bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR/Cas9 and Agrobacterium tumefaciens virulence proteins synergistically increase efficiency of precise genome editing via homology directed repair in plants
Authors: Tang Ye , Zhang Zhennan , Yang Zhiyuan , Wu Jiahe 
Published: March 2023

Abstract
CRISPR/Cas9 genome editing and Agrobacterium tumefaciens-mediated genetic transformation are widely-used plant biotechnology tools derived from bacterial immunity-related systems, each involving DNA modification. The Cas9 endonuclease introduces DNA double-strand breaks (DSBs), and the A. tumefaciens T-DNA is released by the VirD2 endonuclease assisted by VirDl and attached by VirE2, transferred to the plant nucleus and integrated into the genome. Here, we explored the potential for synergy between the two systems and found that Cas9 and three virulence (Vir) proteins achieve precise genome editing via the homology directed repair (HDR) pathway in tobacco and rice plants. Compared with Cas9T (Cas9, VirD1, VirE2) and CvD (Cas9-VirD2) systems, the HDR frequencies of a foreign GFPm gene in the CvDT system (Cas9-VirD2, VirD1, VirE2) increased 52-fold and 22-fold, respectively. Further optimization of the CvDT process with a donor linker (CvDTL) achieved a remarkable increase in the efficiency of HDR-mediated genome editing. Additionally, the HDR efficiency of the three rice endogenous genes ACETOLACTATE SYNTHASE (ALS), PHYTOENE DESATURASE (PDS), and NITROGEN TRANSPORTER 1.1 B (NRT1.1B) increased 24-, 32- and 16-fold, respectively, in the CvDTL system, compared with corresponding Cas9TL (Cas9T process with a donor linker). Our results suggest that collaboration between CRISPR/Cas9 and Agrobacterium-mediated genetic transformation can make great progress towards highly efficient and precise genome editing via the HDR pathway.
Intellectual property protection for traditional medical knowledge in China’s context: a round peg in a square hole?
Authors: Xia Nan 
Published: March 2023

Abstract
This article is an examination of the extent to which traditional medical knowledge in China can be protected by intellectual property laws. The analysis begins by providing a global picture with regard to the historic origin of intellectual property, exploring the reasons why China does not have indigenous counterparts to the western system of intellectual property rights protecting its traditional knowledge (including traditional medical knowledge) and stating the problems of transplanting western intellectual property standards in China. A discussion follows on how China, under foreign pressure, has made efforts to comply with the changing standards mandated by various international, regional, and bilateral arrangements related to intellectual property, with examples of the development of China’s patent law. China’s approach towards the protection of traditional medical knowledge in various international fora related to intellectual property is explored. Finally, there is a specific examination of the compatibilities between the western system of intellectual property rights and traditional medical knowledge in China, at the national and community levels. This article argues that the system of intellectual property rights does not easily fit with China’s traditional medical knowledge because of China’s unique cultural traits, distinctive historical context and wide ethnic, religious, and local community diversity.
Study of the radial dependence of Forbush decreases at 0.28–1 au using data from the Helios 1 and 2 spacecraft
Authors: Belov Anatoly , Shlyk Nataly , Abunina Maria , Abunin Artem , Papaioannou Athanasios , Richardson Ian G , Lario David 
Published: March 2023

ABSTRACT
We identify and investigate cosmic ray Forbush decreases (FDs) observed in the E &gt; 50 MeV data from the Helios 1 and 2 spacecraft, spanning from 1974–1985 and covering heliocentric distances in the range 0.28–1 au. A Helios FD catalogue is compiled, including the characteristics of the cosmic ray variations, as well as those of the solar wind (SW) and the interplanetary magnetic field (IMF) of the associated interplanetary disturbances. An extended statistical study considers the radial dependence of the FD magnitude, the SW velocity, and the IMF intensity in these disturbances. It is found that the Helios FD sizes at different distances from the Sun are determined by the parameters of the interplanetary disturbances. In particular, the FD magnitudes observed at Helios, as well as near Earth, correlate well with VB, which is the product of the maximum SW velocity and the IMF intensity when normalized by the average values of these parameters at the radial distance of the observations. However, we found that, on average, the Helios FD sizes are statistically independent of the radial distance in the range of 0.28–1 au.
Testosterone Coordinates Gene Expression Across Different Tissues to Produce Carotenoid-Based Red Ornamentation
Authors: Khalil Sarah , Enbody Erik D , Frankl-Vilches Carolina , Welklin Joseph F , Koch Rebecca E , Toomey Matthew B , Sin Simon Yung Wa , Edwards Scott V , Gahr Manfred , Schwabl Hubert , Webster Michael S , Karubian Jordan 
Published: March 2023

