bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-strategy approach towards optimization of maturation and germination in radiata pine somatic embryogenesis.
Authors: Castander-Olarieta Ander , Montalbán Itziar Aurora , Moncaleán Paloma 
Published: November 2022

Abstract
Somatic embryogenesis is a powerful technique for forestry improvement programs when implementing multi-varietal forestry. However, it still faces some bottlenecks to be efficient in many forestry species. In this work we have studied the effect of some physico-chemical modifications at proliferation, maturation and germination stages of Pinus radiata D. Don somatic embryogenesis, as well as the impact of this modifications on plant conversion, survival, and on the morphology and biochemical profile (carbohydrate and amino acid analysis) of the resulting plantlets. Given the long culture period needed for maturation and germination in radiata pine, an increase of the plant yield could be very beneficial for its commercial application. A preculture of 14 days without plant growth regulators before maturation seems to be beneficial for the development and germination of somatic embryos. Before germination, a cold storage at 4ºC had no detrimental effect and even increased plant conversion in some embryogenic cell lines. During germination, supplementation of the culture medium with glutamine and a reduction of the sucrose content can improve the greenhouse acclimatization of the plants. Similarly, germinants were demonstrated to be influenced by the light source: fluorescent light enhanced root formation, whereas blue LED light increased the shoot height of somatic plants. Moreover, the highest plants showed lower contents of arginine, asparagine and total carbohydrates.
Phage tRNAs evade tRNA-targeting host defenses through anticodon loop mutations
Authors: Berg Daan F. van den , Steen Baltus A. van der , Costa Ana Rita , Brouns Stan J. J. 
Published: November 2022

Abstract

tRNAs in bacteriophage genomes are widespread across bacterial genera, but their exact function has remained unclear for more than 50 years. Multiple hypotheses have been proposed, with the most established being codon compensation, where codons more rarely used by the host but necessary for the phage are supplemented by tRNAs encoded by the phage. Here, we combine several observations and propose a new hypothesis that phage-encoded tRNAs are a means to counteract the tRNA-depleting strategies of the host to defend from viral infection. Based on mutational patterns of tRNA anticodon loops, we predict that phage tRNAs are insensitive to the host tRNAses. For tRNAs targeted in the anticodon itself, we observe phage counter-selection of targeted isoacceptor tRNAs, further supporting the hypothesis that phage tRNAs are selected to be insensitive to host anticodon nucleases. Importance The presence of tRNAs in phages was discovered more than 50 years ago and their function has been debated ever since. Here, we propose that phage tRNAs counteract the tRNAse activities of the host, which may represent a depletion strategy of essential cellular components to stop translation and thereby phage infection.
Effectiveness and toxicity of re-irradiation after breast conserving surgery for recurrent or new primary breast cancer: a multi-institutional study
Authors: Abeloos Camille Hardy , Xiao Julie , Oh Cheongeun , Barbee David , Perez Carmen A , Oratz Ruth , Schnabel Freya , Axelrod Deborah , Guth Amber , Braunstein Lior , Khan Atif , Choi Isabelle , Gerber Naamit 
Published: November 2022

