bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning for fast low-field MRI acquisitions
Authors: Ayde Reina , Senft Tobias , Salameh Najat , Sarracanie Mathieu 
Published: July 2022

AbstractLow-field (LF) MRI research currently gains momentum from its potential to offer reduced costs and reduced footprints translating into wider accessibility. However, the impeded signal-to-noise ratio inherent to lower magnetic fields can have a significant impact on acquisition times that challenges LF clinical relevance. Undersampling is an effective way to speed up acquisitions in MRI, and recent work has shown encouraging results when combined with deep learning (DL). Yet, training DL models generally requires large databases that are not yet available at LF regimes. Here, we demonstrate the capability of Residual U-net combined with data augmentation to reconstruct magnitude and phase information of undersampled LF MRI scans at 0.1 T with a limited training dataset (n = 10). The model performance was first evaluated in a retrospective study for different acceleration rates and sampling patterns. Ultimately, the DL approach was validated on prospectively acquired, fivefold undersampled LF data. With varying performances associated to the adopted sampling scheme, our results show that the approach investigated can preserve the global structure and the details sharpness in the reconstructed magnitude and phase images. Overall, promising results could be obtained on acquired LF MR images that may bring this research closer to clinical implementation.
Ironing out the wrinkles and folds in the epidemiology of skin fold dermatitis in dog breeds in the UK
Authors: O’NeillI Dan G. , Rowe Dara , Brodbelt Dave C. , Pegram Camilla , Hendricks Anke 
Published: July 2022

AbstractSkin fold dermatitis (intertrigo) is an inflammatory process of closely apposing skin surfaces. Extreme conformations towards folded skin in many dog breeds are linked with higher risk. Using anonymised primary-care veterinary data from the VetCompass Programme, this study aimed to report the frequency, demographic risk factors and clinical management for skin fold dermatitis in the UK. Risk factor analysis used random effects multivariable logistic regression modelling. From a study population of 905,553 dogs, the one-year period prevalence in dogs overall was 0.37% (95% CI 0.35–0.39). Diagnosis was supported by laboratory testing in 4.21% cases. Systemic antibiosis was used in 42.30% cases. Compared with crossbreed dogs, the most highly predisposed breeds were English Bulldog (odds ratio [OR] 49.07, 95% CI 37.79–63.70), French Bulldog (OR 25.92, 95% CI 19.62–34.26,) and Pug (OR 16.27, 95% CI 12.20–21.69). The most protected breeds were Yorkshire Terrier (OR 0.14, 95% CI 0.03–0.56), Border Collie (OR 0.31, 95% CI 0.11–0.84), Jack Russell Terrier (OR 0.53, 95% CI 0.30–0.92) and Labrador Retriever (OR 0.57, 95% CI 0.35–0.93). This study adds further evidence to the welfare concerns around high popularity of dog breeds with extreme conformations. The three breeds with by far the highest odds of skin fold dermatitis represent an extreme brachycephalic conformation.
Acidic condition accelerates cation release from purple rock in Southwestern China
Authors: Zhao Jixia , Li Chunpei , Lu Chuanhao , Deng Limei , Liu Gangcai , Fan Maopan 
Published: July 2022

AbstractIn spite of the fact that rock weathering performs an essential task in the evolution of the Earth’s surface, the quantitative assessment between pH and rates of chemical weathering remain unclear. This study aims to characterize the chemical weathering rate of purple rocks and then develops a model to calculate the release rates of cations (K+, Na+, Ca2+and Mg2+) under various pH conditions. Two types of purple rock were sampled from the Shaximiao Group (J2s) and Penglaizhen Group (J3p), and a series of laboratory experiments were performed by soaking the purple rocks in solutions with pHs from 2.5 to 7.0, over 24 treatment cycles. The results showed that the release rates of cations apparently increased as the pH decreased. The release of Ca2+was the dominant process of chemical weathering in J3p under various pH treatments, while K+and Na+were remarkably high in J2s (with the exception of the pH 2.5 treatment). Quantitative analysis revealed that the rate of cation release was significantly related to the H+concentration (p < 0.001) and the air temperature (p < 0.001). The relationship between cation release and acidity was found to be an exponential function. Our results suggested that solution acidity serves as an important driving force for cation release rates from purple rocks and that environmental acidification would enhance rock weathering.
Assessing Asiatic cheetah’s individual diet using metabarcoding and its implication for conservation
Authors: Khalatbari Leili , Egeter Bastian , Abolghasemi Hamed , Hakimi Ehsan , Ghadirian Taher , Khaleghi Hamidi Amir Hosein , Jowkar Houman , Breitenmoser Urs , Brito José Carlos 
Published: July 2022