AbstractCarotenoid pigments underlie most of the red, orange, and yellow visual signals used in mate choice in vertebrates. However, many of the underlying processes surrounding the production of carotenoid-based traits remain unclear due to the complex nature of carotenoid uptake, metabolism, and deposition across tissues. Here, we leverage the ability to experimentally induce the production of a carotenoid-based red plumage patch in the red-backed fairywren (Malurus melanocephalus), a songbird in which red plumage is an important male sexual signal. We experimentally elevated testosterone in unornamented males lacking red plumage to induce the production of ornamentation and compared gene expression in both the liver and feather follicles between unornamented control males, testosterone-implanted males, and naturally ornamented males. We show that testosterone upregulates the expression of CYP2J19, a gene known to be involved in ketocarotenoid metabolism, and a putative carotenoid processing gene (ELOVL6) in the liver, and also regulates the expression of putative carotenoid transporter genes in red feather follicles on the back, including ABCG1. In black feathers, carotenoid-related genes are downregulated and melanin genes upregulated, but we find that carotenoids are still present in the feathers. This may be due to the activity of the carotenoid-cleaving enzyme BCO2 in black feathers. Our study provides a first working model of a pathway for carotenoid-based trait production in free-living birds, implicates testosterone as a key regulator of carotenoid-associated gene expression, and suggests hormones may coordinate the many processes that underlie the production of these traits across multiple tissues.
Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation
Authors: Nisler Collin R , Narui Yoshie , Scheib Emily , Choudhary Deepanshu , Bowman Jacob D , Mandayam Bharathi Harsha , Lynch Vincent J , Sotomayor Marcos 
Published: March 2023

AbstractThe sensory epithelium of the inner ear, found in all extant lineages of vertebrates, has been subjected to over 500 million years of evolution, resulting in the complex inner ear of modern vertebrates. Inner-ear adaptations are as diverse as the species in which they are found, and such unique anatomical variations have been well studied. However, the evolutionary details of the molecular machinery that is required for hearing are less well known. Two molecules that are essential for hearing in vertebrates are cadherin-23 and protocadherin-15, proteins whose interaction with one another acts as the focal point of force transmission when converting sound waves into electrical signals that the brain can interpret. This "tip-link" interaction exists in every lineage of vertebrates, but little is known about the structure or mechanical properties of these proteins in most non-mammalian lineages. Here, we use various techniques to characterize the evolution of this protein interaction. Results show how evolutionary sequence changes in this complex affect its biophysical properties both in simulations and experiments, with variations in interaction strength and dynamics among extant vertebrate lineages. Evolutionary simulations also characterize how the biophysical properties of the complex in turn constrain its evolution and provide a possible explanation for the increase in deafness-causing mutants observed in cadherin-23 relative to protocadherin-15. Together, these results suggest a general picture of tip-link evolution in which selection acted to modify the tip-link interface, although subsequent neutral evolution combined with varying degrees of purifying selection drove additional diversification in modern tetrapods.
DNA i-motif formation at neutral pH is driven by kinetic partitioning
Authors: Školáková Petra , Gajarský Martin , Palacký Jan , Šubert Denis , Renčiuk Daniel , Trantírek Lukáš , Mergny Jean-Louis , Vorlíčková Michaela 
Published: March 2023

