bluuebunny/crossref_metadata_2025_split huggingface dataset:
The motor neuron disease mouse model hSOD1-G93A presents a non-canonical profile of senescence biomarkers in the spinal cord
Authors: Torres Pascual , Anerillas Carlos , Encinas Mario , Povedano Monica , Andrés-Benito Pol , Ferrer Isidro , Ayala Victòria , Pamplona Reinald , Portero-Otin Manuel 
Published: February 2021

Abstract
Recent evidence demonstrates a pathological role for senescent cells in Alzheimer’s and Parkinson’s diseases. The present study aimed to show senescence mechanisms including senescence-associated secretory phenotype (SASP) in the familial amyotrophic lateral sclerosis (ALS) transgenic mouse model hSOD1-G93A. We evaluated, as senescence biomarkers, the expression of p16 and p21 with reverse-transcriptase quantitative PCR (RT-qPCR), immunofluorescence (IF), and immunohistochemistry (IHC), as well as the senescence-associated b galactosidase (SA-b-gal) activity in the lumbar spinal cords (LSC) of this model. As SASP markers, we quantified the mRNA levels of Il1a, Il6, Ifna, and Ifnb. Furthermore, we explored if an alteration of alternative splicing is associated with senescence phenomena in this model. Thus, we quantified the Adipor2 cryptic exon inclusion levels, a specific splicing variant repressed by TAR-DNA binding of 43 kDa (TDP-43), using RT-qPCR. Our results show an atypical senescence-profile in LSC from transgenic mice, increasing p16 and p21 mRNA and protein levels in glial cells with a mostly cytoplasmic pattern, without the canonical increase in SA-beta-gal activity in these cells. Consistent with enhanced SASP, there is an increase in Il1a and Il6 expression. Also, TDP-43 splicing activity is compromised in this ALS model, in a direct relationship with the increase in p16 expression. However, senolytic drug Navitoclax -with reported benefits in Alzheimer and Parkinson disease mouse models - does not alter the present model’s disease progression. Navitoclax neither eliminates cells expressing senescence and nor represses the expression of SASP related genes. Globally, our findings support the existence of a non-canonical profile of senescence biomarkers in the LSC of the ALS model hSOD1-G93A.
Selenogenome and AMPK signal insight into the protective effect of dietary Se on chronic heat stress-induced hepatic metabolic disorder in growing pigs
Authors: Liu Yan , Tang Jiayong , He Ying , Jia Gang , Liu Guangmang , Tian Gang , Chen Xiaoling , Cai Jingyi , Kang Bo , Hua Zhao 
Published: February 2021

Abstract
Background:Chronic heat stress (CHS) disrupts hepatic metabolic homeostasis and jeopardizes product quality of pigs. Selenium (Se) may regulate the metabolic state through affect selenoprotein. Thus, we investigate the protective effect of dietary hydroxy-4-methylselenobutanoic acid (HMSeBA) on CHS induced hepatic metabolic disorder in growing pigs, and the corresponding response of selenoprotein. Methods:Forty crossbreed growing pigs were randomly assigned to five groups: control group raised in the thermoneutral environment (22 ± 2 oC) with basal diet; four CHS groups raised in hyperthermal condition (33 ± 2 oC) with basal diet and supplied with 0.0, 0.2, 0.4 and 0.6 mg Se/kg HMSeBA, respectively. The trial lasted 28 days. The serum biochemical, hepatic metabolism related enzyme, protein and gene expression and 25 selenoproteins in liver tissue were determined by real-time PCR, ELISA and western blot.Results:CHS significantly increased the rectal temperature, respiration rate, serum aspartate aminotransferase (AST) and low-density lipoprotein cholesterol (LDL-C) of pigs, up-regulated hepatic heat shock protein 70 (HSP70) and induced lower liver weight, glycogen content, hepatic glucokinase and glutathione peroxidase (GSH-Px). The CHS-induced liver metabolic disorder was associated with the aberrant expression of 6 metabolism-related gene and 11 selenoprotein encoding genes, and decreased the protein abundance of GCK, GPX4 and SELENOS. HMSeBA improved anti-oxidative capacity of liver. 0.4 or 0.6 mg Se/kg HMSeBA supplementation recovered the liver weight, glycogen content and rescue of mRNA abundance of genes related to metabolism and protein levels of GCK. HMSeBA supplementation changed expressions of 15 selenoprotein encoding genes, and enhanced protein expression of GPX1, GPX4 and SELENOS in the liver affected by CHS. CHS alone showed no impact while HMSeBA supplementation increased protein levels of p-AMPKα in the liver. Conclusions:In summary, HMSeBA supplementation beyond nutrient requirement mitigates CHS-induced hepatic metabolic disorder, recovered the liver glycogen content and the processes are associated with the activation of AMPK signal and regulation of selenoproteins in the liver of growing pigs.
DenovoProfiling: a webserver for de novo generated molecule library profiling
Authors: Liu Zhihong , Du Jiewen , Liu Bingdong , Cui Zongbin , Fang Jiansong , Xie Liwei 
Published: February 2021

