bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exogenous enzymes and probiotics alter digestion kinetics, volatile fatty acid content and microbial interactions in the gut of Nile tilapia
Authors: Maas Roel M. , Deng Yale , Dersjant-Li Yueming , Petit Jules , Verdegem Marc C. J. , Schrama Johan W. , Kokou Fotini 
Published: April 2021

AbstractSustainable aquafeed production requires fishmeal replacement, leading to an increasing use of plant-derived ingredients. As a consequence, higher levels of antinutritional substances, such as non-starch polysaccharides and phytate, are present in aquafeeds, with negative effects on fish performance, nutrient digestibility and overall gut health. To alleviate these negative effects, providing exogenous digestive enzymes and/or probiotics can be an effective solution. In this study, we tested the effect of dietary supplementation of enzymes (phytase and xylanase) and probiotics (three strains of Bacillus amyloliquefaciens) on nutrient digestion kinetics and volatile fatty acid content along the gut, and the distal gut microbiome diversity in Nile tilapia. Chyme volatile fatty content was increased with probiotic supplementation in the proximal gut, while lactate content, measured for the first time in vivo in fish, decreased with enzymes along the gut. Enzyme supplementation enhanced crude protein, Ca and P digestibility in proximal and middle gut. Enzymes and probiotics supplementation enhanced microbial interactions as shown by network analysis, while increased the abundance of lactic acid bacteria and Bacillus species. Such results suggest that supplementation with exogenous enzymes and probiotics increases nutrient availability, while at the same time benefits gut health and contributes to a more stable microbiome environment.
Antimicrobial susceptibility, serotype distribution, virulence profile and molecular typing of piliated clinical isolates of pneumococci from east coast, Peninsular Malaysia
Authors: Dzaraly Nurul Diana , Mohd Desa Mohd Nasir , Muthanna AbdulRahman , Masri Siti Norbaya , Taib Niazlin Mohd , Suhaili Zarizal , Sulaiman Nurshahira , Baharin Nurul Hana Zainal , Shuan Cheah Yun , Ariffin Zarina , Rahman Nor Iza A. , Mohd Rani Farahiyah , Palanisamy Navindra Kumari , Soh Tuan Suhaila Tuan , Abdullah Fatimah Haslina 
Published: April 2021

AbstractPilus has been recently associated with pneumococcal pathogenesis in humans. The information regarding piliated isolates in Malaysia is scarce, especially in the less developed states on the east coast of Peninsular Malaysia. Therefore, we studied the characteristics of pneumococci, including the piliated isolates, in relation to antimicrobial susceptibility, serotypes, and genotypes at a major tertiary hospital on the east coast of Peninsular Malaysia. A total of 100 clinical isolates collected between September 2017 and December 2019 were subjected to serotyping, antimicrobial susceptibility test, and detection of pneumococcal virulence and pilus genes. Multilocus sequence typing (MLST) and phylogenetic analysis were performed only for piliated strains. The most frequent serotypes were 14 (17%), 6A/B (16%), 23F (12%), 19A (11%), and 19F (11%). The majority of isolates were resistant to erythromycin (42%), tetracycline (37%), and trimethoprim-sulfamethoxazole (24%). Piliated isolates occurred in a proportion of 19%; 47.3% of them were multidrug-resistant (MDR) and a majority had serotype 19F. This study showed ST236 was the most predominant sequence type (ST) among piliated isolates, which was related to PMEN clone Taiwan19F-14 (CC271). In the phylogenetic analysis, the piliated isolates were grouped into three major clades supported with 100% bootstrap values. Most piliated isolates belonged to internationally disseminated clones of S. pneumoniae, but pneumococcal conjugate vaccines (PCVs) have the potential to control them.
Novel application of automated machine learning with MALDI-TOF-MS for rapid high-throughput screening of COVID-19: a proof of concept
Authors: Tran Nam K. , Howard Taylor , Walsh Ryan , Pepper John , Loegering Julia , Phinney Brett , Salemi Michelle R. , Rashidi Hooman H. 
Published: April 2021

