bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a genetic linkage map and QTL mapping of the agronomic traits in Foxtail millet (Setaria italica)
Authors: Gao Lulu , Zhu Qianxue , Li Huan , Wang Shiyuan , Fan Jiahui , Wang Tianguo , Yang Lejie , Zhao Yuqin , Ma Yixuan , Chen Lu , Li Xiaorui , Dong Shuqi , Chu Xiaoqian , Diao Xianmin , Yuan Xiangyang , Wang Jiagang , Yang Guanghui 
Published: November 2024

Abstract

Foxtail millet (Setaria italica) is one of the most ancient cultivated cereal crops and is ideal for the functional genomics of the Panicoideae crops. In the present study, we generated an F2 population derived from a cross between an elite foxtail millet variety Jingu28 and a backbone line Ai88 and constructed a genetic linkage map with 213 published SSR markers and two InDel markers. Quantitative trait locus (QTL) mapping identified 46 QTL for 12 agronomic traits, including 13 major effect QTL. Meanwhile, 40 QTL controlling different traits formed 13 co-located QTL clusters. Moreover, one putative candidate gene Seita.9G020100 for qHD9-1 with conserved CCT (constans, constans-like, and timing of chlorophyll A/B binding) motif and a gibberellin biosynthesis related GA20 oxidase gene Seita.5G404900 for qPH5-1 were identified based on homologous gene comparison. The 277 bp insertion/deletion on the promoter of Seita.9G020100 and the one-base (G) insertion/deletion in the third exon of Seita.5G404900 might be candidate functional sites. Furthermore, two markers (Ghd7InDel and GA20oxSTARP-1) were developed based on these two variation sites, respectively. These results will help to elucidate the genetic basis of important agronomic traits in foxtail millet and be useful for marker-assisted selection of varieties with ideal plant architecture and high yield potential.
A single-vector system for tunable and homogeneous dual gene expression in Escherichia coli
Authors: Živič Z. , Lipoglavšek L. , Lah J. , Hadži S. 
Published: November 2024

Abstract

Expression of recombinant genes can be controlled using inducible promoters. However, the most commonly used IPTG- and arabinose-inducible promoters result in an 'all-or-nothing' response, leading to fully induced and uninduced bacterial subpopulations. Here, we investigate whether appropriate modifications to these promoter systems can be combined into a single vector system, enabling homogenous expression of two genes of interest that can be precisely tuned using inducer concentration. We show that modifications of positive feedback loops related to inducer uptake result in homogeneous gene expression in both the T7 lactose and pBAD arabinose systems. Furthermore, these two modified systems were combined into a single vector, pRAT-sfGFP that provides the desired tunable expression of two genes of interest. Finally, we test this single-vector system as a tool for studying two-component genetic circuits, using toxin-antitoxin modules as model systems. This novel low-copy single vector expression system opens up new possibilities for investigating the function of two-component bacterial genetic circuits.
Rapid determination of insect lipids and their fatty acid profile in doughs using hand-held and portable infrared spectrometers
Authors: Mendez-Sanchez Carmen , Ranasinghe Madushika K. , Güell Maria Carme , Ferrando Montserrat , Rodriguez-Saona Luis , Castellvi Silvia Lamo 
Published: November 2024

Abstract

The objective of the study was to evaluate infrared (IR) spectroscopy in combination with pattern recognition analysis as a rapid technique to quantify the percentage of insect lipid added into chickpea-based dough as well as dough’s fatty acid profile. Several chickpea-based doughs were prepared with a variable amount of Tenebrio molitor, Alphitobius diaperinus, and Acheta domesticus lipid fraction (0, 2.9%, 5.8%, 8.7% and 11.6%) replacing the same amount of olive and sunflower oil. The raw doughs were analyzed using portable Fourier transform mid infrared (FT-MIR) and handheld FT-NIR spectrometers. Fatty acid profile was determined by using fatty acid methyl esters (FAME) methods. Partial least squares regression (PLSR) was used to build up a model to predict the percentage of insect lipid added showing a low standard error of cross-validation (SECV≤0.71%), strong correlation (RCV≥0.85) and great predictive ability (RPD: 5.21-5.53). The saturated (SFA), monounsaturated (MUFA), polyunsaturated (PUFA) fatty acids as well as the content of palmitic, oleic and linoleic were correctly predicted with values of SECV≤5.64% and an RCV≥0.88. Nonetheless, the FT-MIR device tested, showed higher performance to predict SFA, MUFA, PUFA and fatty acids reaching values of 0.97 in coefficient of correlation (RP) and 2.81% in standard error in prediction (SEP).
The assessment of root apical curvature of maxillary lateral incisors phenotypes reveals side and gender difference
Authors: Kuchler Erika , Neto Mario Pereira Couto , Stroparo Jeferson Luis Oliveira , Scariot Rafaela , Beisel-Memmert Svenja , Schroder Angela Graciela Deliga , Roskamp Liliane , Hemming Daniel , Matsumoto Mirian Nakane , Mattos Natanael Henrique Ribeiro , Kirschneck Christian , Baratto-Filho Flares 
Published: November 2024

