bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal drought analysis in Bangladesh using the standardized precipitation index (SPI) and standardized precipitation evapotranspiration index (SPEI)
Authors: Kamruzzaman Mohammad , Almazroui Mansour , Salam M. A. , Mondol Md Anarul Haque , Rahman Md. Mizanur , Deb Limon , Kundu Palash Kumar , Zaman Md. Asad Uz , Islam Abu Reza Md. Towfiqul 
Published: November 2022

AbstractCountries depending on small-scale agriculture, such as Bangladesh, are susceptible to climate change and variability. Changes in the frequency and intensity of drought are a crucial aspect of this issue and the focus of this research. The goal of this work is to use SPI (standardized precipitation index) and SPEI (standardized precipitation evapotranspiration index) to investigate the differences in drought characteristics across different physiognomy types in Bangladesh and to highlight how drought characteristics change over time and spatial scales when considering different geomorphologies. This study used monthly precipitation and temperature data from 29 metrological stations for 39 years (1980–2018) for calculating SPI and SPEI values. To determine the significance of drought characteristic trends over different temporal and spatial scales, the modified Mann–Kendall trend test and multivariable linear regression (MLR) techniques were used. The results are as follows: (1) Overall, decreasing dry trend was found in Eastern hill regions, whereas an increasing drought trends were found in the in the rest of the regions in all time scaless (range is from − 0.08 decade−1 to − 0.15 decade−1 for 3-month time scale). However, except for the one-month time scale, the statistically significant trend was identified mostly in the north-central and northeast regions, indicating that drought patterns migrate from the northwest to the center region. (2) SPEI is anticipated to be better at capturing dry/wet cycles in more complex regions than SPI. (3) According to the MLR, longitude and maximum temperature can both influence precipitation. (4) Drought intensity increased gradually from the southern to the northern regions (1.26–1.56), and drought events occurred predominantly in the northwestern regions (27–30 times), indicating that drought meteorological hotspots were primarily concentrated in the Barind Tract and Tista River basin over time. Findings can be used to improve drought evaluation, hazard management, and application policymaking in Bangladesh. This has implications for agricultural catastrophe prevention and mitigation.
Structural analysis of the 2-oxoglutarate binding site of the circadian rhythm linked oxygenase JMJD5
Authors: Islam Md. Saiful , Markoulides Marios , Chowdhury Rasheduzzaman , Schofield Christopher J. 
Published: November 2022

AbstractJmjC (Jumonji-C) domain-containing 5 (JMJD5) plays important roles in circadian regulation in plants and humans and is involved in embryonic development and cell proliferation. JMJD5 is a 2-oxoglutarate (2OG) and Fe(II) dependent oxygenase of the JmjC subfamily, which includes histone Nε-methyl lysine-demethylases (KDMs) and hydroxylases catalysing formation of stable alcohol products. JMJD5 is reported to have KDM activity, but has been shown to catalyse C-3 hydroxylation of arginine residues in sequences from human regulator of chromosome condensation domain-containing protein 1 (RCCD1) and ribosomal protein S6 (RPS6) in vitro. We report crystallographic analyses of human JMJD5 complexed with 2OG analogues, including the widely used hypoxia mimic pyridine-2,4-dicarboxylate, both D- and L-enantiomers of the oncometabolite 2-hydroxyglutarate, and a cyclic N-hydroxyimide. The results support the assignment of JMJD5 as a protein hydroxylase and reveal JMJD5 has an unusually compact 2OG binding pocket suitable for exploitation in development of selective inhibitors. They will be useful in the development of chemical probes to investigate the physiologically relevant roles of JMJD5 in circadian rhythm and development and explore its potential as a medicinal chemistry target.
Wild microbiomes of striped plateau lizards vary with reproductive season, sex, and body size
Authors: Bunker Marie E. , Arnold A. Elizabeth , Weiss Stacey L. 
Published: November 2022

