bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualizing translation dynamics at atomic detail inside a bacterial cell
Authors: Xue Liang , Lenz Swantje , Zimmermann-Kogadeeva Maria , Tegunov Dimitry , Cramer Patrick , Bork Peer , Rappsilber Juri , Mahamid Julia 
Published: September 2022

AbstractTranslation is the fundamental process of protein synthesis and is catalysed by the ribosome in all living cells1. Here we use advances in cryo-electron tomography and sub-tomogram analysis2,3 to visualize the structural dynamics of translation inside the bacterium Mycoplasma pneumoniae. To interpret the functional states in detail, we first obtain a high-resolution in-cell average map of all translating ribosomes and build an atomic model for the M. pneumoniae ribosome that reveals distinct extensions of ribosomal proteins. Classification then resolves 13 ribosome states that differ in their conformation and composition. These recapitulate major states that were previously resolved in vitro, and reflect intermediates during active translation. On the basis of these states, we animate translation elongation inside native cells and show how antibiotics reshape the cellular translation landscapes. During translation elongation, ribosomes often assemble in defined three-dimensional arrangements to form polysomes4. By mapping the intracellular organization of translating ribosomes, we show that their association into polysomes involves a local coordination mechanism that is mediated by the ribosomal protein L9. We propose that an extended conformation of L9 within polysomes mitigates collisions to facilitate translation fidelity. Our work thus demonstrates the feasibility of visualizing molecular processes at atomic detail inside cells.
LRRC15+ myofibroblasts dictate the stromal setpoint to suppress tumour immunity
Authors: Krishnamurty Akshay T. , Shyer Justin A. , Thai Minh , Gandham Vineela , Buechler Matthew B. , Yang Yeqing Angela , Pradhan Rachana N. , Wang Amber W. , Sanchez Patricia L. , Qu Yan , Breart Beatrice , Chalouni Cécile , Dunlap Debra , Ziai James , Elstrott Justin , Zacharias Neelie , Mao Weiguang , Rowntree Rebecca K. , Sadowsky Jack , Lewis Gail D. , Pillow Thomas H. , Nabet Barzin Y. , Banchereau Romain , Tam Lucinda , Caothien Roger , Bacarro Natasha , Roose-Girma Merone , Modrusan Zora , Mariathasan Sanjeev , Müller Sören , Turley Shannon J. 
Published: September 2022

AbstractRecent single-cell studies of cancer in both mice and humans have identified the emergence of a myofibroblast population specifically marked by the highly restricted leucine-rich-repeat-containing protein 15 (LRRC15)1–3. However, the molecular signals that underlie the development of LRRC15+ cancer-associated fibroblasts (CAFs) and their direct impact on anti-tumour immunity are uncharacterized. Here in mouse models of pancreatic cancer, we provide in vivo genetic evidence that TGFβ receptor type 2 signalling in healthy dermatopontin+ universal fibroblasts is essential for the development of cancer-associated LRRC15+ myofibroblasts. This axis also predominantly drives fibroblast lineage diversity in human cancers. Using newly developed Lrrc15–diphtheria toxin receptor knock-in mice to selectively deplete LRRC15+ CAFs, we show that depletion of this population markedly reduces the total tumour fibroblast content. Moreover, the CAF composition is recalibrated towards universal fibroblasts. This relieves direct suppression of tumour-infiltrating CD8+ T cells to enhance their effector function and augments tumour regression in response to anti-PDL1 immune checkpoint blockade. Collectively, these findings demonstrate that TGFβ-dependent LRRC15+ CAFs dictate the tumour-fibroblast setpoint to promote tumour growth. These cells also directly suppress CD8+ T cell function and limit responsiveness to checkpoint blockade. Development of treatments that restore the homeostatic fibroblast setpoint by reducing the population of pro-disease LRRC15+ myofibroblasts may improve patient survival and response to immunotherapy.
Awake perception is associated with dedicated neuronal assemblies in the cerebral cortex
Authors: Filipchuk Anton , Schwenkgrub Joanna , Destexhe Alain , Bathellier Brice 
Published: September 2022

