bluuebunny/crossref_metadata_2025_split huggingface dataset:
Preconditioning in hypoxic-ischemic neonate mice triggers Na+-Ca2+ exchanger-dependent neurogenesis
Authors: Brancaccio P. , Anzilotti S. , Cuomo O. , Vinciguerra A. , Campanile M. , Herchuelz A. , Amoroso S. , Annunziato L. , Pignataro G. 
Published: July 2022

AbstractTo identify alternative interventions in neonatal hypoxic-ischemic encephalopathy, researchers’ attention has been focused to the study of endogenous neuroprotective strategies. Based on the preconditioning concept that a subthreshold insult may protect from a subsequent harmful event, we aimed at identifying a new preconditioning protocol able to enhance Ca2+-dependent neurogenesis in a mouse model of neonatal hypoxia ischemia (HI). To this purpose, we also investigated the role of the preconditioning-linked protein controlling ionic homeostasis, Na+/Ca2+ exchanger (NCX). Hypoxic Preconditioning (HPC) was reproduced by exposing P7 mice to 20’ hypoxia. HI was induced by isolating and cutting the right common carotid artery. A significant reduction in ischemic damage was observed in mice subjected to 20’ hypoxia followed,3 days later, by 60’ HI, thus suggesting that 20’ hypoxia functions as preconditioning stimulus. HPC promoted neuroblasts proliferation in the dentate gyrus mirrored by an increase of NCX1 and NCX3-positive cells and an improvement of behavioral motor performances in HI mice. An attenuation of HPC neuroprotection as well as a reduction in the expression of neurogenesis markers, including p57 and NeuroD1, was observed in preconditioned mice lacking NCX1 or NCX3. In summary, PC in neonatal mice triggers a neurogenic process linked to ionic homeostasis maintenance, regulated by NCX1 and NCX3.
A deep-learning estimate of the decadal trends in the Southern Ocean carbon storage
Authors: Zemskova Varvara E. , He Tai-Long , Wan Zirui , Grisouard Nicolas 
Published: July 2022

AbstractUptake of atmospheric carbon by the ocean, especially at high latitudes, plays an important role in offsetting anthropogenic emissions. At the surface of the Southern Ocean south of 30∘S, the ocean carbon uptake, which had been weakening in 1990s, strengthened in the 2000s. However, sparseness of in-situ measurements in the ocean interior make it difficult to compute changes in carbon storage below the surface. Here we develop a machine-learning model, which can estimate concentrations of dissolved inorganic carbon (DIC) in the Southern Ocean up to 4 km depth only using data available at the ocean surface. Our model is fast and computationally inexpensive. We apply it to calculate trends in DIC concentrations over the past three decades and find that DIC decreased in the 1990s and 2000s, but has increased, in particular in the upper ocean since the 2010s. However, the particular circulation dynamics that drove these changes may have differed across zonal sectors of the Southern Ocean. While the near-surface decrease in DIC concentrations would enhance atmospheric CO2 uptake continuing the previously-found trends, weakened connectivity between surface and deep layers and build-up of DIC in deep waters could reduce the ocean’s carbon storage potential.
CD8 lymphocytes mitigate HIV-1 persistence in lymph node follicular helper T cells during hyperacute-treated infection
Authors: Baiyegunhi Omolara O. , Mann Jaclyn , Khaba Trevor , Nkosi Thandeka , Mbatha Anele , Ogunshola Funsho , Chasara Caroline , Ismail Nasreen , Ngubane Thandekile , Jajbhay Ismail , Pansegrouw Johan , Dong Krista L. , Walker Bruce D. , Ndung’u Thumbi , Ndhlovu Zaza M. 
Published: July 2022

AbstractHIV persistence in tissue sites despite ART is a major barrier to HIV cure. Detailed studies of HIV-infected cells and immune responses in native lymph node tissue environment is critical for gaining insight into immune mechanisms impacting HIV persistence and clearance in tissue sanctuary sites. We compared HIV persistence and HIV-specific T cell responses in lymph node biopsies obtained from 14 individuals who initiated therapy in Fiebig stages I/II, 5 persons treated in Fiebig stages III-V and 17 late treated individuals who initiated ART in Fiebig VI and beyond. Using multicolor immunofluorescence staining and in situ hybridization, we detect HIV RNA and/or protein in 12 of 14 Fiebig I/II treated persons on suppressive therapy for 1 to 55 months, and in late treated persons with persistent antigens. CXCR3+ T follicular helper cells harbor the greatest amounts of gag mRNA transcripts. Notably, HIV-specific CD8+ T cells responses are associated with lower HIV antigen burden, suggesting that these responses may contribute to HIV suppression in lymph nodes during therapy. These results reveal HIV persistence despite the initiation of ART in hyperacute infection and highlight the contribution of virus-specific responses to HIV suppression in tissue sanctuaries during suppressive ART.
The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment
Authors: Huang Zhou , Liu Hejun , Nix Jay , Xu Rui , Knoverek Catherine R. , Bowman Gregory R. , Amarasinghe Gaya K. , Sibley L. David 
Published: July 2022