AbstractKnowledge on diet composition allows defining well-targeted conservation measures of large carnivores. Little is known about ecology of critically endangered Asiatic cheetah, especially the overall diet and its possible regional differences. We used cheetah scats, metabarcoding technique and microsatellite markers to assess the individual and overall diet composition of the species across its entire range in Asia. Cheetahs were primarily predating on mouflon; following by ibex, cape hare and goitered gazelle. Despite their high availability, small-sized livestock was never detected. Goitered gazelles were only detected in an area where the habitat is mainly flatlands. In hilly areas, mouflon was the most frequent prey item taken. Ibex was typically taken in rugged terrain, but mouflon was still the most frequently consumed item in these habitats. High consumption of mouflon in comparison to goitered gazelle suggests that human pressure on lowland habitats has possibly forced Asiatic cheetahs to occupy suboptimal habitats where gazelles are less abundant. The protection of flatlands and the removal of livestock from them are needed to ensure the long-term survival of Asiatic cheetah. The laboratory and bioinformatics pipelines used in this study are replicable and can be used to address similar questions in other threatened carnivores.
Structural and biochemical analysis reveals how ferulic acid improves catalytic efficiency of Humicola grisea xylanase
Authors: Oliveira Izadora Cristina Moreira , Garay Aisel Valle , Souza Amanda Araújo , Valadares Napoleão Fonseca , Barbosa João Alexandre Ribeiro Gonçalves , Faria Fabrícia Paula , Freitas Sonia Maria 
Published: July 2022

AbstractHumicolagriseavar.thermoideais an aerobic and thermophilic fungus that secretes the GH11 xylanase HXYN2 in the presence of sugarcane bagasse. In this study, HXYN2 was expressed inPichiapastorisand characterized biochemically and structurally in the presence of beechwood xylan substrate and ferulic acid (FA). HXYN2 is a thermally stable protein, as indicated by circular dichroism, with greater activity in the range of 40–50 °C and pH 5.0–9.0, with optimal temperature and pH of 50 °C and 6.0, respectively. FA resulted in a 75% increase in enzyme activity and a 2.5-fold increase in catalytic velocity, catalytic efficiency, and catalytic rate constant (kcat), with no alteration in enzyme affinity for the substrate. Fluorescence quenching indicated that FA forms a complex with HXYN2 interacting with solvent-exposed tryptophan residues. The binding constants ranged from moderate (pH 7.0 and 9.0) to strong (pH 4.0) affinity. Isothermal titration calorimetry, structural models and molecular docking suggested that hydrogen bonds and hydrophobic interactions occur in the aglycone region inducing conformational changes in the active site driven by initial and final enthalpy- and entropy processes, respectively. These results indicate a potential for biotechnological application for HXYN2, such as in the bioconversion of plant residues rich in ferulic acid.
Genome-wide identification and in silico analysis of NPF, NRT2, CLC and SLAC1/SLAH nitrate transporters in hexaploid wheat (Triticum aestivum)
Authors: Kumar Aman , Sandhu Nitika , Kumar Pankaj , Pruthi Gomsie , Singh Jasneet , Kaur Satinder , Chhuneja Parveen 
Published: July 2022

