bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ångström-resolution fluorescence microscopy
Authors: Reinhardt Susanne C. M. , Masullo Luciano A. , Baudrexel Isabelle , Steen Philipp R. , Kowalewski Rafal , Eklund Alexandra S. , Strauss Sebastian , Unterauer Eduard M. , Schlichthaerle Thomas , Strauss Maximilian T. , Klein Christian , Jungmann Ralf 
Published: May 2023

AbstractFluorescence microscopy, with its molecular specificity, is one of the major characterization methods used in the life sciences to understand complex biological systems. Super-resolution approaches1–6 can achieve resolution in cells in the range of 15 to 20 nm, but interactions between individual biomolecules occur at length scales below 10 nm and characterization of intramolecular structure requires Ångström resolution. State-of-the-art super-resolution implementations7–14 have demonstrated spatial resolutions down to 5 nm and localization precisions of 1 nm under certain in vitro conditions. However, such resolutions do not directly translate to experiments in cells, and Ångström resolution has not been demonstrated to date. Here we introdue a DNA-barcoding method, resolution enhancement by sequential imaging (RESI), that improves the resolution of fluorescence microscopy down to the Ångström scale using off-the-shelf fluorescence microscopy hardware and reagents. By sequentially imaging sparse target subsets at moderate spatial resolutions of >15 nm, we demonstrate that single-protein resolution can be achieved for biomolecules in whole intact cells. Furthermore, we experimentally resolve the DNA backbone distance of single bases in DNA origami with Ångström resolution. We use our method in a proof-of-principle demonstration to map the molecular arrangement of the immunotherapy target CD20 in situ in untreated and drug-treated cells, which opens possibilities for assessing the molecular mechanisms of targeted immunotherapy. These observations demonstrate that, by enabling intramolecular imaging under ambient conditions in whole intact cells, RESI closes the gap between super-resolution microscopy and structural biology studies and thus delivers information key to understanding complex biological systems.
Microbial carbon use efficiency promotes global soil carbon storage
Authors: Tao Feng , Huang Yuanyuan , Hungate Bruce A. , Manzoni Stefano , Frey Serita D. , Schmidt Michael W. I. , Reichstein Markus , Carvalhais Nuno , Ciais Philippe , Jiang Lifen , Lehmann Johannes , Wang Ying-Ping , Houlton Benjamin Z. , Ahrens Bernhard , Mishra Umakant , Hugelius Gustaf , Hocking Toby D. , Lu Xingjie , Shi Zheng , Viatkin Kostiantyn , Vargas Ronald , Yigini Yusuf , Omuto Christian , Malik Ashish A. , Peralta Guillermo , Cuevas-Corona Rosa , Di Paolo Luciano E. , Luotto Isabel , Liao Cuijuan , Liang Yi-Shuang , Saynes Vinisa S. , Huang Xiaomeng , Luo Yiqi 
Published: May 2023

AbstractSoils store more carbon than other terrestrial ecosystems1,2. How soil organic carbon (SOC) forms and persists remains uncertain1,3, which makes it challenging to understand how it will respond to climatic change3,4. It has been suggested that soil microorganisms play an important role in SOC formation, preservation and loss5–7. Although microorganisms affect the accumulation and loss of soil organic matter through many pathways4,6,8–11, microbial carbon use efficiency (CUE) is an integrative metric that can capture the balance of these processes12,13. Although CUE has the potential to act as a predictor of variation in SOC storage, the role of CUE in SOC persistence remains unresolved7,14,15. Here we examine the relationship between CUE and the preservation of SOC, and interactions with climate, vegetation and edaphic properties, using a combination of global-scale datasets, a microbial-process explicit model, data assimilation, deep learning and meta-analysis. We find that CUE is at least four times as important as other evaluated factors, such as carbon input, decomposition or vertical transport, in determining SOC storage and its spatial variation across the globe. In addition, CUE shows a positive correlation with SOC content. Our findings point to microbial CUE as a major determinant of global SOC storage. Understanding the microbial processes underlying CUE and their environmental dependence may help the prediction of SOC feedback to a changing climate.
Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum
Authors: González Alexis , Covarrubias-Pinto Adriana , Bhaskara Ramachandra M. , Glogger Marius , Kuncha Santosh K. , Xavier Audrey , Seemann Eric , Misra Mohit , Hoffmann Marina E. , Bräuning Bastian , Balakrishnan Ashwin , Qualmann Britta , Dötsch Volker , Schulman Brenda A. , Kessels Michael M. , Hübner Christian A. , Heilemann Mike , Hummer Gerhard , Dikić Ivan 
Published: May 2023