Abstract

BACKGROUND Maxillary lateral incisors root angulation is a common developmental aspect characterized by an alteration in the axial inclination between the crown and root of the incisor, in which a curvature of varied angle of the dental root is observed. This study investigated if root apical curvature of maxillary lateral incisors has gender and side preference as observed in patients with cleft lip and/or palate. METHODS Panoramic radiographs from 230 orthodontic patients were investigated. The method described by Schneider method (1971) was used for the estimation of the degree of root apical curvature of maxillary lateral incisors and to classify the root as straight (5° or less) or curved (higher than 5°). To compare curvature degree among genders, t test was used, and to compare left and right degree differences, a paired t-test was used. Chi-squared test and Odds ratio were used to calculate gender and laterality differences among straight or curved root groups. The established alpha was 5%. RESULTS Ninety-seven were males and 133 were females. A total 198 left maxillary incisors and 201 right maxillary incisors were measured. A statistical difference was observed, in which straight root was more common in the left side (p = 0.028; odds ratio = 1.5, confidence interval 95%: 1.1–2.4). On left incisors, the mean curvature degree was 5.9° (SD = 4.4°) in males, while the mean curvature degree was 7.5° (SD = 5.3°) in females (p = 0.030). Means comparisons between left and right incisor regardless the gender showed a statistical significant difference between sides (p = 0.0001). CONCLUSIONS Our study confirmed the hypotheses that root apical curvature of maxillary lateral incisors has gender and side preference in the general population.
Combined Lipid Metabolism Indicators and CT Deep Learning Model to Predict Rectal Cancer Prognosis
Authors: Zhou Chuan , He Wan-Bin , Zhang Yun-Feng , Yang Zhi-Jun , Yang Jin , Miao Guo-Liang , Zhou FengHai , Da Ming-Xu 
Published: November 2024

Abstract

Objective
Colorectal cancer (CRC) is a common malignant tumor, and its prognosis is closely associated with abnormalities in lipid metabolism; meanwhile, CT imaging-based radiomics also demonstrates significant advantages in the evaluation of CRC. This study aims to investigate the application value of lipid metabolism indicators and CT deep learning models in prognostic assessment of colorectal cancer.
Materials and Methods
We retrospectively collected clinical data, lipid metabolism indicator data, and CT imaging data of patients diagnosed with rectal cancer by pathology at Gansu Provincial People's Hospital from January 2019 to May 2021. First, we analyzed the patients' lipid metabolism indicators, including serum lipid levels and metabolic-related biomarkers. Next, we delineated regions of interest (ROIs) from the patients' CT images. After delineation, we used a cropping tool to extract the tumor's maximum ROI cross-section for deep learning model training. We trained deep learning models using the ResNet and DenseNet series, plotted ROC curves, and calculated the AUC (area under the curve) to evaluate the performance of the predictive models. We also plotted calibration curves and DCA (decision curve analysis) curves to assess the model's fit and clinical value, and drew KM curves to evaluate its relationship with prognosis. Finally, we used a nomogram to integrate lipid metabolism indicators and the CT deep learning model at the outcome level, establishing a combined model for predicting rectal cancer prognosis.
Results
The predictive model based on lipid metabolism indicators achieved an AUC of 0.700. The CT-based deep learning model achieved an AUC of 0.746 on the test set. The combined model achieved an AUC of 0.863. Calibration curve analysis demonstrated superior accuracy of the combined model, while decision curve analysis (DCA) indicated better clinical utility. Kaplan-Meier curves showed that risk stratification based on the combined model accurately assessed patients' prognosis.
Conclusion
The combined model based on lipid metabolism indicators and CT deep learning has certain predictive value for the prognosis of rectal cancer.
Latent Profile Analysis of Spinal Deep Muscle Strength and Physical Fitness in Elite Taekwondo Athletes
Authors: Lee Jae-Hoon , Kim Taehwan , Lee Minchul , Ha Min-Seong 
Published: November 2024

