bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-term Push-pull Cropping System Shifts Rhizosphere and Maize-root Microbiome Diversity Paving Way To Resilient Farming System
Authors: Jalloh Abdul A , Khamis Fathiya , Yusuf Abdullahi , Subramanian Sevgan , Mutyambai Daniel Munyao 
Published: September 2023

Abstract
Background: The rhizosphere biota consists of a complex assembly of microbial communities and other organisms that vary significantly across farming systems and influence soil health and plant productivity. How different cropping systems manipulates soil and plant microbiomes is little understood. In this study, we investigated soil physicochemical properties, rhizosphere and maize-root microbiomes in an agroecological cereal-legume companion cropping system known as push-pull technology (PPT) which has been in use in farmer fields for over two decades for insect-pest management, soil health improvement, and weed control in sub-Saharan Africa. We compared this with the maize-monoculture (Mono) cropping system.
Results: PPT cropping system positively impacted the abundance and diversity of soil and maize-root microbial communities and influenced soil physicochemical characteristics compared to Mono. Specific genera of both bacterial and fungal communities drove the variation in diversity of the microbial communities in these cropping systems. Soil and maize-root from the PPT cropping system had enriched Trichoderma, Mortierella, and Bionectria fungal genera while Streptomyces, RB41, and Nitrospira, among other bacterial genera linked to essential ecosystem services like plant protection, decomposition, carbon utilization, production of bioinsecticides, nitrogen fixation, nematode suppression, phytohormone production, and bioremediation. Bacterial from the genus Bryobacter linked to plant pathogenesis was more abundant in Mono-root. Similarly, fungal genera such as Gibberella, Neocosmospora, and Aspergillus, linked to plant pathogenesis and food contamination, were abundant in Mono. Notable differences were observed in the overall diversity of metabiome functional protein pathways, such as syringate degradation, L-methionine biosynthesis I, and inosine 5'-phosphate degradation.
Conclusion: Push-pull cropping system improves soil physicochemical properties and shifts soil and maize-root microbiomes in farmer fields in favour of microbial communities involved in important ecological services. The current findings add to the diversification of ecosystem services provided by this cropping system where it is practiced and contributes to the system’s resilience and functional redundancy. Underpinning the mechanism through PPT affects the soil and maize-root microbial communities – whether it is through the influence of plant metabolites from the intercrop root exudates or is the alteration of the soil nutritional status which affects microbial enzymatic activities should be the future focus.
Rising Public Cost of Preterm Infant Hospitalization: A nationwide observational study in South Korea
Authors: Lee Ji Young , Park Joonsik , Lee Myeongjee , Han Minkyung , Lim Sung Min , Baek Jee Yeon , Kang Ji-Man , Park Min Soo , Jung Inkyung , Ahn Jong Gyun 
Published: September 2023

Abstract
Objective: Despite the decline in the overall birth rate, increasing preterm births and associated medical costs pose a national concern. We analyze hospitalization costs covered by national public insurance for preterm infants.
Methods: Population-based data, obtained from the National Health Insurance Service (NHIS), which is operated by the Health Insurance Review and Assessment Service, were used for the study. Preterm births from January 1, 2008 to December 31, 2020 were included, using International Classification of Diseases and Related Health Problems, 10th edition (P0.72, extremely preterm <28 weeks gestational age, P07.3, non-extremely preterm). The primary outcomes related to cost from the first hospitalization due to preterm births and medication, and laboratory, radiological, and functional tests by gestational age and birth weight. Additionally, we assessed the readmission rates of preterm infants and the associated medical costs.
Results: A total of 5,312,886 live infants were born, of which 90,575 were claimed as preterm birth hospitalization. The total medical cost per patient increased almost three-fold from $7,390.90 to $20,209.59 from 2008 to 2020; for the extremely preterm group, it increased four-fold ($13,961.03 to $55,984.47 $). The readmission rate within 90 days of discharge was 62.5%; however, a greater proportion of the extremely preterm, as compared to the non-extremely preterm (16.1% vs. 8.32%, P < 0.001) group was readmitted within 30 days,. The extremely preterm group also incurred higher costs associated with readmission (mean $4293.8 vs. $2975.4, P < 0.001).
Conclusion: This study reveals not only the increase in preterm birth rate in South Korea, but also in the associated medical costs. Further attention should be paid to efficient resource allocation at the national level to relieve the medical burden of preterm births.
Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato
Authors: Clot Corentin R. , Vexler Lea , Leyva-Perez Maria de La O , Bourke Peter M. , Engelen Christel J.M. , Hutten Ronald C.B. , de Belt José van , Wijnker Erik , Milbourne Dan , Visser Richard G.F. , Juranić Martina , Eck Herman J. van 
Published: September 2023