AbstractNeural activity in the sensory cortex combines stimulus responses and ongoing activity, but it remains unclear whether these reflect the same underlying dynamics or separate processes. In the present study, we show in mice that, during wakefulness, the neuronal assemblies evoked by sounds in the auditory cortex and thalamus are specific to the stimulus and distinct from the assemblies observed in ongoing activity. By contrast, under three different anesthetics, evoked assemblies are indistinguishable from ongoing assemblies in the cortex. However, they remain distinct in the thalamus. A strong remapping of sensory responses accompanies this dynamic state change produced by anesthesia. Together, these results show that the awake cortex engages dedicated neuronal assemblies in response to sensory inputs, which we suggest is a network correlate of sensory perception.
Healthcare workers’ self-regulatory eating behaviours are associated with being stress-free during the Covid-19 lockdown in Singapore
Authors: Huang Zhongwei , Tan Pei Ting , Kua Zaylea , Ong Li Jiuen , Hamzah Fadzil Bin Mohamed , Tan Benedict 
Published: September 2022

AbstractOur study sought to examine the impact of the pandemic and the Circuit-breaker (CB) measures on dietary behaviours of healthcare workers (HCW). In addition, the association between self-regulatory eating behaviours and psychological stress was explored. Our study employed a cross-sectional anonymous survey that examined the demographics, dietary habits, self-regulatory eating behaviours (SR) and their association to stress levels of healthcare workers (HCWs) before and during the Circuit Breaker (CB) in Singapore. The survey was conducted over four weeks from May 17 to June 18, 2020. Snowball sampling was performed in the final week. A total of 707 participants took part in the survey. Due to the CB measures and modifications of work scope and work areas, there were significant changes in their dietary behaviors before CB versus during the CB period (n = 707), with many reducing the intake of vegetables (p = 0.018) while increasing their intake of unhealthy food choices such as canned drinks (p = 0.002), convenience food (p ≤ 0.001) and alcoholic drinks (p = 0.034). Before the CB period, 91.8% (602/656) of participants who intended to have a healthy diet were classified in medium-to-high SR groups whereas during the CB period, 87.7% (575/656) were in medium-to-high SR groups and the difference was statistically significant (p = 0.011). Nurses, administrative staff, HCWs of Chinese and Indian ethnicities, staff who did not complete university education and those who did not have domestic helpers were more likely to have reduced SR. Importantly, amongst participants who intended to have a healthy diet, 70.9% displayed no change or improved eating habits and showed medium-to-high levels of SR during CB. Participants with no changes in SR were 2.11 times more likely to be stress-free as compared to those who had deteriorated SR (OR 2.11 95% CI 1.27–3.48, p = 0.004). Due to CB measures and work modifications, dietary behaviours of HCWs deteriorated with increased intake of unhealthy food choices. HCWs who maintain their self-regulatory eating behaviour are more likely to be stress-free. Short screening questionnaires based on SR changes should be developed and explored as surveillance tools for assessment of HCWs’ general well-being such that personalized interventions to vulnerable groups of workers could be implemented effectively on the ground.
Multiparameter analysis of timelapse imaging reveals kinetics of megakaryocytic erythroid progenitor clonal expansion and differentiation
Authors: Scanlon Vanessa M. , Thompson Evrett N. , Lawton Betty R. , Kochugaeva Maria , Ta Kevinminh , Mayday Madeline Y. , Xavier-Ferrucio Juliana , Kang Elaine , Eskow Nicole M. , Lu Yi-Chien , Kwon Nayoung , Laumas Anisha , Cenci Matthew , Lawrence Kalyani , Barden Katie , Larsuel Shannon T. , Reed Fiona E. , Peña-Carmona Gabriela , Ubbelohde Ashley , Lee June P. , Boobalan Shakthi , Oppong Yvette , Anderson Rachel , Maynard Colby , Sahirul Kaylie , Lajeune Callista , Ivathraya Varsha , Addy Tiffany , Sanchez Patricia , Holbrook Colin , Van Ho Andrew Tri , Duncan James S. , Blau Helen M. , Levchenko Andre , Krause Diane S. 
Published: September 2022

AbstractSingle-cell assays have enriched our understanding of hematopoiesis and, more generally, stem and progenitor cell biology. However, these single-end-point approaches provide only a static snapshot of the state of a cell. To observe and measure dynamic changes that may instruct cell fate, we developed an approach for examining hematopoietic progenitor fate specification using long-term (> 7-day) single-cell time-lapse imaging for up to 13 generations with in situ fluorescence staining of primary human hematopoietic progenitors followed by algorithm-assisted lineage tracing. We analyzed progenitor cell dynamics, including the division rate, velocity, viability, and probability of lineage commitment at the single-cell level over time. We applied a Markov probabilistic model to predict progenitor division outcome over each generation in culture. We demonstrated the utility of this methodological pipeline by evaluating the effects of the cytokines thrombopoietin and erythropoietin on the dynamics of self-renewal and lineage specification in primary human bipotent megakaryocytic-erythroid progenitors (MEPs). Our data support the hypothesis that thrombopoietin and erythropoietin support the viability and self-renewal of MEPs, but do not affect fate specification. Thus, single-cell tracking of time-lapse imaged colony-forming unit assays provides a robust method for assessing the dynamics of progenitor self-renewal and lineage commitment.
An ultrasound-induced wireless power supply based on AlN piezoelectric micromachined ultrasonic transducers
Authors: Rong Zhicong , Zhang Menglun , Ning Yuan , Pang Wei 
Published: September 2022

