bluuebunny/crossref_metadata_2025_split huggingface dataset:
Facing the challenges to shorten the diagnostic odyssey: first Whole Genome Sequencing experience of a Colombian cohort with suspected rare diseases
Authors: Velasco Harvy Mauricio , Bertoli-Avella Aida , Jaramillo Carolina Jaramillo , Cardona Danny Styvens , González Leonel Andrés , Vanegas Melisa Naranjo , Arango Juan Pablo Valencia , Buitrago Cesar Augusto , González Jorge Alberto Gutiérrez , Marcello Jonas , Bauer Peter , Moncada Juliana Espinosa 
Published: June 2024

AbstractExome and genome sequencing (ES/GS) are routinely used for the diagnosis of genetic diseases in developed countries. However, their implementation is limited in countries from Latin America. We aimed to describe the results of GS in patients with suspected rare genetic diseases in Colombia. We studied 501 patients from 22 healthcare sites from January to December 2022. GS was performed in the index cases using dried blood spots on filtercards. Ancestry analysis was performed under iAdmix. Multiomic testing was performed when needed (biomarker, enzymatic activity, RNA-seq). All tests were performed at an accredited genetic laboratory. Ethnicity prediction data confirmed that 401 patients (80%) were mainly of Amerindian origin. A genetic diagnosis was established for 142 patients with a 28.3% diagnostic yield. The highest diagnostic yield was achieved for pathologies with a metabolic component and syndromic disorders (p < 0.001). Young children had a median of 1 year of diagnostic odyssey, while the median time for adults was significantly longer (15 years). Patients with genetic syndromes have spent more than 75% of their life without a diagnosis, while for patients with neurologic and neuromuscular diseases, the time of the diagnostic odyssey tended to decrease with age. Previous testing, specifically karyotyping or chromosomal microarray were significantly associated with a longer time to reach a definitive diagnosis (p < 0.01). Furthermore, one out of five patients that had an ES before could be diagnosed by GS. The Colombian genome project is the first Latin American study reporting the experience of systematic use of diagnostic GS in rare diseases.
Calibration-independent bound on the unitarity of a quantum channel with application to a frequency converter
Authors: Bock Matthias , Sekatski Pavel , Bancal Jean-Daniel , Kucera Stephan , Bauer Tobias , Sangouard Nicolas , Becher Christoph , Eschner Jürgen 
Published: June 2024

AbstractWe report on a method to certify a unitary operation with the help of source and measurement apparatuses whose calibration throughout the certification process needs not be trusted. As in the device-independent paradigm our certification method relies on a Bell test and requires no assumption on the underlying Hilbert space dimension, but it removes the need for high detection efficiencies by including the single additional assumption that non-detected events are independent of the measurement settings. The relevance of the proposed method is demonstrated experimentally by bounding the unitarity of a quantum frequency converter. The experiment starts with the heralded creation of a maximally entangled two-qubit state between a single 40Ca+ ion and a 854 nm photon. Entanglement preserving frequency conversion to the telecom band is then realized with a non-linear waveguide embedded in a Sagnac interferometer. The resulting ion-telecom photon entangled state is assessed by means of a Bell-CHSH test from which the quality of the frequency conversion is quantified. We demonstrate frequency conversion with an average certified fidelity of ≥84% and an efficiency ≥3.1 × 10−6 at a confidence level of 99%. This ensures the suitability of the converter for integration in quantum networks from a trustful characterization procedure.
A study on interoperability between two Personal Health Train infrastructures in leukodystrophy data analysis
Authors: Welten Sascha , de Arruda Botelho Herr Marius , Hempel Lars , Hieber David , Placzek Peter , Graf Michael , Weber Sven , Neumann Laurenz , Jugl Maximilian , Tirpitz Liam , Kindermann Karl , Geisler Sandra , Bonino da Silva Santos Luiz Olavo , Decker Stefan , Pfeifer Nico , Kohlbacher Oliver , Kirsten Toralf 
Published: June 2024

