bluuebunny/crossref_metadata_2025 huggingface dataset:
The Institutional Environment, Human Capital Development, and Productivity-Enhancing Factors: Evidence from ASEAN Countries
Authors: Tasane Helery , Srun Sopheak
Published: March 2023

We explored the nexus between the quality of human capital, productivity-enhancing factors, and the quality of institutions in nine Association of Southeast Asian Nations (ASEAN) countries using canonical correlation and principal component analysis of country-level data for 2007–2017 from the World Bank, World Economic Forum, and Penn World Tables databases. We found that an unequal development of human capital in the ASEAN countries is clearly linked to their heterogeneous institutional conditions and that the quality of human capital drives technology absorption and innovation. The four transition economies in the region—Laos, Cambodia, Vietnam, and Myanmar—are facing particularly difficult challenges in developing institutional environments that stimulate human capital development to reach higher levels of knowledge intensity of their economies and achieve the resulting competitive advantages.
Interacting Effects of Watershed and Coastal Processes on the Evolution of Compound Flooding During Hurricane Irene
Authors: Deb Mithun , Sun Ning , Yang Zhaoqing , Wang Taiping , Judi David , Xiao Ziyu , Wigmosta Mark S.
Published: March 2023

In low‐lying estuarine regions, compound flooding (CF) is caused by the co‐occurrence of extreme precipitation, river flooding and storm surge. In recent decades, there has been a rise in the frequency and intensity of pluvial‐coastal CF events in different parts of the U.S. due to the increased frequency of intense precipitation and storm surge events. However, in estuarine and deltaic regions, the CF characteristics depend mainly on the storm tide and river flow interaction. Understanding how the fluvial‐coastal CF may respond to changes to watershed and estuarine characteristics is essential for future CF hazard prediction. This study examined two critical processes: (a) the interplay between antecedent soil moisture conditions and peak river flow, and (b) how the impact of sea level rise (SLR) on storm surge and river flood distribution alters the CF in complex estuaries. As the study area, we selected the Delaware Bay and River, a shallow and convergent estuary in the US Mid‐Atlantic region—where flood hazards during a CF can become more significant than the surge and river flood processes occurring in isolation. For the focal event for the study, we selected Hurricane Irene (2011) because it reportedly produced the most extreme CF over the past two decades in the same region. Ultimately, our results illustrated that the potential changes to the catchment and bay characteristics from the global temperature increase and SLR could significantly modulate the fluvial‐coastal CF variability. The potential increase in global temperature and rainfall intensity might not always exacerbate the CF.
A Review of Speleothems as Archives for Paleofire Proxies, With Australian Case Studies
Authors: Campbell Micheline , McDonough Liza , Treble Pauline C. , Baker Andy , Kosarac Nevena , Coleborn Katie , Wynn Peter M. , Schmitt Axel K.
Published: March 2023

Wildfires affect 40% of the earth's terrestrial biome, but much of our knowledge of wildfire activity is limited to the satellite era. Improved understanding of past fires is necessary to better forecast how fire regimes might change with future climate change, to understand ecosystem resilience to fire, and to improve data‐model comparisons. Environmental proxy archives can extend our knowledge of past fire activity. Speleothems, naturally occurring cave formations, are widely used in paleoenvironmental research as they are absolutely dateable, occur on every ice‐free continent, and include multiple proxies. Recently, speleothems have been shown to record past fire events (Argiriadis et al., 2019, https://doi.org/10.1021/acs.analchem.9b00767; McDonough et al., 2022, https://doi.org/10.1016/j.gca.2022.03.020; Homann et al., 2022, https://doi.org/10.1038/s41467-022-34950-x). Here we present a review of this emerging application in speleothem paleoenvironmental science. We give a concise overview of fire regimes and common paleofire proxies, describe past attempts to use stalagmites to investigate paleofire, and describe the physical basis through which speleothems can record past fires. We then describe the ideal speleothem sample for paleofire research and offer a summary of applicable laboratory and statistical methods. Finally, we present four case studies from southwest Australia which: (a) explore the geochemistry of ash leachates, (b) detail how sulfate isotopes may be a proxy for post fire ecological recovery, (c) demonstrate how a catastrophic paleofire was linked to changes in climate and land management, and (d) investigate whether deep caves can record past fire events. We conclude the paper by outlining future research directions for paleofire applications.
Veterinary Antibiotics Reduce Soil Carbon Sequestration Capacity
Authors: Pardikar Rishika
Published: March 2023

Livestock grazing areas sequester less carbon than those under wild herbivores.
Artificial-intelligence-assisted mass fabrication of nanocantilevers from randomly positioned single carbon nanotubes
Authors: Tadokoro Yukihiro , Funayama Keita , Kawano Keisuke , Miura Atsushi , Hirotani Jun , Ohno Yutaka , Tanaka Hiroya
Published: March 2023