AbstractCytosine-rich DNA regions can form four-stranded structures based on hemi-protonated C.C+ pairs, called i-motifs (iMs). Using CD, UV absorption, NMR spectroscopy, and DSC calorimetry, we show that model (CnT3)3Cn (Cn) sequences adopt iM under neutral or slightly alkaline conditions for n &gt; 3. However, the iMs are formed with long-lasting kinetics under these conditions and melt with significant hysteresis. Sequences with n &gt; 6 melt in two or more separate steps, indicating the presence of different iM species, the proportion of which is dependent on temperature and incubation time. At ambient temperature, kinetically favored iMs of low stability are formed, most likely consisting of short C.C+ blocks. These species act as kinetic traps and prevent the assembly of thermodynamically favored, fully C.C+ paired iMs. A higher temperature is necessary to unfold the kinetic forms and enable their substitution by a slowly developing thermodynamic structure. This complicated kinetic partitioning process considerably slows down iM folding, making it much slower than the timeframes of biological reactions and, therefore, unlikely to have any biological relevance. Our data suggest kinetically driven iM species as more likely to be biologically relevant than thermodynamically most stable iM forms.
Discovery of natural non-circular permutations in non-coding RNAs
Authors: Eckert Iris , Friedrich Richard , Weinberg Christina E , Weinberg Zasha 
Published: March 2023

AbstractResearch in the last two decades has increasingly demonstrated that RNA has capabilities comparable to those of proteins, for example the ability to form intricate 3D structures necessary for catalysis. Numerous protein domains are known in varied within-domain rearrangements, called permutations, that change the N- to C-terminal order of important amino acids inside the domain, but maintain their 3D locations. In RNAs, by contrast, only simple circular permutations are known, in which 5′ and 3′ portions of the molecule are merely swapped. Here, we computationally find and experimentally validate naturally occurring RNAs exhibiting non-circular permutations of previously established hammerhead ribozyme RNAs. In addition to the rearranged RNAs, a bioinformatics-based search uncovered many other new conserved RNA structures that likely play different biological roles. Our results further demonstrate the structural sophistication of RNA, indicate a need for more nuance in the analysis of pseudoknots, and could be exploited in RNA-based biotechnology applications.
Tissue-specific regulation of gene expression via unproductive splicing
Authors: Mironov Alexei , Petrova Marina , Margasyuk Sergey , Vlasenok Maria , Mironov Andrey A , Skvortsov Dmitry , Pervouchine Dmitri D 
Published: March 2023

Abstract
Eukaryotic gene expression is regulated post-transcriptionally by a mechanism called unproductive splicing, in which mRNA is triggered to degrade by the nonsense-mediated decay (NMD) pathway as a result of regulated alternative splicing (AS). Only a few dozen unproductive splicing events (USEs) are currently documented, and many more remain to be identified. Here, we analyzed RNA-seq experiments from the Genotype-Tissue Expression (GTEx) Consortium to identify USEs, in which an increase in the NMD isoform splicing rate is accompanied by tissue-specific down-regulation of the host gene. To characterize RNA-binding proteins (RBPs) that regulate USEs, we superimposed these results with RBP footprinting data and experiments on the response of the transcriptome to the perturbation of expression of a large panel of RBPs. Concordant tissue-specific changes between the expression of RBP and USE splicing rate revealed a high-confidence regulatory network including 27 tissue-specific USEs with strong evidence of RBP binding. Among them, we found previously unknown PTBP1-controlled events in the DCLK2 and IQGAP1 genes, for which we confirmed the regulatory effect using small interfering RNA (siRNA) knockdown experiments in the A549 cell line. In sum, we present a transcriptomic pipeline that allows the identification of tissue-specific USEs, potentially many more than were reported here using stringent filters.
Insights into translocation mechanism and ribosome evolution from cryo-EM structures of translocation intermediates of Giardia intestinalis
Authors: Majumdar Soneya , Emmerich Andrew , Krakovka Sascha , Mandava Chandra Sekhar , Svärd Staffan G , Sanyal Suparna 
Published: March 2023