Abstract
In diploid potato the production of unreduced gametes with a diploid (2n) rather than a haploid (n) number of chromosomes has been widely reported. Besides their evolutionary important role in sexual polyploidisation, unreduced gametes also have a practical value for potato breeding as a bridge between diploid and tetraploid germplasm. Although early articles argued for a monogenic recessive inheritance, the genetic basis of unreduced pollen production in potato has remained elusive. Here, three diploid full-sib populations were genotyped with an amplicon sequencing approach and phenotyped for unreduced pollen production across two growing seasons. We identified two minor-effect and three major-effect QTLs regulating this trait. The two QTLs with the largest effect displayed a recessive inheritance and an additive interaction. Both QTLs co-localised with genes encoding for putative AtJAS homologs, a key regulator of meiosis II spindle orientation in Arabidopsis thaliana. The function of these candidate genes is consistent with the cytological phenotype of mis-oriented metaphase II plates observed in the parental clones. The alleles associated with elevated levels of unreduced pollen showed deleterious mutation events: an exonic transposon insert causing a premature stop, and an amino acid change within a highly conserved domain. Taken together, our findings shed light on the natural variation underlying unreduced pollen production in potato and will facilitate interploidy breeding by enabling marker assisted selection for this trait.
Comparative Analysis of Molecular Testing Methods for FGFR2 Fusion/Rearrangement in Intrahepatic Cholangiocarcinoma
Authors: Zhang Xin , Bai Qianming , Wang Yulin , Jiang Zhengzeng , Han Jing , Xue Cheng , Huang Kai , Luan Lijuan , Huang Xiaoyong , Huang Xiaowu , Shi Guoming , Hou Yingyong , Ji Yuan 
Published: September 2023

Abstract
Backgrounds: Targeted therapies for intrahepatic cholangiocarcinoma (ICC) patients with FGFR2 fusion/rearrangement have shown significant effectiveness. Reliable and efficient testing strategies for detecting FGFR2 fusion/rearrangement are crucial following FDA and NMPA approval.
Methods: A cohort of 226 cases underwent RNA-based NGS, DNA-based NGS, and break-apart FISH analysis to evaluate FGFR2 fusion/rearrangement. The fusion detection rates, fusion partner identification, and concordance between the methods were analyzed.
Results: The positive rates for each method were as follows: RNA-based NGS − 9.8% (22/225), DNA-based NGS − 7.1% (16/226), and break-apart FISH − 10.2% (23/226). The integrated approach increased the prevalence rate of FGFR2 fusion/rearrangement to 11.5% (26/226). Among the 26 positive cases detected by any of the three methods, only 15 cases (57.7%) showed positive results for all three techniques, resulting in an overall concordance rate of 95.1% (215/226). RNA-based NGS played a critical role in confirming the presence of oncogenic FGFR2 fusion in 77% (20/26) of the fusion-positive cases and uncovered five novel putative oncogenic fusions involving FGFR2 (A1CF, ANKS1B, FOXP1, TFEC, and DAAM2). The combination of RNA- and DNA-based NGS detected a total of 29 FGFR2 fusion/rearrangements in 23 out of 226 cases (10.2%), involving 23 partner genes. The most frequent fusion partner was BICC1 (21.7%), while others varied. Relative to the oncogenic FGFR2 fusions identified by the RNA-based NGS assay, DNA-based NGS exhibited a sensitivity of 70.0% and specificity of 99.0%, while FISH showed a sensitivity of 99.0% and specificity of 98.1%. Among the 23 cases with positive FGFR2-FISH results, 18 cases (78%) demonstrated the typical split 3'/5' pattern with a signal distance of ≥ 2, while 5 cases (22%) displayed atypical patterns, including 1 case with short split signals (signal distance < 2) and 4 cases with a single 5' signal.
Conclusion: FGFR2 fusion/rearrangement exhibits genetic heterogeneity. Although DNA-based NGS is highly specific and FISH is highly sensitive, the use of RNA-based NGS is crucial for detecting FGFR2 fusion/rearrangement. A combined approach utilizing RNA-based NGS, DNA-based NGS, and FISH assay is recommended to enhance the accuracy of identifying FGFR2 fusions.
Investigation of the radiation Shielding Behavior of Monocrystalline and Polycrystalline solar cell Using experimental, Geant4 Simulation Code and WinXCOM Database
Authors: Al-zaidi Ghsson Ali , Saudi H. A. , Nassar Ibrahim A. , Sedeek K. 
Published: September 2023