AbstractNitrogen transport is one of the most important processes in plants mediated by specialized transmembrane proteins. Plants have two main systems for nitrogen uptake from soil and its transport within the system—a low-affinity transport system and a high-affinity transport system. Nitrate transporters are of special interest in cereal crops because large amount of money is spent on N fertilizers every year to enhance the crop productivity. Till date four gene families of nitrate transporter proteins; NPF (nitrate transporter 1/peptide transporter family), NRT2 (nitrate transporter 2 family), the CLC (chloride channel family), and the SLAC/SLAH (slow anion channel-associated homologues) have been reported in plants. In our study, in silico mining of nitrate transporter genes along with their detailed structure, phylogenetic and expression analysis was carried out. A total of 412 nitrate transporter genes were identified in hexaploid wheat genome using HMMER based homology searches in IWGSC Refseq v2.0. Out of those twenty genes were root specific, 11 leaf/shoot specific and 17 genes were grain/spike specific. The identification of nitrate transporter genes in the close proximity to the previously identified 67 marker-traits associations associated with the nitrogen use efficiency related traits in nested synthetic hexaploid wheat introgression library indicated the robustness of the reported transporter genes. The detailed crosstalk between the genome and proteome and the validation of identified putative candidate genes through expression and gene editing studies may lay down the foundation to improve nitrogen use efficiency of cereal crops.
Noninvasive prenatal diagnosis of genetic diseases induced by triplet repeat expansion by linked read haplotyping and Bayesian approach
Authors: Liautard-Haag C. , Durif G. , VanGoethem C. , Baux D. , Louis A. , Cayrefourcq L. , Lamairia M. , Willems M. , Zordan C. , Dorian V. , Rooryck C. , Goizet C. , Chaussenot A. , Monteil L. , Calvas P. , Miry C. , Favre R. , Le Boette E. , Fradin M. , Roux A. F. , Cossée M. , Koenig M. , Alix-Panabière C. , Guissart C. , Vincent M. C. 
Published: July 2022

AbstractThe field of noninvasive prenatal diagnosis (NIPD) has undergone significant progress over the last decade. Direct haplotyping has been successfully applied for NIPD of few single-gene disorders. However, technical issues remain for triplet-repeat expansions. The objective of this study was to develop an NIPD approach for couples at risk of transmitting dynamic mutations. This method includes targeted enrichment for linked-read libraries and targeted maternal plasma DNA sequencing. We also developed an innovative Bayesian procedure to integrate the Hoobari fetal genotyping model for inferring the fetal haplotype and the targeted gene variant status. Our method of directly resolving parental haplotypes through targeted linked-read sequencing was smoothly performed using blood samples from families with Huntington’s disease or myotonic dystrophy type 1. The Bayesian analysis of transmission of parental haplotypes allowed defining the genotype of five fetuses. The predicted variant status of four of these fetuses was in agreement with the invasive prenatal diagnosis findings. Conversely, no conclusive result was obtained for the NIPD of fragile X syndrome. Although improvements should be made to achieve clinically acceptable accuracy, our study shows that linked-read sequencing and parental haplotype phasing can be successfully used for NIPD of triplet-repeat expansion diseases.Trial registration: NCT04698551_date of first registration: 07/01/2021.
A thorough annotation of the krill transcriptome offers new insights for the study of physiological processes
Authors: Urso Ilenia , Biscontin Alberto , Corso Davide , Bertolucci Cristiano , Romualdi Chiara , De Pittà Cristiano , Meyer Bettina , Sales Gabriele 
Published: July 2022

AbstractThe krill species Euphausia superba plays a critical role in the food chain of the Antarctic ecosystem. Significant changes in climate conditions observed in the Antarctic Peninsula region in the last decades have already altered the distribution of krill and its reproductive dynamics. A deeper understanding of the adaptation capabilities of this species is urgently needed. The availability of a large body of RNA-seq assays allowed us to extend the current knowledge of the krill transcriptome. Our study covered the entire developmental process providing information of central relevance for ecological studies. Here we identified a series of genes involved in different steps of the krill moulting cycle, in the reproductive process and in sexual maturation in accordance with what was already described in previous works. Furthermore, the new transcriptome highlighted the presence of differentially expressed genes previously unknown, playing important roles in cuticle development as well as in energy storage during the krill life cycle. The discovery of new opsin sequences, specifically rhabdomeric opsins, one onychopsin, and one non-visual arthropsin, expands our knowledge of the krill opsin repertoire. We have collected all these results into the KrillDB2 database, a resource combining the latest annotation of the krill transcriptome with a series of analyses targeting genes relevant to krill physiology. KrillDB2 provides in a single resource a comprehensive catalog of krill genes; an atlas of their expression profiles over all RNA-seq datasets publicly available; a study of differential expression across multiple conditions. Finally, it provides initial indications about the expression of microRNA precursors, whose contribution to krill physiology has never been reported before.
Next-generation 2D optical strain mapping with strain-sensing smart skin compared to digital image correlation
Authors: Meng Wei , Pal Ashish , Bachilo Sergei M. , Weisman R. Bruce , Nagarajaiah Satish 
Published: July 2022

