bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of sample preparation methods on single cell X-ray microscopy and light elemental analysis evaluated by combined Low Energy X-ray Fluorescence, STXM and AFM
Authors: Merolle Lucia , Pascolo Lorella , Zupin Luisa , Parisse Pietro , Bonanni Valentina , Gariani Gianluca , Kenig Sasa , Bedolla Diana , Crovella Sergio , Ricci Giuseppe , Iotti Stefano , Malucelli Emil , Kourousias George , Gianoncelli Alessandra 
Published: July 2022

Abstract
Background X-ray Fluorescence (XRF) microscopy has become a widespread method to observe the location of elemental components within cell. Although it is becoming a widely used technique in many laboratories and synchrotron facilities, sample preparation for this microscopy remains one of the main concerns. Indeed, the information available to researchers on how to treat samples are insufficient and not clear, sometimes leading to waste of time and/or compromising the success of the experiment. It is indeed recognised that a correct sample preparation is the first important step in performing a successful and meaningful analysis, i.e. achieving a condition in which the cells are closer to their physiological state. The majority of the commonly used protocols of cell fixation for X-ray microscopy have been mainly imported and adapted from immunocytochemistry. Therefore, many fixation methods are described, but none of them have been tested in a systematic way and declared the most eligible for synchrotron-based X-ray microscopy. Methods HEC-1-A endometrial cell line, human spermatozoa and Human Embryonic Kidney HEK-293 cell line were chosen as cellular models; all type of cells were fixed using both organic solvents and cross-linking methods, as follow: 70% ethanol, paraphormaldehyde at 3.7 % and 2%; in addition HEK-293 cells were also subjected to methanol/acetone treatment and to cryofixation. Comparison among the different fixation methods was conducted by coupling Low Energy X-ray fluorescence (LEXRF), with Scanning Transmission X-ray Microscopy (STXM) and Atomic Force Microscopy (AFM). Results Organic solvents induce greater cellular dehydration, with the maximal impact on the distribution and depletion of the diffusive elements. Paraphormaldehyde seems to be able to provide robust and replicable data. Finally, the cryofixed cells give the best results both in terms of morphology and elemental content. Conclusion Although cryofixation appears to be the most appropriate method as it allows the cell to be kept closer to physiological conditions, it has some technical limitations. PFA, when used at conventional concentration of 3.7%, is also an excellent alternative method for X-ray microscopy.
Tyrosine phosphorylation of CARM1 promotes its enzymatic activity and alters its target specificity
Authors: Itonaga Hidehiro , Mookhtiar Adnan , Greenblatt Sarah , Liu Fan , Martinez Concepcion , Grozovsky Renata , Bilbao Daniel , Rains Masai , Hamard Pierre-Jacques , Sun Jun , Umeano Afoma , Duffort Stephanie , Chen Chuan , Man Na , Mas Gloria , Schurer Stephan , Nimer Stephen 
Published: July 2022

Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1) is overexpressed in cancer, and it has emerged as an important target in acute myeloid leukemia and other hematologic malignancies. Janus kinase 2 (JAK2), that is activated by mutation in a variety of myeloid malignancies, can dictate chromatin structure via multiple effects. Here, we find that the hyperactivated JAK2-V617F mutant kinase phosphorylates CARM1, increasing its methyltransferase activity and altering its target specificity. Phospho-CARM1 binds and methylates the RUNX1 transcription factor, and the asymmetric dimethylation of R223 and R319 in RUNX1 is lost in engineered to express only non-phosphorylatable CARM1 mutant proteins in JAK2-V617F+ cell lines. The decreased CARM1 activity found in these cell lines impairs cell-cycle progression and induces apoptosis. We have established a link between activated JAK2 and CARM1 activity, and demonstrate that dual targeting of JAK2 and CARM1 is more effective than monotherapy in phospho-CARM1+ cell lines.
A Light-weighted Network Traffic Intrusion Detection Method Based on Grid-Density Peak Clustering
Authors: Zhang Zedong , Wei Songjie 
Published: July 2022