Abstract
This study focuses on the radiation shielding characteristics of monocrystalline and polycrystalline Si solar cells. The linear attenuation coefficient (µ) for both cell types has been measured. By measuring the cell density, the mass attenuation coefficient (µ/ρ) has been calculated. The photon absorption capacity of polycrystalline solar cells is detected to be higher than that of monocrystalline solar ones. Lattice disordering and grain-boundary defects may enhance gamma absorption. Theoretical calculations have been carried out using Win X-Com and GEANT4 code computer programs at various photon energies ranging from 80 to 2614 keV. A great agreement was found with the experimental results at all energies. Some shielding parameters based on the measured attenuation coefficient such as the effective atomic number (Zeff), the effective electron density (Nel), half value layer (HVL), and mean free path (MFP) have been calculated at different energies. Polycrystalline solar cells were found to have better shielding properties than monocrystalline cells since they have lower MFP values. Macroscopic effective removal cross sections (ΣR) for fast neutrons have been also calculated by applying the win X-com software. Polycrystalline solar cells have a higher ΣR value than monocrystalline cells. We can conclude that, in addition to energy conversion, photovoltaic systems are superior shielding materials for both gamma rays and neutrons.
TPI/LDPE/OC composites preparation and the properties of shape memory research
Authors: Zhang Tao , Jia Yuhui , Shen Ruibing , Zhao W , Liang Yurong 
Published: September 2023

Abstract
Triple shape memory materials currently have a wide range of applications in aerospace and healthcare, however, the lack of their mechanical properties limits their wider application. In order to overcome the problem of low mechanical properties of the triple shape memory composites, in this study, organoclay (OC), which is low-cost and has an intercalation-type structure, was introduced as a reinforcing phase in a trans-isoprene (TPI) with regular molecular chains and a low-crosslinking low-density polyethylene (LDPE) matrix. TPI/LDPE/OC shape memory composites (SMP) were prepared by melt blending and vulcanized by dynamic vulcanization technique. Since different OC contents have different effects on the properties of the composites, it is particularly important to select the appropriate OC content. A series of experiments were conducted to reveal the effect of OC content on the mechanical and shape memory properties of TPI/LDPE/OC composites. The results show that OC can form a stable and homogeneous intercalation structure in the composites when the OC incorporation amount is 2 phr, and the mechanical properties and triple shape memory properties of the composites are optimized. This study demonstrates that OC can improve the crystallinity and cross-linking of TPI/LDPE composites, thus providing potential value for the study of multiple shape memory material applications.
Preliminary report on ultrashort perioperative partial-breast irradiation with multicatheter interstitial brachytherapy for early-stage breast cancer
Authors: Sato Kazuhiko , Fuchikami Hiromi , Takeda Naoko , Natsume Nana , Kato Masahiro 
Published: September 2023

