bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome Analysis of Heterosis for Young Spikes in Sorghum Hybrid and Its Parents
Authors: Zhang Yizhong , Wang Huiyan , Fan Xinqi , Liang Du , Guo Qi , Zhang Xiaojuan , Nie Mengen , Yang Huiyong , Yang Bin , Yang Tingting , Wu Yuxiang , Liu Qingshan 
Published: February 2023

Abstract
Background
Heterosis has been widely used for breeding high-yield crops, changes crop breeding and agricultural production by increasing yield. Transcriptome profiles of sorghum spikes in hybrid Jinnuo 3 and its parents 10480A and L17R were performed by RNA sequencing technology at secondary branch and spikelet differentiation period.
Results
During above two differentiation period, there were 2,641 and 2,175 differentially expressed genes (DEGs) between Jinnuo 3 and 10480A, respectively. Meanwhile, there were 1,387 and 1,094 DEGs between Jinnuo 3 and L17R, respectively. These indicated that massive DEGs were existed between hybird and its parents, and a more similar expression pattern was presented between hybrid and male parent. Gene expression inheritance analysis showed that most of genes were expressed additively, suggesting that the complementary effect may play a foundation role in sorghum spike heterosis. Among non-additive expression genes, L17R-dominant genes were predominant, indicating that male parent may provide beneficial alleles with great contribution to heterosis. GO and KEGG analysis suggested that metabolic pathways, such as photosynthetic antenna protein, photosynthesis, carbon fixation in photosynthetic organisms, amino acid metabolism, glycolysis, and endoplasmic reticulum protein processing, would participate in yield heterosis formation in hybrid Jinnuo 3. Further analysis showed that photosynthesis-related genes PsbW, PsbR, Lhca2, Lhcb1 and LAX3, spike structure development-related genes MADS1, MADS7, MADS16 and MADS55, as well as stress resistance-related genes WRKY14, WRKY35, HSFB2C and HSP70, might play an important role in yield heterosis formation in hybrid Jinnuo 3.
Conclusion
Hybrids Jinnuo 3 increased yield by simultaneously increasing source (photosynthetic efficiency-related genes), library (spike development-related genes), and resistance (inresistance-related genes). This molecular mechanism could provide new clues for sorghum heterosis utilization and high-yield breeding.
Revealing Potential Diagnostic Biomarkers of Idiopathic Pulmonary Fibrosis Based on Machine Learning Analysis
Authors: wu zenan , Chen Huan , Ke Shiwen , Mo Lisha , Qiu Mingliang , Zhu Guoshuang , Zhu Wei , Liu Liangji 
Published: February 2023

Abstract

BackgroundIdiopathic pulmonary fibrosis (IPF) is the most common and serious type of idiopathic interstitial pneumonia, characterized by chronic, progressive, and low survival rates, while unknown disease etiology. Until recently, patients with idiopathic pulmonary fibrosis have a poor prognosis, high mortality, and limited treatment options, due to the lack of effective early diagnostic and prognostic tools. Therefore, we aimed to identify biomarkers for idiopathic pulmonary fibrosis based on multiple machine-learning approaches and to evaluate the role of immune infiltration in the disease.MethodNext, the differentially expressed genes (DEGs) with the threshold of FDR < 0.05 and |log2 foldchange (FC)| > 0.585 were analyzed via R package “DESeq2” and GO enrichment and KEGG pathways were run in R software. Then, least absolute shrinkage and selection operator (LASSO) logistic regression, support vector machine-recursive feature elimination (SVM-RFE) and random forest (RF) algorithms were combined to screen the key potential biomarkers of idiopathic pulmonary fibrosis. The diagnostic performance of these biomarkers was evaluated through receiver operating characteristic (ROC) curves. Moreover, the CIBERSORT algorithm was employed to assess the infiltration of immune cells and the relationship between the infiltrating immune cells and the diagnostic biomarkers. Finally, we sought to understand the role of the diagnostic biomarker (SLAIN1) in idiopathic pulmonary fibrosis pathogenesis using a mouse model and cellular model.ResultsA total of 3658 differentially expressed genes of idiopathic pulmonary fibrosis were identified, including 2359 upregulated genes and 1299 downregulated genes. FHL2, HPCAL1, RNF182, and SLAIN1 were identified as diagnostic biomarkers of idiopathic pulmonary fibrosis using LASSO logistic regression, RF, and SVM-RFE algorithms. The ROC curves confirmed the predictive accuracy of these diagnostic biomarkers both in the training set and test set. Immune cell infiltration analysis suggested that patients with idiopathic pulmonary fibrosis had a higher level of B cells memory, Plasma cells, T cells CD8, T cells follicular helper, T cells regulatory (Tregs), Macrophages M0, and Mast cells resting compared with the control group. Correlation analysis demonstrated that FHL2 was significantly associated with the infiltrating immune cells. qPCR and western blotting analysis suggested that SLAIN1 might be a signature for the diagnosis of idiopathic pulmonary fibrosis.ConclusionIn this study, we developed a diagnostic model to identify four diagnostic biomarkers (FHL2, HPCAL1,RNF182 and SLAIN1) and validated the role of SLAIN1 in the pathogenesis of idiopathic pulmonary fibrosis, which may be great significance in guiding the prognosis and treatment of idiopathic pulmonary fibrosis.
High-Throughput Reprogramming of an NRPS Condensation Domain
Authors: Folger Ines , Frota Natália , Pistofidis Angelos , Niquille David , Hansen Douglas , Schmeing T. Martin , Hilvert Donald 
Published: February 2023