Abstract
With the advances of deep learning techniques, various architectures for molecular generation have been proposed for de novo drug design. Successful cases from academia and industrial demonstrated that the deep learning-based de novo molecular design could efficiently accelerate the drug discovery process. The flourish of the de novo molecular generation methods and applications created a great demand for the visualization and functional profiling for the de novo generated molecules. The rising of publicly available chemogenomic databases lays good foundations and creates good opportunities for comprehensive profiling of the de novo library. In this paper, we present DenovoProfiling, a webserver dedicated to de novo library visualization and functional profiling. Currently, DenovoProfiling contains six modules: (1) identification & visualization, (2) chemical space, (3) scaffold analysis, (4) molecular alignment, (5) drugs mapping, and (6) target & pathway. DenovoProfiling could provide structural identification, chemical space exploration, drug mapping, and target & pathway information. The comprehensive annotated information could give users a clear picture of their de novo library and could guide the further selection of candidates for synthesis and biological confirmation. DenovoProfiling is freely available at http://denovoprofiling.xielab.net.
Perceptual Factors (Awareness, Attitude) and Positive, Indeterminate and Negative Nurturing Factors Affecting Physical Activity of Pregnant Women Visiting Health-care Centers in Tehran: Examination and Analyses
Authors: Kianfard Leila , SHokravi Farkhonde Amin , Rakhshanderou Sakineh , Niknami Shamsaddin 
Published: February 2021

Abstract
Background: The purpose of this study was to examine the effect of perceptual factors (awareness, attitude) and positive, intermediate and negative nurturing factors on the physical activity of pregnant women visiting health centers in Tehran. Methods: The present research was an applied study in which a quasi-experimental research design (pre-test-post-test) with a control group was employed. The Pregnancy Physical Activity Questionnaire (PPAQ) and a questionnaire designed based on the results of needs assessment and dimensions of the PEN-3 model were used for this study. This study is a randomized control trial (RCT). Results: The results indicated that the intervention based on E-learning has a statistically significant effect on perceptual factors (awareness, attitude) in increasing physical activity of pregnant women in the experimental group. Furthermore, the e-learning-based intervention has a significant effect on increasing physical activity of pregnant women in the experimental group compared to the control group.Conclusion: Based on the research results, it can be said that there is a statistically significant difference between the experimental and control groups in the scores obtained from perceptual factors (awareness, attitude) in the pre-test and the experimental group. Furthermore, it can be said that there is a statistically significant difference between the experimental and control groups in the scores obtained from perceptual factors (awareness, attitude) in the pre-test and the experimental group.
Exploring ligand binding pathways on proteins using hypersound–accelerated molecular dynamics
Authors: Araki Mitsugu , Matsumoto Shigeyuki , Bekker Gert-Jan , Isaka Yuta , Sagae Yukari , Kamiya Narutoshi , Okuno Yasushi 
Published: February 2021