AbstractThe development of platforms for distributed analytics has been driven by a growing need to comply with various governance-related or legal constraints. Among these platforms, the so-called Personal Health Train (PHT) is one representative that has emerged over the recent years. However, in projects that require data from sites featuring different PHT infrastructures, institutions are facing challenges emerging from the combination of multiple PHT ecosystems, including data governance, regulatory compliance, or the modification of existing workflows. In these scenarios, the interoperability of the platforms is preferable. In this work, we introduce a conceptual framework for the technical interoperability of the PHT covering five essential requirements: Data integration, unified station identifiers, mutual metadata, aligned security protocols, and business logic. We evaluated our concept in a feasibility study that involves two distinct PHT infrastructures: PHT-meDIC and PADME. We analyzed data on leukodystrophy from patients in the University Hospitals of Tübingen and Leipzig, and patients with differential diagnoses at the University Hospital Aachen. The results of our study demonstrate the technical interoperability between these two PHT infrastructures, allowing researchers to perform analyses across the participating institutions. Our method is more space-efficient compared to the multi-homing strategy, and it shows only a minimal time overhead.
Chromosome-level assembly of the synthetic hexaploid wheat-derived cultivar Chuanmai 104
Authors: Liu Zehou , Yang Fan , Deng Cao , Wan Hongshen , Tang Hao , Feng Junyan , Wang Qin , Yang Ning , Li Jun , Yang Wuyun 
Published: June 2024

AbstractSynthetic hexaploid wheats (SHWs) are effective genetic resources for transferring agronomically important genes from wild relatives to common wheat (Triticum aestivum L.). Dozens of reference-quality pseudomolecule assemblies of hexaploid wheat have been generated, but none is reported for SHW-derived cultivars. Here, we generated a chromosome-scale assembly for the SHW-derived cultivar ‘Chuanmai 104’ based on PacBio HiFi reads and chromosome conformation capture sequencing. The total assembly size was 14.81 Gb with a contig N50 length of 58.25 Mb. A BUSCO analysis yielded a completeness score of 99.30%. In total, repetitive elements comprised 81.36% of the genome and 122,554 high-confidence protein-coding gene models were predicted. In summary, the first chromosome-level assembly for a SHW-derived cultivar presents a promising outlook for the study and utilization of SHWs in wheat improvement, which is essential to meet the global food demand.
Multi-year aboveground data of minirhizotron facilities in Selhausen
Authors: Nguyen Thuy Huu , Lopez Gina , Seidel Sabine J. , Lärm Lena , Bauer Felix Maximilian , Klotzsche Anja , Schnepf Andrea , Gaiser Thomas , Hüging Hubert , Ewert Frank 
Published: June 2024

AbstractImproved understanding of crops’ response to soil water stress is important to advance soil-plant system models and to support crop breeding, crop and varietal selection, and management decisions to minimize negative impacts. Studies on eco-physiological crop characteristics from leaf to canopy for different soil water conditions and crops are often carried out at controlled conditions. In-field measurements under realistic field conditions and data of plant water potential, its links with CO2 and H2O gas fluxes, and crop growth processes are rare. Here, we presented a comprehensive data set collected from leaf to canopy using sophisticated and comprehensive sensing techniques (leaf chlorophyll, stomatal conductance and photosynthesis, canopy CO2 exchange, sap flow, and canopy temperature) including detailed crop growth characteristics based on destructive methods (crop height, leaf area index, aboveground biomass, and yield). Data were acquired under field conditions with contrasting soil types, water treatments, and different cultivars of wheat and maize. The data from 2016 up to now will be made available for studying soil/water-plant relations and improving soil-plant-atmospheric continuum models.
Estimating bee distributions and their functional range to map important areas for protecting bee species and their functions
Authors: Suzuki-Ohno Yukari , Ishihama Fumiko , Yokoyama Jun , Inoue Maki N. , Nakashizuka Tohru , Kawata Masakado 
Published: June 2024

AbstractThe decline of wild bee populations causes the decline of bee-pollinated plant populations through the deterioration of pollination services. Since high bee species richness generally involves high functional group diversity, protecting areas of high bee species richness will help to maintain pollination services for plants. However, those areas do not always include the habitats of bee species with specialized functions that expand the range of plants being pollinated. To map important areas for protecting native bee species and their functions, we estimated the distributions and functional range of 13 bumble bee species and 1 honey bee species in Japan. The distributions were estimated from an ensemble of six species distribution models using bee occurrence data and environmental data. The functional range of bee species was estimated by combining the estimated distributions and proboscis length, which frequently corresponds to the floral shape of the plant species they pollinate. The estimated species richness was high in western Hokkaido and the estimated functional range was wide in central Honshu. Our method is useful to see whether areas important for high species richness of pollinators differ from those for rare species or their functions.
Synergistic and potential antifungal properties of tailored, one pot multicomponent monoterpenes co-delivered with fluconazole encapsulated nanostructure lipid carrier
Authors: Radwan Ibrahim Taha , El-Sherbiny Ibrahim M. , Metwally Nadia Hanafy 
Published: June 2024