Abstract

Engineered biosynthetic assembly lines could revolutionize the sustainable production of bioactive natural product analogues. While yeast display is a proven, powerful tool for altering the substrate specificity of gatekeeper adenylation domains in nonribosomal peptide synthetases (NRPSs), comparable strategies for other components of these megaenzymes have not been described. Here we report a high-throughput approach for engineering condensation (C) domains responsible for peptide elongation. We show that a 120-kDa NRPS module, displayed in functional form on yeast, can productively interact with an upstream module, provided in solution, to produce amide products tethered to the yeast surface. Using this system to screen a large C domain library, we reprogrammed a surfactin synthetase module to accept a fatty acid donor, increasing catalytic efficiency for this noncanonical substrate >40-fold. Since C domains can function as selectivity filters in NRPSs, this methodology should facilitate precision engineering of these molecular assembly lines.
Technical acoustic measurements combined with clinical parameters for differential diagnosis of nonalcoholic steatohepatitis
Authors: Zhao Yanan , Qiu Chen , Dong Yiping , Wang Xuchu , Chen Jifan , Yao Jianting , Jiang Yifan , Zhang Chao , Weng Huifang , Liu Yajing , Wong Yik Ning , Huang Pintong 
Published: February 2023

Abstract
Background and aim
Diagnosing NASH is challenging. This study intended to explore the diagnostic value of multiple technical acoustic measurements in the diagnosis of NASH, and to establish a diagnostic model combining technical acoustic measurements with clinical parameters to improve the diagnostic efficacy of NASH.
Methods
We consecutively enrolled 75 patients with clinically suspected NAFLD who underwent percutaneous liver biopsy in our hospital from June 2020 to December 2021. All cases underwent multiple advanced acoustic measurements for liver such as SWD, SWS, ATI, NLV, and Ratio examination before liver biopsies. A nomogram prediction model combining the technical acoustic measurements and clinical parameters was established and the model is proposed to improve the diagnostic performance of NASH.
Results
A total of 75 cases were included in this study. Classification of Pathological grade for NASH was as follows: normal liver, (n=15, 20%), NAFL, (n=44, 58.7%), and NASH, (n=16, 21.3%). There were statistically significant differences in SWS (p=0.002), AC (p=0.018), NLV (p=0.033), age (p=0.013) and Glucose (Glu) (p=0.049) between NASH and non-NASH. A nomogram model which includes SWS, AC, NLV, age and Glu was built to predict NASH, and the calibration curves showed good calibrations in both training and validation sets. The AUCs of the combined nomogram model for the training set and validation set were 0.8597 and 0.7794, respectively.
Conclusion
There were statistically significant differences in SWS, AC, NLV, age and Glu between NASH and non-NASH. A nomogram model which includes SWS, AC, NLV, age and Glu was built to predict NASH. The predictive model has a higher diagnostic performance than a single factor model in the diagnosis of NASH, and has a good clinical application prospect.
Differential expression and co-localization of transcription factors during the indirect de novo shoot organogenesis in the fern Ceratopteris richardii
Authors: Xiao Yuan-Le , Li Gui-Sheng 
Published: February 2023

