bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Dynamics Study on Tip-Based Nanomachining: A Review
Authors: Li Zihan , Yan Yongda , Wang Jiqiang , Geng Yanquan 
Published: October 2020

AbstractTip-based nanomachining (TBN) approaches has proven to be a powerful and feasible technique for fabrication of microstructures. The molecular dynamics (MD) simulation has been widely applied in TBN approach to explore the mechanism which could not be fully revealed by experiments. This paper reviews the recent scientific progress in MD simulation of TBN approach. The establishing methods of the simulation model for various materials are first presented. Then, the analysis of the machining mechanism for TBN approach is discussed, including cutting force analysis, the analysis of material removal, and the defects analysis in subsurface. Finally, current shortcomings and future prospects of the TBN method in MD simulations are given. It is hopeful that this review can provide certain reference for the follow-up research.
Hierarchical Porous MoS2/C Nanospheres Self-Assembled by Nanosheets with High Electrochemical Energy Storage Performance
Authors: Liu Hongdong , Lin Ye , Zhang Lei 
Published: October 2020

AbstractTo overcome the deficiency of the volume expansion of MoS2as the anode material for lithium-ion batteries (LIBs), an effective strategy was developed to design hierarchical porous MoS2/carbon nanospheres via a facile, easy-operated hydrothermal method followed by annealing. FESEM and TEM images clearly showed that nanospheres are composed of ultra-thin MoS2/C nanosheets coated with carbon layer and possess an expanded interlayer spacing of 0.98 nm. As anodes for LIBs, MoS2/carbon nanospheres deliver an initial discharge capacity of 1307.77 mAh g−1at a current density of 0.1 A g−1. Moreover, a reversible capacity of 612 mAh g−1was obtained even at 2 A g−1and a capacity retention of 439 mAh g−1after 500 cycles at 1 A g−1. The improved electrochemical performance is ascribed to the hierarchical porous structure as well as the intercalation of carbon into lattice spacing of MoS2, which offers fast channels for ion/electron transport, relieves the influence of volume change and increases electrical conductivity of electrode. Meanwhile, the expanded interlayer spacing of MoS2in MoS2/C can decrease the ion diffusion resistance and alleviate the volumetric expansion during discharge/charge cycles.
Proteomic profiling reveals differentially expressed proteins associated with amylose accumulation during rice grain filling
Authors: Zhang Hengdong , Chen Jiana , Shan Shuanglü , Cao Fangbo , Chen Guanghui , Zou Yingbin , Huang Min , Abou-Elwafa Salah F. 
Published: October 2020

Abstract
Background
Amylose accumulation in rice grains is controlled by genetic and environmental factors. Amylose content is a determinant factor of rice quality in terms of cooking and eating. Great variations in amylose content in indica rice cultivars have been observed. The current study was to identify differentially expressed proteins in starch and sucrose metabolism and glycolysis/gluconeogenesis pathways and their relationships to amylose synthesis using two rice cultivars possess contrasting phenotypes in grain amylose content.

Results
Synthesis and accumulation of amylose in rice grains significantly affected the variations between rice cultivars in amylose contents. The high amylose content cultivar has three down-regulated differentially expressed proteins, i.e., LOC_Os01g62420.1, LOC_Os02g36600.1, and LOC_Os08g37380.2 in the glycolysis/gluconeogenesis pathway, which limit the glycolytic process and decrease the glucose-1-phosphate consumption. In the starch and sucrose metabolic pathway, an up-regulated protein, i.e., LOC_Os06g04200.1 and two down-regulated proteins, i.e., LOC_Os05g32710.1 and LOC_Os04g43360.1 were identified (Figure 4). Glucose-1-phosphate is one of the first substrates in starch synthesis and glycolysis that are catalyzed to form adenosine diphosphate glucose (ADPG), then the ADPG is catalyzed by granule-bound starch synthase I (GBSS I) to elongate amylose.

Conclusions
The results indicate that decreasing the consumption of glucose-1-phosphate in the glycolytic process is essential for the formation of ADPG and UDPG, which are substrates for amylose synthesis. In theory, amylose content in rice can be regulated by controlling the fate of glucose-1-phosphate.
Gut microbiota characteristics in mice with antibiotic-associated diarrhea
Authors: Shao Haoqing , Zhang Chenyang , Xiao Nenqun , Tan Zhoujin 
Published: October 2020

Abstract
Background
Antibiotic-associated diarrhea (AAD), defined as diarrhea that occurs in association with the administration of antibiotics and without another clear etiology, is one of the most common adverse drug events of antibiotics therapy. We established a diarrhea model induced by gentamycin and cefradine to investigate the microbiota characteristics in the intestinal lumen of mice with AAD and provide insights into noteworthy bacteria related to gentamicin and cefradine-associated diarrhea.

