bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bio-electricity production from Fibroblasts and their cultivation media
Authors: Shlosberg Yaniv , Lesman Ayelet 
Published: January 2024

AbstractThe recent understanding of the critical future damage that might happen on earth by climate change has urged scientists to initiate new creative ideas for clean energy technologies that will reduce carbon emissions. A promising approach is the utilization of living cells as electron donors in bio-electrochemical cells (BECs). This concept has been intensively studied for micro-organisms such as non-photosynthetic bacteria, cyanobacteria, and microalgae, but not for mammalian cells. In this work, we report for the first-time integrating live fibroblast cells in a BEC to produce electrical current that is about 3 times higher than intact micro-organisms. Furthermore, we apply 2D-fluorescence and electrochemical measurements to show that like in micro-organisms based BECs, NADH and flavins play a role in the electron mediation between the cells and the anode. Finally, we show that the cultivation medium of fibroblasts also consists of redox species that may produce dark and photocurrent.
Efficient value encoding through convergence of tactile and visual value information in the primate putamen
Authors: Hwang Seong-Hwan , Park Doyoung , Lee Ji-Woo , Lee Sue-Hyun , Kim Hyoung F. 
Published: January 2024

AbstractThe processing of diverse sensory values by a limited number of basal ganglia neurons raises the question of whether each value is processed independently or combined as the number of neurons decreases from the cortex to downstream structures. Here, we discovered that tactile and visual values were partially converged in the primate putamen, enhancing its efficiency in encoding values while preserving modality information. Humans and monkeys performed tactile and visual value discrimination tasks. Notably, the human putamen selectively represented both tactile and visual values in fMRI scans. Single-unit electrophysiology further revealed that half of the individual neurons in the macaque putamen encoded both tactile and visual values, and the other half encoded each value separately. The bimodal value neurons enable more efficient value encoding using fewer neurons than the modality-selective value neurons. Our data suggest that the basal ganglia system uses modality convergence to efficiently encode values with limited resources.
Reconstructing fresh green leaf spectra in the SWIR-2 region (2001–2500 nm) collected in a humid environment by referring to publicly available green leaf spectral databases
Authors: Denaro Lino Garda , Li Hsin-Ju , Chong Jie-Yun , Huang Cho-ying 
Published: January 2024

AbstractLeaf spectra (reflectance and transmittance) are key parameters for land surface physical and biogeochemical modeling and are commonly measured using a portable spectroradiometer and an integrating sphere or contact probe with an artificial light source. However, spectral data may be obscured mainly because of water vapor and low signal-to-noise ratios, especially in the shortwave infrared-2 region (SWIR-2, 2001–2500 nm). This erroneous pattern is particularly pronounced in humid conditions, such as in many tropical and subtropical regions, making data unusable in SWIR-2. In this study, we proposed a statistical/mathematical spectral reconstruction approach to retrieve noise-free SWIR-2 fresh green leaf spectra by referring to the available previously published quality-controlled fresh green leaf reflectance and transmittance reference databases. We processed 896 pairs of fresh tea (Camellia sinensisvar.sinensis) leaf reflectance and transmittance data from Alishan in central Taiwan. The spectral data were acquired by a field spectroradiometer with an integrating sphere. We selected a subset (500–1900 nm) of the spectra in the visible, near-infrared, and SWIR-1 regions (VNS-1) that was relatively insensitive to atmospheric conditions. Then, we applied a Gaussian fitting function to smooth the spectral profile. We matched those spectra with publicly available, quality-controlled, and Gaussian fitting function smoothed reference green leaf spectral databases obtained from Italy (LOPEX), Panama (SLZ), and Puerto Rico (G-LiHT) (1694 reflectance and 997 transmittance samples) and selected the one that was most similar (yielding the highest correlation coefficient) to each smoothed Alishan VNS-1 spectrum. We then used multivariable linear regression, linear parameter multiplication, and spectral reversion to reconstruct SWIR-2 spectra based on VNS-1 spectra. To assess the validity of the proposed SWIR-2 reconstruction method, we acquired an independent set of green leaf spectral databases from France (Angers) with SWIR-2 of 2001– 2450 nm. We found that the performance of the SWIR-2 reconstruction approach was satisfactory, with mean (± standard deviation) root-mean-square errors (RMSEs) of 0.0041 ± 0.0019 (reflectance, 3.0% of the mean SWIR-2 of the test data) and 0.0054 ± 0.0027 (transmittance, 2.5%) for each spectrum and RMSEs of 0.0058 ± 0.0027 (reflectance, 4.2%) and 0.0055 ± 0.0043 (transmittance, 2.5%) for each SWIR-2 band. The proposed approach successfully modeled SWIR-2 of the test spectra, which could be further improved with the availability of a more comprehensive set of green leaf reference spectral databases.
Hormetic effect induced byBeauveria bassianainMyzus persicae
Authors: Arinanto Leonhard Satrio , Hoffmann Ary Anthony , Ross Perran Albert , Gu Xinyue 
Published: January 2024