AbstractThis study reports next generation optical strain measurement with “strain-sensing smart skin” (S4) and a comparison of its performance against the established digital image correlation (DIC) method. S4 measures strain-induced shifts in the emission wavelengths of single-wall carbon nanotubes embedded in a thin film on the specimen. The new S4 film improves spectral uniformity of the nanotube sensors, avoids the need for annealing at elevated temperatures, and allows for parallel DIC measurements. Noncontact strain maps measured with the S4 films and point-wise scanning were directly compared to those from DIC on acrylic, concrete, and aluminum test specimens, including one with subsurface damage. Strain features were more clearly revealed with S4 than with DIC. Finite element method simulations also showed closer agreement with S4 than with DIC results. These findings highlight the potential of S4 strain measurement technology as a promising alternative or complement to existing technologies, especially when accumulated strains must be detected in structures that are not under constant observation.
Irigenin, a novel lead from Iris confusa for management of Helicobacter pylori infection with selective COX-2 and HpIMPDH inhibitory potential
Authors: Abdel-Baki Passent M. , El-Sherei Moshera M. , Khaleel Amal E. , Abdel-Aziz Marwa M. , Okba Mona M. 
Published: July 2022

AbstractThe development of new natural drugs for Helicobacter pylori (H. pylori) management has recently received significant attention. Iris confusa (I. confusa) was long used for the treatment of bacterial infections and gastritis. This study aimed at evaluating its effect on management of H. pylori infection and exploring its bioactive metabolites. The inhibitory potential of the polar (PF), non-polar (NPF) fractions and the isolated compounds against H. pylori using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assay in addition to their cyclooxygenases (COX-1 and COX-2), and nitric oxide (NO) inhibitory activities were assessed. The most biologically active compound was tested for its selective H. pylori inosine-5′-monophosphate dehydrogenase (HpIMPDH) inhibitory potential. Chromatographic purification of PF and NPF allowed isolation of tectoridin, orientin, irigenin, tectorigenin, isoarborinol and stigmasterol. The PF exhibited significant anti-H. pylori (MIC 62.50 µg/mL), COX-1, COX-2 (IC50 of 112.08 ± 0.60 and 47.90 ± 1.50 µg/mL respectively, selectivity index SI of 2.34), and NO (IC50 47.80 ± 0.89 µg/mL) inhibitory activities, while irigenin was the most potent isolated compound. Irigenin was found to have a promising activity against HpIMPDH enzyme (IC50 of 2.07 ± 1.90 μM) with low activity against human hIMPDH2 (IC50 > 10 μM) than clarithromycin, assuring its selectivity. Overall, I. confusa and its isolated compounds may serve as a potential source of plant-based drugs for H. pylori control. This study scientifically validated the claimed anti-bacterial activity of I. confusa and revealed irigenin potential as a novel lead exhibiting anti H. pylori activity in a first record.
Histological and electrophysiological evidence on the safe operation of a sharp-tip multimodal optrode during infrared neuromodulation of the rat cortex
Authors: Horváth Á. Cs. , Borbély S. , Mihók F. , Fürjes P. , Barthó P. , Fekete Z. 
Published: July 2022

