bluuebunny/crossref_metadata_2025_split huggingface dataset:
An ATEM 1D inversion based on K-Means clustering and MLP deep learning
Authors: Shi Mingzhi , Cao Hui 
Published: July 2022

Abstract
Traditional geophysical inversion methods rely on an assumption of prior knowledge, starting from the establishment of the initial model and ending with the model being modified many times. This iterative process makes the forward modelling results move increasingly closer to the observed data. However, each inversion step requires multiple forward calculations, which consumes considerable time and computing resources. This is the greatest obstacle to real-time inversion at present. Airborne transient electromagnetic (ATEM) response data are collected in a time-channel manner. The different stratigraphic structures reveal different time-varying electromagnetic response laws. In this paper, deep learning technology is used to advance the ‘model correction-forward iteration’ step in the geophysical inversion process to the data preprocessing stage, to better adapt to the specialty of ATEM, improve the efficiency of the inversion and shorten the inversion time. In this method, a sample set composed of a ‘stratigraphic texture model—ATEM response’ is established, the K-Means clustering technique of unsupervised learning is used to complete the sample tag attachment, and the multilayer perceptron (MLP) deep learning network with supervised learning is used to complete the multiclassification tasks. Then, the sample sets are input into the deep learning network for training to build the inversion from the input response data to the output of the stratigraphic model. Finally, the inversion flow is verified with test set samples. The prediction results are consistent with the simulated data, and the inversion, from the test data to the prediction model, is implemented efficiently.
‘His utter unfitness for a commercial collector’
Authors: Alcorn Keith 
Published: July 2022

Abstract
Non-European or ‘exotic’ plants became prestigious collectable items in the early nineteenth century. Although unpaid collectors contributed greatly to the discovery of new plants, systematic sponsored collecting became increasingly important after 1800 in Britain. While sharing features of natural history collecting, the organization and sponsorship of exotic plant collecting in the first half of the nineteenth century in Britain exhibits several distinctive features, notably the involvement of commercial sponsors and cooperation between commercial and scientific bodies. Using the Directors’ Correspondence of the Royal Botanic Gardens, Kew, this article describes how individuals, consortia of sponsors and subscription systems assembled finance for plant collecting. The article demonstrates the extent to which plant introductions depended on a structured trade in plants, in which commercial nurseries played a central role. Plant collecting must be understood as an episode not only in the history of garden design, but also in the history of collections.
Estimation of projection parameter distribution and initial model generation in single-particle analysis
Authors: Mamizu Nobuya , Yasunaga Takuo 
Published: July 2022

Abstract
This study focused on the problem of projection parameter search in 3D reconstruction using single-particle analysis. We treated the sampling distribution for the parameter search as a prior distribution and designed a probabilistic model for efficient parameter estimation. Using our method, we showed that it is possible to perform 3D reconstruction from synthetic and actual electron microscope images using an initial model and to generate the initial model itself. We also examined whether the optimization function used in the stochastic gradient descent method can be applied with loose constraints to improve the convergence of initial model generation and confirmed the effect. In order to investigate the advantage of generating a smooth sampling distribution from the stochastic model, we compared the distribution of estimated projection directions with the conventional method of performing a global search using spherical gridding. As a result, our method, which is simple in both mathematical model and implementation, showed no algorithmic artifacts.
Tau Pathology in Chronic Traumatic Encephalopathy is Primarily Neuronal
Authors: Butler Morgane L M D , Dixon Erin , Stein Thor D , Alvarez Victor E , Huber Bertrand , Buckland Michael E , McKee Ann C , Cherry Jonathan D 
Published: July 2022