AbstractThe endoplasmic reticulum (ER) undergoes continuous remodelling via a selective autophagy pathway, known as ER-phagy1. ER-phagy receptors have a central role in this process2, but the regulatory mechanism remains largely unknown. Here we report that ubiquitination of the ER-phagy receptor FAM134B within its reticulon homology domain (RHD) promotes receptor clustering and binding to lipidated LC3B, thereby stimulating ER-phagy. Molecular dynamics (MD) simulations showed how ubiquitination perturbs the RHD structure in model bilayers and enhances membrane curvature induction. Ubiquitin molecules on RHDs mediate interactions between neighbouring RHDs to form dense receptor clusters that facilitate the large-scale remodelling of lipid bilayers. Membrane remodelling was reconstituted in vitro with liposomes and ubiquitinated FAM134B. Using super-resolution microscopy, we discovered FAM134B nanoclusters and microclusters in cells. Quantitative image analysis revealed a ubiquitin-mediated increase in FAM134B oligomerization and cluster size. We found that the E3 ligase AMFR, within multimeric ER-phagy receptor clusters, catalyses FAM134B ubiquitination and regulates the dynamic flux of ER-phagy. Our results show that ubiquitination enhances RHD functions via receptor clustering, facilitates ER-phagy and controls ER remodelling in response to cellular demands.
Walking naturally after spinal cord injury using a brain–spine interface
Authors: Lorach Henri , Galvez Andrea , Spagnolo Valeria , Martel Felix , Karakas Serpil , Intering Nadine , Vat Molywan , Faivre Olivier , Harte Cathal , Komi Salif , Ravier Jimmy , Collin Thibault , Coquoz Laure , Sakr Icare , Baaklini Edeny , Hernandez-Charpak Sergio Daniel , Dumont Gregory , Buschman Rik , Buse Nicholas , Denison Tim , van Nes Ilse , Asboth Leonie , Watrin Anne , Struber Lucas , Sauter-Starace Fabien , Langar Lilia , Auboiroux Vincent , Carda Stefano , Chabardes Stephan , Aksenova Tetiana , Demesmaeker Robin , Charvet Guillaume , Bloch Jocelyne , Courtine Grégoire 
Published: May 2023

AbstractA spinal cord injury interrupts the communication between the brain and the region of the spinal cord that produces walking, leading to paralysis1,2. Here, we restored this communication with a digital bridge between the brain and spinal cord that enabled an individual with chronic tetraplegia to stand and walk naturally in community settings. This brain–spine interface (BSI) consists of fully implanted recording and stimulation systems that establish a direct link between cortical signals3 and the analogue modulation of epidural electrical stimulation targeting the spinal cord regions involved in the production of walking4–6. A highly reliable BSI is calibrated within a few minutes. This reliability has remained stable over one year, including during independent use at home. The participant reports that the BSI enables natural control over the movements of his legs to stand, walk, climb stairs and even traverse complex terrains. Moreover, neurorehabilitation supported by the BSI improved neurological recovery. The participant regained the ability to walk with crutches overground even when the BSI was switched off. This digital bridge establishes a framework to restore natural control of movement after paralysis.
Gap junctions desynchronize a neural circuit to stabilize insect flight
Authors: Hürkey Silvan , Niemeyer Nelson , Schleimer Jan-Hendrik , Ryglewski Stefanie , Schreiber Susanne , Duch Carsten 
Published: May 2023

AbstractInsect asynchronous flight is one of the most prevalent forms of animal locomotion used by more than 600,000 species. Despite profound insights into the motor patterns1, biomechanics2,3 and aerodynamics underlying asynchronous flight4,5, the architecture and function of the central-pattern-generating (CPG) neural network remain unclear. Here, on the basis of an experiment–theory approach including electrophysiology, optophysiology, Drosophila genetics and mathematical modelling, we identify a miniaturized circuit solution with unexpected properties. The CPG network consists of motoneurons interconnected by electrical synapses that, in contrast to doctrine, produce network activity splayed out in time instead of synchronized across neurons. Experimental and mathematical evidence support a generic mechanism for network desynchronization that relies on weak electrical synapses and specific excitability dynamics of the coupled neurons. In small networks, electrical synapses can synchronize or desynchronize network activity, depending on the neuron-intrinsic dynamics and ion channel composition. In the asynchronous flight CPG, this mechanism translates unpatterned premotor input into stereotyped neuronal firing with fixed sequences of cell activation that ensure stable wingbeat power and, as we show, is conserved across multiple species. Our findings prove a wider functional versatility of electrical synapses in the dynamic control of neural circuits and highlight the relevance of detecting electrical synapses in connectomics.
A Pseudomonas aeruginosa small RNA regulates chronic and acute infection
Authors: Cao Pengbo , Fleming Derek , Moustafa Dina A. , Dolan Stephen K. , Szymanik Kayla H. , Redman Whitni K. , Ramos Anayancy , Diggle Frances L. , Sullivan Christopher S. , Goldberg Joanna B. , Rumbaugh Kendra P. , Whiteley Marvin 
Published: May 2023