Abstract
Giardia intestinalis is a protozoan parasite that causes diarrhea in humans. Using single-particle cryo-electron microscopy, we have determined high-resolution structures of six naturally populated translocation intermediates, from ribosomes isolated directly from actively growing Giardia cells. The highly compact and uniquely GC-rich Giardia ribosomes possess eukaryotic rRNAs and ribosomal proteins, but retain some bacterial features. The translocation intermediates, with naturally bound tRNAs and eukaryotic elongation factor 2 (eEF2), display characteristic ribosomal intersubunit rotation and small subunit’s head swiveling—universal for translocation. In addition, we observe the eukaryote-specific ‘subunit rolling’ dynamics, albeit with limited features. Finally, the eEF2·GDP state features a uniquely positioned ‘leaving phosphate (Pi)’ that proposes hitherto unknown molecular events of Pi and eEF2 release from the ribosome at the final stage of translocation. In summary, our study elucidates the mechanism of translocation in the protists and illustrates evolution of the translation machinery from bacteria to eukaryotes from both the structural and mechanistic perspectives.
Almonertinib Combined with Anlotinib and Temozolomide in a Patient with Recurrent Glioblastoma with EGFR L858R Mutation
Authors: Hou Zhiwei , Wu Huaguo , Luo Ningning , Li Shuo , Zhang Xiang , Dong Shuai , Zhu Dongyuan , Zhang Hui , Tao Rongjie 
Published: March 2023

Abstract
Glioblastoma (GBM) is the most common primary brain tumor, and patients with GBM have a universally poor prognosis. Genomic profiling has detected epidermal growth factor receptor (EGFR) gene alterations in more than half of GBMs. Major genetic events include amplification and mutation of EGFR. Interestingly, we identified an EGFR p.L858R mutation in a patient with recurrent GBM for the first time. Based on the genetic testing results, almonertinib combined with anlotinib and temozolomide was administered and obtained 12 months of progression-free survival after the diagnosis of recurrence as the fourth-line treatment. This is the first report that an EGFR p.L858R mutation was identified in a patient with recurrent GBM. Furthermore, this case report represents the first study applying the third-generation TKI inhibitor almonertinib in the treatment of recurrent GBM. The results of this study indicate that EGFR might be a new marker for the treatment of GBM with almonertinib.
Analysis of companion cell and phloem metabolism using a transcriptome-guided model of Arabidopsis metabolism
Authors: Hunt Hilary , Brueggen Nico , Galle Alexander , Vanderauwera Sandy , Frohberg Claus , Fernie Alisdair R , Sonnewald Uwe , Sweetlove Lee J 
Published: March 2023

AbstractCompanion cells and sieve elements play an essential role in vascular plants, and yet the details of the metabolism that underpins their function remain largely unknown. Here, we construct a tissue-scale flux balance analysis (FBA) model to describe the metabolism of phloem loading in a mature Arabidopsis (Arabidopsis thaliana) leaf. We explore the potential metabolic interactions between mesophyll cells, companion cells, and sieve elements based on the current understanding of the physiology of phloem tissue and through the use of cell type–specific transcriptome data as a weighting in our model. We find that companion cell chloroplasts likely play a very different role to mesophyll chloroplasts. Our model suggests that, rather than carbon capture, the most crucial function of companion cell chloroplasts is to provide photosynthetically generated ATP to the cytosol. Additionally, our model predicts that the metabolites imported into the companion cell are not necessarily the same metabolites that are exported in phloem sap; phloem loading is more efficient if certain amino acids are synthesized in the phloem tissue. Surprisingly, in our model predictions, the proton-pumping pyrophosphatase (H+-PPiase) is a more efficient contributor to the energization of the companion cell plasma membrane than the H+-ATPase.
THE NATIONAL RESEARCH COUNCIL OF CANADA MANGANESE BATH SYSTEM
Authors: Archambault J P 
Published: March 2023