Results
The number of OTUs in the model group and the normal group was 983 and 2107, respectively, and 872 identical OTUs were shared between two groups. Species richness and species diversity of intestinal microbe were altered by antibiotics administration. PCoA showed a clear separation between AAD and health control. The dominant phyla of AAD mice were Firmicutes (52.63%) and Proteobacteria (46.37%). Among the genus with top 20 abundance, the relative abundance of 7 genera, Ruminococcus, Blautia, Enterococcus, Eubacterium, Clostridium, Coprococcus, and Aerococcus, were enriched in the model group. Based upon the LEfSe analysis, Enterococcus, Eubacterium, Ruminococcus, and Blautia were identified as potential biomarkers for AAD.

Conclusions
The bacterial diversity of the intestinal lumen was diminished after gentamicin and cefradine administration. The alterations in the abundance and composition of gut microbiota further led to the dysfunction of gut microbiota. More specifically, gentamicin and cefradine significantly increased the abundance of the opportunistic pathogens, of which Enterococcus and Clostridium were the most prominent and most worthy of attention.
Genome-wide identification and comparative analysis of diacylglycerol kinase (DGK) gene family and their expression profiling in Brassica napus under abiotic stress
Authors: Tang Fang , Xiao Zhongchun , Sun Fujun , Shen Shulin , Chen Si , Chen Rui , Zhu Meichen , Zhang Qianwei , Du Hai , Lu Kun , Li Jiana , Qu Cunmin 
Published: October 2020

AbstractBackgroundDiacylglycerol kinases (DGKs) are signaling enzymes that play pivotal roles in response to abiotic and biotic stresses by phosphorylating diacylglycerol (DAG) to form phosphatidic acid (PA). However, no comprehensive analysis of theDGKgene family had previously been reported inB. napusand its diploid progenitors (B. rapaandB. oleracea).ResultsIn present study, we identified 21, 10, and 11DGKgenes fromB. napus,B. rapa, andB. oleracea, respectively, which all contained conserved catalytic domain and were further divided into three clusters. Molecular evolutionary analysis showed that speciation and whole-genome triplication (WGT) was critical for the divergence of duplicatedDGKgenes. RNA-seq transcriptome data revealed that, with the exception ofBnaDGK4andBnaDGK6,BnaDGKgenes have divergent expression patterns in most tissues. Furthermore, someDGKgenes were upregulated or downregulated in response to hormone treatment and metal ion (arsenic and cadmium) stress. Quantitative real-time PCR analysis revealed that differentBnaDGKgenes contribute to seed oil content.ConclusionsTogether, our results indicate thatDGKgenes have diverse roles in plant growth and development, hormone response, and metal ion stress, and in determining seed oil content, and lay a foundation for further elucidating the roles ofDGKsinBrassicaspecies.
Influence of cigarette smoking on biventricular systolic function independent of respiratory function: a cross-sectional study
Authors: Watanabe Yusuke , Tajiri Kazuko , Suzuki Atsuko , Nagata Hiroyuki , Kojima Masayuki 
Published: October 2020

Abstract
Background
Cigarette smoking harms nearly every organ, including the heart and lungs. A comprehensive assessment of both cardiac and respiratory function is necessary for evaluating the direct effects of tobacco on the heart. However, few previous studies examining the effects of cigarette smoking on cardiac function included an assessment of lung function. This cross-sectional study investigated the influence of cigarette smoking on cardiac function, independent of respiratory function.

Methods
We retrospectively reviewed the medical records of 184 consecutive cases that underwent both spirometry and transthoracic echocardiography around the same time (within 1 month) in one hospital from April 2019 to March 2020. Participants were classified into three groups based on lifetime smoking exposure (pack-years): non-smoker (n = 49), low exposure (1–20 pack-years, n = 40), and high exposure (≥ 20 pack years, n = 95). Multiple linear regression analysis was used to assess the relationship among cigarette smoking, and cardiac and respiratory functions. The relationship between selected dependent variables and lifetime pack-years was assessed in two models with multiple linear regression analysis. Model 1 was adjusted for age and male sex; and Model 2 was adjusted for Model 1 plus forced expiratory volume percentage in 1 s and forced vital capacity percentage.