Abstract
Background Regeneration can be achieved through various approaches in flowering plants and different sets of transcription factors are involved in those processes. Ceratopteris richardii is one of the water ferns and can obtain intact plantlets from the callus, thus providing an opportunity for comprehensively understanding plant regeneration.
Results The callus could be induced from the aerial part and the putative embedded root primordia in emergent leaves within this fern, with formation of shoot pro-meristems and meristems verifying an indirect de novo shoot organogenesis. Differentially expressed genes identified by RNA-seq indicated that photosynthesis including both light and dark reaction, response to stimuli, and transmembrane signaling were immediately altered upon transition of the callus from proliferation to differentiation. Moreover, genes concerning hormones and transcription factors were up- or down-regulated, with a suggestion that mechanisms controlling this transition was partly conserved across green plants. Three STM-, ANT-, and ESE3-like transcription factors differentially expressed were all localized at the presumptive vascular-initial-like cells but not in the other callus tissues as indicated by in situ hybridization, thus identifying a putative mechanism underlying callus development.
Conclusions This work provided a basis for studying regeneration in ferns and generated a hypothesis related to callus development.
A Novel Application of Quantum Speed Limit to String Theory
Authors: Lone Arshid Shabir , Wani Salman Sajad , Ali Raja Nisar , Kannan Suresh , Sheikh Aasiya , Faizal Mir , Sheikh Javid , Rubab Seemin , Al-Kuwari Saif 
Published: February 2023

Abstract
In this work, we investigate the implications of the concept of quantum speed limit in string field theory. We adopt a novel approach to the problem of time on world-sheet based on Fisher information, and arrive at a minimum time for a particle state to evolve into another particle state. This is done using both the Mandelstam-Tamm bound and the Margolus-Levitin bound. This implies that any interaction has to be smeared over such an interval, and any interaction in the effective quantum field theory has to be non-local. As non-local quantum field theories are known to be finite, it is expected that divergences should be removed from effective quantum field theories due to the quantum speed limit of string theory.
Reusable suction tips can be a source of infection in joint arthroplasty: Tips for reducing periprosthetic joint infection
Authors: Song Joo-Hyoun , Koh Hae Seok , Jeong Jinyoung , Kim Soo-Young , Jung Hye Seon , Park Chan Jin , Ahn Jae Hyun , Park Hyun Woo , Oh Seungbae 
Published: February 2023

Abstract
The purpose of this study was to analyze whether actual reusable suction tips can be a source of infection by incubating material on suction tips before and after surgery. A prospective study was planned, and 142 orthopedic patients scheduled for surgery were selected. Before and after surgery, the material from the reusable suction tips of the study group was incubated and analyzed by operation time to confirm whether the actual bacterial culture was positive. At the beginning of surgery, a culture-positive finding was seen in seven patients (5.1%). The suction tip investigation at the end of surgery showed bacterial contamination in only two patients (1.4%). Among the patients who were positive on the preoperative evaluation, none of them were positive in postoperative culture findings. None of the patients with positive postoperative culture had an operation time of less than three hours. To reduce the risk of infection when performing joint arthroplasty, great effort should be made to sterilize the surgical instruments, and it is recommended that the surgery be performed in a short time with a well-designed heating, ventilation, and air conditioning (HVAC) system.
Assessing thermal imagery integration into object detection methods on air-based collection platforms
Authors: Gallagher James E. , Oughton Edward J. 
Published: February 2023

Abstract
Object detection models commonly focus on utilizing the visible spectrum via Red-Green-Blue (RGB) imagery. Due to various limitations with this approach in low visibility settings, there is growing interest in fusing RGB with thermal long wave infrared (LWIR) (7.5–13.5 µm) images to increase object detection performance. However, we still lack baseline performance metrics evaluating RGB, LWIR and RGB-LWIR fused object detection machine learning models, especially from air-based platforms. This study undertakes such an evaluation finding that a blended RGB-LWIR model generally exhibits superior performance compared to traditional RGB or LWIR approaches. For example, an RGB-LWIR blend only performed 1–5% behind the RGB approach in predictive power across various altitudes and periods of clear visibility. Yet, RGB fusion with a thermal signature overlayed provides edge redundancy and edge emphasis, both which are vital in supporting edge detection machine learning algorithms. This approach has the ability to improve object detection performance for a range of use cases in industrial, consumer, government, and military applications. Finally, this research additionally contributes a novel open labeled training dataset of 6,300 images for RGB, LWIR, and RGB-LWIR fused imagery, collected from air-based platforms, enabling further multispectral machine-driven object detection research.
A Pilot Single-Site Randomized Control Trial: Investigating the Use of Donor Milk in the Late Preterm and Term Infant in the Neonatal Intensive Care Unit
Authors: Pithia Neema , Grogan Tristan , Garg Meena , Kesavan Kalpashri , Calkins Kara 
Published: February 2023

