bluuebunny/crossref_metadata_2025_split huggingface dataset:
REDCap and the National Mesothelioma Virtual Bank—a scalable and sustainable model for rare disease biorepositories
Authors: Rashid Rumana , Copelli Susan , Silverstein Jonathan C , Becich Michael J 
Published: July 2023

Abstract

Objective
Rare disease research requires data sharing networks to power translational studies. We describe novel use of Research Electronic Data Capture (REDCap), a web application for managing clinical data, by the National Mesothelioma Virtual Bank, a federated biospecimen, and data sharing network.

Materials and Methods
National Mesothelioma Virtual Bank (NMVB) uses REDCap to integrate honest broker activities, enabling biospecimen and associated clinical data provisioning to investigators. A Web Portal Query tool was developed to source and visualize REDCap data in interactive, faceted search, enabling cohort discovery by public users. An AWS Lambda function behind an API calculates the counts visually presented, while protecting record level data. The user-friendly interface, quick responsiveness, automatic generation from REDCap, and flexibility to new data, was engineered to sustain the NMVB research community.

Results
NMVB implementations enabled a network of 8 research institutions with over 2000 mesothelioma cases, including clinical annotations and biospecimens, and public users’ cohort discovery and summary statistics. NMVB usage and impact is demonstrated by high website visits (&gt;150 unique queries per month), resource use requests (&gt;50 letter of interests), and citations (&gt;900) to papers published using NMVB resources.

Discussion
NMVB’s REDCap implementation and query tool is a framework for implementing federated and integrated rare disease biobanks and registries. Advantages of this framework include being low-cost, modular, scalable, and efficient. Future advances to NVMB’s implementations will include incorporation of -omics data and development of downstream analysis tools to advance mesothelioma and rare disease research.

Conclusion
NVMB presents a framework for integrating biobanks and patient registries to enable translational research for rare diseases.
Super-resolution fusion optimization for poultry detection: a multi-object chicken detection method
Authors: Wu Zhenlong , Zhang Tiemin , Fang Cheng , Yang Jikang , Ma Chuang , Zheng Haikun , Zhao Hongzhi 
Published: July 2023

Abstract
Accurate poultry detection is crucial for studying poultry behavior using computer vision and video surveillance. However, in free-range farming environments, detecting chickens can often be challenging due to their small size and mutual occlusion. The current detection algorithms exhibit a low level of accuracy, with a high probability of false and missed detections. To address this, we proposed a multi-object chicken detection method named Super-resolution Chicken Detection, which utilizes super-resolution fusion optimization. The algorithm employs the residual–residual dense block to extract image features and used a generative adversarial network to compensate for the loss of details during deep convolution, producing high-resolution images for detection. The proposed algorithm was validated with the B1 data set and the MC1 multi-object data set, demonstrating that the reconstructed images possessed richer pixel features compared to original images, specifically it improved detection accuracy and reduced the number of missed detections. The structural similarity of the reconstructed images was 99.9%, and the peak signal-to-noise ratio was above 30. The algorithm improved the Average Precision50:95 of all You Only Look Once Version X (YOLOX) models, with the largest improvement for the B1 data set with YOLOX-Large (+6.3%) and for the MC1 data set with YOLOX-Small (+4.1%). This was the first time a super-resolution reconstruction technique was applied to multi-object poultry detection. Our method will provide a fresh approach for future poultry researchers to improve the accuracy of object detection using computer vision and video surveillance.
‘Enraged, But Only Out of Love’: Sītā’s Disagreement With Rāma in the Ayodhyākāṇḍa of the Vālmīki-Rāmāyaṇa
Authors: Saxena Shishir 
Published: July 2023