AbstractThe 2019 novel coronavirus infectious disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created an unsustainable need for molecular diagnostic testing. Molecular approaches such as reverse transcription (RT) polymerase chain reaction (PCR) offers highly sensitive and specific means to detect SARS-CoV-2 RNA, however, despite it being the accepted “gold standard”, molecular platforms often require a tradeoff between speed versus throughput. Matrix assisted laser desorption ionization (MALDI)—time of flight (TOF)—mass spectrometry (MS) has been proposed as a potential solution for COVID-19 testing and finding a balance between analytical performance, speed, and throughput, without relying on impacted supply chains. Combined with machine learning (ML), this MALDI-TOF-MS approach could overcome logistical barriers encountered by current testing paradigms. We evaluated the analytical performance of an ML-enhanced MALDI-TOF-MS method for screening COVID-19. Residual nasal swab samples from adult volunteers were used for testing and compared against RT-PCR. Two optimized ML models were identified, exhibiting accuracy of 98.3%, positive percent agreement (PPA) of 100%, negative percent agreement (NPA) of 96%, and accuracy of 96.6%, PPA of 98.5%, and NPA of 94% respectively. Machine learning enhanced MALDI-TOF-MS for COVID-19 testing exhibited performance comparable to existing commercial SARS-CoV-2 tests.
Crop response to El Niño-Southern Oscillation related weather variation to help farmers manage their crops
Authors: Chapman Ross , Cock James , Samson Marianne , Janetski Noel , Janetski Kate , Gusyana Dadang , Dutta Sudarshan , Oberthür Thomas 
Published: April 2021

AbstractAlthough weather is a major driver of crop yield, many farmers don’t know in advance how the weather will vary nor how their crops will respond. We hypothesized that where El Niño-Southern Oscillation (ENSO) drives weather patterns, and data on crop response to distinct management practices exists, it should be possible to map ENSO Oceanic Index (ENSO OI) patterns to crop management responses without precise weather data. Time series data on cacao farm yields in Sulawesi, Indonesia, with and without fertilizer, were used to provide proof-of-concept. A machine learning approach associated 75% of cacao yield variation with the ENSO patterns up to 8 and 24 months before harvest and predicted when fertilizer applications would be worthwhile. Thus, it’s possible to relate average cacao crop performance and management response directly to ENSO patterns without weather data provided: (1) site specific data exist on crop performance over time with distinct management practices; and (2) the weather patterns are driven by ENSO OI. We believe that the principles established here can readily be applied to other crops, particularly when there’s little data available on crop responses to management and weather. However, specific models will be required for each crop and every recommendation domain.
Reduced evoked activity and cortical oscillations are correlated with anisometric amblyopia and impairment of visual acuity
Authors: Julku Hanna , Rouhinen Santeri , Huttunen Henri J. , Lindberg Laura , Liinamaa Johanna , Saarela Ville , Karvonen Elina , Booms Sigrid , Mäkelä Jyrki P. , Uusitalo Hannu , Castrén Eero , Palva J. Matias , Palva Satu 
Published: April 2021

AbstractAmblyopia is a developmental disorder associated with abnormal visual experience during early childhood commonly arising from strabismus and/or anisometropia and leading to dysfunctions in visual cortex and to various visual deficits. The different forms of neuronal activity that are attenuated in amblyopia have been only partially characterized. In electrophysiological recordings of healthy human brain, the presentation of visual stimuli is associated with event-related activity and oscillatory responses. It has remained poorly understood whether these forms of activity are reduced in amblyopia and whether possible dysfunctions would arise from lower- or higher-order visual areas. We recorded neuronal activity with magnetoencephalography (MEG) from anisometropic amblyopic patients and control participants during two visual tasks presented separately for each eye and estimated neuronal activity from source-reconstructed MEG data. We investigated whether event-related and oscillatory responses would be reduced for amblyopia and localized their cortical sources. Oscillation amplitudes and evoked responses were reduced for stimuli presented to the amblyopic eye in higher-order visual areas and in parietal and prefrontal cortices. Importantly, the reduction of oscillation amplitudes but not that of evoked responses was correlated with decreased visual acuity in amblyopia. These results show that attenuated oscillatory responses are correlated with visual deficits in anisometric amblyopia.
Sustained intrinsic WNT and BMP4 activation impairs hESC differentiation to definitive endoderm and drives the cells towards extra-embryonic mesoderm
Authors: Markouli C. , De Deckersberg E. Couvreu , Dziedzicka D. , Regin M. , Franck S. , Keller A. , Gheldof A. , Geens M. , Sermon K. , Spits C. 
Published: April 2021

