bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrahepatic cholangiocyte regeneration from an Fgf‐dependent extrahepatic progenitor niche in a zebrafish model of Alagille Syndrome
Authors: Zhao Chengjian , Lancman Joseph J. , Yang Yi , Gates Keith P. , Cao Dan , Barske Lindsey , Matalonga Jonathan , Pan Xiangyu , He Jiaye , Graves Alyssa , Huisken Jan , Chen Chong , Dong P. Duc Si 
Published: September 2021

Abstract

Background and Aims
Alagille Syndrome (ALGS) is a congenital disorder caused by mutations in the Notch ligand gene JAGGED1, leading to neonatal loss of intrahepatic duct (IHD) cells and cholestasis. Cholestasis can resolve in certain patients with ALGS, suggesting regeneration of IHD cells. However, the mechanisms driving IHD cell regeneration following Jagged loss remains unclear. Here, we show that cholestasis due to developmental loss of IHD cells can be consistently phenocopied in zebrafish with compound jagged1b and jagged2b mutations or knockdown.

Approach and Results
Leveraging the transience of jagged knockdown in juvenile zebrafish, we find that resumption of Jagged expression leads to robust regeneration of IHD cells through a Notch‐dependent mechanism. Combining multiple lineage tracing strategies with whole‐liver three‐dimensional imaging, we demonstrate that the extrahepatic duct (EHD) is the primary source of multipotent progenitors that contribute to the regeneration, but not to the development, of IHD cells. Hepatocyte‐to‐IHD cell transdifferentiation is possible but rarely detected. Progenitors in the EHD proliferate and migrate into the liver with Notch signaling loss and differentiate into IHD cells if Notch signaling increases. Tissue‐specific mosaic analysis with an inducible dominant‐negative Fgf receptor suggests that Fgf signaling from the surrounding mesenchymal cells maintains this extrahepatic niche by directly preventing premature differentiation and allocation of EHD progenitors to the liver. Indeed, transcriptional profiling and functional analysis of adult mouse EHD organoids uncover their distinct differentiation and proliferative potential relative to IHD organoids.

Conclusions
Our data show that IHD cells regenerate upon resumption of Jagged/Notch signaling, from multipotent progenitors originating from an Fgf‐dependent extrahepatic stem cell niche. We posit that if Jagged/Notch signaling is augmented, through normal stochastic variation, gene therapy, or a Notch agonist, regeneration of IHD cells in patients with ALGS may be enhanced.
Morphologic characterization and fractal analysis of lapped and polished surfaces of quartz single crystals
Authors: Ţălu Ştefan , Guzzo Pedro L. , Salerno Marco , Bramowicz Miroslaw , Kulesza Slawomir 
Published: September 2021

AbstractLapping and polishing are industrial processes sometimes used alternatively for surface finishing of hard and brittle materials. This article presents advanced image analysis of surfaces of quartz crystal blanks finished by lapping and polishing. Scanning electron micrographs were obtained from workpiece surfaces parallel to Y‐, AT‐, and Z‐cut crystal planes treated with different normal stress and abrasive grit size, and stereometric and fractal/multifractal approaches were used to analyze the respective surfaces. Fractal dimensions and segmentation parameters were able to decode the effect of normal stress increasing on the surface roughness of lapped and polished samples. Moreover, the texture isotropy and the bifractal—hence agglomerated—nature of the surface patterns, suggest that both treatments dismiss the anisotropic signature of hardness and fracture toughness inherent to each crystal plane. This study provides promising results regarding the applicability of fractal analysis in the assessment of surfaces severely worn by the combined effect of brittle microcracking and plastic deformation mechanisms.
Symmetries of the honeycomb toroidal graphs
Authors: Šparl Primož 
Published: September 2021

AbstractHoneycomb toroidal graphs are a family of cubic graphs determined by a set of three parameters that have been studied over the last three decades both by mathematicians and computer scientists. They all can be embedded on a torus and coincide with the cubic Cayley graphs of generalized dihedral groups with respect to a set of three reflections. In a recent survey paper B. Alspach gathered most known results on this intriguing family of graphs and suggested a number of research problems regarding them. In this paper we solve two of these problems by determining the full automorphism group of each honeycomb toroidal graph.
Genetic variation in the E6 and E7 genes of human papillomavirus type 16 in northeastern Argentina
Authors: Totaro M. Elina , Gili Juan A. , Liotta D. Javier , Schurr Theodore G. , Picconi Maria A. , Badano Inés 
Published: September 2021