Abstract
PURPOSE
Perioperative partial-breast irradiation (PBI) with multicatheter interstitial brachytherapy (MIB) is less invasive and more convenient. This study aimed to compare ultrashort perioperative MIB-PBI and conventional MIB-PBI (cPBI).
METHODS
The trial was conducted on patients aged ≥ 40 years and those with T0–2 (≤ 3 cm), N0-mi, and negative margins on mammography. The locoregional recurrence (LRR) and toxicity rates were compared between ultrashort perioperative MIB-PBI (uPBI) at a dose of 25.2 Gy in 4 fractions and cPBI at a dose of 32 Gy in 8 fractions.
RESULTS
In total, 198 patients (151 with uPBI and 47 with cPBI) were evaluated. At a median follow-up of 20.1 months, one (0.66%) patient in the uPBI group had LRR. The 2-year ipsilateral breast tumor recurrence-free survival rates of the uPBI and cPBI groups were 98.7% and 100%, respectively. The highest toxicity grades were grade 1 in 23 (15.2%) and grade 2 in 2 (1.3%) patients in the uPBI group, and grade 1 in 8 (17.0%) and grade 2 in 1 (2.1%) patient in the cPBI group. None of the patients in the two groups presented with grade 3 and higher toxicities. The toxicity rates between the two groups did not significantly differ. Further, 22 (14.6%) patients in the uPBI group and 8 (17.0%) in the cPBI group, and 3 (2.0%) patients in the uPBI group and 1 (2.1%) in the cPBI had acute and late toxicities, respectively. Toxicities commonly occurred at ≤ 3 months after PBI. Nevertheless, the timing of toxicity development between the two groups did not significantly differ.
CONCLUSIONS
This preliminary report included a small sample size and had a short follow-up period. However, the local control and toxicity rates were similar between the uPBI and cPBI groups. Therefore, an ultrashort hypofraction schedule is feasible and safe for perioperative MIB-PBI.
Aspect-based sentiment analysis with weighted relational convolutional network and complementary learning
Authors: Yu Bengong , Chen Mingyue 
Published: September 2023

Abstract
Aspect-based sentiment analysis in the sight of fine-grained sentiment detects the sentiment polarities towards given aspects terms. The syntactic information of the dependency tree is utilized in existing methods mainly by modeling the equality of different dependencies, which lacks the ability to capture aspect-related globally syntactic information and ignores the importance of considering contextual information of specific aspects. To alleviate the above problems, we propose WRCN-CL with two tasks: Weighted Relational Convolutional Network (WRCN) and auxiliary task complementary learning (CL); Weighted Relational Convolutional Network dynamically assigns weights to prune the dependency tree by considering positional weights and semantic structure simultaneously; Complementary representation is an auxiliary task for knowledge enhancement by obtaining grammatical information related to specific aspects of words. The experimental results prove the effectiveness of the model, and by observing the results on all datasets its state-of-the-art performance proved.
Scanpro: robust proportion analysis for single cell resolution data
Authors: Looso Mario , Alayoubi Yousef , Bentsen Mette 
Published: September 2023

Abstract

In higher organisms, individual cells respond to signals and perturbations by epigenetic regulation or transcriptional adaptation. However, in addition to shifting the expression level of individual genes, the adaptive response of cells can also lead to shifts in the proportions of different cell types. Recent methods such as scRNA-seq allow for the interrogation of expression on the single cell level, and can quantify individual cell type clusters within complex tissue samples. In order to identify clusters showing differential composition between different biological conditions, differential proportion analysis has recently been introduced. However, bioinformatics tools for robust proportion analysis of both replicated and unreplicated single cell datasets are critically missing. In this manuscript, we present Scanpro, a modular tool for proportion analysis, seamlessly integrating into widely accepted frameworks in the Python environment. Scanpro is fast, accurate, supports datasets without replicates, and is intended to be used by bioinformatics experts and beginners alike.
IMPATIENT-qPCR: melting-temperature-shift based evolution monitoring of successful aptamer development in SELEX processes
Authors: Kissmann Ann-Kathrin , Bolotnikov Grigory , Li Runliu , Müller Franziska , Xing Hu , Krämer Markus , Gottschalk Kay-E. , Zaiser Emmily , Andersson Jakob , Weil Tanja , Rosenau Frank 
Published: September 2023