Results
Compared with the non-smokers, the participants with high smoking exposure had lower left ventricular (LV) systolic function and larger LV size. Multiple linear regression analysis revealed a negative association of cumulative lifetime pack-years with LV and right ventricular (RV) systolic functions, even after adjustment for age, sex, and spirometric parameters (forced expiratory volume percentage in 1 s and forced vital capacity percentage). Meanwhile, there was no significant association of smoking exposure with LV diastolic function (E/e′ and E/A) and RV diastolic function (e′t and e′t/a′t).

Conclusions
Cumulative smoking exposure was associated with a negative effect on biventricular systolic function in patients with relatively preserved cardiac function, independent of respiratory function.
An evaluation of DistillerSR’s machine learning-based prioritization tool for title/abstract screening – impact on reviewer-relevant outcomes
Authors: Hamel C. , Kelly S. E. , Thavorn K. , Rice D. B. , Wells G. A. , Hutton B. 
Published: October 2020

Abstract
Background
Systematic reviews often require substantial resources, partially due to the large number of records identified during searching. Although artificial intelligence may not be ready to fully replace human reviewers, it may accelerate and reduce the screening burden. Using DistillerSR (May 2020 release), we evaluated the performance of the prioritization simulation tool to determine the reduction in screening burden and time savings.

Methods
Using a true recall @ 95%, response sets from 10 completed systematic reviews were used to evaluate: (i) the reduction of screening burden; (ii) the accuracy of the prioritization algorithm; and (iii) the hours saved when a modified screening approach was implemented. To account for variation in the simulations, and to introduce randomness (through shuffling the references), 10 simulations were run for each review. Means, standard deviations, medians and interquartile ranges (IQR) are presented.

Results
Among the 10 systematic reviews, using true recall @ 95% there was a median reduction in screening burden of 47.1% (IQR: 37.5 to 58.0%). A median of 41.2% (IQR: 33.4 to 46.9%) of the excluded records needed to be screened to achieve true recall @ 95%. The median title/abstract screening hours saved using a modified screening approach at a true recall @ 95% was 29.8 h (IQR: 28.1 to 74.7 h). This was increased to a median of 36 h (IQR: 32.2 to 79.7 h) when considering the time saved not retrieving and screening full texts of the remaining 5% of records not yet identified as included at title/abstract. Among the 100 simulations (10 simulations per review), none of these 5% of records were a final included study in the systematic review. The reduction in screening burden to achieve true recall @ 95% compared to @ 100% resulted in a reduced screening burden median of 40.6% (IQR: 38.3 to 54.2%).

Conclusions
The prioritization tool in DistillerSR can reduce screening burden. A modified or stop screening approach once a true recall @ 95% is achieved appears to be a valid method for rapid reviews, and perhaps systematic reviews. This needs to be further evaluated in prospective reviews using the estimated recall.
Extracting medication information from unstructured public health data: a demonstration on data from population-based and tertiary-based samples
Authors: Chen Robert , Ho Joyce C. , Lin Jin-Mann S. 
Published: October 2020

Abstract
Background
Unstructured data from clinical epidemiological studies can be valuable and easy to obtain. However, it requires further extraction and processing for data analysis. Doing this manually is labor-intensive, slow and subject to error. In this study, we propose an automation framework for extracting and processing unstructured data.

Methods
The proposed automation framework consisted of two natural language processing (NLP) based tools for unstructured text data for medications and reasons for medication use. We first checked spelling using a spell-check program trained on publicly available knowledge sources and then applied NLP techniques. We mapped medication names into generic names using vocabulary from publicly available knowledge sources. We used WHO’s Anatomical Therapeutic Chemical (ATC) classification system to map generic medication names to medication classes. We processed the reasons for medication with the Lancaster stemmer method and then grouped and mapped to disease classes based on organ systems. Finally, we demonstrated this automation framework on two data sources for Mylagic Encephalomyelitis/ Chronic Fatigue Syndrome (ME/CFS): tertiary-based (n = 378) and population-based (n = 664) samples.