AbstractWireless power transfer is one of the enabling technologies for powering implantable biomedical devices. Biocompatibility and CMOS compatibility of wireless power transfer devices are highly desired due to safety and footprint concerns. Toward implantable applications, this paper presents an ultrasound-induced wireless power supply based on AlN piezoelectric micromachined ultrasonic transducer (PMUT). The wireless power supply integrates wireless power transfer, power management and energy storage functions. The PMUT array is used as a passive wireless power receiver, followed by electrical impedance matching networks and a voltage multiplier for efficient power transmission and rectification. The output power intensity of the wireless receiver reaches 7.36 μW/mm2with an incident ultrasound power below the FDA safety limit. The output power of the wireless power supply reaches 18.8 μW and a 100-μF capacitor is fully charged to 3.19 V after power management, which are sufficient to power many low-power implantable biomedical devices such as for neural electrical stimulation, biosensors and intrabody communication applications. The wireless power supply is implemented in a PCB with a diameter of 1 cm. With biocompatibility and CMOS compatibility of AlN thin film compared to commonly used PZT, the proposed solution paves the way for safer and ultraminiaturized wireless power supplies with further development incorporating all the functions on a monolithic chip in the future.
Effect of processing parameters on texture and variant selection of as-built 300 maraging steel processed by laser powder bed fusion
Authors: Eres-Castellanos Adriana , Santana Ana , De-Castro David , Jimenez Jose Antonio , Rementeria Rosalia , Capdevila Carlos , Caballero Francisca G. 
Published: September 2022

AbstractAmong the materials that might be manufactured with laser powder bed fusion (LPBF), one can highlight maraging steels, with excellent weldability, strength and fracture toughness. However, the effects of the processing parameters and the mechanisms governing the as-built texture are not clear yet. A recent publication showed a low texture index in the prior austenite, in contrast to other alloys subjected to LPBF with the same strategy. Authors suggested several hypotheses, although no conclusions were drawn. This work aims to investigate these findings by using a 300 maraging steel processed under different conditions, i.e. different printer, powder layer thickness and laser emission mode. To do so, X-Ray Diffraction, Electron Backscattered Diffraction and Scanning Electron Microscopy have been used. Results show that the heat treatment intrinsic to the LPBF process does not affect the prior austenite grains, whose texture and morphology remain unchanged throughout the process. Also, for the studied ranges, the microstructure texture is not related to the powder layer thickness or to the laser emission mode, although it could be affected by the laser power or the scan strategy. Finally, a low degree of variant selection has been observed, where the selected variants are those that contribute to a martensite cubic rotated texture.
Attomolar sensitivity microRNA detection using real-time digital microarrays
Authors: Ekiz Kanik Fulya , Celebi Iris , Sevenler Derin , Tanriverdi Kahraman , Lortlar Ünlü Nese , Freedman Jane E. , Ünlü M. Selim 
Published: September 2022