Abstract
Objective: We aimed to study the use of donor milk (DM) in term and late preterm infants (LPIs) when mother’s own milk (MOM) was unavailable. We hypothesized this study would be feasible and breastfeeding attempts and the percentage of MOM (MOM%) would increase with DM without adversely affecting growth.
Study Design: This was a pilot study (n=32). Infants with gestational age >34 weeks admitted to the neonatal intensive care unit were included. Infants were randomized to: the human milk (MOM+DM) or formula (MOM+F) groups.
Result: Consent rate was 52%. Breastfeeding attempts increased significantly over time in the MOM+DM group compared to the MOM+F group (group p=0.41, time p =0.02, group*time p=0.01). Growth at multiple time points was similar when the two groups were compared.
Conclusion: A study randomizing term infants and LPIs to DM or formula when MOM is unavailable is feasible. DM may increase breastfeeding attempts without compromising growth.
Spatio-temporal dynamics of nutrients at the water-sediment interface: case of the Nokoue lagoon in southern Benin
Authors: AMADOU Akilou SOCOHOU , Djihouessi Metogbe Belfrid , Tigo Beatrix Amen , Viainon Vignon Mechtilde , Adandedji Firmin Mahoutin , Adounkpe Julien , Aina Martin Pépin 
Published: February 2023

Abstract
Lake Nokoué, a major component of the hydrographic system of the Ouémé delta, is the largest lagoon-estuarine ecosystem in Benin. Recent studies have shown that benthic processes would actively participate in the maintenance of eutrophication and biogeochemical cycle of this ecosystem. In order to understand the implication of the bottom on the quality of the waters of the lake, a monthly follow-up of ten (10) parameters of quality of the waters of the bottom was undertaken from July 2020 to December 2021 on a network of nineteen (19) stations distributed on the whole lake. Univariate and multivariate analysis techniques were used to assess the spatial and temporal dynamics of these waters. The Kruskal-Walis test, PCA, correlation analysis and discriminant analysis all showed a very marked influence of the hydrological regime on the concentration of nutrients compared to the influence of anthropogenic activities around the lake and an influence of climatic conditions on internal processes. Indeed, les water inflows from the Ouémé watershed are the main contributors of phosphorus in the lake while benthic processes are the most important contributors of nitrogen. Cluster analysis defined three significantly different areas in Lake Nokoué: the channel, the center of the lake and the river mouth. A single station in each cluster could be used for a spatial assessment of water quality over the entire lake.
Synergistic chemical and structural colorations in early polychromic ceramic glazes over 1000 years ago
Authors: Yin Xuesong , Alcaide Berta Mañas , Pesme Christel , Li Qiang , Zhang Jingyi , HUI Hui Kim , Hnin Yu Yu Ko , Lim Poh Chong , Ding Ning , Zhu Qiang , Tham Nguk Neng , Chiam Sing Yang , Luo Hongjie 
Published: February 2023

Abstract

Ancient ceramics have profound influences on the living habits of human beings. The emergence of high-fired polychromic glazes during Tang period (618–907 AD) highlights a significant advancement in ceramic history that reflected inter-civilizational communications more than 1000 years ago. However, the understanding of colouration mechanisms in Tang glazes are still not satisfactory. In this work, we unravel the mysteries of colourful Tang glazes through a comparative study of Tang Sancai and Changsha kiln samples. Multiple chemical and structural factors, including colourants in varied concentrations and oxidation states as well as microstructures resulted from phase separation, impurity and corrosion, are found responsible for the glaze appearance. More importantly, the combination of different coloration ingredients brings about additional colours and optical effects that any individual factor can hardly generate. These fresh observations and comprehensive analyses provide an insightful assessment of the diversity of Tang glazes and promote the perception of ancient ceramics in a more scientific manner. The knowledge and methodology revealed here are expected to inspire more studies of heritage materials.
Lithium carbonate accelerates the healing of apical periodontitis
Authors: Kagioka Takumi , Itoh Shousaku , Hue Mai Thi , Abe Makoto , Hayashi Mikako 
Published: February 2023