ABSTRACTMyzus persicae, a serious sap-sucking pest of a large variety of host plants in agriculture, is traditionally controlled using chemical insecticides but there is interest in using biopesticides as restrictions are increasingly placed on the use of broad-spectrum pesticides. Here we show that in petri dish experiments high concentrations of the fungal entomopathogenBeauveria bassiana(strain PRRI 5336) lead to rapid mortality ofM. persicaebut at a low concentration (1 × 104conidia mL−1) there is a hormetic effect where longevity and fecundity are enhanced. Hormetic effects persisted across a generation with reduced development times and increased fecundity in the offspring ofM. persicaeexposed toB. bassiana. Whole plant experiments point to a hormetic effect being detected in two out of three tested lines. The impact of these effects might also depend on whetherM. persicaewas transinfected with the endosymbiontRickettsiella viridis, which decreases fecundity and survival compared to aphids lacking this endosymbiont. This fecundity cost was ameliorated in the generation following exposure to the entomopathogen. WhileB. bassianais effective in controllingM. persicaeespecially at higher spore concentrations, utilization of this entomopathogen requires careful consideration of hormetic effects at lower spore concentrations, and further research to optimize its application for sustainable agriculture is recommended.AUTHOR SUMMARYBiopesticides such asBeauveria bassianacan be effective alternatives to chemical insecticides to control insect pests. We tested the efficacy of this biopesticide against the important agricultural pest aphidMyzus persicaein laboratory experiments. We also tested whether the potential biological control agent and endosymbiontRickettsiella viridiscould provide protection against mortality caused byB. bassiana. While high doses ofB. bassianacaused rapid mortality in aphids, low doses enhanced aphid fecundity and survival. This enhancement persisted into the next generation, with shortened development times and increased fecundity regardless, even when high doses were used in the previous generation. The endosymbiontR. viridisdid not provide clear protection againstB. bassiana, in contrast to previous studies in other aphid species, but beneficial effects at low doses also occurred in this aphid line. We also observed hormesis on experiments on whole plants, but only for some aphid genotypes. To a lesser extent, we also observed beneficial effects of low doses ofB. bassianain experiments on whole plants, but only in some aphid genotypes. Fitness enhancement by biopesticides at low doses raises concerns for field applications but further research is required to understand its underlying mechanisms.
Detailed mechanisms for unintended large DNA deletions with CRISPR, base editors, and prime editors
Authors: Hwang Gue-ho , Lee Seok-Hoon , Oh Minsik , Kim Segi , Habib Omer , Jang Hyeon-Ki , Kim Heon Seok , Kim Chan Hyuk , Kim Sun , Bae Sangsu 
Published: January 2024

AbstractCRISPR-Cas9 nucleases are versatile tools for genetic engineering cells and function by producing targeted double-strand breaks (DSBs) in the DNA sequence. However, the unintended production of large deletions (>100 bp) represents a challenge to the effective application of this genome-editing system. We optimized a long-range amplicon sequencing system and developed a k-mer sequence-alignment algorithm to simultaneously detect small DNA alteration events and large DNA deletions. With this workflow, we determined that CRISPR-Cas9 induced large deletions at varying frequencies in cancer cell lines, stem cells, and primary T cells. With CRISPR interference screening, we determined that end resection and the subsequent TMEJ [DNA polymerase theta-mediated end joining] repair process produce most large deletions. Furthermore, base editors and prime editors also generated large deletions despite employing mutated Cas9 “nickases” that produce single-strand breaks. Our findings reveal an important limitation of current genome-editing tools and identify strategies for mitigating unwanted large deletion events.
Innate Immune Activation and Mitochondrial ROS Invoke Persistent Cardiac Conduction System Dysfunction after COVID-19
Authors: Ashok Deepthi , Liu Ting , Criscione Joseph , Prakash Meghana , Kim Byunggik , Chow Julian , Craney Morgan , Papanicolaou Kyriakos N. , Sidor Agnieszka , Brian Foster D. , Pekosz Andrew , Villano Jason , Kim Deok-Ho , O’Rourke Brian 
Published: January 2024