AbstractWe identified a human embryonic stem cell subline that fails to respond to the differentiation cues needed to obtain endoderm derivatives, differentiating instead into extra-embryonic mesoderm. RNA-sequencing analysis showed that the subline has hyperactivation of the WNT and BMP4 signalling. Modulation of these pathways with small molecules confirmed them as the cause of the differentiation impairment. While activation of WNT and BMP4 in control cells resulted in a loss of endoderm differentiation and induction of extra-embryonic mesoderm markers, inhibition of these pathways in the subline restored its ability to differentiate. Karyotyping and exome sequencing analysis did not identify any changes in the genome that could account for the pathway deregulation. These findings add to the increasing evidence that different responses of stem cell lines to differentiation protocols are based on genetic and epigenetic factors, inherent to the line or acquired during cell culture.
Proteomic profiling of the rat hippocampus from the kindling and pilocarpine models of epilepsy: potential targets in calcium regulatory network
Authors: Sadeghi Leila , Rizvanov Albert Anatolyevich , Dabirmanesh Bahareh , Salafutdinov Ilnur Ildusovich , Sayyah Mohammad , Shojaei Amir , Zahiri Javad , Mirnajafi-Zadeh Javad , Khorsand Babak , Khajeh Khosro , Fathollahi Yaghoub 
Published: April 2021

AbstractHerein proteomic profiling of the rat hippocampus from the kindling and pilocarpine models of epilepsy was performed to achieve new potential targets for treating epileptic seizures. A total of 144 differently expressed proteins in both left and right hippocampi by two-dimensional electrophoresis coupled to matrix-assisted laser desorption-mass spectrometry were identified across the rat models of epilepsy. Based on network analysis, the majority of differentially expressed proteins were associated with Ca2+ homeostasis. Changes in ADP-ribosyl cyclase (ADPRC), lysophosphatidic acid receptor 3 (LPAR3), calreticulin, ubiquitin carboxyl-terminal hydrolase L1 (UCH-L1), synaptosomal nerve-associated protein 25 (SNAP 25) and transgelin 3 proteins were probed by Western blot analysis and validated using immunohistochemistry. Inhibition of calcium influx by 8-Bromo-cADP-Ribose (8-Br-cADPR) and 2-Aminoethyl diphenylborinate (2-APB) which act via the ADPRC and LPAR3, respectively, attenuated epileptic seizures. Considering a wide range of molecular events and effective role of calcium homeostasis in epilepsy, polypharmacy with multiple realistic targets should be further explored to reach the most effective treatments.
Tissue plasminogen activator is a ligand of cation-independent mannose 6-phosphate receptor and consists of glycoforms that contain mannose 6-phosphate
Authors: Miller James J. , Bohnsack Richard N. , Olson Linda J. , Ishihara Mayumi , Aoki Kazuhiro , Tiemeyer Michael , Dahms Nancy M. 
Published: April 2021