AbstractThe ability to switch between different lifestyles allows bacterial pathogens to thrive in diverse ecological niches1,2. However, a molecular understanding of their lifestyle changes within the human host is lacking. Here, by directly examining bacterial gene expression in human-derived samples, we discover a gene that orchestrates the transition between chronic and acute infection in the opportunistic pathogenPseudomonas aeruginosa. The expression level of this gene, here namedsicX, is the highest of theP. aeruginosagenes expressed in human chronic wound and cystic fibrosis infections, but it is expressed at extremely low levels during standard laboratory growth. We show thatsicXencodes a small RNA that is strongly induced by low-oxygen conditions and post-transcriptionally regulates anaerobic ubiquinone biosynthesis. Deletion ofsicXcausesP. aeruginosato switch from a chronic to an acute lifestyle in multiple mammalian models of infection. Notably,sicXis also a biomarker for this chronic-to-acute transition, as it is the most downregulated gene when a chronic infection is dispersed to cause acute septicaemia. This work solves a decades-old question regarding the molecular basis underlying the chronic-to-acute switch inP. aeruginosaand suggests oxygen as a primary environmental driver of acute lethality.
Asphericity derived from [18F]FDG PET as a new prognostic parameter in cervical cancer patients
Authors: Cegla Paulina , Hofheinz Frank , Burchardt Ewa , Czepczyński Rafał , Kubiak Anna , van den Hoff Jörg , Nikulin Pavel , Bos-Liedke Agnieszka , Roszak Andrzej , Cholewinski Witold 
Published: May 2023

AbstractThe objective of this study was to assess the prognostic value of asphericity (ASP) and standardized uptake ratio (SUR) in cervical cancer patients. Retrospective analysis was performed on a group of 508 (aged 55 ± 12 years) previously untreated cervical cancer patients. All patients underwent a pretreatment [18F]FDG PET/CT study to assess the severity of the disease. The metabolic tumor volume (MTV) of the cervical cancer was delineated with an adaptive threshold method. For the resulting ROIs the maximum standardized uptake value (SUVmax) was measured. In addition, ASP and SUR were determined as previously described. Univariate Cox regression and Kaplan–Meier analysis with respect to event free survival (EFS), overall survival (OS), freedom from distant metastasis (FFDM) and locoregional control (LRC) was performed. Additionally, a multivariate Cox regression including clinically relevant parameters was performed. In the survival analysis, MTV and ASP were shown to be prognostic factors for all investigated endpoints. Tumor metabolism quantified with the SUVmax was not prognostic for any of the endpoints (p > 0.2). The SUR did not reach statistical significance either (p = 0.1, 0.25, 0.066, 0.053, respectively). In the multivariate analysis, the ASP remained a significant factor for EFS and LRC, while MTV was a significant factor for FFDM, indicating their independent prognostic value for the respective endpoints. The alternative parameter ASP has the potential to improve the prognostic value of [18F]FDG PET/CT for event-free survival and locoregional control in radically treated cervical cancer patients.
Integration analysis of miRNA–mRNA expression exploring their potential roles in intrahepatic cholangiocarcinoma
Authors: Liu Liyan , Shi Yajun , Zhang Pengjie , Zhang Xing 
Published: May 2023

AbstractIntrahepatic cholangiocarcinoma (ICC) is the second common primary hepatic malignancy tumor. In this study, an integrative analysis of differentially expressed genes (DEGs) and miRNAs from the ICC onset and adjacent normal tissues were performed to explore the regulatory roles of miRNA–mRNA interaction. A total of 1018 DEGs and 39 miRNAs were likely involved in ICC pathogenesis, suggesting the changes in cell metabolism in ICC development. The built network indicated that 30 DEGs were regulated by 16 differentially expressed miRNA. The screened DEGs and miRNA together were probably considered the biomarkers of ICC, and their important roles in ICC pathogenesis remain to be elucidated. This study could provide a good basis to uncover the regulatory mechanism of miRNA and mRNAs in ICC pathogenesis.
Intravenous sildenafil for treatment of early pulmonary hypertension in preterm infants
Authors: Schroeder Lukas , Monno Paulina , Strizek Brigitte , Dresbach Till , Mueller Andreas , Kipfmueller Florian 
Published: May 2023