Abstract
Capturing the dynamic processes of biomolecular systems in atomistic detail remains difficult despite recent experimental advances. Although molecular dynamics (MD) techniques enable atomic-level observations, simulations of “slow” biomolecular processes (with timescales longer than submilliseconds) are challenging, due to current computer speed limitations. Therefore, we developed a new method to accelerate MD simulations by high-frequency ultrasound perturbation. The binding events between the protein CDK2 and its small-molecule inhibitors were nearly undetectable in 100-ns conventional MD, but the new method successfully accelerated their slow binding rates by up to 10–20 times. The accelerated MD simulations revealed a variety of microscopic kinetic features of the inhibitors on the protein surface, such as the existence of different binding pathways to the active site. Moreover, the simulations allowed estimating the corresponding kinetic parameters and exploring other druggable pockets. This method can thus provide deeper insight into the microscopic interactions controlling biomolecular processes.
Towards Improving Edge Quality using Combinatorial Optimization and a Novel Skeletonize Algorithm
Authors: Arnold Marvin , Hattab Georges , Speidel Stefanie 
Published: February 2021

Abstract
Background: Object detection and image segmentation of regions of interest provide the foundation for numerous pipelines across disciplines. Robust and accurate computer vision methods are needed to properly solve image-based tasks. Multiple algorithms have been developed to solely detect edges in images. Constrained to the problem of creating a thin, one-pixel wide, edge from a predicted object boundary, we require an algorithm that removes pixels while preserving the topology. Thanks to skeletonize algorithms, an object boundary is transformed into an edge; contrasting uncertainty with exact positions.Methods: To extract edges from boundaries generated from different algorithms, we present a computational pipeline that relies on: a novel skeletonize algorithm, a non-exhaustive discrete parameter search to find the optimal parameter combination of a specific post-processing pipeline, and an extensive evaluation using three data sets from the medical and natural image domains (kidney boundaries, NYU-Depth V2, BSDS 500). While the skeletonize algorithm was compared to classical topological skeletons, the validity of our post-processing algorithm was evaluated by integrating the original post-processing methods from six different works.Results: Using the state of the art metrics, precision and recall based Signed Distance Error (SDE) and the Intersection over Union bounding box (IOU-box), our results indicate that the SDE metric for these edges is improved up to 2.3 times.Conclusions: Our work provides guidance for parameter tuning and algorithm selection in the post-processing of predicted object boundaries.
Angular and Linear Speed Cells in the Parahippocampal Circuits
Authors: Spalla Davide , Treves Alessandro , Boccara Charlotte 
Published: February 2021

Abstract
An essential role of the hippocampal region is to integrate information to compute and update representations. How this transpires is highly debated. Many theories hinge on the integration of self-motion signals and the existence of continuous attractor networks (CAN). CAN models hypothesise that neurons coding for navigational correlates – such as position and direction – receive inputs from cells conjunctively coding for position, direction and self-motion. As yet, such conjunctive coding had not been found in the hippocampal region. Here, we report neurons coding for angular and linear velocity, distributed across the medial entorhinal cortex, the presubiculum and the parasubiculum. These self-motion neurons often conjunctively encoded position and/or direction, yet lacked a structured organisation, calling for the revision of current CAN models. These results offer insights as to how linear/angular speed – derivative in time of position/direction – may allow the updating of spatial representations, possibly uncovering a generalised algorithm to update any representation.
Clinical Features and Development of Sepsis in Klebsiella Pneumoniae Infected Liver Abscess Patients: A Retrospective Analysis of 135 Cases
Authors: Li Shixiao , Yu Sufei , Peng Minfei , Qin Jiajia , Xu Chunyan , Qian Jiao , He Minmin , Zhou Peng 
Published: February 2021

Abstract
Background

Klebsiella pneumoniae is a primary pathogen of pyogenic liver abscess (PLA). However, little data are available on combination with sepsis. In this study, we aimed to evaluate the clinical characteristics and prognostic differences of PLA patients with sepsis.
Methods

This retrospective cohort study was conducted to investigate 135 patients with confirmed Klebsiella pneumoniae-caused liver abscesses (KPLA) from a tertiary teaching hospital, from 2013 to 2019. The patients were divided into two groups based on comorbidity with sepsis. The demographic characteristics, clinical features as well as laboratory and microbiologic findings was analyzed.
Results