Abstract
The malicious traffic generated by attack behaviors shows similarity in character distribution, and specific types of malicious traffic also have differences in spatial distribution due to their formation methods and attack methods. Aiming at these two characteristics, we propose a network traffic intrusion detection method based on grid-density peak clustering(GDPC). It uses grid clustering to form clusters, and then uses the density peak clustering algorithm to distinguish different local densities belong the clusters. We apply the Autoencoder to reduce the dimensionality of the data. After learning and recording the malicious traffic distribution, our saved data only contains less than 500 records of cluster information, which is light-weighted. In the experiment on the CIC-IDS2018 dataset, the classification accuracy of six types of malicious traffic is not less than 95%, and the classification accuracy of unknown malicious traffic has reached 80%. Experiment shows that our proposed method has smaller time complexity than other common cluster algorithms, and our GDPC is not only effective in the known malicious traffic but also has better identification ability for unknown malicious traffic, which is a feasible intrusion detection method.
Enhancing Context-aware Recommendation using Trust-based Contextual Attentive Autoencoder
Authors: S ABINAYA , A SHERLY ALPHONSE , S ABIRAMI , M.K. KAVITHADEVI 
Published: July 2022

Abstract
Context-aware recommender systems (CARS) are intended primarily to consider the circumstances under which a user encounters an item to provide better-personalized recommendations. Users acquire point-of-interest, movies, products, and various online resources as suggestions. Classical collaborative filtering algorithms are shown to be satisfactory in a variety of recommendation activities processes, but cannot often capture complicated interactions between item and user, along with sparsity and cold start constraints. Hence it becomes a surge to apply a deep learning-based recommender model owing to its dynamic modeling potential and sustained success in other fields of application. In this work, a Trust-based Attentive Contextual Denoising Autoencoder(TACDA) for enhanced Top-N context-aware recommendation is proposed. Specifically, the TCADA model takes the sparse preference of the user that is integrated with trust data as input into the autoencoder to prevail over the cold start and sparsity obstacle and efficiently accumulates the context condition into the model via attention framework. Thereby, the attention technique is used to encode context features into a latent space of the user's trust data that is integrated with their preferences, which interconnects personalized context circumstances with active user's choice to deliver recommendations suited to that active user. Experiments conducted on Epinions and Caio dataset make obvious the efficiency of the TACDA model persistently outperforms the state-of-the-art methods.
Defining post-acute COVID-19 syndrome (PACS) by an epigenetic biosignature in peripheral blood mononuclear cells
Authors: Nikesjö Frida , Sayyab Shumaila , Karlsson Lovisa , Apostolou Eirini , Rosén Anders , Hedman Kristofer , Lerm Maria 
Published: July 2022

Abstract
Post-Acute COVID-19 Syndrome (PACS) has been defined as symptoms persisting after clearance of a COVID-19 infection. We have previously demonstrated that alterations in DNA methylation (DNAm) status persists in individuals who recovered from a COVID-19 infection, but it is currently unknown if PACS is associated with epigenetic changes. We compared DNAm patterns in patients with PACS with those in controls and in healthy COVID-19 convalescents and found a unique DNAm signature in PACS patients. This signature unravelled modified pathways that regulate angiotensin II and muscarinic receptor signalling and protein-protein interaction networks that have bearings on vesicle formation and mitochondrial function.
Using Electrical Resistivity Tomography (ERT) to assess the effectiveness of capping in old unlined landfills
Authors: Morita Alice K. M. , Pelinson Natalia S. , Wendland Edson 
Published: July 2022

Abstract
Engineered capping systems are efficient tools for the safety concept for landfills and contaminated land, consisting of multilayer barriers installed at the top of the deposited waste, even years after its closure. The efficiency of such systems is closely associated with avoiding rainwater infiltration into the waste body, a process that can be assessed and monitored with geophysical methods, such as Electrical Resistivity Tomography (ERT). A surface geomembrane capping of approximately 900m² was installed over an abandoned unlined landfill in southeastern Brazil and ERT surveys were adopted to assay the effectiveness of the intervention measure. It was possible to verify significantly more resistive regions below the geomembrane and an increase in conductivity values only at approximately 6 m, at the groundwater level of the area. Thus, the reduction of rainwater input possibly, even in the short term, reduces the moisture content and prevents the formation of leachate sheets in unlined landfills, leading the deposit to be more isolated from the surroundings. Lateral flow affected distances as far as 2.5 m from the capping borders, showing that about 70% of the capped area was effectively isolated from the rainfall infiltration. Therefore, capping contributed to reducing leachate production and can be considered an effective method for mitigating impacts from old unlined landfills.
The Quantum Realization of Image Linear Gray Enhancement
Authors: Liu Kai , Li Hai-Sheng 
Published: July 2022