Abstract
Purpose:
Breast reirradiation (reRT) after breast conserving surgery (BCS) has emerged as a viable alternative to mastectomy for women presenting with recurrent or new primary breast cancer. There are limited data on safety of different fractionation regimens. This multi-institutional study reports safety and efficacy among women treated with repeat BCS and reRT.
Methods and Materials:
Patients who underwent repeat BCS followed by RT from 2015–2021 at 2 institutions were analyzed. Univariate logistic regression models were used to identify predictors of acute and late toxicities. Kaplan Meier estimates were used to evaluate overall survival (OS), distant metastasis free survival (DMFS) and locoregional recurrence-free survival (LR-RFS).
Results:
Sixty-six patients were reviewed with median follow-up of 16 months (range: 3–60 months). At time of first recurrence, 41% had invasive carcinoma with a ductal carcinoma in situ (DCIS) component, 41% had invasive carcinoma alone and 18% had DCIS alone. All were clinically node negative. For the reirradiation course, 95% received partial breast irradiation (PBI) (57.5% with 1.5Gy BID; 27% with 1.8Gy daily; 10.5% with hypofractionation), and 5% received whole breast irradiation (1.8-2Gy/fx), all of whom had received PBI for initial course. One patient experienced grade 3 fibrosis, and one patient experienced grade 3 telangiectasia. None had grade 4 or higher late adverse events. We found no association between the fractionation of the second course of RT or the cumulative dose (measured as EQD2) with acute or late toxicity. At 2 years, OS was 100%, DMFS was 91.6%, and LR-RFS was 100%.
Conclusion:
In this multi-institutional series of patients with recurrent or new primary breast cancer, a second breast conservation surgery followed by reirradiation was effective with no local recurrences and an acceptable toxicity profile across a range of available fractionation regimens.
Molecular phylogeny of mega-diverse Carabus attests late Miocene evolution of alpine environments in the Himalayan-Tibetan Orogen
Authors: Schmidt Joachim , Opgenoorth Lars , Mao Kangshan , Baniya Chitra B. , Hofmann Sylvia 
Published: November 2022

Abstract
The timing, sequence, and scale of uplift of the Himalayan-Tibetan Orogen (HTO) are controversially debated. Many geoscientific studies assume paleoelevations close to present-day elevations and the existence of alpine environments across the HTO already in the late Paleogene, contradicting fossil data. Using molecular genetic data of ground beetles we reconstruct the paleoenvironmental history of the HTO, focusing on its southern margin (Himalayas, South Tibet). Based on a comprehensive sampling of extratropical Carabus, and ~ 10,000 bp of mitochondrial and nuclear DNA we applied Bayesian and Maximum likelihood phylogenetics. We show that Carabus arrived in the HTO at the Oligocene-Miocene boundary. During the early Miocene, five lineages diversified in different parts of the HTO, initially in its southern center and on its eastern margin. Evolution of subalpine-alpine taxa occurred during the late Miocene. There were apparently no habitats for Carabus before the late Oligocene. Until the Late Oligocene elevations must have been low throughout the HTO. Temperate forests emerged in South Tibet in the late Oligocene at the earliest. Alpine environments developed in the HTO from the late Miocene and, in large scale, during the Pliocene-Quaternary. Findings are consistent with fossil records but contrast with uplift models recovered from stable isotope paleoaltimetry.
Experimental Study on Impermeability of Loess Liner Mixed with Bentonite-HDTMA
Authors: Zhang Ming , Dongke Hu , Shaoyu Pan , Guozhou Chen 
Published: November 2022

Abstract
Permeability tests are performed by using the flexible wall permeameter to study the influence of bentonite-HDTMA on the permeability performance of loess as a lining material in landfills. Results show, the impermeability of compacted Malan loess in the middle and lower reaches of the Yellow River in China does not meet the code requirement as a landfill liner. The permeability of Malan loess mixed with more than 10% bentonite ratio is less than 1.0 ×10− 7 cm·s− 1. The permeability of modified loess increases slightly after mixing a small amount of HDTMA. The impermeability of loess mixed with some bentonite-HDTMA ratio still meet the requirement of China code. The SEMs show that the bentonite clay particle can fill the pores between loess coarse particles and improve the impermeability performance of the material. The HDTMA may destroy the soil aggregate structure and increase the soil permeate channel. The digital photos show that HDTMA can effectively resist the development of soil macro-cracks induced by wetting-drying cycles, better for liner to maintain good impermeability. On this basis, the relationship between the hydraulic conductivity of bentonite-HDTMA modified loess and dry density is constructed. From this study, loess can be used as a lining material for landfills, when mixed with bentonite/HDTMA at ratios of 10%/0% or 14%/2%.
Risk factors of pelvic organ prolapse: an ultrasound based retrospective study
Authors: Fang Jianqi , Zhang Ronghua , Weng Yilin , Lin Yang , Chen Yi , Wang Miao , Lu Yao , Lin Juan , Cai Shuhe 
Published: November 2022