AbstractMicroRNAs (miRNAs) are a family of noncoding, functional RNAs. With recent developments in molecular biology, miRNA detection has attracted significant interest, as hundreds of miRNAs and their expression levels have shown to be linked to various diseases such as infections, cardiovascular disorders and cancers. A powerful and high throughput tool for nucleic acid detection is the DNA microarray technology. However, conventional methods do not meet the demands in sensitivity and specificity, presenting significant challenges for the adaptation of miRNA detection for diagnostic applications. In this study, we developed a highly sensitive and multiplexed digital microarray using plasmonic gold nanorods as labels. For proof of concept studies, we conducted experiments with two miRNAs, miRNA-451a (miR-451) and miRNA-223-3p (miR-223). We demonstrated improvements in sensitivity in comparison to traditional end-point assays that employ capture on solid phase support, by implementing real-time tracking of the target molecules on the sensor surface. Particle tracking overcomes the sensitivity limitations for detection of low-abundance biomarkers in the presence of low-affinity but high-abundance background molecules, where endpoint assays fall short. The absolute lowest measured concentration was 100 aM. The measured detection limit being well above the blank samples, we performed theoretical calculations for an extrapolated limit of detection (LOD). The dynamic tracking improved the extrapolated LODs from femtomolar range to $$\sim$$
∼
10 attomolar (less than 1300 copies in 0.2 ml of sample) for both miRNAs and the total incubation time was decreased from 5 h to 35 min.
Hand dexterity, daily functioning and health-related quality of life in kidney transplant recipients
Authors: Knobbe Tim J. , Kremer Daan , Eisenga Michele F. , Corpeleijn Eva , Annema Coby , Spikman Joke M. ,   Transplantlines Investigators, Annema Coby , Bakker Stephan J. L. , Berger Stefan P. , Blokzijl Hans , Bodewes Frank , de Boer Marieke T. , Damman Kevin , de Borst Martin H. , Diepstra Arjan , Dijkstra Gerard , Douwes Rianne M. , Eisenga Michele F. , Erasmus Michiel E. , Tji Gan C. , Gomes Neto Antonio W. , Grootjans Heleen , Hak Eelko , Rebecca Heiner-Fokkema M. , Hepkema Bouke G. , Klont Frank , Knobbe Tim J. , Kremer Daan , Leuvenink Henri G. D. , Lexmond Willem S. , de Meijer Vincent E. , Niesters Hubert G. M. , van Pelt L. Joost , Pol Robert J. , Porte Robert J. , Ranchor Adelita V. , Sanders Jan Stephan F. , Schutten Joëlle C. , Siebelink Marion J. , Slart Riemer J. H. J. A. , Casper Swarte J. , Timens Wim , Touw Daan J. , van den Heuvel Marius C. , van Leer-Buter Coretta C. , van Londen Marco , Verschuuren Erik A. M. , Vos Michel J. , Weersma Rinse K. , Navis Gerjan , Berger Stefan P. , Bakker Stephan J. L. 
Published: September 2022

AbstractImpaired interplay between sensory and motor function may be an important, often overlooked cause of the decreased daily functioning and impaired health-related quality of life (HRQoL) of kidney transplant recipients (KTR). We assessed this interplay using a hand dexterity test, and investigated its potential associations with daily functioning and HRQoL among KTR enrolled at the TransplantLines Biobank and Cohort Study. A total of 309 KTR (58% male, mean age 56 ± 13 years) at median 4 [IQR: 1–11] years after transplantation were included. Impaired hand dexterity, as defined by a test performance slower than the 95th percentile of an age- and sex-specific reference population, was observed in 71 (23%) KTR. Worse hand dexterity was independently associated with worse performance on almost all measures of physical capacity, activities of daily living and societal participation. Finally, hand dexterity was independently associated with physical HRQoL (standardized beta − 0.22, 95%CI − 0.34 to − 0.09, P < 0.001). In conclusion, impaired interplay between sensory and motor function, as assessed by hand dexterity, is prevalent among KTR. In addition, poor hand dexterity was associated with impaired daily functioning and limited physical HRQoL. Impaired interplay between sensory and motor function may be therefore an important, hitherto overlooked, phenomenon in KTR.
Synthesis, biological evaluation, and molecular modeling studies of new benzoxazole derivatives as PARP-2 inhibitors targeting breast cancer
Authors: El-Ghobashy Nadeen M. , El-Sayed Selwan M. , Shehata Ihsan A. , El-Ashmawy Mahmoud B. 
Published: September 2022

AbstractMany benzoxazole-based and similar scaffolds were reported to have wide-range of anticancer activities. In this study, four series of benzoxazole derivatives were designed by combining benzoxazole scaffold with different amines via a reversed phenyl amide linker to produce the compounds of series A, B and C. A fourth new hybrid of benzoxazole with 1,2,3 triazole ring (series D) was also designed. The designed compounds were synthesized and screened for their anti-breast cancer activity against MDA-MB-231 and MCF-7 cell lines using MTT assay. The most potent cytotoxic compounds; 11–14, 21, 22, 25–27 were further evaluated for their in vitro PARP-2 enzyme inhibition. Compounds 12 and 27 proved to be the most active PARP-2 inhibitors with IC50 values of 0.07 and 0.057 µM, respectively. Compounds 12 and 27 caused cell cycle arrest in mutant MCF-7 cell line at G2/M and G1/S phase, respectively and they possessed significant apoptosis-promoting activity. Docking results of compounds 12 and 27 into PARP-2 pocket demonstrated binding interactions comparable to those of olaparib. Their predicted pharmacokinetic parameters and oral bioavailability appeared to be appropriate. Collectively, it could be concluded that compounds 12 and 27 are promising anti-breast cancer agents that act as PARP-2 inhibitors with potent apoptotic activity.
Probiotics suppress nonalcoholic steatohepatitis and carcinogenesis progression in hepatocyte-specific PTEN knockout mice
Authors: Arai Naoshi , Miura Kouichi , Aizawa Kenichi , Sekiya Mariko , Nagayama Manabu , Sakamoto Hirotsugu , Maeda Hiroshi , Morimoto Naoki , Iwamoto Sadahiko , Yamamoto Hironori 
Published: September 2022