The 135 patients were analyzed, with a mean age of 60.9 ± 12.7 years, and 59.3% were men. Among them, 37/135 (27.4%) had comorbid sepsis and mortality rate was 1.5%. The most common symptom was fever (91.1%). KPLA patients with sepsis had a significantly higher proportion of frailty, diarrhea, fatty liver, chronic renal insufficiency, and hepatic dysfunction (p < 0.05). Antibiotic therapy and percutaneous drainage were most frequently used. The incidences of sepsis shock, acute respiratory distress syndrome was higher in the sepsis group compared to the non-sepsis group. As for metastatic infections, the lung was the most common site. Respiratory symptoms were found in 11 patients, and endophthalmitis coexisted in 4 patients, and meningitis occurred in 1 patient.
Conclusion

Our findings emphasize that KPLA patients combined with and without sepsis have different clinical features, but KPLA patients with sepsis have a high rate of complications and metastatic infections. Further surveillance and control of septic spread is essential in KPLA patients.
Real-time automatic identification ear diseases using a deep learning model
Authors: Zeng Xinyu , Jiang Zifan , Luo Wen , Li Honggui , Li Hongye , Li Guo , Shi Jingyong , Wu Kangjie , Liu Tong , Lin Xing , Wang Fusen , Li Zhenzhang 
Published: February 2021

Abstract
Early detection and appropriate medical treatment is of great use for ear disease. However, a new diagnostic strategy is necessary in the absence of experts and relatively low diagnostic accuracy, in which deep learning plays an important role. This paper puts forward a mechanic learning model which uses abundant otoscope image data gained in the clinical cases in order to achieve automatic diagnosis of ear diseases in real time. A total of 20,542 endoscopic images were employed to train nine common deep convolution neural networks. According to the characteristics of eardrum and external auditory canal, eight kinds of ear diseases were classified, involving the majority of ear diseases, such as normal, Cholestestoma of middle ear, Chronic suppurative otitis media, External auditory cana bleeding, Impacted cerumen, Otomycosis external, Secretory otitis media, Tympanic membrane calcification. After we evaluate these optimization schemes, two best performance models are selected to combine the ensemble classifiers with real-time automatic classification. Based on accuracy and training time, we choose a transferring learning model based on DensNet-BC169 and DensNet-BC1615, getting a result that each model has obvious improvement by using these two ensemble classifiers, and has average accuracy of 95.59%. Considering the dependence of classifier performance on data size in transfer learning, we evaluate the high accuracy of the current model that can be attributed to large databases. Current studies are unparalleled regarding disease diversity and diagnostic precision. The real-time classifier trains the data under different acquisition conditions, which is suitable for the real cases. According to this study, in the clinical case, deep learning model is of great use in early detection and remedy of ear diseases.
The ameliorative role of ascorbic acid against blood disorder, immunosuppression and oxidative damage of oxytetracycline in rainbow trout (Oncorhynchus mykiss)
Authors: Moradi Saeed , javanmardi sina , Gholamzadeh Pooria , Tavabe Kamran Rezaei 
Published: February 2021

Abstract
This experiment aimed to determine the possible beneficial effects of dietary ascorbic acid (AA) on hematological indices, immune responses, and antioxidative capacity of Oncorhynchus mykiss treated with antibiotic oxytetracycline (OTC). 150 fish were divided evenly among five experimental groups (30 fish of each, in 3 replicates) receiving diets containing OTC (0 and 100 mg per kg fish weight) and AA (100, 200, 400 and 800 mg per kg fish diet) for 28 days. Treatments include group A or control (100 mg AA without OTC), group B (100 mg AA with OTC), group C (200 mg AA with OTC), group D (400 mg AA with OTC), and group E (800 mg AA with OTC). The results obtained showed that the hematological indices (red blood cells, white blood cells, hematocrit, hemoglobin and neutrophils), immunological parameters (plasma lysozyme, plasma complement and skin mucus alkaline phosphatase activities), and antioxidant enzymes activities (superoxide dismutase and catalase) were significantly decreased by OTC in O. mykiss fed control diet (P < 0.05). The results also revealed that OTC significantly increased the activity of biochemical enzymes (aspartate aminotransferase, alanine aminotransferase and alkaline phosphatase) in the plasma of O. mykiss fed control diet (P < 0.05). However, in comparison to the control diet, feeding fish with higher amounts of AA (400 and 800 mg/kg diet) significantly restored the hematological, immunological, and antioxidative responses in OTC treated groups (p < 0.05). These findings show that the dietary supplementation of AA at 400 or 800 mg/kg diet is beneficial in relieving O. mykiss from OTC-induced oxidative stress and immunosuppression.
Economic Growth and Carbon Emission Nexus: A Survey
Authors: Li Rongrong , Wang Qiang , Zhan Lina 
Published: February 2021