Nanoscale cantilevers (nanocantilevers) made from carbon nanotubes (CNTs) provide tremendous benefits in sensing and electromagnetic applications. This nanoscale structure is generally fabricated using chemical vapor deposition and/or dielectrophoresis, which contain manual, time-consuming processes such as the placing of additional electrodes and careful observation of single-grown CNTs. Here, we demonstrate a simple and Artificial Intelligence (AI)-assisted method for the efficient fabrication of a massive CNT-based nanocantilever. We used randomly positioned single CNTs on the substrate. The trained deep neural network recognizes the CNTs, measures their positions, and determines the edge of the CNT on which an electrode should be clamped to form a nanocantilever. Our experiments demonstrate that the recognition and measurement processes are automatically completed in 2 s, whereas comparable manual processing requires 12 h. Notwithstanding the small measurement error by the trained network (within 200 nm for 90% of the recognized CNTs), more than 34 nanocantilevers were successfully fabricated in one process. Such high accuracy contributes to the development of a massive field emitter using the CNT-based nanocantilever, in which the output current is obtained with a low applied voltage. We further showed the benefit of fabricating massive CNT-nanocantilever-based field emitters for neuromorphic computing. The activation function, which is a key function in a neural network, was physically realized using an individual CNT-based field emitter. The introduced neural network with the CNT-based field emitters recognized handwritten images successfully. We believe that our method can accelerate the research and development of CNT-based nanocantilevers for realizing promising future applications.
BrainGENIE: The Brain Gene Expression and Network Imputation Engine
Authors: Hess Jonathan L. , Quinn Thomas P. , Zhang Chunling , Hearn Gentry C. , Chen Samuel ,   Neuropsychiatric Consortium for Analysis and Sharing of Transcriptomes, Beveridge Natalie Jane , Carr Vaughan , de Jong Simone , Gardiner Erin , Kelly Brian , Kumarasinghe Nishantha , Ophoff Roel , Schall Ulrich , Scott Rodney , Stamova Boryana , Tooney Paul , Kong Sek Won , Cairns Murray , Tsuang Ming T. , Faraone Stephen V. , Glatt Stephen J.
Published: March 2023

In vivo experimental analysis of human brain tissue poses substantial challenges and ethical concerns. To address this problem, we developed a computational method called the Brain Gene Expression and Network-Imputation Engine (BrainGENIE) that leverages peripheral-blood transcriptomes to predict brain tissue-specific gene-expression levels. Paired blood–brain transcriptomic data collected by the Genotype-Tissue Expression (GTEx) Project was used to train BrainGENIE models to predict gene-expression levels in ten distinct brain regions using whole-blood gene-expression profiles. The performance of BrainGENIE was compared to PrediXcan, a popular method for imputing gene expression levels from genotypes. BrainGENIE significantly predicted brain tissue-specific expression levels for 2947–11,816 genes (false-discovery rate-adjusted p < 0.05), including many transcripts that cannot be predicted significantly by a transcriptome-imputation method such as PrediXcan. BrainGENIE recapitulated measured diagnosis-related gene-expression changes in the brain for autism, bipolar disorder, and schizophrenia better than direct correlations from blood and predictions from PrediXcan. We developed a convenient software toolset for deploying BrainGENIE, and provide recommendations for how best to implement models. BrainGENIE complements and, in some ways, outperforms existing transcriptome-imputation tools, providing biologically meaningful predictions and opening new research avenues.
Satellites reveal hotspots of global river extent change
Authors: Wu Qianhan , Ke Linghong , Wang Jida , Pavelsky Tamlin M. , Allen George H. , Sheng Yongwei , Duan Xuejun , Zhu Yunqiang , Wu Jin , Wang Lei , Liu Kai , Chen Tan , Zhang Wensong , Fan Chenyu , Yong Bin , Song Chunqiao
Published: March 2023

Rivers are among the most diverse, dynamic, and productive ecosystems on Earth. River flow regimes are constantly changing, but characterizing and understanding such changes have been challenging from a long-term and global perspective. By analyzing water extent variations observed from four-decade Landsat imagery, we here provide a global attribution of the recent changes in river regime to morphological dynamics (e.g., channel shifting and anabranching), expansion induced by new dams, and hydrological signals of widening and narrowing. Morphological dynamics prevailed in ~20% of the global river area. Booming reservoir constructions, mostly skewed in Asia and South America, contributed to ~32% of the river widening. The remaining hydrological signals were characterized by contrasting hotspots, including prominent river widening in alpine and pan-Arctic regions and narrowing in the arid/semi-arid continental interiors, driven by varying trends in climate forcing, cryospheric response to warming, and human water management. Our findings suggest that the recent river extent dynamics diverge based on hydroclimate and socio-economic conditions, and besides reflecting ongoing morphodynamical processes, river extent changes show close connections with external forcings, including climate change and anthropogenic interference.
Assessment of community efforts to advance network-based prediction of protein–protein interactions
Authors: Wang Xu-Wen , Madeddu Lorenzo , Spirohn Kerstin , Martini Leonardo , Fazzone Adriano , Becchetti Luca , Wytock Thomas P. , Kovács István A. , Balogh Olivér M. , Benczik Bettina , Pétervári Mátyás , Ágg Bence , Ferdinandy Péter , Vulliard Loan , Menche Jörg , Colonnese Stefania , Petti Manuela , Scarano Gaetano , Cuomo Francesca , Hao Tong , Laval Florent , Willems Luc , Twizere Jean-Claude , Vidal Marc , Calderwood Michael A. , Petrillo Enrico , Barabási Albert-László , Silverman Edwin K. , Loscalzo Joseph , Velardi Paola , Liu Yang-Yu
Published: March 2023