AbstractNonalcoholic fatty liver disease (NAFLD), a hepatic characteristic of metabolic syndrome, received significant attention in clinical settings. The multiple-hit theory is one of the proposed mechanisms of NAFLD, and gut dysbiosis is considered a hit. Thus, controlling gut microbiota is a potential target in the management of NAFLD, and probiotics can be used as a treatment agent for NAFLD. The current study aimed to investigate the efficacy of probiotics against nonalcoholic steatohepatitis in a hepatocyte-specific PTEN knockout mouse model that mimics the characteristics of human NAFLD. Probiotics were administered to male knockout mice for 8 or 40 weeks. Next, we assessed hepatic inflammation, fibrosis, carcinogenesis, and oxidative stress. Probiotics were found to reduce serum transaminase levels, NAFLD activity score, and the gene expression of pro-inflammatory cytokines. In addition, they decreased liver fibrosis grade, which was examined via Sirius red staining, gene expression of fibrotic markers, and hydroxyproline. Furthermore, probiotics suppressed the number of liver tumors, particular in HCC. Probiotics reduced oxidative stresses, including glutathione levels, and anti-oxidative stress marker, which may be an underlying mechanism for their beneficial effects. In conclusion, probiotics treatment had beneficial effects against NAFLD and carcinogenesis in hepatocyte-specific PTEN knockout mice.
Application of machine learning in predicting oil rate decline for Bakken shale oil wells
Authors: Bhattacharyya Subhrajyoti , Vyas Aditya 
Published: September 2022

AbstractCommercial reservoir simulators are required to solve discretized mass-balance equations. When the reservoir becomes heterogeneous and complex, more grid blocks can be used, which requires detailed and accurate reservoir information, for e.g. porosity, permeability, and other parameters that are not always available in the field. Predicting the EUR (Estimated Ultimate Recovery) and rate decline for a single well can therefore take hours or days, making them computationally expensive and time-consuming. In contrast, decline curve models are a simpler and speedier option because they only require a few variables in the equation that can be easily gathered from the wells' current data. The well data for this study was gathered from the Montana Board of Oil and Gas Conservation's publicly accessible databases. The SEDM (Stretched Exponential Decline Model) decline curve equation variables specifically designed for unconventional reservoirs variables were correlated to the predictor parameters in a random oil field well data set. The study examined the relative influences of several well parameters. The study's novelty comes from developing an innovative machine learning (ML) (random forest (RF)) based model for fast rate-decline and EUR prediction in Bakken Shale oil wells. The successful application of this study relies highly on the availability of good quality and quantity of the dataset.
Dual attention network for unsupervised medical image registration based on VoxelMorph
Authors: Li Yong-xin , Tang Hui , Wang Wei , Zhang Xiu-feng , Qu Hang 
Published: September 2022

AbstractAn accurate medical image registration is crucial in a variety of neuroscience and clinical studies. In this paper, we proposed a new unsupervised learning network, DAVoxelMorph to improve the accuracy of 3D deformable medical image registration. Based on the VoxelMorph model, our network presented two modifications, one is adding a dual attention architecture, specifically, we model semantic correlation on spatial and coordinate dimensions respectively, and the location attention module selectively aggregates the features of each location by weighting the features of all locations. The coordinate attention module further puts the location information into the channel attention. The other is introducing the bending penalty as regularization in the loss function to penalize the bending in the deformation field. Experimental results show that DAVoxelMorph achieved better registration performance including average Dice scores (0.714) and percentage of locations with non-positive Jacobian (0.345) compare with VoxelMorph (0.703, 0.355), CycleMorph (0.705, 0.133), ANTs SyN (0.707, 0.137) and NiftyReg (0.694, 0.549). Our model increases both model sensitivity and registration accuracy.