Abstract
Apical periodontitis is a disease caused by bacterial invasions through the root canals. Our previous study reported that lithium chloride (LiCl) had a healing effect on apical periodontitis. The aim of this report is to investigate the healing properties and mechanism of lithium ion (Li+) for apical periodontitis using rat root canal treatment model. 10-week-old male Wistar rat’s mandibular first molars with experimentally induced apical periodontitis underwent root canal treatment and were applied lithium carbonate (Li2CO3) containing intracanal medicament. Base material of the medicament was used as a control. Subject teeth were scanned by micro-CT every week and the periapical lesion volume was evaluated. The lesion volume of Li2CO3 group was significantly smaller than that of the control group. Histological analysis showed that in Li2CO3 group, M2 macrophages and regulatory T cells were induced in the periapical lesion. In situ hybridization experiments revealed a greater expression of Col1a1 in Li2CO3 group compared with the control group. At 24 h after application of intracanal medicament, Axin2-positive cells were distributed in Li2CO3 group. In conclusion, Li2CO3 stimulates Wnt/β-catenin signaling pathway and accelerate the healing process of apical periodontitis, modulating the immune system and the bone metabolism.
Effects of Different Endotracheal Tube Cuff Pressure Management Modes on Postoperative Sore Throat in Patients undergoing Endotracheal Intubation for General Anesthesia
Authors: Liu Jing , Li Hongzhi , Ren Wei , Wang Tingting , Yang Zaiqi 
Published: February 2023

Abstract

Objective To evaluate the effects of different methods of tube cuff pressure management on postoperative sore throat (POST). Methods One hundred and twenty patients, American Society of Anesthesiologists physical status I–II, who were scheduled for elective surgery under general anesthesia, were randomly divided into three groups: the minimum hermetically sealed pressure group (MOP group, n = 40), the measure and control endotracheal tube cuff group (ETTc group, n = 40) and the control group (Con group, n = 40). Midazolam, propofol, cisatracurium, and sufentanil were used to induce anesthesia in all three groups, while propofol, remifentanil, and atracurium were used to maintain anesthesia. We observed the peak airway pressure (Pmax), mean airway pressure (Pmean), partial respiratory CO2 pressure (PETCO2), mean arterial pressure (MAP), heart rate (HR), pulse oxygen saturation (SpO2), and tube cuff pressure at 1 min (T0), 5 min (T1), 30 min (T2), and 60 min (T3) after intubation, and at 5 min before extubation min (T4). The circulating respiratory index was maintained stable during the operation. POST was evaluated by the Prince Henry Hospital pain scale. Results The total incidence of POST was 40%, while it was 20% in the MOP group, 37.5% in the ETTc group, and 62.5% in the Control group. The incidence of POST was positively related to the cuff pressure, particularly at 24 h after the operation. The severity of POST differed with cuff pressure, particularly at 24 h after the operation. Conclusion Application of MOP is advantageous for maintaining the airway during the operation.
Activation mechanisms of Cu 2+ and Pb 2+ in stibnite flotation
Authors: Xiao Youming , Cui Yiqi , Tong Xiong , Wang Jing , Huang Dianqiang , Zhang Yang 
Published: February 2023

Abstract
Different activation mechanisms of Cu2+ and Pb2+ in stibnite flotation were studied via microflotation and adsorption capacity tests and density functional theory (DFT). Microflotation experiments indicated that the recovery rate of stibnite flotation with butyl xanthate (BX) was activated 7.82% higher by Pb2+ than Cu2+. The presence of Pb2+ increased the amount of adsorbed BX on the stibnite surface. The results of DFT also suggested stronger activation by Pb2+. Cu2+ activation induced the formation of Cu-S bonds between the double-bonded S1 atom of BX with Cu, resulting in electron gain. Pb2+ activation was followed by the formation of a stable chelating structure between single-bond S1 and double-bond S2 atoms of BX, resulting in electron loss. This system also facilitated dixanthate formation on the mineral surface via interaction between BX and oxygen, thus improving the floatability of stibnite. This study lays a theoretical foundation for the efficient recovery of stibnite.