AbstractThe province of Misiones is considered a region with a high mortality rate due to cervical cancer (CC). To gain insight into this problem, we explored the association between genetic variation in the E6 and E7 oncogenes of HPV16 and the risk of CC. We studied 160 women with cytological diagnoses of negative for intraepithelial lesion or malignity, low‐grade squamous intraepithelial lesion, and high‐grade squamous intraepithelial lesion/CC and a positive test for HPV16 infection. The genetic characterization of E6 and E7 genes was undertaken through PCR amplification and direct Sanger sequencing. Phylogenetic classification was conducted using Bayesian methods. To estimate the odds ratio (OR) for an association between genetic variants in the E6 and E7 genes and the risk of CC, we used ordinal logistic regression adjusted by age. The final data set comprised 112 samples. Diagnostic single‐nucleotide polymorphisms (SNPs) and phylogenetic trees confirmed the presence of Lineage A (95.5%) and D (4.5%) in the samples. For the E6 gene, we identified eleven different sequences, with the most common ones being Lineage A E6 350G (58.9%) and E6 350T (37.5%). The E6 350G was associated with progression to HSIL/CC, with an OR of 19.41 (4.95–76.10). The E7 gene was more conserved than E6, probably due to the functional constraints of this small protein. Our results confirmed the association of the E6 350G SNP with a higher risk of developing CC. These data will contribute to understanding the biological bases of CC incidence in this region.
Incorporation of white tea extract in nano‐liposomes: optimization, characterization, and stability
Authors: Ahmadi Elham , Elhamirad Amir Hossein , Mollania Nasrin , Saeidi Asl Mohammad Reza , Pedramnia Ahmad 
Published: September 2021

AbstractBACKGROUNDIn the present study, an extraction method affected by sonication intensity (40%, 70% and 100%), sonication time (5, 10 and 15 min) and different solvents (ethanol, methanol and a combination of ethanol/methanol) was optimized to extract the white tea with the greatest polyphenolic compounds using a response surface methodology. To prepare the nano‐liposomal vesicles, phospholipids and cholesterol in various proportions (60:0, 40:20, 30:30 and 20:40) were applied based on thin‐film hydration and ultrasound method. The nano‐capsules enriched in bioactive compounds were examined through particle characteristics, encapsulation efficiency, morphological analysis, thermal properties and Fourier transform infrared spectroscopy.RESULTSThe observations showed that the extraction yield highly depended on the type of solvent with varying permeability, sonication time and power. The highest total phenolic content (68.38 mg GA g–1) and free radical scavenging activity (77.65%) were observed for the following optimal conditions: 70% for sonication intensity, 15 min for sonication time and methanol as solvent. Characteristics of nanoliposomes within a compositional ratio of lecithin/cholesterol (40:20) and with a zeta potential of −56 ± 0.01 mV, as well as white tea extract (WTE) samples with an average particle diameter of 82.20 ± 0.08, microencapsulation efficiency of 76.5% ± 0.081, polydispersity index of 0.06 ± 0.02 and span value of 0.69 ± 0.03. are used as the optimal formulation for microencapsulation of antioxidant WTE. The results demonstrated an increment in thermal stability of liposomal WTE samples compared to other samples.CONCLUSIONThe findings of the present study indicated that nano‐liposomes comprise an effective technology for coating the WTE, as well as to increasing its stability and thermal properties. © 2021 Society of Chemical Industry.
Salvage pulmonary resection in stages IIIb–IV lung cancer after treatment with immune checkpoint inhibitors case series and literature review
Authors: Smith Alex , Wali Anuj , Montes Ana , Hadaki Maher , Harrison‐Phipps Karen , Karapanagiotou Eleni M. , Bille Andrea 
Published: September 2021