Abstract

Objective: To analyse the risk factors of pelvic organ prolapse in postpartum period.
Methods: This retrospective study included 4965 participants who visited Fujian Maternity and Child Health Hospital from December 2019 to March 2022. All participants were assessed by medical professionals for general information and Pelvic floor 3D ultrasound.
Results: Logistic regression analysis showed that age and body mass index had a negative impact on cystocele, perineal hypermobility, hiatal ballooning, rectocele (BMI only), levator avulsion (age only). In contrast, education was a protective factor of uterine prolapse, perineal hypermobility, and hiatal ballooning. Multiparas were more likely to develop cystocele, while multiparas were less likely to get levator avulsion. Vaginal delivery was a risk factor of most of pelvic floor injury, including cystocele, uterine prolapse, perineal hypermobility, hiatal ballooning, and levator avulsion. Similarly, neonatal weight was also a negative factor of levator avulsion. No specific association was found between these factors and anterior, middle and posterior pelvic prolapse.
Conclusions: We found that age, body mass index, parity, vaginal delivery, and neonatal weight were the risk factors of pelvic organ prolapse or levator avulsion. But education and parity was the protective factor of pelvic organ prolapse and levator avulsion respectively.
Biomechanical investigation of long spinal fusion models using three-dimensional finite element analysis
Authors: Oku Norihiro , Demura Satoru , Tawara Daisuke , Kato Satoshi , Shinmura Kazuya , Yokogawa Noriaki , Yonezawa Noritaka , Shimizu Takaki , Kitagawa Ryo , Handa Makoto , Ryohei Annen , Tsuchiya Hiroyuki 
Published: November 2022

Abstract
Background: This study represents the first finite element (FE) analysis of long-instrumented spinal fusion from the thoracic vertebrae to the pelvis in the context of adult spinal deformity (ASD) with osteoporosis. We aimed to evaluate the mechanical stress in long spinal instrumentation for models that differ in terms of spinal balance, fusion length, and implant type.
Methods: In this three-dimensional FE analysis, FE models were developed based on computed tomography images from a patient with osteoporosis. Mechanical stress was compared for three different sagittal vertical axes (SVAs) (0, 50, and 100 mm), two different fusion lengths (from the pelvis to the second [T2-S2AI] or 10th thoracic vertebra [T10-S2AI]), and two different types of implants (pedicle screw or transverse hook) in the upper instrumented vertebra (UIV). We created 12 models based on combinations of these conditions.
Results: The overall mechanical stress was 3.1 times higher on the vertebrae and 3.9 times higher on implants for the 50-mm SVA models than that for the 0-mm SVA models. Similarly, the values were 5.0 times higher on the vertebrae and 6.9 times higher on implants for the 100-mm SVA models than that for the 0-mm SVA models. Higher SVA was associated with greater stress below the fourth lumbar vertebrae and implants. In the T2-S2AI models, the peaks of vertebral stress were observed at the UIV, at the apex of kyphosis, and below the lower lumbar spine. In the T10-S2AI models, the peaks of mechanical stress were observed at the UIV and below the lower lumbar region. Mechanical stress in the UIV was also higher for the screw models than for the hook models.
Conclusion: Higher SVA is associated with greater mechanical stress on the vertebrae and implants. Mechanical stress on the UIV is greater for the T10-S2AI models than for the T2-S2AI models. Using transverse hooks instead of screws at the UIV may reduce mechanical stress in patients with osteoporosis.
Highly Robust Electronic Skin based on Carbon Nanomaterials and SEBS for Object Recognition of Robot Hand: Proximity and Pressure Sensing Array
Authors: Sang Shengbo , Zhang Qiang , Zhang Rui , Lv Bohan , Chen Zhihong , Zhang Fan , Ji Chao , Zhang Chunyan , Fu Zhiyuan , Yang Kun 
Published: November 2022

