bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combination Ad26.RSV.preF/preF protein vaccine induces superior protective immunity compared with individual vaccine components in preclinical models
Authors: Saeland Eirikur , van der Fits Leslie , Bolder Renske , Heemskerk-van der Meer Marjolein , Drijver Joke , van Polanen Yolinda , Vaneman Cornelis , Tettero Lisanne , Cox Freek , Serroyen Jan , Jorgensen Matthew J. , Langedijk Johannes P. M. , Schuitemaker Hanneke , Callendret Benoit , Zahn Roland C. 
Published: March 2023

AbstractRespiratory syncytial virus (RSV) is a leading cause of severe respiratory disease for which no licensed vaccine is available. We have previously shown that a prefusion (preF) conformation-stabilized RSV F protein antigen and an adenoviral vector encoding RSV preF protein (Ad26.RSV.preF) are immunogenic and protective in animals when administered as single components. Here, we evaluated a combination of the 2 components, administered as a single injection. Strong induction of both humoral and cellular responses was shown in RSV-naïve and pre-exposed mice and pre-exposed African green monkeys (AGMs). Both components of the combination vaccine contributed to humoral immune responses, while the Ad26.RSV.preF component was the main contributor to cellular immune responses in both mice and AGMs. Immunization with the combination elicited superior protection against RSV A2 challenge in cotton rats. These results demonstrate the advantage of a combination vaccine and support further clinical development.
Real-time detection of ammonium in soil pore water
Authors: Yupiter Rotem , Arnon Shlomi , Yeshno Elad , Visoly-Fisher Iris , Dahan Ofer 
Published: March 2023

AbstractThe development of technologies for continuous measurement of nitrogen forms in the soil is essential for optimizing the application of fertilizers in agriculture and preventing water-resource pollution. However, there is no effective commercial technology available for continuous monitoring of ammonium species in soil pore water. This work investigates an approach for real-time measurement of ammonium in soil water using near-infrared transmission spectroscopy and partial least squares regression (PLSR) for spectral analysis. The PLSR model was trained using soil pore water collected from various soils spiked with ammonium to achieve a wide concentration range. The monitoring approach was then validated through transport experiments in a soil column. The results demonstrated capabilities for real-time tracking of the temporal variation in soil ammonium concentration and potential utilization in agronomical or environmental sensing.
How autoreactive thymocytes differentiate into regulatory versus effector CD4+ T cells after avoiding clonal deletion
Authors: Tai Xuguang , Indart Alyssa , Rojano Mirelle , Guo Jie , Apenes Nicolai , Kadakia Tejas , Craveiro Marco , Alag Amala , Etzensperger Ruth , Badr Mohamed Elsherif , Zhang Flora , Zhang Zhongmei , Mu Jie , Guinter Terry , Crossman Assiatu , Granger Larry , Sharrow Susan , Zhou Xuyu , Singer Alfred 
Published: March 2023

AbstractThymocytes bearing autoreactive T cell receptors (TCRs) are agonist-signaled by TCR/co-stimulatory molecules to either undergo clonal deletion or to differentiate into specialized regulatory T (Treg) or effector T (Teff) CD4+ cells. How these different fates are achieved during development remains poorly understood. We now document that deletion and differentiation are agonist-signaled at different times during thymic selection and that Treg and Teff cells both arise after clonal deletion as alternative lineage fates of agonist-signaled CD4+CD25+ precursors. Disruption of agonist signaling induces CD4+CD25+ precursors to initiate Foxp3 expression and become Treg cells, whereas persistent agonist signaling induces CD4+CD25+ precursors to become IL-2+ Teff cells. Notably, we discovered that transforming growth factor-β induces Foxp3 expression and promotes Treg cell development by disrupting weaker agonist signals and that Foxp3 expression is not induced by IL-2 except under non-physiological in vivo conditions. Thus, TCR signaling disruption versus persistence is a general mechanism of lineage fate determination in the thymus that directs development of agonist-signaled autoreactive thymocytes.
High-resolution calibrated and validated Synthetic Aperture Radar Ocean surface wind data around Australia
Authors: Khan Salman , Young Ian , Ribal Agustinus , Hemer Mark 
Published: March 2023

AbstractThe dataset consists of ocean surface wind speed and direction at 10 m height and 1 km spatial resolution around the wider Australian coastal areas, spanning 4 years (2017 to 2021) of measurements from Sentinel-1 A and B imaging Synthetic Aperture Radar (SAR) platforms. The winds have been derived using a consistent SAR wind retrieval algorithm, processing the full Sentinel-1 archive in this region. The data are appropriately quality controlled, flagged, and archived as NetCDF files representing SAR wind field maps aligned with satellite along-track direction. The data have been calibrated against Metop-A/B Scatterometer buoy-calibrated, wind measurements and examined for potential changes in calibration over the duration of the data. The calibrated data are further validated by comparisons against independent Altimeter (Cryosat-2, Jason-2, Jason-3, and SARAL) wind speeds. Several methods for data access are also listed. The database is potentially useful for offshore industries (oil and gas, fisheries, shipping, offshore wind energy), public recreational activities (fishing, sailing, surfing), and protection and management of coasts and natural habitats.
Geosmin suppresses defensive behaviour and elicits unusual neural responses in honey bees
Authors: Scarano Florencia , Deivarajan Suresh Mukilan , Tiraboschi Ettore , Cabirol Amélie , Nouvian Morgane , Nowotny Thomas , Haase Albrecht 
Published: March 2023

AbstractGeosmin is an odorant produced by bacteria in moist soil. It has been found to be extraordinarily relevant to some insects, but the reasons for this are not yet fully understood. Here we report the first tests of the effect of geosmin on honey bees. A stinging assay showed that the defensive behaviour elicited by the bee’s alarm pheromone component isoamyl acetate (IAA) is strongly suppressed by geosmin. Surprisingly, the suppression is, however, only present at very low geosmin concentrations, and disappears at higher concentrations. We investigated the underlying mechanisms at the level of the olfactory receptor neurons by means of electroantennography, finding the responses to mixtures of geosmin and IAA to be lower than to pure IAA, suggesting an interaction of both compounds at the olfactory receptor level. Calcium imaging of the antennal lobe (AL) revealed that neuronal responses to geosmin decreased with increasing concentration, correlating well with the observed behaviour. Computational modelling of odour transduction and coding in the AL suggests that a broader activation of olfactory receptor types by geosmin in combination with lateral inhibition could lead to the observed non-monotonic increasing–decreasing responses to geosmin and thus underlie the specificity of the behavioural response to low geosmin concentrations.
Functional sugar-free chewing gum infused with spices bolsters antioxidant capacity and phenolic content of saliva
Authors: Crowe-White Kristi M. , Jung Seung Eun , Bragg Anna , Senkus Katelyn E. 
Published: March 2023

AbstractOral and vascular diseases are seemingly disparate conditions, yet individuals with poor oral health are at increased risk for cardiovascular events. Spice-derived bioactive polyphenols with antioxidant functionality may attenuate mechanisms linking the diseases, namely oxidative stress and inflammation. Acknowledging that novel approaches to increase antioxidant intake are warranted, the purpose of this study was to evaluate the influence of two functional sugar-free gums infused with spices on antioxidant capacity and phenolic content of saliva using the oxygen radical absorbance capacity and Folin-Ciocalteu assays, respectively. Unstimulated followed by stimulated saliva was collected according to a validated method across a prescribed five minute chewing period. Both gums significantly increased hydrophilic, lipophilic, and total antioxidant capacity of saliva (p < 0.05) yet to varying extents. Phenolic content of saliva was significantly higher (p < 0.001) post-chew for both gums. Results suggest spices infused into sugar-free chewing gum bolster the antioxidant capacity of saliva, thereby promoting oral health. Research evaluating the sublingual absorption of spice-derived antioxidants in functional gums and their influence on systemic oxidative stress is warranted.
Investigating livestock management in the early Neolithic archaeological site of Cabecicos Negros (Almería, Spain) from the organic residue analysis in pottery
Authors: Tarifa-Mateo N. , Saña M. , Clop X. , Rosell-Melé A. , Camalich-Massieu M. D. , Martín-Socas D. 
Published: March 2023

AbstractThis paper seeks to reconstruct the management of food resources in the early Neolithic site of Cabecicos Negros in southeastern Spain. For this purpose, we have studied 29 potsherds from Cabecicos Negros (Andalusia, Spain). Applying the methods of gas chromatography and mass spectrometry we were able to recompose the daily use of the sherds related to the consumption and storage of food products. Among the results obtained in this work, we were able to show new evidence of the exploitation of dairy products in the south of the Iberian Peninsula, as well as provide information on the exploitation and management of the early domestic animals herds. To improve the archaeological results obtained, isotopic results were compared with a modern reference of 53 fat samples from the adipose tissue of domestic pigs and wild boars.
Growth and characterization of thorium-doped calcium fluoride single crystals
Authors: Beeks Kjeld , Sikorsky Tomas , Rosecker Veronika , Pressler Martin , Schaden Fabian , Werban David , Hosseini Niyusha , Rudischer Lukas , Schneider Felix , Berwian Patrick , Friedrich Jochen , Hainz Dieter , Welch Jan , Sterba Johannes H. , Kazakov Georgy , Schumm Thorsten 
Published: March 2023

AbstractWe have grown $$^{232}$$

232

Th:CaF$$_2$$

2

and $$^{229}$$

229

Th:CaF$$_2$$

2

single crystals for investigations on the VUV laser-accessible first nuclear excited state of $$^{229}$$

229

Th, with the aim of building a solid-state nuclear clock. To reach high doping concentrations despite the extreme scarcity (and radioactivity) of $$^{229}$$

229

Th, we have scaled down the crystal volume by a factor 100 compared to established commercial or scientific growth processes. We use the vertical gradient freeze method on 3.2 mm diameter seed single crystals with a 2 mm drilled pocket, filled with a co-precipitated CaF$$_2$$

2

:ThF$$_4$$

4

:PbF$$_2$$

2

powder in order to grow single crystals. Concentrations of $$4\cdot 10^{19}$$

4
·

10
19

cm$$^{-3}$$

-
3

have been realized with $$^{232}$$

232

Th with good (> 10%) VUV transmission. However, the intrinsic radioactivity of $$^{229}$$

229

Th drives radio-induced dissociation during growth and radiation damage after solidification. Both lead to a degradation of VUV transmission, currently limiting the $$^{229}$$

229

Th concentration to $$<5\times 10^{17}$$

<
5
×

10
17

cm$$^{-3}$$

-
3

.
Circulating tumor DNA in molecular assessment feasibly predicts early progression of pancreatic cancer that cannot be identified via initial imaging
Authors: Watanabe Fumiaki , Suzuki Koichi , Aizawa Hidetoshi , Endo Yuhei , Takayama Yuji , Kakizawa Nao , Kato Takaharu , Noda Hiroshi , Rikiyama Toshiki 
Published: March 2023

AbstractMolecular assessment using circulating tumor DNA (ctDNA) has not been well-defined. We recruited 61 pancreatic cancer (PC) patients who underwent initial computed tomography (CT) imaging study during first-line chemotherapy. Initial molecular assessment was performed using droplet digital PCR and defined as the change in KRAS-mutated ctDNA before and after treatments, which was classified into five categories: mNT, molecular negative; mCR, complete response; mPR, partial response; mSD, stable disease; mPD, progressive disease. Of 61 patients, 14 diagnosed with PD after initial CT imaging showed significantly worse therapeutic outcomes than 47 patients with disease control. In these 47 patients, initial molecular assessment exhibited significant differences in therapeutic outcomes between patients with and without ctDNA (mPD + mSD vs. mCR + mNT; 13.2 M vs. 21.7 M, P = 0.0029) but no difference between those with mPD and mSD + mCR + mNT, suggesting that the presence of ctDNA had more impact on the therapeutic outcomes than change in its number. Multivariate analysis revealed that it was the only independent prognostic factor (P = 0.0405). The presence of ctDNA in initial molecular assessment predicted early tumor progression and identified PC patients more likely to benefit from chemotherapy.
Embryo morphokinetics derived from fresh and vitrified bovine oocytes predict blastocyst development and nuclear abnormalities
Authors: Angel-Velez Daniel , De Coster Tine , Azari-Dolatabad Nima , Fernández-Montoro Andrea , Benedetti Camilla , Pavani Krishna , Van Soom Ann , Bogado Pascottini Osvaldo , Smits Katrien 
Published: March 2023

AbstractEmbryo development is a dynamic process and critical stages may go unnoticed with the use of traditional morphologic assessments, especially the timing of embryonic divisions and aberrant zygotic cleavage patterns. Bovine embryo development is impaired after oocyte vitrification, but little is known about the underlying morphokinetic behavior. Here, bovine zygotes from fresh (n = 708) and vitrified oocytes (n = 182) were monitored by time-lapse imaging and the timing and nature of early blastomere divisions were modeled to find associations with blastocyst development at day 8. The predictive potential of morphokinetic parameters was analyzed by logistic regression and receiver operating characteristic curve analysis to determine optimal cut-off values. Lag-phase was highly correlated with embryo development. Remarkably, 100% of zygotes that reached the blastocyst stage showed a lag-phase. Fast first cleavage increased the chance of blastocyst development to 30% with a cut-off of 32 h and 22 min. Aberrant zygotic cleavage events, including multipolar division, unequal blastomere sizes, and membrane ruffling resulted in decreased blastocyst development. Multipolar division leads to uneven blastomeres, which was associated with anuclear and multinuclear blastomeres, indicating genome segregation errors. Moreover, we described for the first time morphokinetics of embryos derived from vitrified bovine oocytes. Vitrification severely affected blastocyst development, although lower cryoprotectant concentration in equilibration solutions seems to be less detrimental for embryo yield. Impaired development was linked to slow cleavages, lower lag-phase incidence, and increased early embryonic arrest. Typically, less than 15% of the embryos produced from vitrified oocytes reached more than eight cells. Interestingly, the rate of abnormal first cleavage events was not affected by oocyte vitrification. In conclusion, time to first cleavage, the presence of a lag-phase, and the absence of aberrant zygotic cleavage were the best predictors of bovine blastocyst development for both fresh and vitrified oocytes.
High-precision measurements of the hyperfine structure of cobalt ions in the deep ultraviolet range
Authors: Koszorús Á. , Block M. , Campbell P. , Cheal B. , de Groote R. P. , Gins W. , Moore I. D. , Ortiz-Cortes A. , Raggio A. , Warbinek J. 
Published: March 2023

AbstractHigh-precision hyperfine structure measurements were performed on stable, singly-charged $$^{59}$$

59

Co ions at the IGISOL facility in Jyväskylä, Finland using the collinear laser spectroscopy technique. A newly installed light collection setup enabled the study of transitions in the 230 nm wavelength range from low-lying states below 6000 cm$$^{-1}$$

-
1

. We report a 100-fold improvement on the precision of the hyperfine A parameters, and furthermore present newly measured hyperfine B paramaters.
Integrative transcriptomic and metabolomic analysis reveals alterations in energy metabolism and mitochondrial functionality in broiler chickens with wooden breast
Authors: Wang Ziqing , Brannick Erin , Abasht Behnam 
Published: March 2023

AbstractThis integrative study of transcriptomics and metabolomics aimed to improve our understanding of Wooden Breast myopathy (WB). Breast muscle samples from 8 WB affected and 8 unaffected male broiler chickens of 47 days of age were harvested for metabolite profiling. Among these 16 samples, 5 affected and 6 unaffected also underwent gene expression profiling. The Joint Pathway Analysis was applied on 119 metabolites and 3444 genes exhibiting differential abundance or expression between WB affected and unaffected chickens. Mitochondrial dysfunctions in WB was suggested by higher levels of monoacylglycerols and down-regulated genes involved in lipid production, fatty acid beta oxidation, and oxidative phosphorylation. Lower levels of carnosine and anserine, along with down-regulated carnosine synthase 1 suggested decreased carnosine synthesis and hence impaired antioxidant capacity in WB. Additionally, Weighted Gene Co-expression Network Analysis results indicated that abundance of inosine monophosphate, significantly lower in WB muscle, was correlated with mRNA expression levels of numerous genes related to focal adhesion, extracellular matrix and intercellular signaling, implying its function in connecting and possibly regulating multiple key biological pathways. Overall, this study showed not only the consistency between transcript and metabolite profiles, but also the potential in gaining further insights from analyzing multi-omics data.
Quantifying progress in research topics across nations
Authors: Asatani Kimitaka , Oki Sumihiro , Momma Takuya , Sakata Ichiro 
Published: March 2023

AbstractA scientist’s choice of research topic affects the impact of their work and future career. While the disparity between nations in scientific information, funding, and facilities has decreased, scientists on the cutting edge of their fields are not evenly distributed across nations. Here, we quantify relative progress in research topics of a nation from the time-series comparison of reference lists from papers, using 71 million published papers from Scopus. We discover a steady leading-following relationship in research topics between Western nations or Asian city-states and others. Furthermore, we find that a nation’s share of information-rich scientists in co-authorship networks correlates highly with that nation’s progress in research topics. These results indicate that scientists’ relationships continue to dominate scientific evolution in the age of open access to information and explain the failure or success of nations’ investments in science.
Image analysis of cutaneous melanoma histology: a systematic review and meta-analysis
Authors: Clarke Emily L. , Wade Ryckie G. , Magee Derek , Newton-Bishop Julia , Treanor Darren 
Published: March 2023

AbstractThe current subjective histopathological assessment of cutaneous melanoma is challenging. The application of image analysis algorithms to histological images may facilitate improvements in workflow and prognostication. To date, several individual algorithms applied to melanoma histological images have been reported with variations in approach and reported accuracies. Histological digital images can be created using a camera mounted on a light microscope, or through whole slide image (WSI) generation using a whole slide scanner. Before any such tool could be integrated into clinical workflow, the accuracy of the technology should be carefully evaluated and summarised. Therefore, the objective of this review was to evaluate the accuracy of existing image analysis algorithms applied to digital histological images of cutaneous melanoma.
Database searching of PubMed and Embase from inception to 11th March 2022 was conducted alongside citation checking and examining reports from organisations. All studies reporting accuracy of any image analysis applied to histological images of cutaneous melanoma, were included. The reference standard was any histological assessment of haematoxylin and eosin-stained slides and/or immunohistochemical staining. Citations were independently deduplicated and screened by two review authors and disagreements were resolved through discussion. The data was extracted concerning study demographics; type of image analysis; type of reference standard; conditions included and test statistics to construct 2 × 2 tables. Data was extracted in accordance with our protocol and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses-Diagnostic Test Accuracy (PRISMA-DTA) Statement. A bivariate random-effects meta-analysis was used to estimate summary sensitivities and specificities with 95% confidence intervals (CI). Assessment of methodological quality was conducted using a tailored version of the Quality Assessment of Diagnostic Accuracy Studies (QUADAS-2) tool. The primary outcome was the pooled sensitivity and specificity of image analysis applied to cutaneous melanoma histological images. Sixteen studies were included in the systematic review, representing 4,888 specimens. Six studies were included in the meta-analysis. The mean sensitivity and specificity of automated image analysis algorithms applied to melanoma histological images was 90% (CI 82%, 95%) and 92% (CI 79%, 97%), respectively. Based on limited and heterogeneous data, image analysis appears to offer high accuracy when applied to histological images of cutaneous melanoma. However, given the early exploratory nature of these studies, further development work is necessary to improve their performance.
Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures
Authors: Ito Yuki , Uda Shinsuke , Kokaji Toshiya , Hirayama Akiyoshi , Soga Tomoyoshi , Suzuki Yutaka , Kuroda Shinya , Kubota Hiroyuki 
Published: March 2023

AbstractInteractions between various molecular species in biological phenomena give rise to numerous networks. The investigation of these networks, including their statistical and biochemical interactions, supports a deeper understanding of biological phenomena. The clustering of nodes associated with molecular species and enrichment analysis is frequently applied to examine the biological significance of such network structures. However, these methods focus on delineating the function of a node. As such, in-depth investigations of the edges, which are the connections between the nodes, are rarely explored. In the current study, we aimed to investigate the functions of the edges rather than the nodes. To accomplish this, for each network, we categorized the edges and defined the edge type based on their biological annotations. Subsequently, we used the edge type to compare the network structures of the metabolome and transcriptome in the livers of healthy (wild-type) and obese (ob/ob) mice following oral glucose administration (OGTT). The findings demonstrate that the edge type can facilitate the characterization of the state of a network structure, thereby reducing the information available through datasets containing the OGTT response in the metabolome and transcriptome.