bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cognitive impairment and associated risk factors in older adult hemodialysis patients: a cross-sectional survey
Authors: Luo Yang , Murray Anne M. , Guo Yi-Dan , Tian Ru , Ye Peng-Peng , Li Xin , Li Guo-Gang , Lu Fang-Ping , Ma Ying-Chun , Sun Yi , Wang Yu-Zhu , Xiao Yue-Fei , Zhang Qi-Meng , Zhao Xue-Feng , Zhao Hai-Dan , Chen Xiang-Mei 
Published: July 2020

AbstractThe clinical epidemiological features of cognitive impairment in Chinese older adult patients undergoing hemodialysis are not clear, we aimed to identify the extent and patterns of cognitive impairment among those patients. We conducted a cross-sectional study of 613 hemodialysis patients aged 50 to 80 from 11 centers in Beijing. A neuropsychological battery of 11 tests covering domains of attention/processing speed, executive function, memory, language, and visuospatial function was applied, patients were classified as none, mild, or major cognitive impairment according to the fifth version of the Diagnostic and Statistical Manual of Mental Disorders criteria for cognitive impairment. Compared with Chinese population norms, 37.2% of the participants had mild cognitive impairment, 43.7% had major cognitive impairment. Memory and language were the most severe impaired domains in the mild cognitive impairment group, attention and visuospatial function domains were the most serious impaired domains in the major cognitive impairment group. Concomitant impairment across multiple cognitive domains was common. Factors associated with major cognitive impairment included age, education level, history of stroke and hypertension, dialysis vintage, and single-pool Kt/V. There is a high frequency of cognitive impairment in Chinese older adult hemodialysis patients, with varying severity and concomitant impairment across multiple domains.
Potential evolutionary impact of integrative and conjugative elements (ICEs) and genomic islands in the Ralstonia solanacearum species complex
Authors: Gonçalves Osiel Silva , de Queiroz Marisa Vieira , Santana Mateus Ferreira 
Published: July 2020

AbstractRalstonia solanacearum, a soil-borne plant pathogen, encompasses a large number of strains known as R. solanacearum species complex (RSSC). Although it has been suggested that mobile genetic elements (MGEs) may play an important role in the RSSC genome, the evolutionary impact of these elements remains unknown. Here, we identified and analysed Integrative and Conjugative Elements (ICEs) and Genomic Islands (GIs) in the 121 genomes published for Ralstonia spp., including RSSC strains and three other non-plant pathogenic Ralstonia spp. Our results provided a dataset of 12 ICEs and 31 GIs distributed throughout Ralstonia spp. Four novel ICEs in RSSC were found. Some of these elements cover 5% of the host genome and carry accessory genes with a potential impact on the fitness and pathogenicity of RSSC. In addition, phylogenetic analysis revealed that these MGEs clustered to the same species, but there is evidence of strains from different countries that host the same element. Our results provide novel insight into the RSSC adaptation, opening new paths to a better understanding of how these elements affect this soil-borne plant pathogen.
Epidemiology and treatment of atrial fibrillation in patients with type 2 diabetes in the UK, 2001–2016
Authors: Alwafi Hassan , Wong Ian C. K. , Banerjee Amitava , Mongkhon Pajaree , Whittlesea Cate , Naser Abdallah Y. , Lau Wallis C. Y. , Wei Li 
Published: July 2020

AbstractPatients with Type 2 diabetes mellitus (T2DM) have an increased risk of atrial fibrillation (AF). The current study aimed to investigate the prevalence and treatment of AF in patients with T2DM, assess the impact of direct oral anticoagulants (DOACs) introduction on oral anticoagulant (OACs) prescribing rates, and factors associated with OAC initiations in patients with T2DM and AF. The Health Improvement Network (THIN) database (2001–2016), was used to examine the annual prevalence and treatment of AF in T2DM. The impact of DOACs introduction on OAC prescribing rates were investigated using interrupted time series analysis (ITS). Factors associated with OAC initiations were also identified using multivariate logistic regression. The prevalence of AF increased from 2.7 [95% confidence intervals (CI) 2.5–2.8] in 2001 to 5.0 (4.9–5.1) in 2016 per 100 persons. OACs prescribing within 30-days of AF diagnosis increased from 21.5% in 2001 to 56.8% in 2016. ITS analysis showed that OAC prescribing increased after DOAC introduction (P < 0.001), however, no immediate change was observed (P = 0.29). T2DM patients with AF, aged 60–79, male gender and BMI ≥ 25 were more likely to receive OAC, adjusted OR 1.3 (1.2–1.5) for aged 60–79, 1.3 (1.2–1.4) for male gender and 2.0 (1.9–2.2) for BMI ≥ 25, respectively. This study highlighted an increase in prevalence of AF in patients with T2DM during the study period. Further studies are warranted to investigate factors contributing to the underuse of OAC in patients with T2DM and AF.
β-hydroxybutyrate and hydroxycarboxylic acid receptor 2 agonists activate the AKT, ERK and AMPK pathways, which are involved in bovine neutrophil chemotaxis
Authors: Carretta María D. , Barría Yonathan , Borquez Katherine , Urra Bárbara , Rivera Andrés , Alarcón Pablo , Hidalgo María A. , Burgos Rafael A. 
Published: July 2020