Abstract
When robot hands work in a com plex environment, it not only needs to sense the objects in contact, but also needs to respond to remote events before physical contact. In this way, robot hands can make prediction, so as to better adapt to the complex environment. In this paper, we have designed a flexible sensor array, which integrates piezoresistive sensor and capacitive sensor for detecting pressure and proximity signals simultaneously. Piezoresistive sensors can detect pressure signals, and capacitive sensors detect pressure and proximity signals. The sensors are arranged in a patterned array and installed on the robot hand to help the robot hand detect the distance and direction of approaching objects, as well as the shape and size of the grasped objects. To avoid mechanical mismatch, piezoresistive sensors and capacitive sensors are fabricated by the same flexible materials. In addition, after extreme pressure tests, the sensors can still work normally, so as to ensure that the robot hands can work normally in complex environments. We also combined the detected signal with machine learning, so that the robot can accurately identify objects of different shapes. In the fruit recognition test, the recognition accuracy reached 90%.
Efficient Multi-Label Attribute Classification and Recognition of Vaginitis Bacteria Based on Deep Learning and model fine-tuning
Authors: Wu Duidi , Huang Haiqing , Zhang Shuo , Qi Jin , Wang Dong , Hu Jie 
Published: November 2022

Abstract
Bacterial vaginosis (BV) is the most common gynecological complaint affecting the health of a large percentage of women worldwide. Traditional manual microscopy methods are expensive and time-consuming, to improve accuracy and efficiency, automated bacterial identification devices with detection intelligence algorithms are urgently needed. We propose a Fine-tuned SmallerVGG (FTS-VGG) convolutional network model-based multi-label classification method for bacteria. Comparison experiments were deployed on several basic backbone networks, including transfer learning on pre-trained VGG19, demonstrating that the proposed method achieves the advantages of being lighter, faster, more accurate, and more efficient. Due to the high cost of time and expertise of experienced clinicians, we use random erasing for data augmentation to address the challenge of dataset collection and annotation, experiments demonstrate its robustness to occlusion. The proposed method has theoretical and practical implications and the potential to be widely extended to other microscopic imaging applications.
Generalized Impedance-Based Transient Analysis for Multi-branched Pipeline Systems
Authors: Kim Sanghyun 
Published: November 2022

Abstract
Transient analysis of multi-branched pipeline systems is generalized by the development of an impedance method. Both open and closed boundaries of branched pipeline elements were implemented in the analytical development of a reservoir pipeline multi-branched pipeline valve systems, in which the performances of the impedance and transient responses were compared with those of conventional approaches. To address realistic boundary conditions along the branched element, a partially-opened boundary condition was implemented in the impedance expression of the branched pipeline system. The performance of the generalized multi-branch impedance was tested on a large water supply system with 10 minor branches from an actual system. The impact of the designated branches was evaluated using the root-mean-square error (RMSE)of the pressure and the difference in the energy spectral density between the original and skeletonized systems. Combinations of multiple branches for certain flow conditions was identified based on the holistic response for both the frequency and time domains. The proposed method can be a useful alternative to effectively address the skeletonization issue for pipeline systems with multi-branched pipeline elements.
Comprehensive Analysis of PHGDH for Predicting Prognosis and Immunotherapy Response in Patients with Endometrial Carcinoma
Authors: Zhang He , Kong Weimin , Zhao Xiaoling , Xie Yunkai , Luo Dan , Chen Shuning 
Published: November 2022