Results
A total of 8681 raw medication records were used for this demonstration. The 1266 distinct medication names (omitting supplements) were condensed to 89 ATC classification system categories. The 1432 distinct raw reasons for medication use were condensed to 65 categories via NLP. Compared to completion of the entire process manually, our automation process reduced the number of the terms requiring manual labor for mapping by 84.4% for medications and 59.4% for reasons for medication use. Additionally, this process improved the precision of the mapped results.

Conclusions
Our automation framework demonstrates the usefulness of NLP strategies even when there is no established mapping database. For a less established database (e.g., reasons for medication use), the method is easily modifiable as new knowledge sources for mapping are introduced. The capability to condense large features into interpretable ones will be valuable for subsequent analytical studies involving techniques such as machine learning and data mining.
Carbon tetrachloride (CCl4) accelerated development of non-alcoholic fatty liver disease (NAFLD)/steatohepatitis (NASH) in MS-NASH mice fed western diet supplemented with fructose (WDF)
Authors: Zhang Guodong , Wang Xiaoli , Chung Tzu-Yang , Ye Weiwei , Hodge Lauren , Zhang Likun , Chng Keefe , Xiao Yong-Fu , Wang Yixin Jim 
Published: October 2020

Abstract
Background
Multiple murine models of nonalcoholic fatty liver disease/steatohepatitis (NAFLD/NASH) have been established by using obesogenic diets and/or chemical induction. MS-NASH mouse (formally FATZO) is a spontaneously developed dysmetabolic strain that can progress from hepatosteatosis to moderate fibrosis when fed a western diet supplemented with 5% fructose (WDF). This study aimed to use carbon tetrachloride (CCl4) to accelerate and aggravate progression of NAFLD/NASH in MS-NASH mouse.

Methods
Male MS-NASH mice at 8 weeks of age were fed WDF for the entire study. Starting at 16 weeks of age, CCl4 was intraperitoneally administered twice weekly at a dose of 0.2 mL/kg for 3 weeks or 0.08 mL/kg for 8 weeks. Obeticholic acid (OCA, 30 mg/kg, QD) was administered in both MS-NASH and C57Bl/6 mice fed WDF and treated with CCl4 (0.08 mL/kg).

Results
WDF enhanced obesity and hepatosteatosis, as well as induced moderate fibrosis in MS-NASH mice similar to previous reports. Administration of CCl4 accelerated liver fibrosis with increased bridging and liver hydroxyproline contents, but had no significant impact on liver steatosis and lipid contents. High dose CCl4 caused high mortality and dramatic elevation of ALT and ASL, while low dose CCl4 resulted in a moderate elevation of ALT and AST with low mortality. Compared to C57BI/6 mice with WDF and CCl4 (0.08 mL/kg), MS-NASH mice had more prominent hepatosteatosis and fibrosis. OCA treatment significantly lowered liver triglycerides, steatosis and fibrosis in both MS-NASH and C57Bl/6 mice fed WDF with CCl4 treatment.

Conclusions
CCl4 reduced induction time and exacerbated liver fibrosis in MS-NASH mice on WDF, proving a superior NASH model with more prominent liver pathology, which has been used favorably in pharmaceutical industry for testing novel NASH therapeutics.
Expression and significance of Her2 and Ki-67 in gastric adenocarcinoma without distant metastasis: a cohort study
Authors: Wei Zhijian , Huang Lei , Zhang Xinyue , Xu Aman 
Published: October 2020

Abstract
Background
The significance of human epidermal growth factor receptor 2 (Her2) and nucleus-associated antigen Ki-67 expression remains controversial in gastric adenocarcinoma (GaC). The aim of this study was to investigate the expression and clinicopathologic and prognostic significance of Her2 and Ki-67 in resected GaC without distant metastasis.

Methods
Malignant tissues and clinicopathologic data were obtained from 195 patients with resected non-metastatic GaC. Immunohistochemistry staining was performed to examine the expression of Her2 and Ki-67; their association with clinicopathologic factors were investigated using logistic regression, and their association with survival was explored using Kaplan–Meier analysis and Cox proportional hazards regression.

Results
Her2 was majorly expressed in cell membrane and Ki-67 in cell nucleus in non-metastatic GaC. Stronger Her2 expression was significantly associated with better tumor differentiation, neurovascular invasion, less advanced pathological tumor (pT) stage, and more advanced pathological node (pN) stage; while Ki-67 expression was not significantly associated with any investigated clinicopathologic factors. Patients with both negative Her2 and negative Ki-67 expression had poorer tumor differentiation, and more advanced pT and pathological tumor-node-metastasis (pTNM) stages; the association with pT and pTNM stages were further confirmed by multivariable analyses, especially in node-negative disease. Her2 or Ki-67 alone was not significantly associated with pTNM stage. A strongly positive (+++) Her2 expression was associated with poorer survival in multivariable analysis only (P = 0.047); while Ki-67 or combined expression was not significantly associated with prognosis.