Comprehensive understanding of the human protein-protein interaction (PPI) network, aka the human interactome, can provide important insights into the molecular mechanisms of complex biological processes and diseases. Despite the remarkable experimental efforts undertaken to date to determine the structure of the human interactome, many PPIs remain unmapped. Computational approaches, especially network-based methods, can facilitate the identification of previously uncharacterized PPIs. Many such methods have been proposed. Yet, a systematic evaluation of existing network-based methods in predicting PPIs is still lacking. Here, we report community efforts initiated by the International Network Medicine Consortium to benchmark the ability of 26 representative network-based methods to predict PPIs across six different interactomes of four different organisms: A. thaliana, C. elegans, S. cerevisiae, and H. sapiens. Through extensive computational and experimental validations, we found that advanced similarity-based methods, which leverage the underlying network characteristics of PPIs, show superior performance over other general link prediction methods in the interactomes we considered.
Insights into receptor structure and dynamics at the surface of living cells
Authors: Steiert Frederik , Schultz Peter , Höfinger Siegfried , Müller Thomas D. , Schwille Petra , Weidemann Thomas
Published: March 2023

Evaluating protein structures in living cells remains a challenge. Here, we investigate Interleukin-4 receptor alpha (IL-4Rα) into which the non-canonical amino acid bicyclo[6.1.0]nonyne-lysine (BCNK) is incorporated by genetic code expansion. Bioorthogonal click labeling is performed with tetrazine-conjugated dyes. To quantify the reaction yield in situ, we develop brightness-calibrated ratiometric imaging, a protocol where fluorescent signals in confocal multi-color images are ascribed to local concentrations. Screening receptor mutants bearing BCNK in the extracellular domain uncovered site-specific variations of both click efficiency and Interleukin-4 binding affinity, indicating subtle well-defined structural perturbations. Molecular dynamics and continuum electrostatics calculations suggest solvent polarization to determine site-specific variations of BCNK reactivity. Strikingly, signatures of differential click efficiency, measured for IL-4Rα in ligand-bound and free form, mirror sub-angstrom deformations of the protein backbone at corresponding locations. Thus, click efficiency by itself represents a remarkably informative readout linked to protein structure and dynamics in the native plasma membrane.
A defect in mitochondrial protein translation influences mitonuclear communication in the heart
Authors: Gao Feng , Liang Tian , Lu Yao Wei , Fu Xuyang , Dong Xiaoxuan , Pu Linbin , Hong Tingting , Zhou Yuxia , Zhang Yu , Liu Ning , Zhang Feng , Liu Jianming , Malizia Andrea P. , Yu Hong , Zhu Wei , Cowan Douglas B. , Chen Hong , Hu Xinyang , Mably John D. , Wang Jian’an , Wang Da-Zhi , Chen Jinghai
Published: March 2023

The regulation of the informational flow from the mitochondria to the nucleus (mitonuclear communication) is not fully characterized in the heart. We have determined that mitochondrial ribosomal protein S5 (MRPS5/uS5m) can regulate cardiac function and key pathways to coordinate this process during cardiac stress. We demonstrate that loss of Mrps5 in the developing heart leads to cardiac defects and embryonic lethality while postnatal loss induces cardiac hypertrophy and heart failure. The structure and function of mitochondria is disrupted in Mrps5 mutant cardiomyocytes, impairing mitochondrial protein translation and OXPHOS. We identify Klf15 as a Mrps5 downstream target and demonstrate that exogenous Klf15 is able to rescue the overt defects and re-balance the cardiac metabolome. We further show that Mrps5 represses Klf15 expression through c-myc, together with the metabolite L-phenylalanine. This critical role for Mrps5 in cardiac metabolism and mitonuclear communication highlights its potential as a target for heart failure therapies.
A helium-burning white dwarf binary as a supersoft X-ray source
Authors: Greiner J. , Maitra C. , Haberl F. , Willer R. , Burgess J. M. , Langer N. , Bodensteiner J. , Buckley D. A. H. , Monageng I. M. , Udalski A. , Ritter H. , Werner K. , Maggi P. , Jayaraman R. , Vanderspek R.
Published: March 2023

Type Ia supernovae are cosmic distance indicators1,2, and the main source of iron in the Universe3,4, but their formation paths are still debated. Several dozen supersoft X-ray sources, in which a white dwarf accretes hydrogen-rich matter from a non-degenerate donor star, have been observed5 and suggested as Type Ia supernovae progenitors6–9. However, observational evidence for hydrogen, which is expected to be stripped off the donor star during the supernova explosion10, is lacking. Helium-accreting white dwarfs, which would circumvent this problem, have been predicted for more than 30 years (refs. 7,11,12), including their appearance as supersoft X-ray sources, but have so far escaped detection. Here we report a supersoft X-ray source with an accretion disk whose optical spectrum is completely dominated by helium, suggesting that the donor star is hydrogen-free. We interpret the luminous and supersoft X-rays as resulting from helium burning near the surface of the accreting white dwarf. The properties of our system provide evidence for extended pathways towards Chandrasekhar-mass explosions based on helium accretion, in particular for stable burning in white dwarfs at lower accretion rates than expected so far. This may allow us to recover the population of the sub-energetic so-called Type Iax supernovae, up to 30% of all Type Ia supernovae13, within this scenario.
RHOJ controls EMT-associated resistance to chemotherapy
Authors: Debaugnies Maud , Rodríguez-Acebes Sara , Blondeau Jeremy , Parent Marie-Astrid , Zocco Manuel , Song Yura , de Maertelaer Viviane , Moers Virginie , Latil Mathilde , Dubois Christine , Coulonval Katia , Impens Francis , Van Haver Delphi , Dufour Sara , Uemura Akiyoshi , Sotiropoulou Panagiota A. , Méndez Juan , Blanpain Cédric
Published: March 2023