AbstractLong-term studies of animal microbiomes under natural conditions are valuable for understanding the effects of host demographics and environmental factors on host-associated microbial communities, and how those effects interact and shift over time. We examined how the cloacal microbiome of wild Sceloporus virgatus (the striped plateau lizard) varies under natural conditions in a multi-year study. Cloacal swabs were collected from wild-caught lizards across their entire active season and over three years in southeastern Arizona, USA. Analyses of 16S rRNA data generated on the Illumina platform revealed that cloacal microbiomes of S. virgatus vary as a function of season, sex, body size, and reproductive state, and do so independently of one another. Briefly, microbial diversity was lowest in both sexes during the reproductive season, was higher in females than in males, and was lowest in females when they were vitellogenic, and microbiome composition varied across seasons, sexes, and sizes. The pattern of decreased diversity during reproductive periods with increased sociality is surprising, as studies in other systems often suggest that microbial diversity generally increases with sociality. The cloacal microbiome was not affected significantly by hibernation and was relatively stable from year to year. This study highlights the importance of long term, wide-scale microbiome studies for capturing accurate perspectives on microbiome diversity and composition in animals. It also serves as a warning for comparisons of microbiomes across species, as each may be under a different suite of selective pressures or exhibit short-term variation from external or innate factors, which may differ in a species-specific manner.
Reduced order modeling for flow and transport problems with Barlow Twins self-supervised learning
Authors: Kadeethum Teeratorn , Ballarin Francesco , O’Malley Daniel , Choi Youngsoo , Bouklas Nikolaos , Yoon Hongkyu 
Published: November 2022

AbstractWe propose a unified data-driven reduced order model (ROM) that bridges the performance gap between linear and nonlinear manifold approaches. Deep learning ROM (DL-ROM) using deep-convolutional autoencoders (DC–AE) has been shown to capture nonlinear solution manifolds but fails to perform adequately when linear subspace approaches such as proper orthogonal decomposition (POD) would be optimal. Besides, most DL-ROM models rely on convolutional layers, which might limit its application to only a structured mesh. The proposed framework in this study relies on the combination of an autoencoder (AE) and Barlow Twins (BT) self-supervised learning, where BT maximizes the information content of the embedding with the latent space through a joint embedding architecture. Through a series of benchmark problems of natural convection in porous media, BT–AE performs better than the previous DL-ROM framework by providing comparable results to POD-based approaches for problems where the solution lies within a linear subspace as well as DL-ROM autoencoder-based techniques where the solution lies on a nonlinear manifold; consequently, bridges the gap between linear and nonlinear reduced manifolds. We illustrate that a proficient construction of the latent space is key to achieving these results, enabling us to map these latent spaces using regression models. The proposed framework achieves a relative error of 2% on average and 12% in the worst-case scenario (i.e., the training data is small, but the parameter space is large.). We also show that our framework provides a speed-up of $$7 \times 10^{6}$$

7
×

10
6

times, in the best case, and $$7 \times 10^{3}$$

7
×

10
3

times on average compared to a finite element solver. Furthermore, this BT–AE framework can operate on unstructured meshes, which provides flexibility in its application to standard numerical solvers, on-site measurements, experimental data, or a combination of these sources.
The spatial and temporal reconstruction of a medieval moat ecosystem
Authors: Antczak-Orlewska Olga , Okupny Daniel , Kruk Andrzej , Bailey Richard Ian , Płóciennik Mateusz , Sikora Jerzy , Krąpiec Marek , Kittel Piotr 
Published: November 2022

AbstractMoats and other historical water features had great importance for past societies. The functioning of these ecosystems can now only be retrieved through palaeoecological studies. Here we aimed to reconstruct the history of a stronghold’s moat during its period of operation. Our spatio-temporal approach allowed mapping of the habitat changes within a medieval moat for the first time. Using data from four cores of organic deposits taken within the moat system, we describe ecological states of the moat based on subfossil Chironomidae and Ceratopogonidae assemblages. We found that over half (57%) of the identified dipteran taxa were indicative of one of the following ecological states: limnetic conditions with or without periodic water inflow, or marshy conditions. Samples representing conditions unfavourable for aquatic insects were grouped in a separate cluster. Analyses revealed that the spatio-temporal distribution of midge assemblages depended mostly on depth differences and freshwater supply from an artificial channel. Paludification and terrestrialization did not happen simultaneously across the moat system, being greatly influenced by human activity. The results presented here demonstrate the importance of a multi-aspect approach in environmental archaeology, focusing not only on the human environment, but also on the complex ecology of the past ecosystems.
Combination of esomeprazole and pirfenidone enhances antifibrotic efficacy in vitro and in a mouse model of TGFβ-induced lung fibrosis
Authors: Ebrahimpour Afshin , Ahir Manisha , Wang Min , Jegga Anil G. , Bonnen Mark D. , Eissa N. Tony , Montesi Sydney B. , Raghu Ganesh , Ghebre Yohannes T. 
Published: November 2022

AbstractIdiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease of unknown etiology. Currently, pirfenidone and nintedanib are the only FDA-approved drugs for the treatment of IPF and are now the standard of care. This is a significant step in slowing down the progression of the disease. However, the drugs are unable to stop or reverse established fibrosis. Several retrospective clinical studies indicate that proton pump inhibitors (PPIs; FDA-approved to treat gastroesophageal reflux) are associated with favorable outcomes in patients with IPF, and emerging preclinical studies report that PPIs possess antifibrotic activity. In this study, we evaluated the antifibrotic efficacy of the PPI esomeprazole when combined with pirfenidone in vitro and in vivo. In cell culture studies of IPF lung fibroblasts, we assessed the effect of the combination on several fibrosis-related biological processes including TGFβ-induced cell proliferation, cell migration, cell contraction, and collagen production. In an in vivo study, we used mouse model of TGFβ-induced lung fibrosis to evaluate the antifibrotic efficacy of esomeprazole/pirfenidone combination. We also performed computational studies to understand the molecular mechanisms by which esomeprazole and/or pirfenidone regulate lung fibrosis. We found that esomeprazole significantly enhanced the anti-proliferative effect of pirfenidone and favorably modulated TGFβ-induced cell migration and contraction of collagen gels. We also found that the combination significantly suppressed collagen production in response to TGFβ in comparison to pirfenidone monotherapy. In addition, our animal study demonstrated that the combination therapy effectively inhibited the differentiation of lung fibroblasts into alpha smooth muscle actin (αSMA)-expressing myofibroblasts to attenuate the progression of lung fibrosis. Finally, our bioinformatics study of cells treated with esomeprazole or pirfenidone revealed that the drugs target several extracellular matrix (ECM) related pathways with esomeprazole preferentially targeting collagen family members while pirfenidone targets the keratins. In conclusion, our cell biological, computational, and in vivo studies show that the PPI esomeprazole enhances the antifibrotic efficacy of pirfenidone through complementary molecular mechanisms. This data supports the initiation of prospective clinical studies aimed at repurposing PPIs for the treatment of IPF and other fibrotic lung diseases where pirfenidone is prescribed.
Organically surface engineered mesoporous silica nanoparticles control the release of quercetin by pH stimuli
Authors: Saputra Ozi Adi , Lestari Windy Ayu , Kurniansyah Viardi , Lestari Witri Wahyu , Sugiura Takashi , Mukti Rino R. , Martien Ronny , Wibowo Fajar Rakhman 
Published: November 2022

AbstractControlling the premature release of hydrophobic drugs like quercetin over physiological conditions remains a challenge motivating the development of smart and responsive drug carriers in recent years. This present work reported a surface modification of mesoporous silica nanoparticles (MSN) by a functional compound having both amines (as a positively charged group) and carboxylic (negatively charged group), namely 4-((2-aminoethyl)amino)-4-oxobut-2-enoic acid (AmEA) prepared via simple mechanochemistry approach. The impact of MSN surface modification on physical, textural, and morphological features was evaluated by TGA, N2 adsorption–desorption, PSA-zeta, SEM, and TEM. The BET surface area of AmEA-modified MSN (MSN-AmEA) was found to be 858.41 m2 g−1 with a pore size of 2.69 nm which could accommodate a high concentration of quercetin 118% higher than MSN. In addition, the colloidal stability of MSN-AmEA was greatly improved as indicated by high zeta potential especially at pH 4 compared to MSN. In contrast to MSN, MSN-AmEA has better in controlling quercetin release triggered by pH, thanks to the presence of the functional groups that have a pose-sensitive interaction hence it may fully control the quercetin release, as elaborated by the DFT study. Therefore, the controlled release of quercetin over MSN-AmEA verified its capability of acting as a smart drug delivery system.
The debate on the earthquake magnitude correlations: a meta-analysis
Authors: Petrillo Giuseppe , Zhuang Jiancang 
Published: November 2022