AbstractFrequent and variant infections are caused by the virtue of opportunistic fungi pathogens. Candidiasis, aspergillosis, and mucormycosis are pathogenic microorganisms that give rise to vast fungal diseases that alternate between moderate to fatal in severity. The use of fluconazole as an antifungal drug was limited due to the acquired resistance in some types of Candida and other fungal species. This study aims to consolidate fluconazole’s biological effectiveness against several pathogenic fungi. Six active monoterpenes (MTs) of carvacrol, linalool, geraniol, α-terpinene, citronellal, and nerolidol were selected and encapsulated in nanostructure lipid carrier (NLC) with (NLC-Flu-MTs) and/without (NLC-MTs) fluconazole in one nanoformulation to determine if they will act synergistically or not? The synthesized nanoformulation NLC-Flu-MTs and NLC-MTs exhibited very good particle size of 144.5 nm and 138.6 nm for size and zeta potential values of (− 23.5 mV) and (− 20.3 mV), respectively. Transmission electron microscope investigation confirmed that the synthesized NLCs have regular and spherical shape. The abundance and concentration of the six released monoterpenes were determined, as a novel approach, using GC–MS with very good results and validity. In-vitro antifungal screening was done before and after nano co-delivery against seven pathogenic, and aggressive fungi of Candida tropicalis, Candida krusei, Candida glabrata, Geotrichum Candidum, Candidaalbicans, Aspergillus Niger, and mucor circinelloides. Inhibition Zone diameter (IZD) and the minimum inhibitory concentration (MIC) were measured. Nanoformulations NLC-Flu-MTs and NLC-MTs manifested potential and unique biological susceptibility against all the tested microorganisms with reduced (MIC) values, especially against Candida Tropicalis (MIC = 0.97 µg/ml) which represents 16-fold of the value shown by NLC-MTs (MIC = 15.6 µg/ml) and 64-fold of fluconazole free before nanoformulation (MIC = 62.5 µg/ml). The efficiency of nanomaterials, particularly NLC-Flu-MTs, has become evident in the diminishing value of MIC which affirmed the synergism between fluconazole and the other six monoterpenes.
Single and combined toxicity of tadalafil (Cilais) and microplastic in Tilapia fish (Oreochromis niloticus)
Authors: Sabra Mahmoud S. , Sayed Alaa El-Din H. , Idriss Shaimaa K. A. , Soliman Hamdy A. M. 
Published: June 2024

AbstractThe joint impact of tadalafil (Cilais) as a pharmaceutical residue and microplastics on fish is not well comprehended. The current study examined haematological, biochemical, and antioxidant parameters, along with immunohistochemical and histological indications in tilapia (Oreochromis niloticus) after being exposed to tadalafil, polyethylene microplastics (PE-MPs), and their mixtures for 15 days. The fish were distributed into 1st group control group (The fish was maintained in untreated water without any supplements); 2nd group exposed to 10 mg/L PE-MPs;3rd group exposed to 20 mg/l tadalafil (Cilais); 4th group exposed to 20 mg/l tadalafil (Cilais) + 10 mg/LPE-MPs (in triplicate). The levels of creatinine, uric acid, glucose, AST, ALT, and albumin in fish treated with tadalafil alone or in combination with PE-MPs were significantly higher than those in the control group. Fish exposed to PE-MPs, tadalafil, and tadalafil plus PE-MPs showed significantly lower levels of RBCs, Hb, Ht, neutrophils, and lymphocytes compared to the control group. Serum levels of total antioxidant capacity and reduced glutathione (GSH) were notably lowered in fish groups subjected to PE-MPs, tadalafil, and tadalafil + PE-MPs combinations in comparison to the control group. Malondialdehyde (MDA) serum levels were notably elevated in fish groups subjected to PE-MPs, tadalafil, and tadalafil + PE-MPs combinations compared to the control group. The most severe impact was observed in the tadalafil + PE-MPs combination group. Interleukin-6 (IL-6) levels were significantly increased in liver tissues following exposure to both tadalafil and microplastics compared to tissues exposed to only one substance or the control group. Changes in the gills, liver, and renal tissues were seen following exposure to PE-MPs, tadalafil, and tadalafil + PE-MPs combination in comparison to the control group of fish. Ultimately, the mixture of tadalafil and PE-MPs resulted in the most detrimental outcomes. Tadalafil and PE-MPs exhibited showed greater adverse effects, likely due to tadalafil being absorbed onto PE-MPs.
Modeling and forecasting the volatility of some industry development indicators in Ethiopia using multivariate GARCH models
Authors: Dagnew Getachew Abate , Alamneh Birhan Walie , Hailu Wosenie Gebireamanuel 
Published: June 2024