Abstract
Millions of individuals are exposed to repetitive head impacts (RHI) each year through contact sports, military blast, and interpersonal violence. RHI is the major risk factor for developing chronic traumatic encephalopathy (CTE), a neurodegenerative tauopathy. Recent consensus criteria defined the pathognomonic lesion in CTE as perivascular, hyperphosphorylated tau (p-tau) in neuronal aggregates. Astroglial p-tau is an inconsistent supporting feature and not in itself diagnostic of CTE. This study quantitated the spatial and cellular distribution of p-tau pathology in postmortem dorsolateral frontal cortex of 150 individuals with CTE, from ages 21 to 80 years old, without comorbid pathology. p-Tau-immunoreactive cells were quantitated in the gray matter sulcus, crest, subpial region, and within pathognomonic CTE lesions. Significantly more neuronal p-tau than astrocytic p-tau was found across all cortical regions (p &lt; 0.0001). Sulcal astrocytic p-tau was primarily (75%, p &lt; 0.0001) localized to subpial regions as thorn-shaped astrocytes, a form of age-related tau astrogliopathy. Neuronal p-tau was significantly associated with age, years of RHI exposure, and CTE severity; astrocytic p-tau pathology was only significantly associated with age. These findings strongly support neuronal degeneration as a driving feature of CTE and will help inform future research and the development of fluid biomarkers for the detection of neuronal degeneration in CTE.
Safety and Acceptance of COVID-19 Vaccination After Multisystem Inflammatory Syndrome in Children (MIS-C) in Spain
Authors: Epalza Cristina , Prieto-Tato Luis , Pino Rosa , Escartín-Paredes Paula , Leoz Inés , Grasa Carlos , Vivanco-Allende Ana , Rivière Jacques G , Carrasco-Colom Jaume , Villate Olatz , Fumadó Victoria , Hermoso-Ibañez Concepción , Herrero Blanca , Aguilera-Alonso David , Tagarro Alfredo , Moraleda Cinta ,   EPICO-AEP Working Group
Published: July 2022

Abstract
In this cohort of 42 adolescents with a previous multisystem inflammatory syndrome (MIS-C) diagnosis, 32 (76.2%) were vaccinated with COVID-19 vaccines, with a low incidence of relevant adverse events. More importantly, no new MIS-C or myocarditis occurred after a median of 10 weeks (range 5.3-19.7) post-vaccination.
Enhanced abundance and activity of the chloroplast ATP synthase in rice through the overexpression of the AtpD subunit
Authors: Ermakova Maria , Heyno Eiri , Woodford Russell , Massey Baxter , Birke Hannah , von Caemmerer Susanne 
Published: July 2022

AbstractATP, produced by the light reactions of photosynthesis, acts as the universal cellular energy cofactor fuelling all life processes. Chloroplast ATP synthase produces ATP using the proton motive force created by solar energy-driven thylakoid electron transport reactions. Here we investigate how increasing abundance of ATP synthase affects leaf photosynthesis and growth of rice, Oryza sativa variety Kitaake. We show that overexpression of AtpD, the nuclear-encoded subunit of the chloroplast ATP synthase, stimulates both abundance of the complex, confirmed by immunodetection of thylakoid complexes separated by Blue Native-PAGE, and ATP synthase activity, detected as higher proton conductivity of the thylakoid membrane. Plants with increased AtpD content had higher CO2 assimilation rates when a stepwise increase in CO2 partial pressure was imposed on leaves at high irradiance. Fitting of the CO2 response curves of assimilation revealed that plants overexpressing AtpD had a higher electron transport rate (J) at high CO2, despite having wild-type-like abundance of the cytochrome b6f complex. A higher maximum carboxylation rate (Vcmax) and lower cyclic electron flow detected in transgenic plants both pointed to an increased ATP production compared with wild-type plants. Our results present evidence that the activity of ATP synthase modulates the rate of electron transport at high CO2 and high irradiance.
The stickers and spacers of Rubiscondensation: assembling the centrepiece of biophysical CO2-concentrating mechanisms
Authors: Ang Warren Shou Leong , How Jian Ann , How Jian Boon , Mueller-Cajar Oliver 
Published: July 2022

Abstract
Aquatic autotrophs that fix carbon using ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) frequently expend metabolic energy to pump inorganic carbon towards the enzyme’s active site. A central requirement of this strategy is the formation of highly concentrated Rubisco condensates (or Rubiscondensates) known as carboxysomes and pyrenoids, which have convergently evolved multiple times in prokaryotes and eukaryotes, respectively. Recent data indicate that these condensates form by the mechanism of liquid–liquid phase separation. This mechanism requires networks of weak multivalent interactions typically mediated by intrinsically disordered scaffold proteins. Here we comparatively review recent rapid developments that detail the determinants and precise interactions that underlie diverse Rubisco condensates. The burgeoning field of biomolecular condensates has few examples where liquid–liquid phase separation can be linked to clear phenotypic outcomes. When present, Rubisco condensates are essential for photosynthesis and growth, and they are thus emerging as powerful and tractable models to investigate the structure–function relationship of phase separation in biology.
Tungsten versus Selenium as a potential source of kilonova nebular emission observed by Spitzer
Authors: Hotokezaka Kenta , Tanaka Masaomi , Kato Daiji , Gaigalas Gediminas 
Published: July 2022