AbstractSignal transducer and activator of transcription (STAT) proteins communicate from cell-surface receptors to drive transcription of immune response genes. The parasiteToxoplasma gondiiblocks STAT1-mediated gene expression by secreting the intrinsically disordered protein TgIST that traffics to the host nucleus, binds phosphorylated STAT1 dimers, and occupies nascent transcription sites that unexpectedly remain silenced. Here we define a core region within internal repeats of TgIST that is necessary and sufficient to block STAT1-mediated gene expression. Cellular, biochemical, mutational, and structural data demonstrate that the repeat region of TgIST adopts a helical conformation upon binding to STAT1 dimers. The binding interface is defined by a groove formed from two loops in the STAT1 SH2 domains that reorient during dimerization. TgIST binding to this newly exposed site at the STAT1 dimer interface alters its conformation and prevents the recruitment of co-transcriptional activators, thus defining the mechanism of blocked transcription.
Selective expression of variant surface antigens enables Plasmodium falciparum to evade immune clearance in vivo
Authors: Chew Marvin , Ye Weijian , Omelianczyk Radoslaw Igor , Pasaje Charisse Flerida , Hoo Regina , Chen Qingfeng , Niles Jacquin C. , Chen Jianzhu , Preiser Peter 
Published: July 2022

AbstractPlasmodium falciparum has developed extensive mechanisms to evade host immune clearance. Currently, most of our understanding is based on in vitro studies of individual parasite variant surface antigens and how this relates to the processes in vivo is not well-understood. Here, we have used a humanized mouse model to identify parasite factors important for in vivo growth. We show that upregulation of the specific PfEMP1, VAR2CSA, provides the parasite with protection from macrophage phagocytosis and clearance in the humanized mice. Furthermore, parasites adapted to thrive in the humanized mice show reduced NK cell-mediated killing through interaction with the immune inhibitory receptor, LILRB1. Taken together, these findings reveal new insights into the molecular and cellular mechanisms that the parasite utilizes to coordinate immune escape in vivo. Identification and targeting of these specific parasite variant surface antigens crucial for immune evasion provides a unique approach for therapy.
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding
Authors: Conte Mattia , Irani Ehsan , Chiariello Andrea M. , Abraham Alex , Bianco Simona , Esposito Andrea , Nicodemi Mario 
Published: July 2022

AbstractLoop-extrusion and phase-separation have been proposed as mechanisms that shape chromosome spatial organization. It is unclear, however, how they perform relative to each other in explaining chromatin architecture data and whether they compete or co-exist at the single-molecule level. Here, we compare models of polymer physics based on loop-extrusion and phase-separation, as well as models where both mechanisms act simultaneously in a single molecule, against multiplexed FISH data available in human loci in IMR90 and HCT116 cells. We find that the different models recapitulate bulk Hi-C and average multiplexed microscopy data. Single-molecule chromatin conformations are also well captured, especially by phase-separation based models that better reflect the experimentally reported segregation in globules of the considered genomic loci and their cell-to-cell structural variability. Such a variability is consistent with two main concurrent causes: single-cell epigenetic heterogeneity and an intrinsic thermodynamic conformational degeneracy of folding. Overall, the model combining loop-extrusion and polymer phase-separation provides a very good description of the data, particularly higher-order contacts, showing that the two mechanisms can co-exist in shaping chromatin architecture in single cells.
GloSEM: High-resolution global estimates of present and future soil displacement in croplands by water erosion
Authors: Borrelli Pasquale , Ballabio Cristiano , Yang Jae E. , Robinson David A. , Panagos Panos 
Published: July 2022