The resistance of cancer cells to therapy is responsible for the death of most patients with cancer1. Epithelial-to-mesenchymal transition (EMT) has been associated with resistance to therapy in different cancer cells2,3. However, the mechanisms by which EMT mediates resistance to therapy remain poorly understood. Here, using a mouse model of skin squamous cell carcinoma undergoing spontaneous EMT during tumorigenesis, we found that EMT tumour cells are highly resistant to a wide range of anti-cancer therapies both in vivo and in vitro. Using gain and loss of function studies in vitro and in vivo, we found that RHOJ—a small GTPase that is preferentially expressed in EMT cancer cells—controls resistance to therapy. Using genome-wide transcriptomic and proteomic profiling, we found that RHOJ regulates EMT-associated resistance to chemotherapy by enhancing the response to replicative stress and activating the DNA-damage response, enabling tumour cells to rapidly repair DNA lesions induced by chemotherapy. RHOJ interacts with proteins that regulate nuclear actin, and inhibition of actin polymerization sensitizes EMT tumour cells to chemotherapy-induced cell death in a RHOJ-dependent manner. Together, our study uncovers the role and the mechanisms through which RHOJ acts as a key regulator of EMT-associated resistance to chemotherapy.
Ultrafast structural changes direct the first molecular events of vision
Authors: Gruhl Thomas , Weinert Tobias , Rodrigues Matthew J. , Milne Christopher J. , Ortolani Giorgia , Nass Karol , Nango Eriko , Sen Saumik , Johnson Philip J. M. , Cirelli Claudio , Furrer Antonia , Mous Sandra , Skopintsev Petr , James Daniel , Dworkowski Florian , Båth Petra , Kekilli Demet , Ozerov Dmitry , Tanaka Rie , Glover Hannah , Bacellar Camila , Brünle Steffen , Casadei Cecilia M. , Diethelm Azeglio D. , Gashi Dardan , Gotthard Guillaume , Guixà-González Ramon , Joti Yasumasa , Kabanova Victoria , Knopp Gregor , Lesca Elena , Ma Pikyee , Martiel Isabelle , Mühle Jonas , Owada Shigeki , Pamula Filip , Sarabi Daniel , Tejero Oliver , Tsai Ching-Ju , Varma Niranjan , Wach Anna , Boutet Sébastien , Tono Kensuke , Nogly Przemyslaw , Deupi Xavier , Iwata So , Neutze Richard , Standfuss Jörg , Schertler Gebhard , Panneels Valerie
Published: March 2023

Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
Influence of Allee effect on the spatiotemporal behavior of a diffusive predator–prey model with Crowley–Martin type response function
Authors: Guin Lakshmi Narayan , Pal Pallav Jyoti , Alzahrani Jawaher , Ali Nijamuddin , Sarkar Krishnendu , Djilali Salih , Zeb Anwar , Khan Ilyas , Eldin Sayed M
Published: March 2023

The present paper is dealt with a predator–prey model in which the growth of the prey population is influenced by the Allee effect while the predator species are contended with the prey population following the Crowley–Martin type response function. The proposed model is comprehensively analyzed in terms of stability and manifestation of bifurcation of the system. The system unveils the bi-stability together with the existence of a separatrix. In view of the eminence of spatial ecology, the dynamical complexity emanating from the induction of the Allee effect in prey species of a Crowley–Martin reaction–diffusion predator–prey model is also investigated profoundly. The results of numerical simulations reveal that the present system dynamics is motivated by both the Allee effect and diffusion-controlled pattern formation growth to hot spots, stripe-hot spot mixtures, stripes, labyrinthine, stripe-cold spot mixtures, and cold spots replication. The theoretical consequences of the spatiotemporal model under study are validated through numerical simulations.
Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing
Authors: Islam Md. Ariful , Kibria Md. Kaderi , Hossen Md. Bayazid , Reza Md. Selim , Tasmia Samme Amena , Tuly Khanis Farhana , Mosharof Md. Parvez , Kabir Syed Rashel , Kabir Md. Hadiul , Mollah Md. Nurul Haque
Published: March 2023