Abstract
Developing better mitigation strategy requires a comprehensive understanding the relationship between economic growth and carbon emission. Through a literature review, we summarized the following five relationship reported in existing studies: (i) a single causal from economic growth to carbon emission, (ii) a single causal from carbon emissions to economic growth, (iii) a bidirectional causality, (iv) the Environmental Kuznets Curve, (v) no obvious relationship. And then, we further quantify contribution of countries, institutes, authors, investigate research hotspot, and explore future research directions of carbon emissions and economic growth nexus using web of science data from 2001-2019. We find regardless of the total number of publications, institutions and highly cited papers, China research on carbon emissions and economic growth has always been among the best. By analyzing the cooperation relationship between countries and institutions, more than half of the institutions are more inclined to cooperate with institutions in their own countries rather than abroad. Through keyword hotspot analysis and keyword trend analysis, we uncovered the future research directions and hotspots of carbon emissions and economic growth: ①What is the relationship between carbon emissions, economic growth and energy consumption. ②The efforts of China in carbon reduction and economic growth. ③How to reduce carbon dioxide emissions while ensuring stable economic growth. ④The research on carbon emissions and economic growth in the fields of urbanization, financial development, renewable energy, and climate change.
Heavy Metals Contamination of River Water and Sediments in The Mangrove Forest Ecosystems in Bangladesh: A Consequence of Oil Spill Incident
Authors: Choudhury Tasrina Rabia , Acter Thamina , Uddin Nizam , Kamal Masud , Chowdhury A.M. Sarwaruddin , Rahman M. Safiur 
Published: February 2021

Abstract
Oil spillage is one of the common pollution events of global water-soil ecosystems. A comprehensive investigation on heavy metals pollution of surface water and sediments was conducted after oil spill incident in Sela River and its tributaries of the Sundarbans mangrove forest ecosystems, Bangladesh. Water and sediment samples were collected from the preselected sampling points in Sela River, and the elemental (Pb, Cd, Cr, Co, Cu, Ni, Fe, As, Hg, Mn, Zn, Ca, Mg, Na, and K) analysis was done using atomic absorption spectrometer (AAS). This study revealed that the descending order for the average concentration of the studied elements were found to be Mg > Co > Na > Ni > K > Ca > Pb > Fe > Mn > Cr > Cd > Zn > Cu respectively, while As and Hg in water samples were found to be below detection limit (BDL). However, some of the toxic elements in the Sela River water samples were exceeded the permissible limit set by the World Health Organization (WHO) with a descending order of Co > Cd > Pb > Ni respectively. Based on the water quality index (WQI), metal pollution index (MPI), and metal quality index (MI), the Sela River water is not suitable for drinking but may be used for irrigating agricultural and vegetable crops. On the other hand, elemental concentration in the sediment samples were found to be the following descending order of Fe > Mg > Na > K > Ca > Mn > Zn > Cr > Cu > Pb > As > Cd respectively. Several pollution assessment indices: contamination factor (Cf), degree of contamination (Cd), modified degree of contamination (mCd), pollution load (PLI), enrichment factor (EF), geo-accumulation (Igeo) indices were followed to assess the sediment systems pollution in the study area. Considering sediment quality indices, this study revealed that the river sediment had higher contamination factor (Cf) values for Cd, moderate values for Pb, Cr, Cu, Zn, Mg, and As, and low values for Mn, Fe, Ca, Na, and K. Among the studied heavy metals, Cd content was highest in both water and sediment samples, which confirming that Cd, insoluble or suspended form, was more likely to be strongly deposited and bound in sediments from water. Principal component and correlation analyses suggested that the sources of heavy metals pollution were mainly anthropogenic along with the geogenic sources in the study area.