AbstractBackgroundCardiac risk rises during acute SARS-CoV-2 infection and in long COVID syndrome in humans, but the mechanisms behind COVID-19-linked arrhythmias are unknown. This study explores the acute and long term effects of SARS-CoV-2 on the cardiac conduction system (CCS) in a hamster model of COVID-19.MethodsRadiotelemetry in conscious animals was used to non-invasively record electrocardiograms and subpleural pressures after intranasal SARS-CoV-2 infection. Cardiac cytokines, interferon-stimulated gene expression, and macrophage infiltration of the CCS, were assessed at 4 days and 4 weeks post-infection. A double-stranded RNA mimetic, polyinosinic:polycytidylic acid (PIC), was used in vivo and in vitro to activate viral pattern recognition receptors in the absence of SARS-CoV-2 infection.ResultsCOVID-19 induced pronounced tachypnea and severe cardiac conduction system (CCS) dysfunction, spanning from bradycardia to persistent atrioventricular block, although no viral protein expression was detected in the heart. Arrhythmias developed rapidly, partially reversed, and then redeveloped after the pulmonary infection was resolved, indicating persistent CCS injury. Increased cardiac cytokines, interferon-stimulated gene expression, and macrophage remodeling in the CCS accompanied the electrophysiological abnormalities. Interestingly, the arrhythmia phenotype was reproduced by cardiac injection of PIC in the absence of virus, indicating that innate immune activation was sufficient to drive the response. PIC also strongly induced cytokine secretion and robust interferon signaling in hearts, human iPSC-derived cardiomyocytes (hiPSC-CMs), and engineered heart tissues, accompanied by alterations in electrical and Ca2+handling properties. Importantly, the pulmonary and cardiac effects of COVID-19 were blunted by in vivo inhibition of JAK/STAT signaling or by a mitochondrially-targeted antioxidant.ConclusionsThe findings indicate that long term dysfunction and immune cell remodeling of the CCS is induced by COVID-19, arising indirectly from oxidative stress and excessive activation of cardiac innate immune responses during infection, with implications for long COVID Syndrome.
Distinct causes underlie double-peaked trilobite morphological disparity
Authors: Drage Harriet B. , Pates Stephen 
Published: January 2024

AbstractTrilobite cephalic morphology impacted the autecology of individuals, and is critical for high- and low-level taxonomic assignments. Disparity in trilobite cephalon shape varied through time and was integral to the occupation of a diversity of ecological niches. To fully appreciate trilobite cephalic evolution, we must understand how this disparity varies, and what factors control cephalon morphometry. We explore the disparity of trilobite cephala through the Palaeozoic, and analyse the associations between cephalic morphometry and taxonomic assignment and geological Period, using a dataset of 983 2D trilobite cephalon outlines. Elliptical Fourier transformation visualised as a Principal Components Analysis suggests significant differences in morphospace occupation for order and Period groups, and comparisons of disparity measures also suggest significantly different disparities between the groups. Trilobite cephalic disparity peaks in the Ordovician and Devonian. The Cambrian–Ordovician expansion of morphospace occupation appears a result of radiation to new niches, and thus all trilobite orders were established by the late Ordovician. In comparison, the morphospace expansion from the Silurian to Devonian seems solely a result of within-niche diversification rather than novel niche occupation. However, analyses interrogating the regions of morphospace occupied, including centroid distances, average pairwise shape comparisons and Linear Discriminant Analysis demonstrate that, except for the order Harpida and the Cambrian and Ordovician Periods, order and geological Period could not be robustly predicted for an unknown trilobite. Further, Kmeans clustering analyses suggest the total dataset naturally subdivides into only seven groups that do not correspond with taxonomic orders, though Kmeans clusters do decrease in number through the Palaeozoic, aligning with findings of decreasing disparity.
Phenylketonuria: modelling cerebral amino acid and neurotransmitter metabolism
Authors: Wegrzyn Agnieszka B. , van Vliet Danique , van Eunen Karen , Heiner-Fokkema M. Rebecca , van der Zee Eddy A. , van Spronsen Francjan J. , Bakker Barbara M. 
Published: January 2024