AbstractBackground and ObjectivesThe role of salvage thoracic surgery in managing advanced‐stage lung cancer following treatment with immune checkpoint inhibitors is currently unclear. We present a series of nine patients with advanced non‐small‐cell lung cancer who underwent pulmonary resection following treatment with pembrolizumab.MethodsWe performed a single‐institution retrospective analysis of pulmonary resection undertaken following treatment with pembrolizumab for advanced‐stage lung cancer. Nine patients met the inclusion criteria.ResultsIn six cases, surgery was indicated for persistent localized disease after treatment, and in three cases for nonresponsive synchronous/metachronous lung nodules while on treatment for stage IV lung cancer. Dense hilar fibrosis was present in all patients. Minimal access surgery was achieved in five cases (video‐assisted n = 2, robotic‐assisted n = 3). There was no in‐hospital mortality. One patient died within 60 days from community‐acquired COVID‐19 pneumonitis. Seven patients remain free of disease between 5 and 22 months follow‐up.ConclusionsPulmonary resection is safe and technically feasible following treatment with immune checkpoint inhibitors. Surgical challenges relate to postimmunotherapy fibrosis, but with increased experience and a robotic approach, minimal access surgery is achievable. Further prospective studies are required to assess the surgical impact on disease control and overall survival in this patient cohort.
Water‐based Cu nanofluid as lubricant for steel hot rolling: Experimental investigation and molecular dynamics simulation
Authors: He Jiaqi , Sun Jianlin , Yang Fulin , Meng Yanan , Jiang Wei 
Published: September 2021

AbstractThe lubrication performance of Cu nanofluid was studied through hot rolling tests and non‐equilibrium molecular dynamics simulation. Results showed that nanofluid with 0.5 wt% Cu nanoparticles possessed the optimal effect in reducing the rolling force, finish rolling thickness and rolled surface roughness. The superior lubrication performance was attributed to the formation of protective tribofilm made of Fe/Cu debris, iron and copper oxides as well as amorphous substances with a thickness of about 24 nm, which avoided the direct contact of steel strip and the roll, thus inhibiting the adhesion wear. Molecular dynamics simulation disclosed that the rolling‐dominated motion pattern of Cu nanoparticles with 74.1% rolling and 25.9% sliding motion contributed to a significant decrease in the friction force. Besides, surface defects including the peaks and valleys were polished and repaired by nanoparticles respectively, thus developing the surface quality of hot rolled products.
Age-0 Silver Carp Otolith Microchemistry and Microstructure Reveal Multiple Early Life Environments and Protracted Spawning in the Upper Mississippi River
Authors: Williams Jesse A. , Whitledge Gregory W. , Knights Brent C. , Bloomfield Nicholas C. , Lamer James T. 
Published: September 2021

Abstract
Silver Carp Hypophthalmichthys molitrix are highly mobile and fecund planktivorous cyprinids that have invaded much of the Mississippi River and are known to alter food webs and compete with native planktivores. In 2016, for the first time, an abundance of age-0 Silver Carp (n = 12,208; 16–231 mm) were captured at many (n = 11) sites upstream of Lock and Dam 19 on the upper Mississippi River. Previous reports were of a few individuals at a few locations; however, effort to capture juveniles of this size was likely less in previous years. Determining the origin, frequency, and timing of the reproductive events that led to this large year-class is important for determining control strategies. We used otolith microstructure and microchemistry from age-0 Silver Carp to estimate timing and frequency of spawning and early life environments of these fish. Hatch dates were determined from the lapillus otoliths of 190 age-0 Silver Carp (16–231 mm), and early life environments were identified from otolith microchemistry for 124 of these fish (64–231 mm). Age-0 Silver Carp were collected from Pools 18 and 19 during July–October 2016 by using a variety of sampling gears. We identified 10 cohorts with hatch dates ranging from May to August 2016 and with main-stem Mississippi River (75%) and tributary (23%) early life signatures. Tributary otolith chemistry signatures were present in all cohorts between May and July (n = 8) but were absent from the August cohorts (n = 2). Our results indicate that tributaries and small tributary streams, in addition to the main-stem river, play an important role in Silver Carp recruitment in areas near the reproductive front, where management actions (e.g., contract removal and deterrents) are often targeted.
Patient safety, quality of care and missed nursing care at a cardiology department during the COVID‐19 outbreak
Authors: Nymark Carolin , von Vogelsang Ann‐Christin , Falk Ann‐Charlotte , Göransson Katarina E 
Published: September 2021