Abstract

In Taekwondo, core stability and physical fitness are vital for performance, with spinal deep muscles playing a key role. This study explored the relationship between spinal deep muscle strength and physical fitness in 104 adolescent Taekwondo athletes, using a cross-sectional design in a laboratory setting. Participants were classified into groups based on spinal muscle strength at various angles, measured with a Centaur 3D machine. Outcome measures included body composition (height, weight, BMI) and physical fitness (grip strength, back muscle strength, endurance, flexibility, balance, and leg strength). Latent profile analysis identified five profiles: G2 and G4 showed higher body weight and skeletal muscle mass, with G2 also having the highest grip, back, and leg strength. No significant relationship was found between spinal muscle strength and balance. The findings suggest spinal muscle strength and physical fitness do not always correlate, highlighting the need for further research to optimize training.
Protective Effects of Notoginsenoside R2 on Reducing Lipid Accumulation and Mitochondrial Dysfunction in Diabetic Nephropathy Through Regulation of c-Src
Authors: Guo Xieyi , Yang Liu , An Xiaoning , Hu Maofang , Shen Yilan , Wang Niansong , Xu Youhua , Gui Dingkun 
Published: November 2024

Abstract

Background
There are few treatment options to delay the progression of diabetic nephropathy (DN), a key contributor to chronic kidney disease (CKD). Previous studies reported that traditional Chinese medicine Panax notoginseng (PNG)exerted beneficial effects on DN. However, the renoprotective effects of Notoginsenoside R2 (NR2), an active component of PNG, on DN have not been previously investigated. This study was designed to assess the therapeutic potential of NR2 in DN and to explore its underlying mechanisms.
Methods
In vivo models were developed using db/db mice, while in vitro models utilized HK-2 cells exposed to high glucose and palmitic acid (HGPA). Online databases and Cytoscape software were employed to predict the potential targets of NR2. The expression of associated proteins was measured using Western blot and immunohistochemistry (IHC) in an effort to clarify the underlying mechanisms. Lipid accumulation, oxidative stress levels, mitochondrial function, and cell apoptosis were also assessed. Small interfering RNA (siRNA) was used in in vitro experiments to confirm the effect of c-Src.
Results
NR2 reduced albuminuria, improved renal function, and ameliorated renal pathology. The activation of c-Src, the predicted target, was suppressed in db/db mice and in HK-2 cells exposed to HGPA. Meanwhile, NR2 inhibited the JNK/STAT1 phosphorylation and CD36 overexpression. Both in vivo and in vitro, NR2 intervention reversed lipid accumulation, oxidative stress, mitochondrial dysfunction, and cell apoptosis. By inhibiting c-Src, HK-2 cells exposed to HGPA experienced less lipid deposition and mitochondrial damage, suggesting the renoprotective effects of NR2 were correlated with the inhibition of c-Src.
Conclusion
NR2 ameliorated mitochondrial dysfunction and delayed the progression of DN partly through suppression of c-Src. The protective effects of NR2 might be related to a reduction in lipid accumulation.
Blind Quality Evaluation for Tone-Mapped Images by Exploiting Statistical Characteristics and Deep Perceptual Features
Authors: Lin Junhao , Ruan Qiuzi , Cai Siwen , Cui Yueli , Wang Yuhe , Xu Jiaming , Cui Yonglong , Li Shuitu , Liu Yadong , Zhang Shiqing 
Published: November 2024