Some recent studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and idiopathic pulmonary fibrosis (IPF) disease might stimulate each other through the shared genes. Therefore, in this study, an attempt was made to explore common genomic biomarkers for SARS-CoV-2 infections and IPF disease highlighting their functions, pathways, regulators and associated drug molecules. At first, we identified 32 statistically significant common differentially expressed genes (cDEGs) between disease (SARS-CoV-2 and IPF) and control samples of RNA-Seq profiles by using a statistical r-package (edgeR). Then we detected 10 cDEGs (CXCR4, TNFAIP3, VCAM1, NLRP3, TNFAIP6, SELE, MX2, IRF4, UBD and CH25H) out of 32 as the common hub genes (cHubGs) by the protein–protein interaction (PPI) network analysis. The cHubGs regulatory network analysis detected few key TFs-proteins and miRNAs as the transcriptional and post-transcriptional regulators of cHubGs. The cDEGs-set enrichment analysis identified some crucial SARS-CoV-2 and IPF causing common molecular mechanisms including biological processes, molecular functions, cellular components and signaling pathways. Then, we suggested the cHubGs-guided top-ranked 10 candidate drug molecules (Tegobuvir, Nilotinib, Digoxin, Proscillaridin, Simeprevir, Sorafenib, Torin 2, Rapamycin, Vancomycin and Hesperidin) for the treatment against SARS-CoV-2 infections with IFP diseases as comorbidity. Finally, we investigated the resistance performance of our proposed drug molecules compare to the already published molecules, against the state-of-the-art alternatives publicly available top-ranked independent receptors by molecular docking analysis. Molecular docking results suggested that our proposed drug molecules would be more effective compare to the already published drug molecules. Thus, the findings of this study might be played a vital role for diagnosis and therapies of SARS-CoV-2 infections with IPF disease as comorbidity risk.
An experimental study of animating-based facial image manipulation in online class environments
Authors: Park Jeong-Ha , Lim Chae-Yun , Kwon Hyuk-Yoon
Published: March 2023

Recent advances in artificial intelligence technology have significantly improved facial image manipulation, which is known as Deepfake. Facial image manipulation synthesizes or replaces a region of the face in an image with that of another face. The techniques for facial image manipulation are classified into four categories: (1) entire face synthesis, (2) identity swap, (3) attribute manipulation, and (4) expression swap. Out of them, we focus on expression swap because it effectively manipulates only the expression of the face in the images or videos without creating or replacing the entire face, having advantages for the real-time application. In this study, we propose an evaluation framework of the expression swap models targeting the real-time online class environments. For this, we define three kinds of scenarios according to the portion of the face in the entire image considering actual online class situations: (1) attendance check (Scenario 1), (2) presentation (Scenario 2), and (3) examination (Scenario 3). Considering the manipulation on the online class environments, the framework receives a single source image and a target video and generates the video that manipulates a face of the target video to that in the source image. To this end, we select two models that satisfy the conditions required by the framework: (1) first order model and (2) GANimation. We implement these models in the framework and evaluate their performance for the defined scenarios. Through the quantitative and qualitative evaluation, we observe distinguishing properties of the used two models. Specifically, both models show acceptable results in Scenario 1, where the face occupies a large portion of the image. However, their performances are significantly degraded in Scenarios 2 and 3, where the face occupies less portion of the image; the first order model causes relatively less loss of image quality than GANimation in the result of the quantitative evaluation. In contrast, GANimation has the advantages of representing facial expression changes compared to the first order model. Finally, we devise an architecture for applying the expression swap model to the online video conferencing application in real-time. In particular, by applying the expression swap model to widely used online meeting platforms such as Zoom, Google Meet, and Microsoft Teams, we demonstrate its feasibility for real-time online classes.
Carbon nanotubes as a nitric oxide nano-reservoir improved the controlled release profile in 3D printed biodegradable vascular grafts
Authors: Kabirian Fatemeh , Baatsen Pieter , Smet Mario , Shavandi Amin , Mela Petra , Heying Ruth
Published: March 2023

Small diameter vascular grafts (SDVGs) are associated with a high failure rate due to poor endothelialization. The incorporation of a nitric oxide (NO) releasing system improves biocompatibility by using the NO effect to promote endothelial cell (EC) migration and proliferation while preventing bacterial infection. To circumvent the instability of NO donors and to prolong NO releasing, S-nitroso-N-acetyl-d-penicillamine (SNAP) as a NO donor was loaded in multi-walled carbon nanotubes (MWCNTs). Successful loading was confirmed with a maximum SNAP amount of ~ 5% (w/w) by TEM, CHNS analysis and FTIR spectra. SDVGs were 3D printed from polycaprolactone (PCL) and coated with a 1:1 ratio of polyethylene glycol and PCL dopped with different concentrations of SNAP-loaded matrix and combinations of MWCNTs-OH. Coating with 10% (w/w) SNAP-matrix-10% (w/w) SNAP-MWCNT-OH showed a diminished burst release and 18 days of NO release in the range of 0.5–4 × 10–10 mol cm−2 min−1 similar to the NO release from healthy endothelium. NO-releasing SDVGs were cytocompatible, significantly enhanced EC proliferation and migration and diminished bacterial viability. The newly developed SNAP-loaded MWCNT-OH has a great potential to develop NO releasing biomaterials with a prolonged, controlled NO release promoting in-situ endothelialization and tissue integration in vivo, even as an approach towards personalized medicine.
Speech therapy to overcome dyslexia in primary schoolers
Authors: Nurseitova Zhanar , Shayakhmetova Aisulu
Published: March 2023