Abstract
Linear gray enhancement is a spatial domain image enhancementtechnique commonly used in classical computers, mainly including image negative, image contrast stretching, and piecewise linear gray transformation. Inorder to realize these three linear gray enhancement techniques in the quantumcomputers, this paper proposes three types of linear gray transformationschemes for quantum images based on the generalized model of novel enhancedquantum image representation(GNEQR), and the quantum circuits that realizethese three transformation methods are constructed according to theschemes. The proposed circuits take advantage of efficient quantum arithmeticoperations and parallel Controlled-NOT modules to factor classical transformationsinto basic unitary operators such as the Controlled-NOT gates andthe Toffoli gates. The results show that the linear gray enhancement algorithmfor quantum images is better than the classical algorithm in both spatialcomplexity and time complexity.
Impact of age on long-term mortality and net survival benefit of radiotherapy for early-stage follicular lymphoma from the SEER database (2000-2015)
Authors: Li Ye-Xiong , Zhong Qiu-Zi , Liu Ye , Wu Yunpeng , Liu Xin , Chen Si-Ye , Chen Bo , Su Fei , Li Gao-Feng , Xu Yonggang , Liu Lipin , Chen Fan , Qi Shu-Nan 
Published: July 2022

Abstract
Background: The effect of age on long-term mortality and net survival benefit of radiotherapy (RT) for early-stage follicular lymphoma (FL) was not evaluated. Methods: 8,803 patients with early-stage FL in the Surveillance, Epidemiology, and End Results (SEER) database (2000-2015) were identified for this study. Primary therapy included RT (27.0%), chemotherapy (CT, 29.3%), observation (24.1%), and other/unknown treatments (19.6%). Inverse probability of treatment weighting (IPTW) was conducted to balance the treatment arms. Relative survival (RS), the standardized mortality ratio (SMR), and transformed Cox regression were used to compare survival differences between treatments.Results: The risk of dying from FL and other causes varied over time, dependent of patient age. RT had significantly higher 10-year OS (77.2%) and RS (96.1%), but lower SMR (1.77), compared with CT (65.2%; 82.6%; 2.92; P<0.001), observation (65.5%; 90.1%; 2.18; P<0.001), and other/unknown treatments (66.5%, P<0.001; 89.9%, P=0.136; 2.05, P<0.001). RT was an independent predictor of better OS and RS in multivariate analyses (P<0.001). No significant interaction between age and RT was identified for RS (Pinteraction=0.305) or OS (Pinteraction= 0.272), indicating similar survival benefits across all-ages patients.Conclusions: RT was associated with long-term OS and net survival benefits in early-stage FL.
The effect of placental transfusion on hemodynamics in premature newborns: a randomized controlled trial
Authors: Farag Marwa Mohamed , Thabet Mohamed Alaa Eldin Hassan , Abd-Almohsen Ali Mohamed , Mohammed Heba Edris Abu Deif 
Published: July 2022