Abstract:
In a moment of great turmoil in the Vālmīki-Rāmāyaṇa (VRām.), Rāma—upon learning of his fourteen-year banishment—attempts to persuade Sītā to stay on in the palace while he will alone proceed into exile. Sītā disagrees entirely with Rāma and argues variously that she should accompany him—until, of course, she succeeds in the end. This is the first moment in the epic when one hears Sītā speak and a careful analysis of her portrayal here is paramount for any serious understanding of her character. Moreover, this episode—of Rāma’s refusal and Sītā’s insistence—when studied closely brings to light various foundational characteristics of their extraordinary relationship. Nevertheless, there are only a handful of studies that have closely engaged with the text’s account of the episode. These few studies also attribute contradictory characteristics to the two protagonists and present entirely contrasting accounts of the situation. I attempt in this paper to demonstrate that an apposite understanding can be attained through a literary analysis of the verses, focusing on the motivating emotions mentioned plainly in the text itself. I argue that Sītā’s disagreement is not grounded in emotional frailty, male honour, or even political fear. Rather, the essential sentiment which permeates this entire episode, including Rāma’s final acceding to Sītā’s request, is—for the VRām.—love.
The right to regulate and the interpretation of the WTO Agreement
Authors: Mitchell Andrew D 
Published: July 2023

ABSTRACT
In contrast to international investment tribunals, World Trade Organization (WTO) adjudicators have been reluctant to acknowledge the inherent right to regulate under international law explicitly. Policy-based considerations arising from such a right have not been viewed as a standalone component under interpretive analyses in WTO dispute settlement. Instead, they have been integrated only to the extent they find expression in the treaty. This article explores how, on occasion, WTO adjudicators have departed from this orthodox approach by choosing to proactively interpret the WTO Covered Agreements in a way that presupposes a States’ right to regulate, even where this may seem contrary to, or unsupported by, the treaty text. In these cases, the question has not been whether such a right subsists within substantive WTO disciplines, but rather how such a right can be read into these disciplines in a manner that comports with the ordinary rules of treaty interpretation. While this unorthodox approach has resulted in interpretations that appear unclear and uncertain, these outcomes are ultimately explicable in terms of a general principle of regulatory autonomy that can form the basis for more principled interpretive choices.
Protecting vulnerable patient populations from climate hazards: the role of the nation’s cancer centers
Authors: Espinel Zelde , Shultz James M , Aubry Vanina Pavia , Abraham Omar Muñoz , Fan Qinjin , Crane Tracy E , Sahar Liora , Nogueira Leticia M 
Published: July 2023

Abstract
Individuals diagnosed with cancer are a vulnerable population during disasters. Emergency preparedness efforts are crucial for meeting the health and safety needs of patients, health-care professionals, health-care facilities, and communities before, during, and after a disaster. Recognizing the importance of advancing emergency preparedness expertise to cancer control efforts nationwide, especially in the era of climate change, we searched National Cancer Institute–designated cancer centers’ websites to examine emergency preparedness information sharing and evidence of research efforts focused on disaster preparedness. Of 71 centers, 56 (78.9%) presented some emergency preparedness information, and 36 (50.7%) presented information specific to individuals diagnosed with cancer. Only 17 (23.9%) centers provided emergency preparedness information for climate-driven disasters. Informed by these data, this commentary describes an opportunity for cancer centers to lead knowledge advancement on an important aspect of climate change adaptation: disaster preparedness.
Low-ionization structures in planetary nebulae – III. The statistical analysis of physico-chemical parameters and excitation mechanisms
Authors: Mari M Belén , Akras Stavros , Gonçalves Denise R 
Published: July 2023