ABSTRACT
Infrared emission lines arising from transitions between fine structure levels of heavy elements are expected to produce kilonova nebular emission. For the kilonova in GW170817, strong emission at $4.5\, {\rm \mu m}$ at late times was detected by the Spitzer Space Telescope but no source was detected at $3.6\, {\rm \mu m}$. This peculiar spectrum indicates that strong line emitters exist around $4.5\, {\rm \mu m}$ and the absence of strong lines around $3.6\, {\rm \mu m}$. To model the spectrum we prepare a line list based on the selection rules in LS coupling from the experimentally calibrated energy levels in the NIST database. This method enables to generate the synthetic spectra with accurate line wavelengths. We find that the spectrum is sensitive to the abundance pattern whether or not the first r-process peak elements are included. In both cases, the synthetic spectra can match the observed data, leading to two possible interpretations. If the first peak elements are abundant, a Se iii line dominates the flux. If otherwise, W iii with Os iii, Rh iii, and Ce iv can be the main sources. Observing nebular spectra for the future kilonova in a wider wavelength range can provide more conclusive elemental identification.
A Secondary Metabolic Enzyme Functioned as an Evolutionary Seed of a Primary Metabolic Enzyme
Authors: Kawaguchi Jun , Mori Hikaru , Iwai Noritaka , Wachi Masaaki 
Published: July 2022

Abstract
The antibiotic alaremycin has a structure that resembles that of 5-aminolevulinic acid (ALA), a universal precursor of porphyrins, and inhibits porphyrin biosynthesis. Genome sequencing of the alaremycin-producing bacterial strain and enzymatic analysis revealed that the first step of alaremcyin biosynthesis is catalysed by the enzyme, AlmA, which exhibits a high degree of similarity to 5-aminolevulinate synthase (ALAS) expressed by animals, protozoa, fungi, and α-proteobacteria. Site-directed mutagenesis of AlmA revealed that the substitution of two amino acids residues around the substrate binding pocket transformed its substrate specificity from that of alaremycin precursor synthesis to ALA synthesis. To estimate the evolutionary trajectory of AlmA and ALAS, we performed an ancestral sequence reconstitution analysis based on a phylogenetic tree of AlmA and ALAS. The reconstructed common ancestral enzyme of AlmA and ALAS exhibited alaremycin precursor synthetic activity, rather than ALA synthetic activity. These results suggest that ALAS evolved from an AlmA-like enzyme. We propose a new evolutionary hypothesis in which a non-essential secondary metabolic enzyme acts as an ‘evolutionary seed’ to generate an essential primary metabolic enzyme.
The HDAC7–TET2 epigenetic axis is essential during early B lymphocyte development
Authors: Azagra Alba , Meler Ainara , de Barrios Oriol , Tomás-Daza Laureano , Collazo Olga , Monterde Beatriz , Obiols Mireia , Rovirosa Llorenç , Vila-Casadesús Maria , Cabrera-Pasadas Mónica , Gusi-Vives Mar , Graf Thomas , Varela Ignacio , Sardina José Luis , Javierre Biola M , Parra Maribel 
Published: July 2022

Abstract
Correct B cell identity at each stage of cellular differentiation during B lymphocyte development is critically dependent on a tightly controlled epigenomic landscape. We previously identified HDAC7 as an essential regulator of early B cell development and its absence leads to a drastic block at the pro-B to pre-B cell transition. More recently, we demonstrated that HDAC7 loss in pro-B-ALL in infants associates with a worse prognosis. Here we delineate the molecular mechanisms by which HDAC7 modulates early B cell development. We find that HDAC7 deficiency drives global chromatin de-condensation, histone marks deposition and deregulates other epigenetic regulators and mobile elements. Specifically, the absence of HDAC7 induces TET2 expression, which promotes DNA 5-hydroxymethylation and chromatin de-condensation. HDAC7 deficiency also results in the aberrant expression of microRNAs and LINE-1 transposable elements. These findings shed light on the mechanisms by which HDAC7 loss or misregulation may lead to B cell–based hematological malignancies.
CGG repeats trigger translational frameshifts that generate aggregation-prone chimeric proteins
Authors: Wright Shannon E , Rodriguez Caitlin M , Monroe Jeremy , Xing Jiazheng , Krans Amy , Flores Brittany N , Barsur Venkatesha , Ivanova Magdalena I , Koutmou Kristin S , Barmada Sami J , Todd Peter K 
Published: July 2022