This research was aimed to investigate changes in the reading technique and in terms of its semantic charge in primary schoolers diagnosed with dyslexia, which occur as a result of the integrated use of speech therapy techniques. The study was performed between 2016 and 2019 in 6 schools of Moscow and Almaty. It enrolled 194 and 200 children, respectively, who were examined with form I to III inclusive. The study revealed that 13% of children had reading speed disorders; they were constituted group 1. Another 11% had reading comprehension disorders; they constituted group 2. In group 1, by form III, the number of reading repetitions increased twofold. In group 2, the number of children, who read in words and phrases, increased by half; in group 1, it doubled. This research showed clear progress in children with technical dyslexia vs. those with semantic dyslexia. Based on the results, it is possible to develop a methodology for speech therapy techniques that can be suitable not only for speech therapists, but also for primary school teachers, as well as for parents of dyslectic children.
Light scattering in stacked mesophyll cells results in similarity characteristic of solar spectral reflectance and transmittance of natural leaves
Authors: Xu Kai , Ye Hong
Published: March 2023

Solar spectral reflectance and transmittance of natural leaves exhibit dramatic similarity. To elucidate the formation mechanism and physiological significance, a radiative transfer model was constructed, and the effects of stacked mesophyll cells, chlorophyll content and leaf thickness on the visible light absorptance of the natural leaves were analyzed. Results indicated that light scattering caused by the stacked mesophyll cells is responsible for the similarity. The optical path of visible light in the natural leaves is increased with the scattering process, resulting in that the visible light transmittance is significantly reduced meanwhile the visible light reflectance is at a low level, thus the visible light absorptance tends to a maximum and the absorption of photosynthetically active radiation (PAR) by the natural leaves is significantly enhanced. Interestingly, as two key leaf functional traits affecting the absorption process of PAR, chlorophyll content and leaf thickness of the natural leaves in a certain environment show a convergent behavior, resulting in the high visible light absorptance of the natural leaves, which demonstrates the PAR utilizing strategies of the natural leaves. This work provides a new perspective for revealing the evolutionary processes and ecological strategies of natural leaves, and can be adopted to guide the improvement directions of crop photosynthesis.
Reduced bimolecular charge recombination in efficient organic solar cells comprising non-fullerene acceptors
Authors: Wu Yue , Li Yungui , van der Zee Bas , Liu Wenlan , Markina Anastasia , Fan Hongyu , Yang Hang , Cui Chaohua , Li Yongfang , Blom Paul W. M. , Andrienko Denis , Wetzelaer Gert-Jan A. H.
Published: March 2023

Bimolecular charge recombination is one of the most important loss processes in organic solar cells. However, the bimolecular recombination rate in solar cells based on novel non-fullerene acceptors is mostly unclear. Moreover, the origin of the reduced-Langevin recombination rate in bulk heterojunction solar cells in general is still poorly understood. Here, we investigate the bimolecular recombination rate and charge transport in a series of high-performance organic solar cells based on non-fullerene acceptors. From steady-state dark injection measurements and drift–diffusion simulations of the current–voltage characteristics under illumination, Langevin reduction factors of up to over two orders of magnitude are observed. The reduced recombination is essential for the high fill factors of these solar cells. The Langevin reduction factors are observed to correlate with the quadrupole moment of the acceptors, which is responsible for band bending at the donor–acceptor interface, forming a barrier for charge recombination. Overall these results therefore show that suppressed bimolecular recombination is essential for the performance of organic solar cells and provide design rules for novel materials.
Learning to predict RNA sequence expressions from whole slide images with applications for search and classification
Authors: Alsaafin Areej , Safarpoor Amir , Sikaroudi Milad , Hipp Jason D. , Tizhoosh H. R.
Published: March 2023

Deep learning methods are widely applied in digital pathology to address clinical challenges such as prognosis and diagnosis. As one of the most recent applications, deep models have also been used to extract molecular features from whole slide images. Although molecular tests carry rich information, they are often expensive, time-consuming, and require additional tissue to sample. In this paper, we propose tRNAsformer, an attention-based topology that can learn both to predict the bulk RNA-seq from an image and represent the whole slide image of a glass slide simultaneously. The tRNAsformer uses multiple instance learning to solve a weakly supervised problem while the pixel-level annotation is not available for an image. We conducted several experiments and achieved better performance and faster convergence in comparison to the state-of-the-art algorithms. The proposed tRNAsformer can assist as a computational pathology tool to facilitate a new generation of search and classification methods by combining the tissue morphology and the molecular fingerprint of the biopsy samples.
Synthesis vs. salvage of ester- and ether-linked phosphatidylethanolamine in the intracellular protozoan pathogen Toxoplasma gondii
Authors: Ren Bingjian , Liang Xiaohan , Brouwers Jos F. , Miron Rosalba Cruz , Shen Bang , Gupta Nishith
Published: March 2023