AbstractData is lacking on the effect of continuous intravenous sildenafil treatment in preterm infants with early pulmonary hypertension (PH), especially in very low birth weight (VLBW) infants. Preterm infants (< 37 weeks of gestational age) with intravenous sildenafil treatment and diagnosis of PH between 01/12 and 12/21 were retrospectively screened for analysis. The primary clinical endpoint was defined as response to sildenafil according to the improvement of the oxygenation index (OI), the saturation oxygenation pressure index (SOPI) and PaO2/FiO2-ratio. Early-PH was defined as diagnosis < 28 day of life (DOL). 58 infants were finally included, with 47% classified as very low birth weight (VLBW) infants. The primary endpoint was reached in 57%. The likelihood to die during in-hospital treatment was more than three times higher (72 vs 21%, p < 0.001) in infants without response to sildenafil. The echocardiographic severity of PH and right-ventricular dysfunction (RVD) decreased significantly from baseline to 24 h (p = 0.045, and p = 0.008, respectively). Sildenafil treatment leads to significant improvement of the oxygenation impairment in 57% of the preterm infants, with similar response rates in VLBW infants. Intravenous sildenafil treatment is associated with a significant decrease of the PH-severity and RVD.
Entropy generation and flow characteristics of Powell Eyring fluid under effects of time sale and viscosities parameters
Authors: Hassan Mohsan , Ahsan Muhammad , Usman  , Alghamdi Metib , Muhammad Taseer 
Published: May 2023

AbstractShear thinning fluids are widely used in the food and polymer industries due to their unique flow characteristics. The flow behavior of these fluids has been commonly studied using the Powell Eyring model under a small shear rate assumption. However, this assumption is not always valid. In this study, we explore the transport characteristics of a Powell Eyring fluid over a variable thicker sheet, not only at small shear rates but also at medium and high shear rates. Furthermore, we calculate the rate of entropy generation based on the assumptions. Generalized Powell–Eyring model of viscosity is used for the fluid, representing the re-arrangements of molecules in the forward and backward directions through the theory of potential energy. The model concludes the sensitivity of the viscosity from zero to infinite shear rate along time sale and exponent parameters. The model is used in the transport phenomena equations. The solution of the equation is obtained by using the numerical method and used to calculate the rate of entropy generation. The results are presented in the form of velocity and temperature profiles, the average rate of entropy generation, skin friction coefficient and Nusselt number under the influence of various viscosity parameters. It is found that velocity and temperature profiles are decreased and increased respectively against the time scale parameter.
Ergebnisse aus der VERSUS-Studie von d-uo am Beispiel des Prostatakarzinoms
Authors: Klier Jörg , König Frank , Johannsen Manfred , Eichenauer Rolf , Schönfelder Robert , Schröder Jörg , Hempel Elke , Doehn Christian 
Published: May 2023

Zusammenfassung
Deutsche Uro-Onkologen (d-uo) hatten bereits Anfang 2017 die Idee, eine Dokumentationsplattform zu konzipieren, mit der die Mitglieder von d-uo einerseits die Meldung an das Krebsregister ermöglicht wird und andererseits Daten in die eigene Datenbank von d-uo überführt werden können – ohne doppelten Aufwand. Das Krebsregister vergütet die Erstmeldung einer Tumorerkrankung mit 18 €. Als weiterhin einziger Anbieter vergütet d-uo seinen Mitgliedern den mit der zusätzlichen Meldung an d-uo verbunden Dokumentationsaufwand mit weiteren 18 €.
Zusätzlich zum einheitlichen Onkologischen Basisdatensatz wurden weitere Parameter von
d-uo definiert. Diese Daten werden im Rahmen der sogenannten VERSUS-Studie erhoben,
ausgewertet und interpretiert.
Ende 2022 waren 14834 Patienten mit einer neu diagnostizierten Tumorerkrankung aus dem urologischen Gebiet in die VERSUS-Studie eingeschlossen. Knapp zwei Drittel aller Patienten hatten ein Prostatakarzinom. Etwa die Hälfte aller Patienten mit einem Prostatakarzinom war im Rahmen einer Früherkennungsmaßnahme aufgefallen. Diese Patienten hatten dann auch günstigere Tumorstadien. Insgesamt hatte fast jeder achte Patient bei Erstdiagnose bereits Metastasen.