AbstractAmong the most important questions that await an answer in seismology, perhaps one is whether there is a correlation between the magnitudes of two successive seismic events. The answer to this question is considered of fundamental importance given the potential effect in forecasting models, such as Epidemic Type Aftershock Sequence models. After a meta-analysis of 29 papers, we speculate that given the lack of studies carried out with realistic physical models and given the possible bias due to the lack of events recorded in the experimental seismic catalogs, important improvements are necessary on both fronts to be sure to provide a statistically relevant answer.
In vitro studies of the protein-interaction network of cell-wall lytic transglycosylase RlpA of Pseudomonas aeruginosa
Authors: Avila-Cobian Luis F. , De Benedetti Stefania , Kim Choon , Feltzer Rhona , Champion Matthew M. , Fisher Jed F. , Mobashery Shahriar 
Published: November 2022

AbstractThe protein networks of cell-wall-biosynthesis assemblies are largely unknown. A key class of enzymes in these assemblies is the lytic transglycosylases (LTs), of which eleven exist in P. aeruginosa. We have undertaken a pulldown strategy in conjunction with mass-spectrometry-based proteomics to identify the putative binding partners for the eleven LTs of P. aeruginosa. A total of 71 putative binding partners were identified for the eleven LTs. A systematic assessment of the binding partners of the rare lipoprotein A (RlpA), one of the pseudomonal LTs, was made. This 37-kDa lipoprotein is involved in bacterial daughter-cell separation by an unknown process. RlpA participates in both the multi-protein and multi-enzyme divisome and elongasome assemblies. We reveal an extensive protein-interaction network for RlpA involving at least 19 proteins. Their kinetic parameters for interaction with RlpA were assessed by microscale thermophoresis, surface-plasmon resonance, and isothermal-titration calorimetry. Notable RlpA binding partners include PBP1b, PBP4, and SltB1. Elucidation of the protein-interaction networks for each of the LTs, and specifically for RlpA, opens opportunities for the study of their roles in the complex protein assemblies intimately involved with the cell wall as a structural edifice critical for bacterial survival.
Decoupling of dust cloud and embedding plasma for high electron depletion in nanodusty plasmas
Authors: Petersen Andreas , Asnaz Oguz Han , Tadsen Benjamin , Greiner Franko 
Published: November 2022

AbstractIn recent years nanoparticles have become key technological products, e.g., as coatings with tunable optical gap in third generation solar cells, as nanocrystals for photonic applications, and as pharmaceutical nanocarriers. In particle sources, that use reactive, nanodusty plasmas, a high dust density changes the properties of the dusty plasma compared to a dust free plasma considerably, as electron depletion leads to a reduced number of free electrons. This is called the Havnes effect and was central for the understanding of the famous spokes in Saturns rings. We see here, that it is also important for technological applications. Using self excited dust density waves (DDW) as a diagnostic tool, we completely characterize an argon discharge with embedded amorphous hydrocarbon nanoparticles of different size and density. The results show, that electron depletion governs the charge of dust grains, while the size of the particles has only a weak influence. The ion density and electric potential profile are almost independent of both, dust size as well as dust density. This suggests, that the rf generated plasma and the dust cloud seem to coexist and coupling of both is weak.
Advanced monitoring of tailings dam performance using seismic noise and stress models
Authors: Ouellet Susanne M. , Dettmer Jan , Olivier Gerrit , DeWit Tjaart , Lato Matthew 
Published: November 2022