Toxoplasma gondii is a prevalent zoonotic pathogen infecting livestock as well as humans. The exceptional ability of this parasite to reproduce in several types of nucleated host cells necessitates a coordinated usage of endogenous and host-derived nutritional resources for membrane biogenesis. Phosphatidylethanolamine is the second most common glycerophospholipid in T. gondii, but how its requirement in the acutely-infectious fast-dividing tachyzoite stage is satisfied remains enigmatic. This work reveals that the parasite deploys de novo synthesis and salvage pathways to meet its demand for ester- and ether-linked PtdEtn. Auxin-mediated depletion of the phosphoethanolamine cytidylyltransferase (ECT) caused a lethal phenotype in tachyzoites due to impaired invasion and cell division, disclosing a vital role of the CDP-ethanolamine pathway during the lytic cycle. In accord, the inner membrane complex appeared disrupted concurrent with a decline in its length, parasite width and major phospholipids. Integrated lipidomics and isotope analyses of the TgECT mutant unveiled the endogenous synthesis of ester-PtdEtn, and salvage of ether-linked lipids from host cells. In brief, this study demonstrates how T. gondii operates various means to produce distinct forms of PtdEtn while featuring the therapeutic relevance of its de novo synthesis.
International corporations trading Brazilian soy are keystone actors for water stewardship
Authors: De Petrillo Elena , Tuninetti Marta , Ridolfi Luca , Laio Francesco
Published: March 2023

Transnational corporations play a major, but poorly constrained, role in reallocating global water resources. Here, we couple high-resolution, company-specific trade data with hydrological and crop models to estimate the virtual water trade of the top 9 transnational corporations that trade Brazilian soy. We identify 4429 virtual water flows connecting 1620 Brazilian municipalities with the top-10 soy importing countries and find that the total virtual water flow increased from 43 billion m3 to 100 billion m3 between 2004 and 2018. We find that the largest soy traders displace on average twice as much virtual water as top-importing countries, excluding China. For example, in 2018 one transnational corporation exported 15 Gm3, almost tripling the Netherlands’s virtual water import (the second largest importer at about 5 Gm3). Our findings highlight the importance of transnational corporations for achieving water stewardship and sustainable supply chains to support water resource security at municipal and international scales.
Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments
Authors: Lynes Mackenzie M , Krukenberg Viola , Jay Zackary J , Kohtz Anthony J , Gobrogge Christine A , Spietz Rachel L , Hatzenpichler Roland
Published: March 2023

Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.
Smartphone-based point-of-care anemia screening in rural Bihar in India
Authors: Haggenmüller Verena , Bogler Lisa , Weber Ann-Charline , Kumar Abhijeet , Bärnighausen Till , Danquah Ina , Vollmer Sebastian
Published: March 2023

Background

The high prevalence of anemia in resource-constrained settings calls for easy-to-use, inexpensive screening tools. The Sanguina Smartphone App, an innovative tool for non-invasive hemoglobin estimation via color-sensitive, algorithm-based analysis of fingernail bed images, was validated in the United States. This study evaluates the performance of the App in a population with different socio-economic, ethnic, demographic and cultural composition in rural Bihar, India.

Methods

For 272 mainly adult patients of a private health centre, hemoglobin measurement with the App is compared with the gold standard laboratory blood analysis. For a second sample of 179 children attending pre-schools, hemoglobin measurement with the App is compared to the results of the HemoCue Hb 301, a point-of-care device using a small blood sample, serving as the reference standard for field-based settings.

Results

The App reaches ±4.43 g/dl accuracy and 0.38 g/dl bias of comparator values in the clinic-based sample, and ±3.54 g/dl and 1.30 g/dl, respectively in the pre-school sample. After retraining the algorithm with the collected data, the validity of the upgraded version is retested showing an improved performance (accuracy of ±2.25 g/dl, bias of 0.25 g/dl), corresponding to the results of the original validation study from the United States.

Conclusions

The initial version of the App does not achieve the accuracy needed for diagnosis or screening. After retraining the algorithm, it achieves an accuracy sufficient for screening. The improved version with the potential for further adaptions is a promising easy-to-use, inexpensive screening tool for anemia in resource-constrained point-of-care settings.
Major depression, physical health and molecular senescence markers abnormalities
Authors: Seitz-Holland Johanna , Mulsant Benoit H. , Reynolds III Charles F. , Blumberger Daniel M. , Karp Jordan F. , Butters Meryl A. , Mendes-Silva Ana Paula , Vieira Erica L. , Tseng George , Lenze Eric J. , Diniz Breno S.
Published: March 2023

Previous studies suggested the role of cellular senescence in late-life depression (LLD). However, it is unclear how this finding relates to common features of LLD, such as medical and cognitive problems. We applied factor analyses to an extensive battery of clinical variables in 426 individuals with LLD. Here we tested the relationship between these factors, age and sex, with an index of cellular senescence based on 22 senescence-associated secretory phenotype proteins. We found four factors: ‘depression and anxiety severity’, ‘cognitive functioning’, ‘cardiovascular and cardiometabolic health’ and ‘blood pressure’. A higher senescence-associated secretory phenotype index was associated with poorer ‘cognitive functioning’ and ‘cardiovascular and cardiometabolic health’ but not with ‘depression and anxiety severity’. These findings highlight the role of cellular senescence in poorer physical and cognitive health in LLD. They are consonant with the viewpoint that co-occurring medical burdens and their associated disabilities are part of a phenotype of accelerated ageing in LLD.
Nitrogen-doped carbon dots/Fe3+-based fluorescent probe for the “off–on” sensing of As(v) in seafood
Authors: Li Zeyi , Cao Yunrui , Feng Tingyu , Wei Tingting , Xue Changhu , Li Zhaojie , Xu Jie
Published: March 2023