Conclusions
In non-metastatic GaC, Her2 expression and combined expression of Her2 and Ki-67 were associated with several clinicopathologic factors including tumor differentiation and stage, and only a +++ Her2 expression was associated with poorer prognosis in multivariable analysis with marginal significance in this study; while Ki-67 alone had both limited clinicopathologic and prognostic values.
Frequency, prognosis and treatment modalities of newly diagnosed small bowel cancer with liver metastases
Authors: Ye Xiaorong , Wang Lifu , Xing Yongjun , Song Chengjun 
Published: October 2020

Abstract
Background
Population-based analysis for the liver metastases of small bowel cancer is currently lacking. This study aimed to analyze the frequency, prognosis and treatment modalities for newly diagnosed small bowel cancer patients with liver metastases.

Methods
Patients with small bowel cancer diagnosed from 2010 to 2015 were extracted from the Surveillance, Epidemiology, and End Results (SEER) database. Binary logistic regression analysis was performed to determine predictors for the presence of liver metastases at diagnosis. Kaplan–Meier method and Cox regression analyses were performed for survival analyses.

Results
A total of 1461 small bowel cancer patients with liver metastases at initial diagnosis were identified, representing 16.5% of the entire set and 63.9% of the subset with metastatic disease to any distant site. Primary tumor with poorer histological type, larger tumor size, later N staging, more extrahepatic metastatic sites, and tumor on lower part of small intestine had increased propensity of developing liver metastases. The combined diagnostic model exhibited acceptable diagnostic efficiency with AUC value equal to 0.749. Patients with liver metastases had significant poorer survival (P < 0.001) than those without liver metastases. In addition, combination of surgery and chemotherapy (HR = 0.27, P < 0.001) conferred the optimal survival for patients with adenocarcinoma, while the optimal treatment options for NEC and GIST seemed to be surgery alone (HR = 0.24, P < 0.001) and chemotherapy alone (HR = 0.08, P = 0.022), respectively.

Conclusions
The combined predictor had a good ability to predict the presence of liver metastases. In addition, those patients with different histologic types should be treated with distinct therapeutic strategy for obtaining optimal survival.
Coverage of non-receipt of cash transfer (Livelihood Empowerment Against Poverty) and associated factors among older persons in the Mampong Municipality, Ghana – a quantitative analysis
Authors: Ottie-Boakye Doris 
Published: October 2020

AbstractBackgroundSocial assistance in the form of cash transfer or in-kind has been recognised as a social protection strategy in many developing countries to tackle poverty and provide protection for individuals and households. Ghana’s cash grant programme, Livelihood Empowerment Against Poverty (LEAP), was introduced in 2008 to support selected households with vulnerable persons including older people 65 years and above, and persons with disabilities. This paper examined the coverage of non-receipt of LEAP, and the associated factors among older persons (65+ years) in the Mampong Municipality, Ghana.MethodsData were extracted from the Ageing, Social Protection and Health Systems (ASPHS) survey carried out between September 2017 and October 2017 among older persons residing in LEAP-targeted communities. Data were analysed using descriptive and sequential logistic regression model techniques.ResultsThe mean age of respondents was 77.0 years and 62.3% were females. Rural residents constituted 59.0%. About 42.0% had no formal education and only 20.5% had no form of caregiving. Non-receipt of LEAP was 82.7% among study respondents. The fully adjusted model showed that being married (AOR = 3.406, CI 1.127–10.290), residing in an urban location (AOR = 3.855, CI 1.752–8.484), having attained primary level of education (AOR = 0.246, CI 0.094–0.642), and not residing in the same household with a primary caregiver (AOR = 6.088, CI 1.814–20.428) were significantly associated with non-receipt of cash grant among older persons.ConclusionThese results provide the first quantitative estimates of non-receipt coverage and its associated factors with the LEAP programme, which can inform the design of government policies related to cash transfers for older persons. The need for further research using different approaches to understand and explain the impact of cash grants on older persons’ well-being is crucial in strengthening old age social support care mechanisms in Ghana.