AbstractAimTo evaluate missed nursing care and patient safety during the first wave of the COVID‐19 pandemic at in‐patient cardiology wards.DesignA cross‐sectional design with a comparative approach.MethodRegistered nurses and nurse assistants at a cardiology department were invited to answer the MISSCARE Survey‐Swedish version, and questions on patient safety and quality of care during the COVID‐19 pandemic. The data were compared with a reference sample.ResultsA total of 43 registered nurses and nurse assistants in the COVID‐19 sample and 59 in the reference sample participated. The COVID‐19 sample reported significantly more overtime hours and more absence from work due to illness in comparison with the reference sample. The patient safety and quality of care were perceived significantly worse, 76.7% (N = 33) versus 94.7% (N = 54), and 85.7% (N = 36) versus 98.3% (N = 58, respectively. The COVID‐19 sample reported more missed nursing care in wound care and in basic nursing.
prPred‐DRLF: Plant R protein predictor using deep representation learning features
Authors: Wang Yansu , Xu Lei , Zou Quan , Lin Chen 
Published: September 2021

AbstractPlant resistance (R) proteins play a significant role in the detection of pathogen invasion. Accurately predicting plant R proteins is a key task in phytopathology. Most plant R protein predictors are dependent on traditional feature extraction methods. Recently, deep representation learning methods have been successfully applied in solving protein classification problems. Motivated by this, we propose a new computational approach, called prPred‐DRLF, which uses deep representation learning feature models to encode the amino acids as numerical vectors. The results show that the fused features of bidirectional long short‐term memory (BiLSTM) embedding and unified representation (UniRep) embedding have a better performance than other features for plant R protein identification using a light gradient boosting machine (LGBM) classifier. The model was evaluated using an independent test achieving an accuracy of 0.956, F1‐score of 0.933, and area under the receiver operating characteristic (ROC) curve (AUC) of 0.997. Meanwhile, compared with the state‐of‐the‐art prPred and HMMER method, prPred‐DRLF shows an overall improvement in accuracy, F1‐score, AUC, and recall. prPred‐DRLF is a higher‐performance plant R protein prediction tool based on two kinds of deep representation learning technologies and offers a user‐friendly interface for inspecting possible plant R proteins. We hope that prPred‐DRLF will become a useful tool for biological research. A user‐friendly webserver for prPred‐DRLF is freely accessible at http://lab.malab.cn/soft/prPred‐DRLF. The Python script can be downloaded from https://github.com/Wangys‐prog/prPred‐DRLF.
Feasibility of nasal NO screening in healthy newborns
Authors: Buechel Flurina , Usemann Jakob , Aline A. , Salfeld Peter , Moeller Alexander , Jung Andreas 
Published: September 2021

AbstractBackgroundNasal nitric oxide (nNO) measurement is recommended as a first line screening test for primary ciliary dyskinesia (PCD). While reliable velum‐ and non‐velum‐closure techniques exist for preschool children and older individuals, no data are available for neonates.AimsTo determine feasibility of nNO screening and nNO concentration in healthy newborns in the first week of life.MethodsNasal NO was analyzed in tidal breathing during natural sleep using a CLD‐88 sp NO analyzer (chemoluminescence sensor) and a NIOX MINO (electrochemical sensor). Test success and nNO concentration were determined and compared between the two devices.ResultsNasal NO was measured in 62 healthy neonates within the first week of life. Feasibility of nNO measurement was 100% for at least one nostril and 85.5% for both nostrils using the chemoluminescence device, but significantly lower with the electrochemical device (85.5% and 53.2%; p < .001). Median nNO concentration was 38 ppb (interquartile range, 27–55; range, 9–100) with the ECOMEDICS device and 23 (15–33, 8–59) with the NIOX MINO (p < .001), with a trend towards higher values for older subjects. None of the subjects exceeded nNO levels of 100 ppb.ConclusionMeasurement of nNO using a chemoluminescence device is highly feasible in newborns during natural sleep. However, nNO levels are considerably lower compared to the published data for older individuals and in the range of a PCD reference group of infants between 4 and 8 weeks of age, potentially resulting in a great overlap with subjects with PCD in this age group. Therefore, screening for PCD using nasal NO might not be useful in the first week of life. Upon clinical suspicion, other diagnostic tests such as high‐speed video analysis of the cilia should be applied.
Effect of Me/B‐Powder on the Ignition of High‐Energy Materials
Authors: Korotkikh Alexander G. , Sorokin Ivan V. 
Published: September 2021