ABSTRACTNearly 30 yr after the first detailed studies of low-ionization structures (LISs) in planetary nebulae (PNe), we perform a statistical analysis of their physical, chemical, and excitation properties, by collecting published data in the literature. The analysis was made through the contrast between LISs and high-ionization structures – rims or shells – for a large sample of PNe, in order to highlight significant differences between these structures. Our motivation was to find robust results based on the largest sample of LISs gathered so far. (i) Indeed, LISs have lower electron densities (Ne[S ii]) than the rims/shells. (ii) The nitrogen electron temperatures (Te[N ii]) are similar between the two groups, while a bimodal distribution is observed for the Te based on [O iii] of the rims/shells, although the high- and low-ionization structures have Te[O iii] of similar median values. (iii) No significant variations are observed in total abundances of He, N, O, Ne, Ar, Cl, and S between the two groups. (iv) Through the analysis of several diagnostic diagrams, LISs are separated from rims/shells in terms of excitation. From two large grids of photoionization and shock models, we show that there is an important overlap between both mechanisms, particularly when low-ionization line ratios are concerned. We found a good tracer of high-velocity shocks, as well as an indicator of high- and low-velocity shocks that depends on temperature-sensitive line ratios. In conclusion, both excitation mechanisms could be present; however, shocks cannot be the main source of excitation for most of the LISs of PNe.
Reconciling the magnetic field in central disc galaxies with the dynamical mass using the cosmological simulations
Authors: Hosseinirad Mohammad , Tabatabaei Fatemeh , Raouf Mojtaba , Roshan Mahmood 
Published: July 2023

ABSTRACT
The Universe is pervaded by magnetic fields in different scales, although for simplicity, they are ignored in most cosmological simulations. In this paper, we use the TNG50, which is a large cosmological galaxy formation simulation that incorporates magnetic fields with an unprecedented resolution. We study the correlation of the magnetic field with various galaxy properties such as the total, stellar, and gaseous mass, circular velocity, size, and star formation rate. We find a linear correlation between the average magnetic field pervading the disc of galaxies in relative isolation and their circular velocities. In addition, we observed that in this sample the average magnetic field in the disc is correlated with the total mass as $\overline{B}\sim M_{\mathrm{tot, R_{\star }}}^{0.2}$. We also find that the massive galaxies with active wind-driven black hole feedback, do not follow this trend, as their magnetic field is substantially affected by this feedback mode in the TNG50 simulation. We show that the correlation of the magnetic field with the star formation rate is a little weaker than the circular velocity. Moreover, we compare the magnetic field components of the above sample with a compiled observational sample of non-cluster non-interacting nearby galaxies. Similar to the observation, we find a coupling between the ordered magnetic field and the circular velocity of the flat part of the rotation curve in the simulation, although contrary to the observation, the ordered component is dominant in the simulation.
Genetically encoded RNA-based sensors with Pepper fluorogenic aptamer
Authors: Chen Zhenyin , Chen Wei , Reheman Zhayila , Jiang Haodong , Wu Jiahui , Li Xing 
Published: July 2023

Abstract
Sensors to measure the abundance and signaling of intracellular molecules are crucial for understanding their physiological functions. Although conventional fluorescent protein-based sensors have been designed, RNA-based sensors are promising imaging tools. Numerous RNA-based sensors have been developed. These sensors typically contain RNA G-quadruplex (RG4) motifs and thus may be suboptimal in living cells. Here we describe RNA-based sensors based on Pepper, a fluorogenic RNA without an RG4 motif. With Pepper, we engineered various sensors for metabolites, synthetic compounds, proteins and metal ions in vitro and in living cells. In addition, these sensors show high activation and selectivity, demonstrating their universality and robustness. In the case of sensors responding to S-adenosylmethionine (SAM), a metabolite produced by methionine adenosyltransferase (MATase), we showed that our sensors exhibited positively correlated fluorescence responding to different SAM levels. Importantly, we revealed the SAM biosynthesis pathway and monitored MATase activity and gene expression spatiotemporally in living individual human cells. Additionally, we constructed a ratiometric SAM sensor to determine the inhibition efficacy of a MATase inhibitor in living cells. Together, these sensors comprising Pepper provide a useful platform for imaging diverse cellular targets and their signaling pathway.
Recovery of protein synthesis to assay DNA repair activity in transcribed genes in living cells and tissues
Authors: van der Woude Melanie , Davó-Martínez Carlota , Thijssen Karen L , Vermeulen Wim , Lans Hannes 
Published: July 2023