AbstractObjectivePhenylketonuria (PKU) is caused by a deficiency of the hepatic enzyme phenylalanine hydroxylase, which primarily converts phenylalanine into tyrosine. Despite a phenylalanine-deprived diet, many adult PKU patients display deficits in executive functions. These are hypothesised to be caused by high cerebral phenylalanine and a shortage of monoaminergic neurotransmitters.MethodTo better understand the relationship between plasma and brain amino acid levels and monoaminergic neurotransmitter biochemistry, we constructed a computational model. The model comprises the transport of large neutral amino acids (LNAA) across the blood-brain barrier as well as cerebral amino acid and monoaminergic neurotransmitter metabolism and was validated by direct measurements of brain amino acid concentrations in PKU mice on various diets.ResultsThe model predicts that brain amino acids are positively controlled by the concentrations of the corresponding amino acids in the blood, and to a lesser extent negatively by other amino acids competing for the transport systems. The model suggests that brain levels of monoaminergic neurotransmitters are controlled more by phenylalanine, probably through non-competitive inhibition of the hydroxylases rather than by their precursor amino acids. Therefore, the model predicts that the decrease of neurotransmitters in PKU cannot be fully rescued by the addition of tyrosine and tryptophan alone, but also benefits from a reduction of the phenylalanine level. Thereby, the model substantiates the experimental data of the synergistic effect of both brain phenylalanine reduction and increased precursor amino acid availability to improve brain neurotransmitters in PKU mice.ConclusionWe present the first complete model of the LNAA transport through the blood-brain barrier and subsequent brain neurotransmitter metabolism in PKU. The model leads to a better understanding of the pathophysiological mechanisms and the influence of individual amino acids in the diet on the underlying brain dysfunction in PKU. Moreover, it identifies gaps in our current knowledge about the LNAA transport across the blood-brain barrier. Furthermore, the model can be readily applied in studies of other neurological disorders in which the relation between diet, gene activities, brain amino acids, and neurotransmitters is important.
CREB activation drives acinar to ductal reprogramming and promote pancreatic cancer progression in animal models of alcoholic chronic pancreatitis
Authors: Srinivasan Supriya , Mehra Siddharth , Bianchi Anna , Singh Samara , Dosch Austin R. , Amirian Haleh , Jinka Sudhakar , Krishnamoorthy Varunkumar , Silva Iago De Castro , Box Edmond Worley , Garrido Vanessa , Totiger Tulasigeri M. , Zhou Zhiqun , Ban Yuguang , Datta Jashodeep , VanSaun Michael , Merchant Nipun , Nagathihalli Nagaraj S. 
Published: January 2024