Abstract
CGG repeat expansions in the FMR1 5’UTR cause the neurodegenerative disease Fragile X-associated tremor/ataxia syndrome (FXTAS). These repeats form stable RNA secondary structures that support aberrant translation in the absence of an AUG start codon (RAN translation), producing aggregate-prone peptides that accumulate within intranuclear neuronal inclusions and contribute to neurotoxicity. Here, we show that the most abundant RAN translation product, FMRpolyG, is markedly less toxic when generated from a construct with a non-repetitive alternating codon sequence in place of the CGG repeat. While exploring the mechanism of this differential toxicity, we observed a +1 translational frameshift within the CGG repeat from the arginine to glycine reading frame. Frameshifts occurred within the first few translated repeats and were triggered predominantly by RNA sequence and structural features. Short chimeric R/G peptides form aggregates distinct from those formed by either pure arginine or glycine, and these chimeras induce toxicity in cultured rodent neurons. Together, this work suggests that CGG repeats support translational frameshifting and that chimeric RAN translated peptides may contribute to CGG repeat-associated toxicity in FXTAS and related disorders.
Top3α is the replicative topoisomerase in mitochondrial DNA replication
Authors: Hangas Anu , Kekäläinen Nina J , Potter Alisa , Michell Craig , Aho Kauko J , Rutanen Chiara , Spelbrink Johannes N , Pohjoismäki Jaakko L , Goffart Steffi 
Published: July 2022

Abstract
Mitochondrial DNA has been investigated for nearly fifty years, but many aspects of the maintenance of this essential small genome remain unknown. Like any genome, mammalian mitochondrial DNA requires the function of topoisomerases to counter and regulate the topological tension arising during replication, transcription, segregation, and repair. However, the functions of the different mitochondrial topoisomerases are poorly understood. Here, we investigate the role of Topoisomerase 3α (Top3α) in mtDNA replication and transcription, providing evidence that this enzyme, previously reported to act in mtDNA segregation, also participates in mtDNA replication fork progression. Top3α knockdown caused replication fork stalling, increased mtDNA catenation and decreased mtDNA levels. Overexpression in contrast induced abundant double-strand breaks around the replication origin OH and abortion of early replication, while at the same time improving the resolution of mtDNA replication termination intermediates. Both Top3α knockdown and overexpression affected mitochondrial RNA transcription, leading to a decrease in steady-state levels of mitochondrial transcripts. Together, our results indicate that the mitochondrial isoform of Top3α is not only involved in mtDNA segregation, as reported previously, but also supports the progression of the replication fork. Mitochondrial Top3α is also influencing the progression of transcription, with its absence affecting downstream transcript levels.
KAP1 is a new non-genetic vulnerability of malignant pleural mesothelioma (MPM)
Authors: Lorenzini Eugenia , Torricelli Federica , Zamponi Raffaella , Donati Benedetta , Manicardi Veronica , Sauta Elisabetta , Faria do Valle Italo , Reggiani Francesca , Gugnoni Mila , Manzotti Gloria , Fragliasso Valentina , Vitale Emanuele , Piana Simonetta , Sancisi Valentina , Ciarrocchi Alessia 
Published: July 2022

Abstract
Malignant pleural mesothelioma (MPM) is a rare and incurable cancer, which incidence is increasing in many countries. MPM escapes the classical genetic model of cancer evolution, lacking a distinctive genetic fingerprint. Omics profiling revealed extensive heterogeneity failing to identify major vulnerabilities and restraining development of MPM-oriented therapies. Here, we performed a multilayered analysis based on a functional genome-wide CRISPR/Cas9 screening integrated with patients molecular and clinical data, to identify new non-genetic vulnerabilities of MPM. We identified a core of 18 functionally-related genes as essential for MPM cells. The chromatin reader KAP1 emerged as a dependency of MPM. We showed that KAP1 supports cell growth by orchestrating the expression of a G2/M-specific program, ensuring mitosis correct execution. Targeting KAP1 transcriptional function, by using CDK9 inhibitors resulted in a dramatic loss of MPM cells viability and shutdown of the KAP1-mediated program. Validation analysis on two independent MPM-patients sets, including a consecutive, retrospective cohort of 97 MPM, confirmed KAP1 as new non-genetic dependency of MPM and proved the association of its dependent gene program with reduced patients’ survival probability. Overall these data: provided new insights into the biology of MPM delineating KAP1 and its target genes as building blocks of its clinical aggressiveness.
Validation of two IgA nephropathy risk-prediction tools using a cohort with a long follow-up
Authors: Haaskjold Yngvar Lunde , Lura Njål Gjærde , Bjørneklett Rune , Bostad Leif , Bostad Lars Sigurd , Knoop Thomas 
Published: July 2022