Abstract
SELEX (Systematic Evolution of Ligands by Exponential enrichment) processes aim on the evolution of high affinity aptamers as binding entities in diagnostics and biosensing. Aptamers can represent game-changers as constituents of diagnostic assays for the management of instantly occurring infectious diseases or other health threats. Without in-process quality control measures SELEX suffers from low overall success rates. We present a quantitative PCR method for fast and easy quantification of aptamers bound to their targets. Simultaneous determination of melting-temperatures (Tm) of each SELEX round delivers information on the evolutionary success via the correlation of increasing GC-content and Tm. Based on nine successful previous processes we show the functionality of the IMPATIENT-qPCR for polyclonal aptamer libraries and resulting individual aptamers. Based on the ease of this new evolution quality control, we hope to introduce it as a valuable tool to accelerate SELEX processes in general.
Combined Action of Pure Oxygen Pretreatment and Near-freezing Temperature Storage on the Quality of Fresh-cut Nectarines
Authors: Li Dandan , Li Lu , Zhao Ruxia , Ding Xu , Du Jin , Liu Tao , Li Xuejin , Pan Na , Zhao Wei , Chen Lan , Li Xihong , Jiang Yuqian 
Published: September 2023

Abstract
Fresh-cut fruits were convenient for consumers but vulnerable to quality deterioration, including browning, softening, and volatile aroma loss. In this study, the effects of pure oxygen (PO) pretreatment and near-freezing temperature (NFT) storage on fresh-cut nectarines were investigated, including changes in browning degree, color shift, enzyme activity, cell membrane permeability, antioxidant activity, and aroma components. Specifically, pure oxygen pretreatment increased the activity of the ROS-scavenger enzymes (POD and CAT), which endows fruit with resistance to environmental stresses before fresh cut and storage. Near-freezing temperature storage is extremely effective in inhibiting browning-related enzyme (PPO) activity and total phenolic content (TPC). Higher antioxidant level and anti-browning effects were observed in fresh-cut nectarines treated with PO + NFT, which demonstrated by the DPPH scavenging action, FRAP, enzyme activity ratios (Ratio 1 and Ratio 2). During the storage for 9 d, firmness of the tissue was preserved, MDA content and membrane permeability were suppressed, which delayed the development of fruit softening and the deformation of cell microstructure. In addition, SSC and TA of fresh-cut nectarines were also well preserved by PO + NFT, which maintained the physiological and metabolic qualities. Electronic nose tests revealed that PO + NFT postponed the volatile aroma deterioration of fresh-cut nectarines. In conclusion, PO + NFT is effective in maintaining the storage quality of fresh-cut nectarines.
Multilingual Image Captioning: Multimodal Framework for Bridging Visual and Linguistic Realms in Tamil and Telugu through Transformers
Authors: B Rohan Reddy , Gunti Swathi , R Prasanna Kumar , S Sridevi 
Published: September 2023

Abstract
Image captioning is a formidable challenge in the realms of computer vision and natural language processing. The limited availability of captioning mechanisms for non-English languages poses significant barriers for nonproficient English speakers. Specifically, Tamil and Telugu the most spoken languages in India, lack image captioning models capable of delivering accurate captions. Moreover, generating captions in Tamil and Telugu is a complex task due to their unique linguistic intricacies. Addressing these challenges requires advanced models capable of capturing long-range dependencies and generating contextually meaningful image captions. This research presents a multimodal deep learning framework that appropriately integrates InceptionV3, VGG16, and ResNet50 convolutional neural network architectures with multihead attention-based transformer architecture. By harnessing the multihead attention mechanism, our model effectively comprehends image context, handles linguistic complexity, and establishes vital multimodal associations between visual and textual features. Extensive experiments were carried out on translated versions of the benchmark datasets such as Flickr8k, Flickr30k, and MSCOCO to evaluate the efficacy of the model. The multimodal technique we suggested produced extraordinary and remarkable results especially in terms of BLEU metrics. The maximum value of the BLEU-1 score achieved by our suggested model reaches 65.16 and 66.79 on Tamil and Telugu caption generation tasks respectively. These findings outperformed the results of existing methods, indicating improved accuracy in generating captions for both Tamil and Telugu languages. Furthermore, a meticulous, manually labored audit of the generated captions confirmed their appropriateness and competence, affirming the robustness of the proposed methodology.