AbstractPlasmin is the key enzyme in fibrinolysis. Upon interaction with plasminogen activators, the zymogen plasminogen is converted to active plasmin. Some studies indicate plasminogen activation is regulated by cation-independent mannose 6-phosphate receptor (CI-MPR), a protein that facilitates lysosomal enzyme trafficking and insulin-like growth factor 2 downregulation. Plasminogen regulation may be accomplished by CI-MPR binding to plasminogen or urokinase plasminogen activator receptor. We asked whether other members of the plasminogen activation system, such as tissue plasminogen activator (tPA), also interact with CI-MPR. Because tPA is a glycoprotein with three N-linked glycosylation sites, we hypothesized that tPA contains mannose 6-phosphate (M6P) and binds CI-MPR in a M6P-dependent manner. Using surface plasmon resonance, we found that two sources of tPA bound the extracellular region of human and bovine CI-MPR with low-mid nanomolar affinities. Binding was partially inhibited with phosphatase treatment or M6P. Subsequent studies revealed that the five N-terminal domains of CI-MPR were sufficient for tPA binding, and this interaction was also partially mediated by M6P. The three glycosylation sites of tPA were analyzed by mass spectrometry, and glycoforms containing M6P and M6P-N-acetylglucosamine were identified at position N448 of tPA. In summary, we found that tPA contains M6P and is a CI-MPR ligand.
Robustness of radiomic features in CT images with different slice thickness, comparing liver tumour and muscle
Authors: Escudero Sanchez Lorena , Rundo Leonardo , Gill Andrew B. , Hoare Matthew , Mendes Serrao Eva , Sala Evis 
Published: April 2021

AbstractRadiomic image features are becoming a promising non-invasive method to obtain quantitative measurements for tumour classification and therapy response assessment in oncological research. However, despite its increasingly established application, there is a need for standardisation criteria and further validation of feature robustness with respect to imaging acquisition parameters. In this paper, the robustness of radiomic features extracted from computed tomography (CT) images is evaluated for liver tumour and muscle, comparing the values of the features in images reconstructed with two different slice thicknesses of 2.0 mm and 5.0 mm. Novel approaches are presented to address the intrinsic dependencies of texture radiomic features, choosing the optimal number of grey levels and correcting for the dependency on volume. With the optimal values and corrections, feature values are compared across thicknesses to identify reproducible features. Normalisation using muscle regions is also described as an alternative approach. With either method, a large fraction of features (75–90%) was found to be highly robust (< 25% difference). The analyses were performed on a homogeneous CT dataset of 43 patients with hepatocellular carcinoma, and consistent results were obtained for both tumour and muscle tissue. Finally, recommended guidelines are included for radiomic studies using variable slice thickness.
Spatio-temporal feature learning with reservoir computing for T-cell segmentation in live-cell $$\hbox {Ca}^{2+}$$ fluorescence microscopy
Authors: Hadaeghi Fatemeh , Diercks Björn-Philipp , Schetelig Daniel , Damicelli Fabrizio , Wolf Insa M. A. , Werner René 
Published: April 2021

AbstractAdvances in high-resolution live-cell$$\hbox {Ca}^{2+}$$Ca2+imaging enabled subcellular localization of early$$\hbox {Ca}^{2+}$$Ca2+signaling events in T-cells and paved the way to investigate the interplay between receptors and potential target channels in$$\hbox {Ca}^{2+}$$Ca2+release events. The huge amount of acquired data requires efficient, ideally automated image processing pipelines, with cell localization/segmentation as central tasks. Automated segmentation in live-cell cytosolic$$\hbox {Ca}^{2+}$$Ca2+imaging data is, however, challenging due to temporal image intensity fluctuations, low signal-to-noise ratio, and photo-bleaching. Here, we propose a reservoir computing (RC) framework for efficient and temporally consistent segmentation. Experiments were conducted with Jurkat T-cells and anti-CD3 coated beads used for T-cell activation. We compared the RC performance with a standard U-Net and a convolutional long short-term memory (LSTM) model. The RC-based models (1) perform on par in terms of segmentation accuracy with the deep learning models for cell-only segmentation, but show improved temporal segmentation consistency compared to the U-Net; (2) outperform the U-Net for two-emission wavelengths image segmentation and differentiation of T-cells and beads; and (3) perform on par with the convolutional LSTM for single-emission wavelength T-cell/bead segmentation and differentiation. In turn, RC models contain only a fraction of the parameters of the baseline models and reduce the training time considerably.
Strain effects on polycrystalline germanium thin films
Authors: Imajo Toshifumi , Suemasu Takashi , Toko Kaoru 
Published: April 2021

AbstractPolycrystalline Ge thin films have attracted increasing attention because their hole mobilities exceed those of single-crystal Si wafers, while the process temperature is low. In this study, we investigate the strain effects on the crystal and electrical properties of polycrystalline Ge layers formed by solid-phase crystallization at 375 °C by modulating the substrate material. The strain of the Ge layers is in the range of approximately 0.5% (tensile) to -0.5% (compressive), which reflects both thermal expansion difference between Ge and substrate and phase transition of Ge from amorphous to crystalline. For both tensile and compressive strains, a large strain provides large crystal grains with sizes of approximately 10 μm owing to growth promotion. The potential barrier height of the grain boundary strongly depends on the strain and its direction. It is increased by tensile strain and decreased by compressive strain. These findings will be useful for the design of Ge-based thin-film devices on various materials for Internet-of-things technologies.
Quantum chemical calculation studies toward microscopic understanding of retention mechanism of Cs radioisotopes and other alkali metals in lichens
Authors: Suno Hiroya , Machida Masahiko , Dohi Terumi , Ohmura Yoshihito 
Published: April 2021

AbstractWe evaluate stability of cesium (Cs) and other alkali-metal cation complexes of lichen metabolites in both gas and aqueous phases to discuss why lichens can retain radioactive Cs in the thalli over several years. We focus on oxalic acid, (+)-usnic acid, atranorin, lecanoric acid, and protocetraric acid, which are common metabolite substances in various lichens including, e.g., Flavoparmelia caperata and Parmotrema tinctorum retaining Cs in Fukushima, Japan. By performing quantum chemical calculations, their gas-phase complexation energies and aqueous-solution complexation free energies with alkali-metal cations are computed for their neutral and deprotonated cases. Consequently, all the molecules are found to energetically favor cation complexations and the preference order is Li$$^+>$$

+

>

Na$$^+>$$

+

>

K$$^+>$$

+

>

Rb$$^+>$$

+

>

Cs$$^+$$

+

for all conditions, indicating no specific Cs selectivity but strong binding with all alkali cations. Comparing complexation stabilities among these metabolites, lecanoric and protocetraric acids seen in medullary layer are found to keep higher affinity in their neutral case, while (+)-usnic acid and atranorin in upper cortex exhibit rather strong affinity only in deprotonated cases through forming stable six atoms’ ring containing alkali cation chelated by two oxygens. These results suggest that the medullary layer can catch all alkali cations in a wide pH range around the physiological one, while the upper cortex can effectively block penetration of metal ions when the metal stress grows. Such insights highlight a physiological role of metabolites like blocking of metal-cation migrations into intracellular tissues, and explain long-term retention of alkali cations including Cs in lichens containing enough such metabolites to bind them.
The anisotropic field of ensemble coding
Authors: Pascucci David , Ruethemann Nadia , Plomp Gijs 
Published: April 2021

AbstractHuman observers can accurately estimate statistical summaries from an ensemble of multiple stimuli, including the average size, hue, and direction of motion. The efficiency and speed with which statistical summaries are extracted suggest an automatic mechanism of ensemble coding that operates beyond the capacity limits of attention and memory. However, the extent to which ensemble coding reflects a truly parallel and holistic mode of processing or a non-uniform and biased integration of multiple items is still under debate. In the present work, we used a technique, based on a Spatial Weighted Average Model (SWM), to recover the spatial profile of weights with which individual stimuli contribute to the estimated average during mean size adjustment tasks. In a series of experiments, we derived two-dimensional SWM maps for ensembles presented at different retinal locations, with different degrees of dispersion and under different attentional demands. Our findings revealed strong spatial anisotropies and leftward biases in ensemble coding that were organized in retinotopic reference frames and persisted under attentional manipulations. These results demonstrate an anisotropic spatial contribution to ensemble coding that could be mediated by the differential activation of the two hemispheres during spatial processing and scene encoding.