AbstractThe study of the ignition characteristics of high‐energy materials (HEMs) is important in solving a number of practical problems related to the assessment of explosion safety, the calculation of transition processes in power installation for various purposes (rocket and space technologies, weapons, pyrotechnics). This paper presents the experimental data on the thermal oxidation of ultrafine powder (UFP) based on Al/B, Ti/B, Ni/B, and Fe/B and the experimental characteristics of the ignition of HEM based on ammonium perchlorate, butadiene rubber, and metal fuel. In the course of processing thermal analysis data, the values of oxidation temperatures, the specific heat effect of the oxidation reaction, and the rate of weight gain of powder during heated at a constant rate of 10 °C/min in air were determined. It was shown that the oxidation of Ti/B and Ni/B UFPs begins at temperature of 490–500 °C, which is 60–70 °C lower than the onset oxidation temperature for boron powder. The use of 15.7 wt.% the mixed UFP based on Al/B, Ti/B, Ni/B or Fe/B in HEM reduces the ignition delay time by 7–50 % compared to boron‐based HEM in the range of heat flux density from 60 to 200 W/cm2. Based on experimental data of the ignition delay time versus the heat flux density, the formal activation energy, the multiplication of the specific heat flux of the reactions by the pre‐exponent and the ignition temperature are calculated which could be used in mathematical modeling of the ignition for composite solid propellant containing metal fuels.
PANNZER—A practical tool for protein function prediction
Authors: Törönen Petri , Holm Liisa 
Published: September 2021

AbstractThe facility of next‐generation sequencing has led to an explosion of gene catalogs for novel genomes, transcriptomes and metagenomes, which are functionally uncharacterized. Computational inference has emerged as a necessary substitute for first‐hand experimental evidence. PANNZER (Protein ANNotation with Z‐scoRE) is a high‐throughput functional annotation web server that stands out among similar publically accessible web servers in supporting submission of up to 100,000 protein sequences at once and providing both Gene Ontology (GO) annotations and free text description predictions. Here, we demonstrate the use of PANNZER and discuss future plans and challenges. We present two case studies to illustrate problems related to data quality and method evaluation. Some commonly used evaluation metrics and evaluation datasets promote methods that favor unspecific and broad functional classes over more informative and specific classes. We argue that this can bias the development of automated function prediction methods. The PANNZER web server and source code are available at http://ekhidna2.biocenter.helsinki.fi/sanspanz/.
Evaluation of different deep convolutional neural networks for detection of broadleaf weed seedlings in wheat
Authors: Zhuang Jiayao , Li Xuehan , Bagavathiannan Muthukumar , Jin Xiaojun , Yang Jie , Meng Wenting , Li Tao , Li Lanxi , Wang Yundi , Chen Yong , Yu Jialin 
Published: September 2021

AbstractBACKGROUNDIn‐field weed detection in wheat (Triticum aestivum L.) is challenging due to the occurrence of weeds in close proximity with the crop. The objective of this research was to evaluate the feasibility of using deep convolutional neural networks for detecting broadleaf weed seedlings growing in wheat.RESULTSThe object detection neural networks, including CenterNet, Faster R‐CNN, TridenNet, VFNet, and You Only Look Once Version 3 (YOLOv3) were insufficient for weed detection in wheat because the recall never exceeded 0.58 in the testing dataset. The image classification neural networks including AlexNet, DenseNet, ResNet, and VGGNet were trained with small (5500 negative and 5500 positive images) or large training datasets (11 000 negative and 11 000 positive images) and three training image sizes (200 × 200, 300 × 300, and 400 × 400 pixels). For the small training dataset, increasing image sizes decreased the F1 scores of AlexNet and VGGNet but generally increased the F1 scores of DenseNet and ResNet. For the large training dataset, no obvious difference was detected between the training image sizes since all neural networks exhibited remarkable classification accuracies with high F1 scores (≥0.96). All image classification neural networks exhibited high F1 scores (≥0.99) when trained with the large training dataset and the training images of 200 × 200 pixels.CONCLUSIONCenterNet, Faster R‐CNN, TridentNet, VFNet, and YOLOv3 were insufficient, while AlexNet, DenseNet, ResNet, and VGGNet trained with a large training dataset were highly effective for detection of broadleaf weed seedlings in wheat. © 2021 Society of Chemical Industry.