Abstract

The tone-mapping operator (TMO) aims to convert high dynamic range images into low dynamic range images, enabling them to be displayed on standard monitors. However, this conversion process inevitably results in a decrease in image quality, such as structural damage, contrast degradation and color artifacts, which impacts human’s visual perception. Evaluating the visual quality of tone-mapped images (TMIs) effectively remains a challenge. To address this issue, this paper proposes a novel blind metric for evaluating the quality of TMIs based on statistical characteristics and deep perceptual features. Specifically, for statistical features, we firstly extract quality-aware features that capture structure-texture variations from local fractal dimension maps and first digit distribution (FDD) statistics from wavelet and gradient domains to capture structural changes in TMIs. Additionally, considering that TMO procedure introduces noticeable color artifacts, we further extract color statistical features to capture color degradation. For deep perceptual features, a pre-trained CNN model is utilized to extract deep learning-based features that represent semantic changes in TMIs. Finally, considering the significant difference between the extracted statistical and deep perceptual features, we leverage an ensemble learning scheme for feature training and quality score generation. Experimental results conducted on two publicly available benchmark databases demonstrate that our method achieves better performance than existing traditional 2D quality metrics and specifically-designed TMI quality metrics.
LEGO-LPPO membrane activity is enhanced by presence of phosphatidylethanolamine but hindered by outer membrane
Authors: Brzobohatá Hana , Dugić Milica , Mojr Viktor , Sahatsapan Nitjawan , Kóšiová Ivana , Křížek Tomáš , Dolejšová Tereza , Lišková Petra , Cwiklik Lukasz , Rejman Dominik , Fišer Radovan , Mikušová Gabriela 
Published: November 2024

Abstract

Finding effective antibiotics against multi-resistant strains of bacteria has been a challenging race. LEGO-lipophosphonoxins (LEGO-LPPOs) are small modular synthetic antibacterial compounds targeting the cytoplasmic membrane. Here we focused on understanding the reasons for the variable efficacy of selected LEGO-LPPOs (LEGO-1, LEGO-2, LEGO-3, and LEGO-4) differing in hydrophobic and linker module structure and length. LEGO-1-4 permeabilized cytoplasmic membrane of Staphylococcus aureus, Bacillus subtilis, Pseudomonas aeruginosa, and Escherichia coli, LEGO-1 with the longest linker module being the most effective. Gram-positive bacteria were more sensitive to LEGO-LPPO action compared to Gram-negatives, which was manifested as a delayed membrane permeabilization, higher minimal inhibitory concentration and lower amount of LEGO-LPPO bound to the cells. Presence of the intact outer membrane had a greater impact on the LEGO-LPPO action than changes in the structure of the hydrophobic modules, considering that the reduced susceptibility of Gram-negatives was attributed to the presence of the outer membrane and its components. Using liposome leakage and in silico simulations, we showed that membranes with major content of phosphatidylethanolamine were more prone to LEGO-LPPO permeabilization.
Epidemiology, clinical spectrum, and outcomes of severe malaria in Eastern Uganda: a prospective study
Authors: Namayanja Cate , Paasi George , Alunyo Jimmy Patrick , Amorut Denis , Okalebo Charles Benard , Okiror William , Ongodia Paul , Abongo Grace , Muhindo Rita , Lubaale Yovani A. M. , Olupot-Olupot Peter 
Published: November 2024

Abstract

Background
In Sub-Saharan Africa, malaria remains a public health problem despite some reports of declining incidence in the period 2000–2018. Since 2019, there are some reports of disease epidemics, resurgences in areas that had registered steep decline and unusual clinical presentation. This study aimed to describe the epidemiology, clinical spectrum, and outcomes of severe malaria in children in malaria-endemic Eastern Uganda, a region that has recently experienced epidemics.
Methodology:
This prospective study was conducted at Mbale Regional Referral Hospital, Uganda, from May 08, 2019 to August 15, 2023 as part of the Malaria Epidemiological, Pathophysiological and Intervention studies in Highly Endemic Eastern Uganda (EDCTP - TMA2016SF-1514-MEPIE Study). Children aged 60 days to 12 years who at admission tested positive for malaria and fulfilled the clinical WHO criteria for surveillance of severe malaria were enrolled into the study following appropriate informed consent. Data were collected using a customised proforma on social demographic characteristics, clinical presentation, treatment, and outcomes. Laboratory analyses included complete blood counts, lactate, glucose, blood gases, electrolytes, metabolites, and coagulation markers. In addition, urinalysis using dipsticks was done. Data were analysed using STATA V15. The study had ethical and regulatory approval before data collection commenced.
Results
A total of 1,379 participants were recruited. The median age was 4 years. Most children 757/1379 (54.9%) were under 5 years, and 825/1379 (59.8%) were males. The common symptoms were fever 1368(99.2%), poor appetite 1095(79.5%), inability to sit upright 1051(76.2%), vomiting 944(68.4%) and yellow eyes 833(60.4%). The common signs included prostration, haemoglobinuria and jaundice. Prolonged hospitalization was found in 284/1339(21.2%) and was associated with impaired consciousness 116/166(30.1%), P = 0.003; haemoglobinuria 514/705 (27.1%), P < 0.001 and jaundice 505/690(26.8%) P < 0.001. The overall mortality was 40/1347 (3.0%). Children who had > 1 severity feature were at a higher risk of mortality.
Conclusion
In this prospective study in children with severe malaria in Eastern Uganda, the overall mortality was 3.0% and the more the disease clinical syndromes the higher the risk of death.
SLC10A7 regulates O-GalNAc glycosylation and Ca2+ homeostasis in the secretory pathway: insights into SLC10A7-CDG
Authors: Durin Zoe , Layotte Aurore , Morelle Willy , Houdou Marine , Folcher Antoine , Legrand Dominique , Lefeber Dirk , Prevarskaya Natalia , Von Blume Julia , Cormier-Daire Valérie , Foulquier Francois 
Published: November 2024