AbstractInfrared neuromodulation is an emerging technology in neuroscience that exploits the inherent thermal sensitivity of neurons to excite or inhibit cellular activity. Since there is limited information on the physiological response of intracortical cell population in vivo including evidence on cell damage, we aimed to create and to validate the safe operation of a microscale sharp-tip implantable optrode that can be used to suppress the activity of neuronal population with low optical power continuous wave irradiation. Effective thermal cross-section and electric properties of the multimodal microdevice was characterized in bench-top tests. The evoked multi-unit activity was monitored in the rat somatosensory cortex, and using NeuN immunocytochemistry method, quantitative analysis of neuronal density changes due to the stimulation trials was evaluated. The sharp tip implant was effectively used to suppress the firing rate of neuronal populations. Histological staining showed that neither the probe insertion nor the heating protocols alone lead to significant changes in cell density in the close vicinity of the implant with respect to the intact control region. Our study shows that intracortical stimulation with continuous-wave infrared light at 1550 nm using a sharp tip implantable optical microdevice is a safe approach to modulate the firing rate of neurons.
Contextual memory reactivation modulates Ca2+-activity network state in a mushroom body-like center of the crab N. granulata
Authors: Maza Francisco Javier , Urbano Francisco José , Delorenzi Alejandro 
Published: July 2022

AbstractHigh-order brain centers play key roles in sensory integration and cognition. In arthropods, much is known about the insect high-order centers that support associative memory processes, the mushroom bodies. The hypothesis that crustaceans possess structures equivalent to the mushroom bodies -traditionally called hemiellipsoid body- has been receiving neuroanatomical endorsement. The recent functional support is limited to the short term: in a structure of the true crab Neohelice granulata that has many insect-like mushroom bodies traits, the plastic learning changes express the context attribute of an associative memory trace. Here, we used in vivo calcium imaging to test whether neuronal activity in this structure is associated with memory reactivation in the long-term (i.e., 24 h after training). Long-term training effects were tested by presenting the training-context alone, a reminder known to trigger memory reconsolidation. We found similar spontaneous activity between trained and naïve animals. However, after training-context presentation, trained animals showed increased calcium events rate, suggesting that memory reactivation induced a change in the underlying physiological state of this center. Reflecting the change in the escape response observed in the paradigm, animals trained with a visual danger stimulus showed significantly lower calcium-evoked transients in the insect-like mushroom body. Protein synthesis inhibitor cycloheximide administered during consolidation prevented calcium mediated changes. Moreover, we found the presence of distinct calcium activity spatial patterns. Results suggest that intrinsic neurons of this crustacean mushroom body-like center are involved in contextual associative long-term memory processes.
Clinical impact of and microbiological risk factors for qacA/B positivity in ICU-acquired ST5-methicillin-resistant SCCmec type II Staphylococcus aureus bacteremia
Authors: Kim Haein , Park Sunghee , Seo Hyeonji , Chung Hyemin , Kim Eun Sil , Sung Heungsup , Kim Mi-Na , Bae Seongman , Jung Jiwon , Kim Min Jae , Kim Sung-Han , Lee Sang-Oh , Choi Sang-Ho , Kim Yang Soo , Chong Yong Pil 
Published: July 2022

AbstractConcern about resistance to chlorhexidine has increased due to the wide use of the latter. The impact of the qacA/B and smr chlorhexidine tolerance genes on the outcome of methicillin-resistant Staphylococcus aureus (MRSA) infections is unclear. We evaluated the prevalence and clinical impact of, and microbiological risk factors for, qacA/B tolerance in MRSA bacteremia. MRSA bacteremia that occurred more than two days after intensive care unit admission between January 2009 and December 2018 was identified from a prospective cohort of S. aureus bacteremia in a tertiary-care hospital from South Korea. A total of 183 MRSA blood isolates was identified, and the major genotype found was ST5-MRSA-II (87.4%). The prevalences of qacA/B and smr were 67.2% and 3.8%, respectively. qacA/B-positive isolates were predominantly ST5-MRSA-II (96.7% [119/123]), the dominant hospital clone. In a homogenous ST5-MRSA-II background, qacA/B positivity was independently associated with septic shock (aOR, 4.85), gentamicin resistance (aOR, 74.43), and non-t002 spa type (aOR, 74.12). qacA/B positivity was found to have decreased significantly in ST5-MRSA-II in association with a decline in qacA/B-positive t2460, despite the increasing use of chlorhexidine since 2010 (P < 0.001 for trend). Continuous surveillance of the qac genes, and molecular characterization of their plasmids, are needed to understand their role in MRSA epidemiology.