Abstract
Background: PHGDH (Phosphoglycerate Dehydrogenase) is the first branch enzyme in the serine biosynthetic pathway and plays a vital role in several cancers. However, little is known about the clinical significance of PHGDH in endometrial cancer.
Methods: Clinicopathological data of endometrial cancer were downloaded from the Cancer Genome Atlas database (TCGA). First, the expression of PHGDH in pan-cancer was investigated, as well as the expression and prognostic value of PHGDH in endometrial cancer. The effect of PHGDH expression on the prognosis of endometrial cancer was analyzed by Kaplan-Meier plotter and Cox regression. The relationship between PHGDH expression and clinical characteristics of endometrial cancer was investigated by logistic regression. Receiver operating characteristic (ROC) curves and nomograms were developed. Possible cellular mechanisms were explored using the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, the Gene Ontology (GO), and gene set enrichment analysis (GSEA). Finally, TIMER and CIBERSORT were used to analyze the relationship between PHGDH expression and immune infiltration. CellMinerTM was used to analyze the drug sensitivity of PHGDH.
Results: The results showed that PHGDH expression was significantly higher in endometrial cancer tissues than in normal tissues at mRNA and protein levels. Kaplan-Meier survival curves showed that patients in the high expression group had shorter overall survival (OS) and disease free survival (DFS) than patients in the low PHGDH expression group. Multifactorial COX regression analysis further supported that high PHGDH expression was an independent risk factor associated with prognosis in patients with endometrial cancer. The results showed estrogen response, mTOR, K-RAS, and epithelial mesenchymal transition (EMT) were differentially elevated in the high-expression group of the PHGDH group. CIBERSORT analysis showed that PHGDH expression is related to the infiltration of multiple immune cells. When PHGDH is highly expressed, the number of CD8+T cells decreases.
Conclusions: PHGDH plays a vital role in the development of endometrial cancer, which is related to tumor immune infiltration, and can be used as an independent diagnostic and prognostic marker for endometrial cancer.
Synthetic consortium of Ganoderma lucidum and Lactobacillus plantarum for enhanced natural products biosynthesis
Authors: Azi Fidelis , Hong Yuxiang , Wu Zizhao , Xu Peng 
Published: November 2022

Abstract
Microbial coculture holds immense promise for biomanufacturing. Herein, we designed a synthetic consortium of G. lucidum and L. plantarum for enhanced natural product biosynthesis. The spatio-temporal alignment of the strains revealed an implicit disposition for transient and long-term mutualistic co-existence in the shared environment. The consortium assembly and biomass growth were driven by an intuitive toggle-switching of carbon/nitrogen sources, multi-metabolite cross-feeding, and TOR signalling. Extracellular electron transfer propelled by redox shuttles facilitated the distribution of high-energy electrons and enhanced the consortium’s robustness. The ROS-scavenging activity of antioxidant enzymes maintained the cells’ viability via intracellular ROS removal. Small-signalling molecules stimulated the biosynthesis of bioactive natural products in the coculture. Over-expression of target genes further enhanced ganoderic acids and exopolysaccharides bioproduction in the coculture system. The study provides insight into the physicochemical and molecular forces that drive cooperative interaction and stimulate natural product biosynthesis in G. lucidum and L. planatarum consortium.
Depositional controls on formation of Quaternary lacustrine Tufa Bent Jedidi spring systems, NE Tunisia
Authors: Tlili Faouzia , Ayari Asma , Regaya Kamel 
Published: November 2022

Abstract
The carbonate Bent Jedidi unit represents middle –late Pleistocene continental carbonate deposits in Northeastern Tunisia. The unit consists of three main facies associations; asymmetrically distributed (1) calcrete-palustrine (2) lacustrine, (3) Tuffa carbonate.This study evaluates variations in petrophysical properties within a lacustrine to palustrine and tufa carbonate. The transition from alluvial environments to lake margins settings displays a shift from conglomerate and silt to lacustrine palustrine mudstones to packstones (1) The palustrine carbonates include features like pseudo-microkarst, root cavities, gypsum, nodular and mottled limestone, (2) The lacustrine deposits include charophytes gastropods and ostracods, oxidation oncoids, oncoliths and recrystallization of calcite.(3) The Tufa deposits include, algae filament, mosse Tufa and laminated structure. The evaluation of the facies associations over time demonstrates an overall fall of the relative lake level. High proportion of low energy facies associated with a deeper lacustrine environment. While at the Top predominate high energy facies associated with a shallow lacustrine environment fluctuations in lake water level enabled land plants to occupy the lake margins during periods of low levels for this reason We found chenal porosity. This study aims to identify the depositional facies and the origin and paleoenvironmental significance of lacustrine /palustrine carbonates and tufas in the Pleistocene Bent Jedidi Lake.