ABSTRACT

Background
Recently, two immunoglobulin A (IgA) nephropathy-prediction tools were developed that combine clinical and histopathologic parameters. The International IgAN Prediction Tool predicts the risk for 50% declines in the estimated glomerular filtration rate or end-stage kidney disease up to 80 months after diagnosis. The IgA Nephropathy Clinical Decision Support System uses artificial neural networks to estimate the risk for end-stage kidney disease. We aimed to externally validate both prediction tools using a Norwegian cohort with a long-term follow-up.

Methods
We included 306 patients with biopsy-proven primary IgA nephropathy in this study. Histopathologic samples were retrieved from the Norwegian Kidney Biopsy Registry and reclassified according to the Oxford Classification. We used discrimination and calibration as principles for externally validating the prognostic models.

Results
The median patient follow-up was 17.1 years. A cumulative, dynamic, time-dependent receiver operating characteristic analysis showed area under the curve values ranging from 0.90 at 5 years to 0.83 at 20 years for the International IgAN Prediction Tool, while time-naive analysis showed an area under the curve value at 0.83 for the IgA Nephropathy Clinical Decision Support System. The International IgAN Prediction Tool was well calibrated, while the IgA Nephropathy Clinical Decision Support System tends to underestimate risk for patients at higher risk and overestimates risk in the lower risk categories.

Conclusions
We have externally validated two prediction tools for IgA nephropathy. The International IgAN Prediction Tool performed well, while the IgA Nephropathy Clinical Decision Support System has some limitations.
Enzymatic and chemo-enzymatic strategies to produce highly valuable chiral amines from biomass with ω-transaminases on 2D zeolites
Authors: Carceller J Miguel , Arias Karen S , Climent Maria J , Iborra Sara , Corma Avelino 
Published: July 2022

Abstract
Amino transaminases (ATAs) have been supported on a 2D ITQ-2 zeolite through electrostatic interactions, resulting in a highly stable active biocatalyst to obtain a variety of valuable chiral amines starting from prochiral ketones derived from biomass. We have extended the biocatalyst applications by designing a chemo-enzymatic process that allows, as the first step, prochiral ketones to be obtained from biomass-derived compounds through an aldol condensation–reduction step using a bifunctional metal/base catalyst. The prochiral ketone is subsequently converted into the chiral amine using the immobilized ATA. We show that it is feasible to couple both steps in a semi-continuous process to produce industrially relevant chiral amines with yields of &gt;95% and ∼100% enantiomer excess.
Extended Remdesivir Infusion for Persistent Coronavirus Disease 2019 Infection
Authors: Martinez Mario A , Chen Ting-Yi , Choi Hosoon , Hwang Munok , Navarathna Dhammika , Hao Linhue , Gale Michael , Camus Gregory , Ramirez Hector E , Jinadatha Chetan 
Published: July 2022

Abstract
Persistent severe acute respiratory syndrome coronavirus 2 infection is difficult to treat. Here, we report a case of 5-month persistent coronavirus disease 2019 in an immunocompromised patient who was successfully treated with 30 consecutive days of remdesivir. Prolonged remdesivir infusion with concurrent cycle threshold monitoring might provide a potential solution to cure these patients with difficult-to-treat infections.
Disseminated Mycobacterium avium Complex Myositis in a Patient With Graft-Versus-Host Disease
Authors: Kompa Kathryn Grace , Trottier Caitlin A , Hyman Charles L , Kohli Rakhi 
Published: July 2022

Abstract
Mycobacterium avium complex (MAC) is a ubiquitous environmental pathogen that was infrequently reported as a cause of disease before the human immunodeficiency virus (HIV)/acquired immune deficiency syndrome epidemic. We present a case of MAC pyomyositis and bacteremia in a 59-year-old man with chronic lymphocytic leukemia in remission after an allogenic stem cell transplant. His posttransplant course was complicated by graft-versus-host disease, requiring treatment with oral steroids and ruxolitinib. In this report, we review the literature on disseminated MAC infection in patients with and without HIV. We also propose a potential mechanism by which this patient may have developed disseminated disease. Disseminated MAC myositis is uncommon in persons without HIV and requires a high index of suspicion for timely diagnosis.