AbstractHealthy soil is the foundation underpinning global agriculture and food security. Soil erosion is currently the most serious threat to soil health, leading to yield decline, ecosystem degradation and economic impacts. Here, we provide high-resolution (ca. 100 × 100 m) global estimates of soil displacement by water erosion obtained using the Revised-Universal-Soil-Loss-Equation-based Global Soil Erosion Modelling (GloSEM) platform under present (2019) and future (2070) climate scenarios (i.e. Shared Socioeconomic Pathway [SSP]1–Representative Concentration Pathway [RCP]2.6, SSP2–RCP4.5 and SSP5–RCP8.5). GloSEM is the first global modelling platform to take into account regional farming systems, the mitigation effects of conservation agriculture (CA), and climate change projections. We provide a set of data, maps and descriptive statistics to support researchers and decision-makers in exploring the extent and geography of soil erosion, identifying probable hotspots, and exploring (with stakeholders) appropriate actions for mitigating impacts. In this regard, we have also provided an Excel spreadsheet that can provide useful insights into the potential mitigating effects of present and future alternative CA scenarios at the country level.
Materials information extraction via automatically generated corpus
Authors: Yan Rongen , Jiang Xue , Wang Weiren , Dang Depeng , Su Yanjing 
Published: July 2022

AbstractInformation Extraction (IE) in Natural Language Processing (NLP) aims to extract structured information from unstructured text to assist a computer in understanding natural language. Machine learning-based IE methods bring more intelligence and possibilities but require an extensive and accurate labeled corpus. In the materials science domain, giving reliable labels is a laborious task that requires the efforts of many professionals. To reduce manual intervention and automatically generate materials corpus during IE, in this work, we propose a semi-supervised IE framework for materials via automatically generated corpus. Taking the superalloy data extraction in our previous work as an example, the proposed framework using Snorkel automatically labels the corpus containing property values. Then Ordered Neurons-Long Short-Term Memory (ON-LSTM) network is adopted to train an information extraction model on the generated corpus. The experimental results show that the F1-score of γ’ solvus temperature, density and solidus temperature of superalloys are 83.90%, 94.02%, 89.27%, respectively. Furthermore, we conduct similar experiments on other materials, the experimental results show that the proposed framework is universal in the field of materials.
Cytopathic SARS-CoV-2 screening on VERO-E6 cells in a large-scale repurposing effort
Authors: Zaliani Andrea , Vangeel Laura , Reinshagen Jeanette , Iaconis Daniela , Kuzikov Maria , Keminer Oliver , Wolf Markus , Ellinger Bernhard , Esposito Francesca , Corona Angela , Tramontano Enzo , Manelfi Candida , Herzog Katja , Jochmans Dirk , De Jonghe Steven , Chiu Winston , Francken Thibault , Schepers Joost , Collard Caroline , Abbasi Kayvan , Claussen Carsten , Summa Vincenzo , Beccari Andrea R. , Neyts Johan , Gribbon Philip , Leyssen Pieter 
Published: July 2022

AbstractWorldwide, there are intensive efforts to identify repurposed drugs as potential therapies against SARS-CoV-2 infection and the associated COVID-19 disease. To date, the anti-inflammatory drug dexamethasone and (to a lesser extent) the RNA-polymerase inhibitor remdesivir have been shown to be effective in reducing mortality and patient time to recovery, respectively, in patients. Here, we report the results of a phenotypic screening campaign within an EU-funded project (H2020-EXSCALATE4COV) aimed at extending the repertoire of anti-COVID therapeutics through repurposing of available compounds and highlighting compounds with new mechanisms of action against viral infection. We screened 8702 molecules from different repurposing libraries, to reveal 110 compounds with an anti-cytopathic IC50 < 20 µM. From this group, 18 with a safety index greater than 2 are also marketed drugs, making them suitable for further study as potential therapies against COVID-19. Our result supports the idea that a systematic approach to repurposing is a valid strategy to accelerate the necessary drug discovery process.
Case study of the convergent evolution in the color patterns in the freshwater bivalves
Authors: Asato Kaito , Nakayama Kentaro , Imai Takuya 
Published: July 2022