Abstract
Introduction Despite of growing evidence of the beneficial effects of placental transfusions techniques, no available sufficient data about their effects on vulnerable hemodynamics and myocardium of premature infants.purposeStudy ventricular functions and hemodynamics after different techniques of placental transfusions techniques, Delayed cord clamping (DCC), Cut cord milking (C-UCM), and intact cord milking (I-UCM).methods: Infants delivered whether by Cs-section or vaginal delivery were randomly assigned to undergo C- UCM (20-30cm), I- UCM (3-4 strippings), and DCC (30–60 seconds). Functional echocardiography was done at 24 hour and 72-96 hours of life. This trial was registered in the clinical trial gov NCT04811872.ResultsOf a total 196 preterm infants ≤32 weeks were enrolled in the study 57 infants were eligible and randomly assigned to the three groups. neonates randomly assigned to DCC had significantly higher superior vena cava flow and lower right ventricular systolic function in the first 24 hours of life. This finding vanished at day 3. Neonates undergone different methods of placental transfusions had similar hemoglobin, admission temperature, and mean blood pressure in the first 24 hours of life. Conclusion Placental transfusion techniques may benefit premature neonates ≤32 weeks, but they have been shown to alter their hemodynamics and myocardial function.
Newton’s law of universal gravitation in ocean dynamics
Authors: Chu Peter C. 
Published: July 2022

Abstract
Oceanographers simplify the Newton’s law of universal gravitation, treat the solid Earth as a point mass located at the Earth’s center, and call it the “gravitational force”. Combination of such defined “gravitational force” with the centrifugal force leads to the effective gravity (geff). This simplification is not feasible because the mass distribution inside the solid Earth is nonuniform. The solid Earth cannot be treated as a point mass. The true gravitational force is the volume integration over all the point masses inside the solid Earth on the point mass in oceans. It leads to the true gravity g. The gravity disturbance vector, δg = g – geff, is a major variable in geodesy and quantified by gravity models with observations. On the contrary, δg is totally neglected in oceanography. After replacement of geff by g (i.e., including δg) in ocean dynamics, new hydrostatic balance, geostrophic balance, thermal wind relation, 1½ layer model with rigid lid, and combined Sverdrup-Stommel-Munk equation are obtained in the effective-geopotential coordinates. Depth dependent nondimensional D-number and depth independent (B, F1, F2) numbers are defined to identify the importance of gravity disturbance vector versus the traditional forcing terms in the thermal wind relation, 1½ layer model, and combined Sverdrup-Stommel-Munk equation, and calculated from three publicly available datasets in climatological, geodetic, and oceanographic communities. Their evidently non-small values demonstrate the urgency to replace geff by g in ocean dynamics.
SLC45A2 Germilne Variants in Colombian Population with Melanoma
Authors: Garcia-Garay Diana , Parra-Tovar David , Gutierrez-Castañeda Luz D 
Published: July 2022

Abstract
The SLC45A2 gene, located at chromosome 5p13.2, is involved in melanin biosynthesis. Single Nucleotide Variant (SNVs) in this gene have been associated with normal variation of skin, eye and hair color in human population. Additionally, there are SNVs like L374F (C/T) and E272K (c/G) that are associated with protection against melanoma. In this project, in a survey of Bogota, Colombia people, both SNVs mentioned before were evaluated in a case and controls study. DNA samples were isolated with commercial kits, prior signing of the informed consent. The genotypification was done through RT-PCR HRM technique. We found that 19% of the individuals were classified as phototype II, 70% phototype III and 11% phototype IV. In addition, 80% of the subjects had brown eyes and dark-brown hair. Both SNVs were in Hardy-Weinberg equilibrium. Allelic frequencies were C=0.644, T=0.356 and C=0.756, G=0.244 for E272K and L374F, respectively. None of the variants analyzed had association with melanoma developing. Haplotype analysis adjusted by sex and phototype shown a higher risk of having melanoma with individuals having CG genotype, OR:2.75 (IC 95% 1.22-6.22 p=0.021). The frequencies found for the variants of SLC45A2 gene in this project is accord with many other studies done with Latin-American population, were phototype II and III are the prevalent in people.
Gender-specific changes of the gut microbiome correlate with tumor development in murine models of pancreatic cancer
Authors: Kaune Tom , Griesmann Heidi , Theuerkorn Katharina , Hämmerle Monika , Laumen Helmut , Krug Sebastian , Plumeier Iris , Kahl Silke , Junca Howard , Borges Luiz , Michl Patrick , Pieper Dietmar H. , Rosendahl Jonas 
Published: July 2022