Abstract
Transcription-coupled nucleotide excision repair (TC-NER) is an important DNA repair mechanism that protects against the negative effects of transcription-blocking DNA lesions. Hereditary TC-NER deficiencies cause pleiotropic and often severe neurodegenerative and progeroid symptoms. While multiple assays have been developed to determine TC-NER activity for clinical and research purposes, monitoring TC-NER is hampered by the low frequency of repair events occurring in transcribed DNA. ’Recovery of RNA Synthesis’ is widely used as indirect TC-NER assay based on the notion that lesion-blocked transcription only resumes after successful TC-NER. Here, we show that measuring novel synthesis of a protein after its compound-induced degradation prior to DNA damage induction is an equally effective but more versatile manner to indirectly monitor DNA repair activity in transcribed genes. This ‘Recovery of Protein Synthesis’ (RPS) assay can be adapted to various degradable proteins and readouts, including imaging and immunoblotting. Moreover, RPS allows real-time monitoring of TC-NER activity in various living cells types and even in differentiated tissues of living organisms. To illustrate its utility, we show that DNA repair in transcribed genes declines in aging muscle tissue of C. elegans. Therefore, the RPS assay constitutes an important novel clinical and research tool to investigate transcription-coupled DNA repair.
A Small Compound, HYGIC, Promotes Hypocotyl Growth Through Ectopic Ethylene Response
Authors: Murao Mizuki , Kato Rika , Kusano Shuhei , Hisamatsu Rina , Endo Hitoshi , Kawabata Yasuki , Kimura Seisuke , Sato Ayato , Mori Hitoshi , Itami Kenichiro , Torii Keiko U , Hagihara Shinya , Uchida Naoyuki 
Published: July 2023

Abstract
Plant seedlings adjust the growth of the hypocotyl in response to surrounding environmental changes. Genetic studies have revealed key players and pathways in hypocotyl growth, such as phytohormones and light signaling. However, because of genetic redundancy in the genome, it is expected that not-yet-revealed mechanisms can be elucidated through approaches different from genetic ones. Here, we identified a small compound, HYGIC (HG), that simultaneously induces hypocotyl elongation and thickening, accompanied by increased nuclear size and enlargement of cortex cells. HG-induced hypocotyl growth required the ethylene signaling pathway activated by endogenous ethylene, involving CONSTITUTIVE PHOTOMORPHOGENIC 1, ETHYLENE INSENSITIVE 2 (EIN2) and redundant transcription factors for ethylene responses, ETHYLENE INSENSITIVE 3 (EIN3) and EIN3 LIKE 1. By using EBS:GUS, a transcriptional reporter of ethylene responses based on an EIN3-binding-cis-element, we found that HG treatment ectopically activates ethylene responses at the epidermis and cortex of the hypocotyl. RNA-seq and subsequent gene ontology analysis revealed that a significant number of HG-induced genes are related to responses to hypoxia. Indeed, submergence, a representative environment where the hypoxia response is induced in nature, promoted ethylene-signaling-dependent hypocotyl elongation and thickening accompanied by ethylene responses at the epidermis and cortex, which resembled the HG treatment. Collectively, the identification and analysis of HG revealed that ectopic responsiveness to ethylene promotes hypocotyl growth, and this mechanism is activated under submergence.
Putative NAD(P)-Binding Rossmann Fold Protein Is Involved in Chitosan-Induced Peroxidase Activity and Lipoxygenase Expression in Physcomitrium patens
Authors: Marttinen Eeva M. , Decker Eva L. , Heinonen Petra , Reski Ralf , Valkonen Jari P. T. 
Published: July 2023