AbstractThe class Bivalvia (phylum Mollusca) is one of the most successful at survival groups of animals with diverse color patterns on their shells, and they are occasionally preserved in the fossil record as residual color patterns. However, the fossil record of the residual color patterns in freshwater bivalves could be traced only to the Miocene, greatly limiting color pattern evolution knowledge. We present the color patterns of the Cretaceous freshwater bivalves belonging to three extinct families of the order Trigoniida (hereinafter the Kitadani Freshwater Bivalves) from Japan, which is the oldest and the second fossil record of freshwater molluscan color patterns. The Kitadani Freshwater Bivalves consists of two types of color patterns: stripes along the growth lines and radial rays tapered toward the umbo, which resemble that of the colored bands of extant freshwater bivalves. This resemblance of the color patterns between the Kitadani Freshwater Bivalves and the extant species indicates that the color patterns of the freshwater bivalves represent the convergent evolution between Trigoniida and Unionida. To explain this convergent evolution, we advocate three conceivable factors: the phylogenetic constraints, monotonous habitats typical of freshwater ecosystems, and the predation pressure by visual predators in freshwater sediments.
Review of some existing QML frameworks and novel hybrid classical–quantum neural networks realising binary classification for the noisy datasets
Authors: Schetakis N. , Aghamalyan D. , Griffin P. , Boguslavsky M. 
Published: July 2022

AbstractOne of the most promising areas of research to obtain practical advantage is Quantum Machine Learning which was born as a result of cross-fertilisation of ideas between Quantum Computing and Classical Machine Learning. In this paper, we apply Quantum Machine Learning (QML) frameworks to improve binary classification models for noisy datasets which are prevalent in financial datasets. The metric we use for assessing the performance of our quantum classifiers is the area under the receiver operating characteristic curve AUC–ROC. By combining such approaches as hybrid-neural networks, parametric circuits, and data re-uploading we create QML inspired architectures and utilise them for the classification of non-convex 2 and 3-dimensional figures. An extensive benchmarking of our new FULL HYBRID classifiers against existing quantum and classical classifier models, reveals that our novel models exhibit better learning characteristics to asymmetrical Gaussian noise in the dataset compared to known quantum classifiers and performs equally well for existing classical classifiers, with a slight improvement over classical results in the region of the high noise.
Cefotaxime removal enhancement via bio-nanophotocatalyst α-Fe2O3 using photocatalytic degradation technique and its echo-biomedical applications
Authors: Al-Hakkani Mostafa F. , Gouda Gamal A. , Hassan Sedky H. A. , Saddik Mohammed S. , El-Mokhtar Mohamed A. , Ibrahim Maggie A. , Mohamed Mahmoud M. A. , Nagiub Adham M. 
Published: July 2022

AbstractThe present paper evaluates the photocatalytic degradation (PCD) performance of the biofabricated hematite nanoparticles (α-HNPs) for the degradation approach of the Cefotaxime (Cfm). The optimum pH of the solution to achieve the best PCD was found to be 10.5. The kinetics study for the PCD of the Cfm via α-HNPs has been investigated and the reaction was found to be fellow pseudo-first-order at R2 = 0.992. The mass loading impact of α-HNPs was investigated and estimated for the maximum degradation of Cfm 0.4 mg/mL. UV–Vis confirmed that α-HNPs had a direct transition bandgap at 3.78 eV at a maximum absorption wavelength of 362 nm with suspension stability for 7 days. The probable mechanism of the Cfm PCD via α-HNPs and the degradation pathway was conducted. The validation of the suspension stability of the α-HNPs (−68.6 ± 11.8 mV) was determined using the zeta potential investigation test. XRD investigation was conducted after Cfm PCD showing an average crystallite size of 27.0 nm. XRD, TEM, SEM, EDX, and FT-IR analyses have been conducted for the α-HNPs before and after Cfm PCD confirming the high efficiency for the reusability of the current biocatalyst α-HNPs for further use. TEM results of the particle sizes of α-HNPs were found at 19.2 ± 4.4 and 20.6 ± 7.4 nm respectively before and after Cfm PCD. The efficiency of the Cfm PCD was found to be 99.1% after 6 h. High potent as an antibacterial agent of α-HNPs was investigated either α-HNPs alone or after its PCD activity against Cfm. The antibacterial activity revealed high sensitivity, especially toward Gram-positive species indicating its promising ability against pathogenic issues. Interestingly, Cfm@α-HNPs showed superior anti-proliferative activity as tested by MTT assay and were able to induce apoptosis in MCF7 and HepG2 cell lines using the flow cytometry technique at 20.7% and 17% respectively. Also, The IC50 of hydrogen peroxide scavenging was estimated and it was manifested that 635.8 and 665.6 μg/mL of α-HNPs before and after the PCD process of Cfm respectively.
Application of machine learning methods for the prediction of true fasting status in patients performing blood tests
Authors: Chang Shih-Ni , Hsiao Ya-Luan , Lin Che-Chen , Sun Chuan-Hu , Chen Pei-Shan , Wu Min-Yen , Chen Sheng-Hsuan , Chiang Hsiu-Yin , Hsiao Chiung-Tzu , King Emily K. , Chang Chun-Min , Kuo Chin-Chi 
Published: July 2022