Aus der VERSUS-Studie Daten für 2167 Operationen eines Prostatakarzinoms mit der Tumorkategorie T2 oder T3 zur Verfügung. Es handelte sich um 1360 Operationen bei Patienten mit einem T2-Tumor (62,8%) und 807 Operationen bei Patienten mit T3-Tumoren (37,2%). Ein positiver Absetzungsrand lag bei 25,5% aller operierten Patienten. Bezogen auf die Tumorkategorien T2 und T3 lag der Anteil eines positiven Absetzungsrandes bei 14,3% bzw. 44,2%.

Die VERSUS-Studie wird weiterhin zu vielen Fragestellungen aus dem uro-onkologischen Feld Antworten mit Bezug zur aktuellen Versorgungsituation in Deutschland liefern.
Corneal Perforation as a Rare and Late Manifestation of Choroidal Melanoma
Authors: Berger Tim , Flockerzi Fidelis , Löw Ursula , Flockerzi Elias , Aljundi Wissam , Abdin Alaadin , Daas Loay , Seitz Berthold 
Published: May 2023

Abstract
Purpose To report a case of corneal perforation as a rare and late manifestation of choroidal melanoma and to highlight the major histopathological findings of this unusual combined
clinical presentation.
Methods A 74-year-old male patient presented to our department due to corneal perforation of the right eye with the absence of light perception for 6 months. The intraocular pressure
was hard on palpation. Because of the protracted finding and reduced visual prognosis, primary enucleation was performed.
Results The histopathological examination revealed choroidal melanoma with epithelioid and spindle cell components at the posterior pole, which was positive for Melan-A, Human
Melanoma Black 45 (HMB45), BAP1, and SOX10. The anterior segment showed complete anterior chamber hemorrhage and blood remnants in the trabecular meshwork. The cornea displayed diffuse blood
staining with hemosiderin and hemosiderin-loaded macrophages and keratocytes. No inflammatory cells were present near the corneal perforation, which had a width of 3 mm. Intraocular
heterotopic ossification was indicative of a long-standing condition. Postoperative cancer staging was normal.
Conclusion Corneal perforation should be considered as a very rare and late manifestation of advanced choroidal melanoma and may result from interaction between intraocular
hemorrhage, elevated IOP, and its secondary signs such as corneal blood staining.
Impact of the COVID-19 pandemic on therapeutic interventional oncology procedures and diagnostic CT/MRI examinations at a German university hospital
Authors: Nebelung Heiner , Radosa Christoph Georg , Schön Felix , Blum Sophia Freya Ulrike , Böhme Christian , Hoffmann Ralf-Thorsten , Plodeck Verena 
Published: May 2023

Purpose The COVID-19 pandemic led to the implementation of severe restrictions on public life in Germany and a reduction in the number of non-COVID patients presenting for care. The aim of this study was to measure the impact on the number of therapeutic interventional oncology procedures in relation to diagnostic imaging studies at a high-volume radiology department.
Materials and Methods The numbers of therapeutic interventional oncology procedures and diagnostic CT/MRI examinations for the years 2010 to 2021 were extracted using the hospital information system. Monthly data from January 2010 to December 2019 were used to build forecasting models for the timeframe from January 2020 to December 2021. Real procedure numbers were compared with predicted numbers to calculate residual differences, which were considered statistically significant if the real number was outside the 95 % confidence interval (p < 0.05).
Results During the first German lockdown (March/April 2020), the number of outpatient CT/MRI examinations decreased significantly, with a less pronounced decrease of overall CT/MRI numbers. The second German lockdown (January-May 2021) led to lower than predicted outpatient CT numbers, whereas outpatient MRI numbers in part even exceeded predicted numbers and overall CT/MRI numbers stayed within confidence limits. The lockdowns had a more pronounced negative effect on the number of oncological MRI examinations compared to CT examinations. The number of therapeutic interventional oncology procedures showed no significant decrease during both lockdowns.
Conclusion Lockdown measures had minor impact on the number of therapeutic interventional oncology procedures, possibly due to a shift from more resource-intensive therapies like surgery towards interventional oncology. The overall numbers of diagnostic imaging decreased during the first lockdown, while the second lockdown had less negative impact. The number of oncological MRI examinations was affected most severely. To avoid adverse outcomes, specific protocols for patient management during future pandemic outbreaks should be implemented and continuously adapted.
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