AbstractBACKGROUND AND AIMSIn vivoinduction of alcoholic chronic pancreatitis (ACP) causes significant acinar damage, increased fibroinflammatory response, and heightened activation of cyclic response element binding protein 1 (CREB) when compared with alcohol (A) or chronic pancreatitis (CP) mediated pancreatic damage. However, the study elucidating the cooperative interaction between CREB and the oncogenicKrasG12D/+(Kras*) in promoting pancreatic cancer progression with ACP remains unexplored.METHODSExperimental ACP induction was established in multiple mouse models, followed by euthanization of the animals at various time intervals during the recovery periods. Tumor latency was determined in these mice cohorts. Here, we established CREB deletion (Crebfl/fl) inPtf1aCreERTM/+;LSL-KrasG12D+/−(KC) genetic mouse models (KCC−/−). Western blot, phosphokinase array, and qPCR were used to analyze the pancreata ofPtf1aCreERTM+/−,KCandKCC−/−mice. The pancreata of ACP-inducedKCmice were subjected to single-cell RNA sequencing (scRNAseq). Further studies involved conducting lineage tracing and acinar cell explant cultures.RESULTSACP induction inKCmice had detrimental effects on the pancreatic damage repair mechanism. The persistent existence of acinar cell-derived ductal lesions demonstrated a prolonged state of hyperactivated CREB. Persistent CREB activation leads to acinar cell reprogramming and increased pro-fibrotic inflammation inKCmice. Acinar-specificCrebablation reduced advanced PanINs lesions, hindered tumor progression, and restored acinar cell function in ACP-induced mouse models.CONCLUSIONSOur findings demonstrate that CREB cooperates withKras*to perpetuate an irreversible ADM and PanIN formation. Moreover, CREB sustains oncogenic activity to promote the progression of premalignant lesions toward cancer in the presence of ACP.
Fish Blood Response to Ash-Induced Environmental Alkalinization, and their Implications to Wildfire-Scarred Watersheds
Authors: Kwan Garfield T. , Sanders Trystan , Huang Sammuel , Kilaghbian Kristen , Sam Cameron , Wang Junhan , Weihrauch Kelly , Wilson Rod W. , Fangue Nann A. 
Published: January 2024

AbstractChanges in land use, warming climate and increased drought have amplified wildfire frequency and magnitude globally. Ash mixing into aquatic systems after wildfires rapidly increases water pH, creating an additional threat to wildlife, especially species that are already threatened, endangered and/or migratory. Here, Chinook salmon (Oncorhynchus tshawytscha) yearlings acclimated to 15 or 20°C were exposed to an environmentally relevant concentration of ash (0.25% w/v) which caused water pH to rapidly rise from ∼8.1 to ∼9.2. Mortalities occurred within the first 12 hours, and was higher at the higher temperature (33 versus 20 %). The greatest differences in blood chemistry between the two temperatures were dramatically greater (∼7.5-fold) and very rapid (within 1 hour) spikes in both plasma total ammonia (to ∼1200 µM) and lactate (to ∼6 mM) in warm-acclimated salmon, whereas cold-acclimated salmon experienced a much smaller and gradual rise in plasma total ammonia. Salmon at both temperatures experienced extracellular and intracellular alkalosis within 1 hour that recovered within 24 hours, but the alkalosis was smaller in magnitude in fish at warmer temperature. Impacts on plasma ion concentrations were relatively mild and plasma glucose increased by 2- to 4-fold at both temperatures. Notably, the increase in plasma total ammonia in fish at the warmer temperature was far faster and much greater than those reported in previous studies exposing fish despite higher water pH (9.4-10.5) induced without using ash. This suggests that ash has physiological impacts that cannot be explained by high water pH alone which may relate to the complex mixture of metals and organic compounds also released from ash. This demonstrates post-wildfire ash input can induce lethal yet previously unexplored physiological disturbances in fish and highlights the complex interaction with warmer temperatures typical of wildfire-scarred landscapes.
ClonalTracker: a tool to elucidate dissemination patterns between vancomycin-resistantEnterococcus faeciumisolates
Authors: Andreu Victoria Pascal 
Published: January 2024

AbstractThe global spread of vancomycin-resistantEnterococcus faecium(VRE), which commonly occurs in hospital environments, has become a major public health concern. To facilitate genomic surveillance and tracking the transmission of VRE, ClonalTracker was designed. This tool assesses the clonal relatedness between two VRE isolates given the respective assembled genomes by analyzing thevanoperon, the respective transposon type and the whole genome similarity. ClonalTracker has been validated using two previously analyzed publicly available datasets and I showcase its applicability on a yet unprocessed third dataset. While the method agrees with previously published results, it is able to provide more resolution at the clustering level even in the absence of plasmid information and using as reference the minimal version of the vancomycin resistance transposon. Within this third dataset composed of 323vanBVRE isolates, ClonalTracker found that clonal expansion is the most common dissemination mode. All in all, this tool provides new bioinformatic means to uncover dissemination patterns and elucidate links between vancomycin-resistance isolates and can be broadly accessible via its webserver hosted atwww.clonaltracker.nl(as of January 2024). The local version of this tool is also available at:https://github.com/victoriapascal/clonaltracker