AbstractThe fasting blood glucose (FBG) values extracted from electronic medical records (EMR) are assumed valid in existing research, which may cause diagnostic bias due to misclassification of fasting status. We proposed a machine learning (ML) algorithm to predict the fasting status of blood samples. This cross-sectional study was conducted using the EMR of a medical center from 2003 to 2018 and a total of 2,196,833 ontological FBGs from the outpatient service were enrolled. The theoretical true fasting status are identified by comparing the values of ontological FBG with average glucose levels derived from concomitant tested HbA1c based on multi-criteria. In addition to multiple logistic regression, we extracted 67 features to predict the fasting status by eXtreme Gradient Boosting (XGBoost). The discrimination and calibration of the prediction models were also assessed. Real-world performance was gauged by the prevalence of ineffective glucose measurement (IGM). Of the 784,340 ontologically labeled fasting samples, 77.1% were considered theoretical FBGs. The median (IQR) glucose and HbA1c level of ontological and theoretical fasting samples in patients without diabetes mellitus (DM) were 94.0 (87.0, 102.0) mg/dL and 5.6 (5.4, 5.9)%, and 92.0 (86.0, 99.0) mg/dL and 5.6 (5.4, 5.9)%, respectively. The XGBoost showed comparable calibration and AUROC of 0.887 than that of 0.868 in multiple logistic regression in the parsimonious approach and identified important predictors of glucose level, home-to-hospital distance, age, and concomitantly serum creatinine and lipid testing. The prevalence of IGM dropped from 27.8% based on ontological FBGs to 0.48% by using algorithm-verified FBGs. The proposed ML algorithm or multiple logistic regression model aids in verification of the fasting status.
The 2019–2020 Australian forest fires are a harbinger of decreased prescribed burning effectiveness under rising extreme conditions
Authors: Clarke Hamish , Cirulis Brett , Penman Trent , Price Owen , Boer Matthias M. , Bradstock Ross 
Published: July 2022

AbstractThere is an imperative for fire agencies to quantify the potential for prescribed burning to mitigate risk to life, property and environmental values while facing changing climates. The 2019–2020 Black Summer fires in eastern Australia raised questions about the effectiveness of prescribed burning in mitigating risk under unprecedented fire conditions. We performed a simulation experiment to test the effects of different rates of prescribed burning treatment on risks posed by wildfire to life, property and infrastructure. In four forested case study landscapes, we found that the risks posed by wildfire were substantially higher under the fire weather conditions of the 2019–2020 season, compared to the full range of long-term historic weather conditions. For area burnt and house loss, the 2019–2020 conditions resulted in more than a doubling of residual risk across the four landscapes, regardless of treatment rate (mean increase of 230%, range 164–360%). Fire managers must prepare for a higher level of residual risk as climate change increases the likelihood of similar or even more dangerous fire seasons.
Biometric and refractive changes following the monocular application of peripheral myopic defocus using a novel augmented-reality optical system in adults
Authors: Kubota Ryo , Joshi Nabin R. , Fitzgerald Tara J. , Samandarova Inna , Oliva Maksud , Selenow Arkady , Gupta Amitava , Ali Steven , Mitchell G. Lynn , Chun Robert , Ciuffreda Kenneth J. 
Published: July 2022

AbstractThe prevalence of myopia is growing at an alarming rate and is associated with axial elongation of the eye. The cause of this undesirable physiological change involves multiple factors. When the magnitude of myopia approaches high levels, this accompanying mechanical effect increases the risk of developing other clinical conditions associated with permanent vision loss. Prior work has investigated how we may halt or reverse this process of axial elongation associated with myopic progression when we expose the eye to a peripheral myopic defocus stimulus. Specifically, the known, short-term response to myopic defocus stimulation is promising and demonstrates the possibility of establishing more permanent effects by regulating the axial length of the eye with specific defocus stimulation. However, how to directly convert these known, short-term effects into more long-term, permanent changes to effectively prevent these unfavourable physiological and refractive changes over time is yet to be understood. Here, we show for the first time that we can produce sustained, long-term reductions in axial length and refractive endpoints with cumulative short-term exposure to specific myopic defocus stimuli using a novel optical design that incorporates an augmented reality optical system. We believe that this technology will have the potential to improve the quality of vision in mankind.