Abstract
Background
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with dismal outcome. Recently, microbiome signatures were demonstrated to influence disease progression or to correlate with PDAC development. To improve understanding of sequential microbiome changes during PDAC development we comprehensively and longitudinally analyzed appropriate mouse models of murine pancreatic carcinogenesis (KC mice recapitulating preinvasive PanIN formation, as well as KPC mice recapitulating invasive PDAC) during early tumor development and subsequent tumor progression.
Results
Diversity and community composition were analyzed depending on factors genotype, age, and gender. All three analyzed factors significantly influenced the overall community composition and diversity. Most prevalent genera (59 of 74) were affected by at least one factor. Bacteroidales were typically affected by all three factors whereas Erysipelotrichiaceae were prone to be influenced by gender and Proteobacteria were mainly affected by genotype. Concerning genotype effects, communities in cancer models differed substantially from communities in Pdx-1-Cre control mice, with KC mice harboring preinvasive PanIN lesions often adopting intermediate stages. Genotype clearly influenced microbiota composition at the genus, but to a lesser extent at higher phylogenetic levels. Ten genera/genus level taxa were influenced by all three factors. Here, Bacteroides, Prevotella and Parabacteroides showed similar effects with increasing abundances during ageing, from Pdx1-Cre over KC to KPC mice and, higher levels were observed in female compared to male mice. In few cases, a significant interaction between factors were observed. A genotype effect on the abundance of Parabacteroides and Prevotella was depicted mainly in female mice. Analysis of species level taxa indicated Bacteroides spp to behave similarly, however, species of other genera displayed very distinct characteristics.
Conclusion
Both mouse models demonstrated concordant abundance changes of several genera influenced by one or more of the investigated factors. Abundance was significantly impacted by gender, highlighting the need to further elucidate the impact of gender differences. Distinct behavior on species level probably enabled to react differently to environmental changes. The findings underline the importance of the microbiome in PDAC development and indicate that microbiological screening of patients at risk and targeting the microbiome in PDAC development may be feasible in future.
Anemoside B4 alleviates neuropathic pain through inhibiting inflammation
Authors: Zhao Minghong , Li Haiyan , Yang Tong , Qiu Chong , Lu Tianming , Wang Qixin , Guo Qiuyan , Wang Jigang 
Published: July 2022

Abstract
Research background: Neuropathic pain (NP), which is caused by nerve injury or other diseases damages patients’ life quality seriously. Anemoside B4 (AB4) is the active component of triterpenoid saponins in traditional Chinese medicine Pulsatilla, with prominent effects of anti-inflammation and analgesia. However, its pharmacological mechanisms acting on NP remains unclear.Methods: The analgesia effects of AB4 against NP were investigated on the basis of the spinal nerve ligation (SNL) rat model by detecting the thresholds of mechanical pain and response times to cold stimulate. The key targets of AB4 acting on NP is selected based on the transcriptomic analysis, and their relative expression level was further verified by RT-qPCR. The binding sites of AB4 to the targets were searched by molecular docking. The regulation effects of AB4 on cytokines including IL-1β, IL-6 and TNF-α in the serum of SNL rats were tested by ELISA.Results: In contrast with normal rats, the thresholds of mechanical pain was decreased, whereas the response times to cold stimulate was increased in SNL rats, and the above phenomenon was reversed by AB4 treatment. The transcriptome sequencing results revealed that AB4 mainly regulated the serotonergic synapse, glutamatergic synapse, GABAergic synapse, dopaminergic synapse and cholinergic synapse pathways which was closely related to neuroinflammation and central pain sensitization. Further overlap analysis selected five genes in the pathway, named Alox15, Gngt1, Gngt2, Gnb3 and Tph1 respectively. Further RT-qPCR confirmed that the gene expression of them was down-regulated in the hippocampus of SNL rats, and up-regulated by AB4 administration. According to the molecular docking results, Anemoside B4 forms tightly bonded hydrogen bonding forces with key target molecules of the synaptic pathway, including Alox15, Gngt1, Gngt2, Gnb3 and Tph1. In addition, AB4 treatment also decreased the contents of inflammatory cytokines IL-1β, IL-6 and TNF-α in the serum of SNL rats.Conclusion: Our findings suggested the possibility of AB4 as a promising candidate for NP treatment by inhibiting inflammation.