Oxidative burst, the rapid production of high levels of reactive oxygen species in response to external stimuli, is an early defense reaction against pathogens. The fungal elicitor chitosan causes an oxidative burst in the moss Physcomitrium patens (formerly Physcomitrella patens), mainly due to the peroxidase enzyme Prx34. To better understand the chitosan responses in P. patens, we conducted a screen of part of a P. patens mutant collection to isolate plants with less peroxidase activity than wild-type (WT) plants after chitosan treatment. We isolated a P. patens mutant that affected the gene encoding NAD(P)-binding Rossmann fold protein (hereafter, Rossmann fold protein). Three Rossmann fold protein-knockout (KO) plants (named Rossmann fold KO lines) were generated and used to assess extracellular peroxidase activity and expression of defense-responsive genes, including alternative oxidase, lipoxygenase (LOX), NADPH oxidase, and peroxidase (Prx34) in response to chitosan treatment. Extracellular (apoplastic) peroxidase activity was significantly lower in Rossmann fold KO lines than in WT plants after chitosan treatments. Expression of the LOX gene in Rossmann fold KO plants was significantly lower before and after chitosan treatment when compared with WT. Peroxidase activity assays together with gene expression analyses suggest that the Rossmann fold protein might be an important component of the signaling pathway leading to oxidative burst and basal expression of the LOX gene in P. patens. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Fungal Microbiome Indicators Are Associated with Genotypic Variation in Pea Root Rot Susceptibility when Intercropped with Barley
Authors: Cadot Selma , Hohmann Pierre , Hsung Ming-Hui , Hartmann Martin , Haug Benedikt , Wille Lukas , Messmer Monika M. , Bodenhausen Natacha 
Published: July 2023

Intercropping of legume and cereal crop species shows potential to reduce root disease pressures by changing root-associated microbiomes and improving nitrogen (N) use via soil N-dependent fixation of atmospheric N2by symbiotic rhizobia. A two-year field study was conducted to evaluate the effect of pea–barley association on crop performance and on the root fungal community. Five pea cultivars (Alvesta, Karpate, Mytic, Respect, and Vitra) were grown either in pure stands or mixed with one variety of barley (Atrika). We measured crop grain yield and root rot incidence and analyzed root fungal communities. In mixed stands, total grain yield was more stable compared with that in each pure stand, but pea root disease incidence was higher except for cultivars Vitra and Karpate. The effect of cropping system on fungal alpha diversity depended on the cultivar, with Vitra showing higher Shannon diversity and Alvesta showing lower richness in mixed compared with pure stands. All four operational taxonomic units (OTUs) belonging to the Didymellaceae family were positively associated with pea root rot, and another disease-associated OTU in pea, Neoascochyta exitialis, was found to be also part of the barley core microbiome. Eleven of twelve OTUs belonging to the Glomeraceae family were associated with healthy roots and abundant in cultivar Vitra. This study shows how the phenotype and fungal microbiome of different pea cultivars respond distinctly to intercropping. Furthermore, the identification of disease- and health-associated taxa in the pea root fungal community refines the characterization of different cultivar candidates for intercropping.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
Evidence that an Unnamed Isometric Virus Associated with Potato Rugose Disease in Peru Is a New Species of Genus Torradovirus
Authors: Alvarez-Quinto Robert , Amao Melody , Muller Giovanna , Fuentes Segundo , Grinstead Samuel , Fuentes-Bueno Irazema , Roenhorst Annelien , Westenberg Marcel , Botermans Marleen , Kreuze Jan , Mollov Dimitre 
Published: July 2023

A previously uncharacterized torradovirus species infecting potatoes was detected by high-throughput sequencing from field samples from Peru and in customs intercepts in potato tubers that originated from South America in the United States of America and the Netherlands. This new potato torradovirus showed high nucleotide sequence identity to an unidentified isometric virus (SB26/29), which was associated with a disease named potato rugose stunting in southern Peru characterized over two decades ago. Thus, this virus is tentatively named potato rugose stunting virus (PotRSV). The genome of PotRSV isolates sequenced in this study were composed of two polyadenylated RNA segments. RNA1 ranges from 7,086 to 7,089 nt and RNA2 from 5,228 to 5,230 nt. RNA1 encodes a polyprotein containing the replication block (helicase-protease-polymerase), whereas RNA2 encodes a polyprotein cleaved into a movement protein and the three capsid proteins (CPs). Pairwise comparison among PotRSV isolates revealed amino acid identity values greater than 86% in the protease-polymerase (Pro-Pol) region and greater than 82% for the combined CPs. The closest torradovirus species, squash chlorotic leaf spot virus, shares amino acid identities of ∼58 and ∼41% in the Pro-Pol and the combined CPs, respectively. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .