bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semi-synthetic terpenoids with differential adjuvant properties as sustainable replacements for shark squalene in vaccine emulsions
Authors: Fisher Karl J. , Kinsey Robert , Mohamath Raodoh , Phan Tony , Liang Hong , Orr Mark T. , Lykins William R. , Guderian Jeffrey A. , Bakken Julie , Argilla David , Ramer-Denisoff Gabi , Larson Elise , Qi Yizhi , Sivananthan Sandra , Smolyar Karina , Carter Darrick , Paddon Christopher J. , Fox Christopher B. 
Published: February 2023

AbstractSynthetic biology has allowed for the industrial production of supply-limited sesquiterpenoids such as the antimalarial drug artemisinin and β-farnesene. One of the only unmodified animal products used in medicine is squalene, a triterpenoid derived from shark liver oil, which when formulated into an emulsion is used as a vaccine adjuvant to enhance immune responses in licensed vaccines. However, overfishing is depleting deep-sea shark populations, leading to potential supply problems for squalene. We chemically generated over 20 squalene analogues from fermentation-derived β-farnesene and evaluated adjuvant activity of the emulsified compounds compared to shark squalene emulsion. By employing a desirability function approach that incorporated multiple immune readouts, we identified analogues with enhanced, equivalent, or decreased adjuvant activity compared to shark squalene emulsion. Availability of a library of structurally related analogues allowed elucidation of structure-function relationships. Thus, combining industrial synthetic biology with chemistry and immunology enabled generation of sustainable terpenoid-based vaccine adjuvants comparable to current shark squalene-based adjuvants while illuminating structural properties important for adjuvant activity.
Organogel delivery vehicles for the stabilization of organolithium reagents
Authors: Slavík Petr , Trowse Benjamin R. , O’Brien Peter , Smith David K. 
Published: February 2023

AbstractOrganolithium reagents are a vital tool in modern organic chemistry, enabling the synthesis of carbon–carbon bonds. However, due to their high reactivity, low temperatures, inert atmospheres and strictly dried solvents are usually necessary for their use. Here we report an encapsulating method for the stabilization of sensitive organolithium reagents—PhLi, n-BuLi and s-BuLi—in a low-cost hexatriacontane (C36H74) organogel. The use of this technology is showcased in nucleophilic addition reactions under ambient conditions, low-temperature bromine–lithium exchange, ortho-lithiation and C–H functionalization. The gel substantially enhances organolithium stability, allows simple storage, handling and delivery, and enables reproducible reagent portioning. The use of gels as easily divided delivery vehicles for hazardous organometallics has the potential to transform this area of synthetic chemistry, making these powerful reactions safer and more accessible to non-specialist researchers, and enabling the more widespread use of these common synthetic methods.
Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC
Authors: Kamrad Stephan , Correia-Melo Clara , Szyrwiel Lukasz , Aulakh Simran Kaur , Bähler Jürg , Demichev Vadim , Mülleder Michael , Ralser Markus 
Published: February 2023

AbstractGenetically identical cells are known to differ in many physiological parameters such as growth rate and drug tolerance. Metabolic specialization is believed to be a cause of such phenotypic heterogeneity, but detection of metabolically divergent subpopulations remains technically challenging. We developed a proteomics-based technology, termed differential isotope labelling by amino acids (DILAC), that can detect producer and consumer subpopulations of a particular amino acid within an isogenic cell population by monitoring peptides with multiple occurrences of the amino acid. We reveal that young, morphologically undifferentiated yeast colonies contain subpopulations of lysine producers and consumers that emerge due to nutrient gradients. Deconvoluting their proteomes using DILAC, we find evidence for in situ cross-feeding where rapidly growing cells ferment and provide the more slowly growing, respiring cells with ethanol. Finally, by combining DILAC with fluorescence-activated cell sorting, we show that the metabolic subpopulations diverge phenotypically, as exemplified by a different tolerance to the antifungal drug amphotericin B. Overall, DILAC captures previously unnoticed metabolic heterogeneity and provides experimental evidence for the role of metabolic specialization and cross-feeding interactions as a source of phenotypic heterogeneity in isogenic cell populations.
Full-length transcriptome from different life stages of cobia (Rachycentron canadum, Rachycentridae)
Authors: Ebeneezar Sanal , Krupesha Sharma S. R. , Vijayagopal P. , Sebastian Wilson , Sajina K. A. , Tamilmani G. , Sakthivel M. , Rameshkumar P. , Anikuttan K. K. , Varghese Eldho , Linga Prabu D. , Jeena N. S. , Sumithra T. G. , Gayathri S. , Iyyapparaja Narasimapallavan G. , Gopalakrishnan A. 
Published: February 2023

AbstractCobia (Rachycentron canadum, Rachycentridae) is one of the prospective species for mariculture. The transcriptome-based study on cobia was hampered by an inadequate reference genome and a lack of full-length cDNAs. We used a long-read based sequencing technology (PacBio Sequel II Iso-Seq3 SMRT) to obtain complete transcriptome sequences from larvae, juveniles, and various tissues of adult cobia, and a single SMRTcell generated 99 gigabytes of data and 51,205,946,694 bases. A total of 8609435, 7441673 and 9140164 subreads were generated from the larval, juvenile, and adult sample pools, with mean sub-read lengths of 2109.9, 1988.2 and 1996.2 bp, respectively. All samples were combined to increase transcript recovery and clustered into 35661 high-quality reads. This is the first report on a full-length transcriptome from R. canadum. Our results illustrate a significant increase in the identified amount of cobia LncRNAs and alternatively spliced transcripts, which will help improve genome annotation. Furthermore, this information will be beneficial for nutrigenomics and functional studies on cobia and other commercially important mariculture species.
GLORIA - A globally representative hyperspectral in situ dataset for optical sensing of water quality
Authors: Lehmann Moritz K. , Gurlin Daniela , Pahlevan Nima , Alikas Krista , Conroy Ted , Anstee Janet , Balasubramanian Sundarabalan V. , Barbosa Cláudio C. F. , Binding Caren , Bracher Astrid , Bresciani Mariano , Burtner Ashley , Cao Zhigang , Dekker Arnold G. , Di Vittorio Courtney , Drayson Nathan , Errera Reagan M. , Fernandez Virginia , Ficek Dariusz , Fichot Cédric G. , Gege Peter , Giardino Claudia , Gitelson Anatoly A. , Greb Steven R. , Henderson Hayden , Higa Hiroto , Rahaghi Abolfazl Irani , Jamet Cédric , Jiang Dalin , Jordan Thomas , Kangro Kersti , Kravitz Jeremy A. , Kristoffersen Arne S. , Kudela Raphael , Li Lin , Ligi Martin , Loisel Hubert , Lohrenz Steven , Ma Ronghua , Maciel Daniel A. , Malthus Tim J. , Matsushita Bunkei , Matthews Mark , Minaudo Camille , Mishra Deepak R. , Mishra Sachidananda , Moore Tim , Moses Wesley J. , Nguyễn Hà , Novo Evlyn M. L. M. , Novoa Stéfani , Odermatt Daniel , O’Donnell David M. , Olmanson Leif G. , Ondrusek Michael , Oppelt Natascha , Ouillon Sylvain , Pereira Filho Waterloo , Plattner Stefan , Verdú Antonio Ruiz , Salem Salem I. , Schalles John F. , Simis Stefan G. H. , Siswanto Eko , Smith Brandon , Somlai-Schweiger Ian , Soppa Mariana A. , Spyrakos Evangelos , Tessin Elinor , van der Woerd Hendrik J. , Vander Woude Andrea , Vandermeulen Ryan A. , Vantrepotte Vincent , Wernand Marcel R. , Werther Mortimer , Young Kyana , Yue Linwei 
Published: February 2023

AbstractThe development of algorithms for remote sensing of water quality (RSWQ) requires a large amount of in situ data to account for the bio-geo-optical diversity of inland and coastal waters. The GLObal Reflectance community dataset for Imaging and optical sensing of Aquatic environments (GLORIA) includes 7,572 curated hyperspectral remote sensing reflectance measurements at 1 nm intervals within the 350 to 900 nm wavelength range. In addition, at least one co-located water quality measurement of chlorophyll a, total suspended solids, absorption by dissolved substances, and Secchi depth, is provided. The data were contributed by researchers affiliated with 59 institutions worldwide and come from 450 different water bodies, making GLORIA the de-facto state of knowledge of in situ coastal and inland aquatic optical diversity. Each measurement is documented with comprehensive methodological details, allowing users to evaluate fitness-for-purpose, and providing a reference for practitioners planning similar measurements. We provide open and free access to this dataset with the goal of enabling scientific and technological advancement towards operational regional and global RSWQ monitoring.
Investigation of the spatial and temporal variation of soil salinity using Google Earth Engine: a case study at Werigan–Kuqa Oasis, West China
Authors: Ma Shilong , He Baozhong , Xie Boqiang , Ge Xiangyu , Han Lijing 
Published: February 2023

AbstractLarge-scale soil salinity surveys are time-costly and labor-intensive, and it is also more difficult to investigate historical salinity, while in arid and semi-arid regions, the investigation of the spatial and temporal characteristics of salinity can provide a scientific basis for the scientific prevention of salinity, With this objective, this study uses multi-source data combined with ensemble learning and Google Earth Engine to build a monitoring model to observe the evolution of salinization in the Werigan–Kuqa River Oasis from 1996 to 2021 and to analyze the driving factors. In this experiment, three ensemble learning models, Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Light Gradient Boosting Machine (LightGBM), were established using data collected in the field for different years and some environmental variables, After the accuracy validation of the model, XGBoost had the highest accuracy of salinity prediction in this study area, with RMSE of 17.62 dS m−1, R2 of 0.73 and RPIQ of 2.45 in the test set. In this experiment, after Spearman correlation analysis of soil Electrical Conductivity (EC) with environmental variables, we found that the near-infrared band in the original band, the DEM in the topographic factor, the vegetation index based on remote sensing, and the salinity index soil EC had a strong correlation. The spatial distribution of salinization is generally characterized by good in the west and north and severe in the east and south. Non-salinization, light salinization, and moderate salinization gradually expanded southward and eastward from the interior of the western oasis over 25 years. Severe and very severe salinization gradually shifted from the northern edge of the oasis to the eastern and southeastern desert areas during the 25 years. The saline soils with the highest salinity class were distributed in most of the desert areas in the eastern part of the Werigan–Kuqa Oasis study area as well as in smaller areas in the west in 1996, shrinking in size and characterized by a discontinuous distribution by 2021. In terms of area change, the non-salinized area increased from 198.25 in 1996 to 1682.47 km2 in 2021. The area of saline soil with the highest salinization level decreased from 5708.77 in 1996 to 2246.87 km2 in 2021. overall, the overall salinization of the Werigan–Kuqa Oasis improved.
Hsa_circ_0128846 knockdown attenuates the progression of pancreatic cancer by targeting miR-1270/NR3C1 axis
Authors: Wang Ming , Li Ming , Liu Zehan , Jiang Cuinan , Lv Hailong , Yang Qin 
Published: February 2023

AbstractThe considerable role of circular RNAs (circRNAs) make them prospective biomarkers in cancer therapy. Our study aimed to unveil the function of circ_0128846 in pancreatic cancer (PC). The expressions of circ_0128846, miR-1270 and NR3C1 mRNA were measured via RT-qPCR. The expressions of NR3C1 protein and apoptosis-related markers (Bax and Bcl-2) were measured via western blotting. CCK-8, colony-forming, or wound healing assay was respectively utilized to identify cell proliferation, growth and migration. Xenograft model was developed to evaluate tumor growth affected by circ_0128846 in vivo. The putative binding between miR-1270 and circ_0128846 or NR3C1 was testified by dual-luciferase reporter, RIP or pull-down assay. Circ_0128846 showed elevated expression in PC. Circ_0128846 deficiency restrained cancer cell proliferation, colony formation and migratory ability, enhanced cell apoptotic rate, and also impeded tumor development in vivo. Circ_0128846 directly targeted miR-1270 whose expression was declined in PC. The suppressive effects of silencing circ_0128846 on PC cell malignant phenotypes were largely reversed by miR-1270 inhibition. NR3C1 was targeted by miR-1270 and was highly regulated in PC. The repressive effects of NR3C1 knockdown on PC cell malignant phenotypes were partly abolished by miR-1270 inhibition. Circ_0128846 deficiency blocked PC progression via mediating the miR-1270/NR3C1 pathway, which partly illustrated PC pathogenesis.
Correlation of monocyte counts with clinical outcomes in idiopathic nonspecific interstitial pneumonia
Authors: Kim Tae Hun , Kim Hyung-Jun , Song Myung Jin , Kwon Byoung Soo , Kim Yeon Wook , Lim Sung Yoon , Lee Yeon Joo , Cho Young-Jae , Lee Jae Ho , Chung Jin-Haeng , Park Jong Sun 
Published: February 2023

AbstractHigher blood monocyte counts are related to worse survival in idiopathic pulmonary fibrosis. However, studies evaluating the association between blood monocyte counts and clinical outcomes of idiopathic nonspecific interstitial pneumonia (iNSIP) are lacking. We evaluated the impact of monocyte counts on iNSIP prognosis. iNSIP patients (n = 126; median age, 60 years; female, n = 64 [50.8%]) diagnosed by surgical lung biopsy were enrolled and categorized into low (monocyte < 600/µL) and high (monocyte ≥ 600/µL) monocyte groups. The median follow-up duration was 53.0 months. After adjusting for age, sex, and smoking history, the annual decline in forced vital capacity (FVC) showed differences between the monocyte groups (Pinteraction = 0.006) (low vs. high; − 28.49 mL/year vs. − 65.76 mL/year). The high-monocyte group showed a worse survival rate (P = 0.01) compared to low monocyte group. The 5-year survival rates were 83% and 72% in the low- and high-monocyte groups, respectively. In the Cox-proportional hazard analysis, older age, male sex, low baseline FVC, and diffusing capacity of the lung for carbon monoxide were independent risk factors for mortality. However, monocyte count (Hazard ratio 1.61, P = 0.126) was not an independent prognostic factor. Although high monocyte count might be associated with faster lung function decline, it could not independently predict survival in iNSIP.
Methodology for estimation of undeformed thickness of arterial tissues
Authors: Schwarz David , Fleisman Jiri , Vitasek Radek , Polzer Stanislav 
Published: February 2023

AbstractSoft tissue sample thickness measurement is one of the major sources of differences between mechanical responses published by different groups. New method for the estimation of unloaded sample thickness of soft tissues is proposed in this study. Ten 30 × 30 mm and ten 20 × 20 mm samples of porcine anterior thoracic aortas were loaded by gradually increased radial force. Their deformed thickness was then recorded in order to generate a pressure-thickness response. Next, the limit pressure to which the response can be considered linear was estimated. Line was fitted to the linear part of the curve and extrapolated towards zero pressure to estimate unloaded thickness (7 kPa fit). For comparison, data near zero pressure were fitted separately and extrapolated towards zero (Near Zero fit). The limit pressure for the linearity of the response was around 7 kPa. The Unloaded thickness for 30 × 30 mm samples was 2.68 ± 0.31 mm and 2.68 ± 0.3 mm for Near Zero fit and 7 kPa fit, respectively. The Unloaded thickness for 20 × 20 mm samples was 2.60 ± 0.35 mm and 2.59 ± 0.35 mm for Near Zero fit and 7 kPa fit, respectively. The median of thickness difference between smaller and larger samples was not found statistically different. Proposed method can estimate unloaded undeformed sample thickness quickly and reliably.
Validity and acceptance of self vs conventional sampling for the analysis of human papillomavirus and Pap smear
Authors: Gibert M. J. , Sánchez-Contador C. , Artigues G. 
Published: February 2023

AbstractThe newest high-risk human papillomavirus (HPV) detection techniques were included for cervical cancer primary screening under the Spanish National Health System in 2019. These analyses allow changing population approaches to foster adherence to screening. Therefore, the validity of self versus conventional sampling for HPV and cytology analyses was appraised. Women's preferences concerning samples and devices were also evaluated. This is a diagnostic accuracy cross-sectional study among 120 women recruited from a colposcopy clinic at a general hospital in Illes Balears, Spain. Participants were given written information and asked for a self-sample. One of two sets containing two devices each were handed. One set was transported dry and the second in liquid medium. Next, clinicians collected vaginal samples that were our gold standards. The agreement between both techniques was examined with the Kappa coefficient (κ). Self-sampling evaluation and preferences for different vaginal devices were also surveyed. The agreement between self and conventional samples concerning HPV positivity was very good (κ 0.86 for Mía by XytoTest® and 0.83 for Viba-Brush®) or reasonable (κ 0.73 for Iune and 0.68 for viscose swab). Pap smears from self-samples exhibited moderate agreement (κ 0.41 for Mía® and 0.51 for Viba-Brush® respectively) for negative versus ASC-US and worse results. Most of the participants considered self-sampling as beneficial (110 or 91.7%) and the advantages were, in decreasing order, scheduling, comfort, intimacy and less fear for pain or disturbance. The priority of choice for the devices was Mía® and viscose swab (chosen in first or second place) in opposition to Iune and Viba-Brush® (chosen in third or fourth place). If Viba-Brush® was to collect the best quality samples, 108 women (94.7%) switched their decisions. Our agreement between self and conventional samples was very good or reasonable for HPV, with the best values for devices in a liquid medium, and moderate for cytology. Even so, reflex cytology on self-samples is a valuable tool in promoting adherence. Self-sampling was widely accepted for smooth and thin devices. However, there is no resistance to change to others if a higher quality of the sample is obtained.
Automatic dispersion, defect, curing, and thermal characteristics determination of polymer composites using micro-scale infrared thermography and machine learning algorithm
Authors: Rahman Md Ashiqur , Rahman Mirza Masfiqur , Ashraf Ali 
Published: February 2023

AbstractInfrared thermography is a non-destructive technique that can be exploited in many fields including polymer composite investigation. Based on emissivity and thermal diffusivity variation; components, defects, and curing state of the composite can be identified. However, manual processing of thermal images that may contain significant artifacts, is prone to erroneous component and property determination. In this study, thermal images of different graphite/graphene-based polymer composites fabricated by hand, planetary, and batch mixing techniques were analyzed through an automatic machine learning model. Filler size, shape, and location can be identified in polymer composites and thus, the dispersion of different samples was quantified with a resolution of ~ 20 µm despite having artifacts in the thermal image. Thermal diffusivity comparison of three mixing techniques was performed for 40% graphite in the elastomer. Batch mixing demonstrated superior dispersion than planetary and hand mixing as the dispersion index (DI) for batch mixing was 0.07 while planetary and hand mixing showed 0.0865 and 0.163 respectively. Curing was investigated for a polymer with different fillers (PDMS took 500 s while PDMS-Graphene and PDMS Graphite Powder took 800 s to cure), and a thermal characteristic curve was generated to compare the composite quality. Therefore, the above-mentioned methods with machine learning algorithms can be a great tool to analyze composite both quantitatively and qualitatively.
Parental education, cognition and functional connectivity of the salience network
Authors: Cermakova Pavla , Chlapečka Adam , Csajbók Zsófia , Andrýsková Lenka , Brázdil Milan , Marečková Klára 
Published: February 2023

AbstractThe aim was to investigate the association of parental education at birth with cognitive ability in childhood and young adulthood and determine, whether functional connectivity of the salience network underlies this association. We studied participants of the Czech arm of the European Longitudinal Study of Pregnancy and Childhood who underwent assessment of their cognitive ability at age 8 (Wechsler Intelligence Scale for Children) and 28/29 years (Wechsler Adult Intelligence Scale) and measurement with resting state functional MRI at age 23/24. We estimated the associations of parental education with cognitive ability and functional connectivity between the seeds in the salience network and other voxels in the brain. We found that lower education of both mothers and fathers was associated with lower verbal IQ, performance IQ and full-scale IQ of the offspring at age 8. Only mother´s education was associated with performance IQ at age 28/29. Lower mother´s education correlated with greater functional connectivity between the right rostral prefrontal cortex and a cluster of voxels in the occipital cortex, which, in turn, was associated with lower performance IQ at age 28/29. We conclude that the impact of parental education, particularly father´s, on offspring´s cognitive ability weakens during the lifecourse. Functional connectivity between the right rostral prefrontal cortex and occipital cortex may be a biomarker underlying the transmission of mother´s education on performance IQ of their offspring.