AbstractIndustry development indicators refer to a set of measures used to assess the performance and growth of industries. The main aim of this study was to assess the relationship between industry development indicators in Ethiopia using a multivariate GARCH model based on World Bank data from 1982 to 2021. A time series technique using annual data for the period 1982–2021 is utilized, and multivariate generalized autoregressive conditional heteroscedasticity was performed for volatility modeling. The results of the diagonal BEKK (1, 1)-GARCH model showed that there is strong evidence for a GARCH effect and the presence of a weaker ARCH effect, Equations show a statistically significant co-variation in shocks, which depends more on their lags than on past errors. Consequently, development indicator shocks are influenced by past information. The cross-volatility effects are higher than the own-volatility effects in Industry GDP, manufacturing GDP, and manufacturing exports. However, past volatility shocks in industry growth have less effect on cross-volatility than its own volatility shock. The implication of the study is that both domestic policymakers and development partners should support and motivate the growth of manufacturing sectors and manufacturing exports, since this is a necessary condition for promoting industry growth.
Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets
Authors: Rönn Tina , Perfilyev Alexander , Oskolkov Nikolay , Ling Charlotte 
Published: June 2024

AbstractType 2 diabetes (T2D) is the fastest growing non-infectious disease worldwide. Impaired insulin secretion from pancreatic beta-cells is a hallmark of T2D, but the mechanisms behind this defect are insufficiently characterized. Integrating multiple layers of biomedical information, such as different Omics, may allow more accurate understanding of complex diseases such as T2D. Our aim was to explore and use Machine Learning to integrate multiple sources of biological/molecular information (multiOmics), in our case RNA-sequening, DNA methylation, SNP and phenotypic data from islet donors with T2D and non-diabetic controls. We exploited Machine Learning to perform multiOmics integration of DNA methylation, expression, SNPs, and phenotypes from pancreatic islets of 110 individuals, with ~ 30% being T2D cases. DNA methylation was analyzed using Infinium MethylationEPIC array, expression was analyzed using RNA-sequencing, and SNPs were analyzed using HumanOmniExpress arrays. Supervised linear multiOmics integration via DIABLO based on Partial Least Squares (PLS) achieved an accuracy of 91 ± 15% of T2D prediction with an area under the curve of 0.96 ± 0.08 on the test dataset after cross-validation. Biomarkers identified by this multiOmics integration, including SACS and TXNIP DNA methylation, OPRD1 and RHOT1 expression and a SNP annotated to ANO1, provide novel insights into the interplay between different biological mechanisms contributing to T2D. This Machine Learning approach of multiOmics cross-sectional data from human pancreatic islets achieved a promising accuracy of T2D prediction, which may potentially find broad applications in clinical diagnostics. In addition, it delivered novel candidate biomarkers for T2D and links between them across the different Omics.
Responses of growth and photosynthesis to alkaline stress in three willow species
Authors: Qiao Shenqi , Ma Changming , Li Hongjiao , Zhang Yu , Zhang Minghui , Zhao Wenhao , Liu Bingxiang 
Published: June 2024