Based on the competition between the electron transfer effect of nitrogen-doped carbon dots (N–CDs)/Fe3+and the complexation reaction of As(v)/Fe3+, an “off–on” fluorescence assay was developed to detect As(v) in complex food substrates.
Controlling the reduction rate and oxidative etching for high yield green synthesis of palladium nanorods in segmented millifluidic flow reactors (SMFRs)
Authors: Basnayake Pussepitiyalage Vindula , Hemmati Shohreh
Published: March 2023

This study explores the green synthesis of palladium nanorods using l-ascorbic acid as a green reducing agent in a segmented millifluidic flow reactor via controlling the reduction rate and oxidative etching.
Toxicological effects of pure and amine-functionalized ZnO nanorods on Daphnia magna and Lactuca sativa
Authors: Oscar Bianca Vicente Costa , Melegari Sílvia Pedroso , Vicentini Denice Schulz , Simioni Carmen , Ouriques Luciane Cristina , Puerari Rodrigo Costa , Matias William Gerson
Published: March 2023

Exposure to ZnO NRs can cause acute and chronic effects on D. magna and it was possible to visualize the internalization of ZnO NRs in the organisms. Effects on the germination, development, and morphology of L. sativa were also observed.
Cellular mechanisms of transcriptional regulation of human cell lines exposed to cadmium-based quantum dots
Authors: Paesano Laura , Vogli Megi , Marmiroli Marta , Bianchi Massimiliano G. , Bussolati Ovidio , Zappettini Andrea , Marmiroli Nelson
Published: March 2023

CdS QDs activate calcium signaling and apoptosis in HepG2 human hepatocytes. CdS QDs trigger inflammatory response and autophagy in THP-1 human macrophages.
Modification of starch by novel and traditional ways: influence on the structure and functional properties
Authors: Suri Shweta , Singh Ajay
Published: March 2023

Starch, a polymeric carbohydrate widely present in plant biomass, has gained popularity owing to its functional characteristics, lower cost and ability to completely decompose without any toxic byproducts.
Ingestion of taxifolin-rich foods affects brain activity, mental fatigue, and the whole blood transcriptome in healthy young adults: a randomized, double-blind, placebo-controlled, crossover study
Authors: Shinozaki Fumika , Kamei Asuka , Shimada Kousuke , Matsuura Hiroshi , Shibata Takeo , Ikeuchi Mayumi , Yasuda Kayo , Oroguchi Takashige , Kishimoto Noriaki , Takashimizu Shinji , Nishizaki Yasuhiro , Abe Keiko
Published: March 2023

Taxifolin, a polyphenol, is a strong antioxidant and is believed to exhibit various functions. This study is the first that showed the possibility of taxifolin to affect brain activity, mental stress and transcriptome in healthy young adults.
Protein powder supplementation in early pregnancy and the risk of gestational diabetes mellitus: a prospective cohort study
Authors: Yang Meng , Cao Zhongqiang , Zhou Jieqiong , Liu Jiuying , Zhong Yuanyuan , Zhou Yan , Cai Xiaonan , Yu Linling , Hu Liqin , Xiao Han , Zhou Aifen
Published: March 2023

Protein powder has attracted attention due to its possible adverse effects.
A 3D flower-like Co/Ni bimetallic organic framework as an excellent material for electrochemical determination of quercetin
Authors: Zheng Shengbiao , Liu Tianna , Zhang Nini , Li Liang , Zhu Yanli , Zhang Erhui , Tang Jing , Guo Jiahao
Published: March 2023

A scheme of the fabrication of 3D flower-like CoNi-MOF nanosheets and their application in electrocatalytic oxidation of quercetin.
A metal-free synthesis of pyrimidines from amidines with α,β-unsaturated ketonesviatandem [3 + 3] annulation and visible-light-enabled photo-oxidation
Authors: Liu Jinshan , Zhuo Jiatian , Tan Qi , Zhou Min , Ma Lin , Zhang Min
Published: March 2023

A facile synthesis of pyrimidines from amidines and α,β-unsaturated ketones, involving a [3 + 3] annulation followed by visible light photo-oxidation using air as terminal oxidant, is reported.
Fluorescent copolymer aggregate sensor for lithium chloride
Authors: Wang Hu , Jones Leighton O. , Zhao Tian , Hwang Inhong , Lynch Vincent M. , Khashab Niveen M. , Schatz George C. , Page Zachariah A. , Sessler Jonathan L.
Published: March 2023

We report a copolymeric lithium chloride selective fluorescent sensor. No fluorescence change is seen upon the addition of NaCl, KCl, MgCl2, or CaCl2, while a fluorescence decrease is seen upon the addition of LiCl.
Surface acoustic wave based microfluidic devices for biological applications
Authors: Liu Xianglian , Chen Xuan , Yang Ziwei , Xia He , Zhang Chuanyu , Wei Xueyong
Published: March 2023

This review chooses types of SAWs as the thread to run through various implements, and the notable set-ups and key features in each category are summarized and discussed in detail.
Developing an electrochemical sensor for thein vivomeasurements of dopamine
Authors: Delmo Naela , Mostafiz Bahar , Ross Ashley E. , Suni Johanna , Peltola Emilia
Published: March 2023

Measurements inside the human body are complicated.