Abstract
The manganese salt bath is considered a primary standard for determining the absolute emission rate of radionuclide neutron sources. The National Research Council of Canada has recently revived its manganese salt bath and a full description of the system is given here. The physical characteristics of the bath, as well as the methods for determining the efficiency of the bath system and the induced activity in the bath, are described. An in-depth analysis of the fraction of neutrons captured in the manganese and the correction factor for neutron losses is also provided. Finally, the results of emission rate measurements of four different sources, complete with an uncertainty budget, are given. The emission rates of three americium-beryllium neutron sources and one californium-252 neutron source were found to agree with the known values, within a standard uncertainty of 1.7%.
Altered Associations Between Motivated Performance and Frontostriatal Functional Connectivity During Reward Anticipation in Schizophrenia
Authors: Smucny Jason , Hanks Timothy D , Lesh Tyler A , O’Reilly Randall C , Carter Cameron S 
Published: March 2023

AbstractBackground and hypothesisThe neuronal mechanisms that underlie deficits in effort cost computation in schizophrenia (SZ) are poorly understood. Given the role of frontostriatal circuits in valence-oriented motivation, we hypothesized that these circuits are either dysfunctional in SZ or do not appropriately predict behavior in SZ when task conditions are difficult and good performance is rewarded.Study designA total of 52 people with recent onset SZ-spectrum disorders and 48 healthy controls (HCs) performed a 3T fMRI task with 2 valence conditions (rewarded vs neutral) and 2 difficulty conditions. Frontostriatal connectivity was extracted during the cue (anticipatory) phase. Individual behavior was fit using a drift-diffusion model, allowing the performance parameter, drift rate (DR), to vary between task conditions. Three models were examined: A group × condition model of DR, a group × condition model of connectivity, and a regression model of connectivity predicting DR depending on group and condition.Study resultsDRs showed the expected positive correlation with accuracy and a negative association with reaction time. The SZ group showed a deficit in DR but did not differ in overall connectivity or show a valence-specific deficit in connectivity. Significant group × valence × difficulty interactions, however, were observed on the relationship between right dorsolateral prefrontal (DLPFC)-striatal connectivity and DR (DLPFC-Caudate: F = 10.92, PFDR = .004; DLPFC-Putamen: F = 5.14, PFDR = .048) driven by more positive relationships between DR and connectivity during cues for the difficult-rewarded condition in HCs compared to SZ.ConclusionsThese findings suggest that frontostriatal connectivity is less predictive of performance in SZ when task difficulty is increased and a reward incentive is applied.
Chest radiograph findings in children with COVID-19—A retrospective analysis from a tertiary care paediatric hospital in South India
Authors: Vendhan Kanimozhi , Kathirrajan Mithra , Kathirvelu Gopinathan , S Balasubramanian 
Published: March 2023

AbstractObjectiveThe primary aim of this study is to document the chest X-ray findings in children with COVID-19 pneumonia. The secondary aim is to correlate chest X-ray findings to patient outcome.MethodsWe performed a retrospective analysis of children (0–18 years) with SARS-CoV-2 admitted to our hospital from June 2020 to December 2021. The chest radiographs were assessed for: peribronchial cuffing, ground-glass opacities (GGOs), consolidation, pulmonary nodules and pleural effusion. The severity of the pulmonary findings was graded using a modification of the Brixia score.ResultsThere were a total of 90 patients with SARS-CoV-2 infection; the mean age was 5.8 years (age range 7 days to 17 years). Abnormalities were seen on the CXR in 74 (82%) of the 90 patients. Bilateral peribronchial cuffing was seen in 68% (61/90), consolidation in 11% (10/90), bilateral central GGOs in 2% (2/90) and unilateral pleural effusion in 1% (1/90). Overall the average CXR score in our cohort of patients was 6. The average CXR score in patients with oxygen requirement was 10. The duration of hospital stay was significantly longer in those patients with CXR score &gt;9.ConclusionThe CXR score has the potential to serve as tool to identify children at high risk and may aid planning of clinical management in such patients.