AbstractTailings dams retain the waste by-products of mining operations and are among the world’s largest engineered structures. Recent tailings dam failures highlight important gaps in current monitoring methods. Here we demonstrate how ambient noise interferometry can be applied to monitor dam performance at an active tailings dam using a geophone array. Seismic velocity changes of less than 1% correlate strongly with water level changes at the adjacent tailings pond. We implement a power-law relationship between effective stress and shear wave velocity, using the pond level recordings with shear wave velocity profiles obtained from cone penetration tests to model changes in shear wave velocities. The resulting one-dimensional model shows good agreement with the seismic velocity changes. As shear wave velocity provides a direct measure of soil stiffness and can be used to infer numerous other geotechnical design parameters, this method provides important advances in understanding changes in dam performance over time.
Les génomes viraux défectueux du virus Chikungunya: Vers une nouvelle approche d’antiviraux à large spectre ?
Authors: Khau Sandra , Lopatynski Cassandra 
Published: November 2022

Le Master 2 « Infectiologie, Immunologie, Vaccinologie et Biomédicaments (I2VB) », dispensé à la faculté de Pharmacie de l’université de Tours, propose de donner les bases conceptuelles et pratiques des différents aspects de l’infectiologie et de l’immunologie dans un contexte d’innovation thérapeutique. Il s’appuie sur une coopération exemplaire entre les équipes de recherche en infectiologie et en immunologie de l’université de Tours, et celles, entre autres, de l’unité « Infectiologie et Santé Publique » (ISP) et de l’unité « Physiologie de la Reproduction et des Comportements » (PRC) du Centre INRAE de Tours-Nouzilly, concrétisée par une profonde interaction entre chercheurs et enseignants-chercheurs. Cette formation aborde aussi bien les aspects fondamentaux et appliqués de l’infectiologie et de l’immunologie, allant de l’étude moléculaire des interactions entre le pathogène et son hôte, jusqu’à la conception et la mise sur le marché des produits de la vaccinologie, des biothérapies anti-infectieuses et des anticorps thérapeutiques.
Le Master 2 I2VB a pour objectif de former :
– de jeunes scientifiques aux enjeux actuels de l’infectiologie et des biomédicaments tels que les anticorps.
– des experts pour gérer les risques d’émergences, et capables de comprendre les interactions complexes entre un agent infectieux et son hôte humain ou animal, capables de proposer des mesures préventives ou des thérapies innovantes.
Valve-Related Complications in TAVI Leading to Emergent Cardiac Surgery
Authors: Conzelmann Lars , Grotherr Philipp , Dapeng Lu , Würth Alexander , Widder Julian , Jacobshagen Claudius , Mehlhorn Uwe 
Published: November 2022

AbstractTranscatheter aortic valve implantation (TAVI) is now a standard procedure for the treatment of symptomatic aortic valve stenosis in many patients. In Germany, according to the annual reports from the German Institute for Quality Assurance and Transparency in Healthcare (Institut für Qualitätssicherung und Transparenz im Gesundheitswesen), the rate of serious intraprocedural complications, such as valve malpositioning or embolization, coronary obstruction, aortic dissection, annular rupture, pericardial tamponade, or severe aortic regurgitation requiring emergency cardiac surgery has decreased markedly in recent years from more than 5.5% in 2012 to 2.0% in 2019. However, with increased use, the total number of adverse events remains about 500 per year, about 100 of which require conversion to sternotomy. These, sometimes, fatal events can occur at any time and are still challenging. Therefore, the interdisciplinary TAVI heart team should be prepared and aware of possible rescue strategies.
A Deeper Curse: A Hirschsprung Patient's Evaluation Unmasks a Rare Association with Congenital Central Hypoventilation Syndrome and Neuroblastoma
Authors: Jacobs Shimon Eric , Tiusaba Laura , Bokova Elizaveta , Al-Shamaileh Tamador , Russell Teresa Lynn , Rutan Emily C. , Haroyan Harutyun , Wang Yong , Feng Christina , Badillo Andrea , Levitt Marc A. 
Published: November 2022

AbstractWe present a rare case of a 2-year-old male patient referred for primary evaluation of constipation and ultimately treatment of Hirschsprung disease (HSCR) whose preoperative workup incidentally revealed a posterior paraspinal mass. Following the biopsy of the mass, the patient exhibited hypoventilation and hypoxia requiring a delayed extubation, raising suspicion for congenital central hypoventilation syndrome (CCHS). We focus on the known history of associations between HSCR and CCHS, in addition to recently found genetic mutations in paired-like homeobox 2B that link HSCR, CCHS, and neuroblastoma.