AbstractInvestigating differences in resistance to alkaline stress among three willow species can provide a theoretical basis for planting willow in saline soils. Therefore we tested three willow species (Salix matsudana, Salix gordejevii and Salix linearistipularis), already known for their high stress tolerance, to alkaline stress environment at different pH values under hydroponics. Root and leaf dry weight, root water content, leaf water content, chlorophyll content, photosynthesis and chlorophyll fluorescence of three willow cuttings were monitored six times over 15 days under alkaline stress. With the increase in alkaline stress, the water retention capacity of leaves of the three species of willow cuttings was as follows: S. matsudana > S. gordejevii > S. linearistipularis and the water retention capacity of the root system was as follows: S. gordejevii > S. linearistipularis > S. matsudana. The chlorophyll content was significantly reduced, damage symptoms were apparent. The net photosynthetic rate (Pn), rate of transpiration (E), and stomatal conductance (Gs) of the leaves showed a general trend of decreasing, and the intercellular CO2 concentration (Ci) of S. matsudana and S. gordejevii first declined and then tended to level off, while the intercellular CO2 concentration of S. linearistipularis first declined and then increased. The quantum yield and energy allocation ratio of the leaf photosystem II (PSII) reaction centre changed significantly (φPo, Ψo and φEo were obviously suppressed and φDo was promoted). The photosystem II (PSII) reaction centre quantum performance index and driving force showed a clear downwards trend. Based on the results it can be concluded that alkaline stress tolerance of three willow was as follows: S. matsudana > S. gordejevii > S. linearistipularis. However, since the experiment was done on young seedlings, further study at saplings stage is required to revalidate the results.
Modified craniotomy procedures and virtual reality technology for accurate localization of the frontal branch of MMA in revascularization surgery
Authors: Chuang-Hong Liu , Hong Xu , Gang Kong 
Published: June 2024

AbstractThe frontal branch of middle meningeal artery (MMA) can easily be damaged during revascularization surgery. To precise locate it and minimize its injury, we propose a set of modified craniotomy procedures combined with simple virtual reality (VR) technology based on three-dimensional (3D) Slicer simply, economically, and efficiently. Patients with Moyamoya disease (MMD) and internal carotid artery occlusion (ICAO) who received revascularization from January 2015 to December 2022 were divided into two groups based on the methods used to locate the MMA: traditional methods and precise MMA locating with VR technology. Patient demographics and clinical characteristics were analyzed to compare the preservation rates of MMA. The distances between this artery and bony anatomical landmarks were also measured to better understand its localization. There was no significant difference in baseline characteristics between the two groups. The precise MMA locating group exhibited a significantly higher preservation rate of the frontal branch of MMA (p = 0.037, 91.7% vs. 68.2%). Over 77% of patients had their frontal branch of MMA partially or completely surrounded by bony structures to varying degrees. Therefore, the combination of modified craniotomy procedures, 3D Slicer, and simple VR technology represents an economical, efficient, and operationally simple strategy.
Design and analysis of an interleaved step-up DC–DC converter with enhanced characteristics
Authors: Hosseinpour Majid , Seifi Elham , Seifi Ali , Shahparasti Mahdi 
Published: June 2024

AbstractIn this paper, an interleaved DC–DC step-up converter with improved characteristics based on a voltage multiplier rectifier is presented. The proposed converter is presented and analyzed for two different operating duty regions including operating region 1 (0 < D ≤ 0.5), and operating region 2 (0.5 ≤ D < 1). This converter can be used in various applications such as energy storage, electric vehicles, and renewable energy systems. This converter is composed of two stages: an interleaved boost stage and a voltage multiplier rectifier stage, which collectively forms its general structure. The interleaved boost stage is a type of two-phase boost converter that transforms the input DC voltage into a high-frequency AC square waveform. This waveform can be readily filtered using smaller capacitors. The square-shaped voltage waveform from the interleaved boost stage is rectified and converted to a high DC voltage by the Voltage Multiplier Rectifier (VMR) stage. The operating regions, the evaluation of the steady-state condition, the voltage gain of the proposed converter's parasitic and ideal models as well as its losses and efficiency analysis have been evaluated. The proposed converter has an efficiency of 97% at the output power of 150 W. The proposed converter is simulated to convert a voltage of 25–159.5 V and to validate the mathematical relationships and simulation results, a laboratory prototype has been developed. The simulation and experimental results show the precision of the performance of the proposed interleaved boost converter.