Abstract

Glycans are known to be fundamental for many cellular and physiological functions. Congenital disorders of glycosylation (CDGs) currently encompassing over 160 subtypes are characterized by glycan synthesis and/or processing defects. Despite the increasing number of CDG patients, therapeutic options remain very limited as our knowledge is often insufficient on the involved molecular and regulatory mechanisms of glycan synthesis. This is worsened by the emergence of significant subgroup of CDG resulting from defects in unexpected regulators of glycosylation such as ER/ Golgi homeostasis defects. SLC10A7 belongs to the SLC10 protein family, known as bile acid and steroid transport family, exhibiting a unique structure and ubiquitous expression. It is linked to negative calcium regulation in cells, but the mechanisms by which SLC10A7 deficiency lead to Golgi glycosylation abnormalities are unknown. The present study identifies major O-glycosylation defects in both SLC10A7 KO HAP1 cells and SLC10A7-CDG patient fibroblasts, as an increased ER and Golgi calcium contents. We also show that the abundance of COSMC and C1GALT1 is altered in SLC10A7-CDG patient cells, as well as the subcellular Golgi localization of the Ca2+-binding Cab45 protein. Finally, we demonstrate that supraphysiological manganese supplementation suppresses the deficient electrophoretic mobility of TGN46 by an aberrant transfer of GalNAc residues, and we reveal the Mn2+ sensitivity of COSMC. These findings provide novel insights into the molecular cause of Golgi glycosylation defects in SLC10A7-deficient cells and show that SLC10A7 is a key Golgi transmembrane protein in maintaining the tight regulation of Ca2+ homeostasis in the ER and Golgi compartments, both essential for glycosylation.
Prevalence, Clinical Correlates, and Sleep Architectures of Asian Patients with Comorbid Insomnia and Obstructive Sleep Apnea: A Prospective Study
Authors: Hoc Tran V. , Lee Hsin-Chien 
Published: November 2024

Abstract

Obstructive sleep apnea (OSA) and insomnia are the two most common sleep disorders. The coexistence of these conditions, termed comorbid insomnia and sleep apnea (COMISA), has been increasingly recognized, with evidence suggesting a bi-directional relationship that exacerbates the severity of each disorder. This prospective recruited 170 consecutive patients with OSA, categorized into OSA alone and COMISA group. Among recruited patients, 68 (40%) were identified with COMISA. No significant differences were found in age, gender, or body mass index between COMISA and OSA alone groups. However, COMISA patients were more likely to have comorbid medical conditions, reported worse sleep quality, and exhibited higher levels of anxiety and depression. Sleep architecture and the distribution of the low arousal threshold endotype, a potential contributor to COMISA, did not significantly differ between patients with COMISA and OSA alone. Our results suggest that OMISA is prevalent among Asian patients with OSA and is associated with worse subjective sleep quality, adverse health conditions, and higher psychological distress. However, objective sleep architecture and arousal threshold endotypes do not significantly differ from OSA alone. Further research is needed to explore the pathophysiological mechanisms underlying COMISA and optimize treatment approaches.