola taxa (up to 58 900 mg kg−1), but concentrations of As were highly variable with V. tricolor subsp. macedonica and V. allchariensis having low As (up to 20.2 and 26.3 mg kg−1, respectively) and V. arsenica having the highest concentrations (up to 381 mg kg−1). The extremely high Tl in all three species is endogenous and not a result of contamination. Arsenic in V. tricolor subsp. macedonica and V. allcharensis is strongly affected by contamination, but not in V. arsenica where it appears to be endogenous. The pattern of As enrichment in V. arsenica is very unusual and coincides with Ca-oxalate deposits and Br hotspots. The results of this study could form the basis for more detailed investigations under controlled conditions, including plant dosing experiments.
Mis-regulation of Zn and Mn homeostasis is a key phenotype of Cu stress in Streptococcus pyogenes
Authors: Hong YoungJin , Mackenzie Eilidh S , Firth Samantha J , Bolton Jack R F , Stewart Louisa J , Waldron Kevin J , Djoko Karrera Y 
Published: October 2023

Abstract
All bacteria possess homeostastic mechanisms that control the availability of micronutrient metals within the cell. Cross-talks between different metal homeostasis pathways within the same bacterial organism have been reported widely. In addition, there have been previous suggestions that some metal uptake transporters can promote adventitious uptake of the wrong metal. This work describes the cross-talk between Cu and the Zn and Mn homeostasis pathways in Group A Streptococcus (GAS). Using a ∆copA mutant strain that lacks the primary Cu efflux pump and thus traps excess Cu in the cytoplasm, we show that growth in the presence of supplemental Cu promotes downregulation of genes that contribute to Zn or Mn uptake. This effect is not associated with changes in cellular Zn or Mn levels. Co-supplementation of the culture medium with Zn or, to a lesser extent, Mn alleviates key Cu stress phenotypes, namely bacterial growth and secretion of the fermentation end-product lactate. However, neither co-supplemental Zn nor Mn influences cellular Cu levels or Cu availability in Cu-stressed cells. In addition, we provide evidence that the Zn or Mn uptake transporters in GAS do not promote Cu uptake. Together, the results from this study strengthen and extend our previous proposal that mis-regulation of Zn and Mn homeostasis is a key phenotype of Cu stress in GAS.
Design of a sorbitol-activated nitrogen metabolism-dependent regulatory system for redirection of carbon metabolism flow in Bacillus licheniformis
Authors: He Hehe , Li Youran , Ma Xufan , Xu Sha , Zhang Liang , Ding Zhongyang , Shi Guiyang 
Published: October 2023

Abstract
Synthetic regulation of metabolic fluxes has emerged as a common strategy to improve the performance of microbial cell factories. The present regulatory toolboxes predominantly rely on the control and manipulation of carbon pathways. Nitrogen is an essential nutrient that plays a vital role in growth and metabolism. However, the availability of broadly applicable tools based on nitrogen pathways for metabolic regulation remains limited. In this work, we present a novel regulatory system that harnesses signals associated with nitrogen metabolism to redirect excess carbon flux in Bacillus licheniformis. By engineering the native transcription factor GlnR and incorporating a sorbitol-responsive element, we achieved a remarkable 99% inhibition of the expression of the green fluorescent protein reporter gene. Leveraging this system, we identified the optimal redirection point for the overflow carbon flux, resulting in a substantial 79.5% reduction in acetoin accumulation and a 2.6-fold increase in acetate production. This work highlight the significance of nitrogen metabolism in synthetic biology and its valuable contribution to metabolic engineering. Furthermore, our work paves the way for multidimensional metabolic regulation in future synthetic biology endeavors.