AbstractElevated plasma concentrations of the ketone body β-hydroxybutyrate (BHB), an endogenous agonist of the hydroxycarboxylic acid receptor 2 (HCA2), is associated with an increased incidence of inflammatory diseases during lactation in dairy cows. In the early stages of this pathology, an increase in neutrophil recruitment is observed; however, the role of BHB remains elusive. This study characterized the effect of BHB and synthetic agonists of the HCA2 receptor on bovine neutrophil chemotaxis and the signaling pathways involved in this process. We demonstrated that treatment with BHB concentrations between 1.2 and 10 mM and two full selective agonists of the HCA2 receptor, MK-1903 and nicotinic acid, increased bovine neutrophil chemotaxis. We also observed that BHB and HCA2 agonists induced calcium release and phosphorylation of AKT, ERK 1/2 and AMPKα. To evaluate the role of these pathways in bovine neutrophil chemotaxis, we used the pharmacological inhibitors BAPTA-AM, pertussis toxin, U73122, LY294002, U0126 and compound C. Our results suggest that these pathways are required for HCA2 agonist-induced bovine neutrophil chemotaxis in non-physiological condition. Concentrations around 1.4 mM of BHB after calving may exert a chemoattractant effect that is key during the onset of the inflammatory process associated with metabolic disorders in dairy cows.
Embossed Mie resonator arrays composed of compacted TiO2 nanoparticles for broadband anti-reflection in solar cells
Authors: Visser Dennis , Chen Ding Yuan , Désières Yohan , Ravishankar Ajith Padyana , Anand Srinivasan 
Published: July 2020

AbstractMie resonator arrays formed by embossing titanium dioxide (TiO2) nanoparticles (NPs) from solution are investigated as optical coatings for anti-reflection applications. Compacted nanoparticle assemblies offer unique possibilities to tailor the effective refractive index (RI). Here, we demonstrate a simple table-top, low pressure, and low temperature method to fabricate structured optical coatings. TiO2 nanostructures in the form of nanodisks support Mie resonances in the visible wavelength spectrum and exhibit strong forward scattering into the high index substrates, making them suitable as broadband anti-reflection coatings for solar cells. TiO2 NP-based nanodisk arrays are designed, fabricated, and characterized regarding their anti-reflection properties on Si, GaAs, and InP substrates and solar cells. Detailed finite-difference time-domain simulations are performed to optimize the TiO2 NP-based Mie resonator arrays for the broadband anti-reflection as well as to explain the measured reflectance spectra. The solar-weighted reflectance is used as a figure of merit (FoM). TiO2 nanodisk arrays on Si show a FoM of ~ 7% in the 400–1,100 nm wavelength spectrum; similar values are obtained for GaAs and InP substrates. TiO2 nanodisk arrays embossed directly on prefabricated planar single-junction Si, GaAs, and InP solar cells result in an appreciable increase (~ 1.3 times) in the short-circuit current densities.
The complete chloroplast genome sequence of the medicinal plant Sophora tonkinensis
Authors: Wei Fan , Tang Danfeng , Wei Kunhua , Qin Fang , Li Linxuan , Lin Yang , Zhu Yanxia , Khan Aziz , Kashif Muhammad Haneef , Miao Jianhua 
Published: July 2020

AbstractSophora tonkinensis belongs to genus Sophora of the Fabaceae family. It is mainly distributed in the ridge and peak regions of limestone areas in western China and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. Furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. Therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. Chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (GC) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSC/IRB boundary, while another copy was absent from the IRA region because of the incomplete structure caused by IR region expansion and contraction. The phylogenetic analysis placed S. tonkinensis in Papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. The complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.
Mutation analysis, treatment and prenatal diagnosis of Chinese cases of methylmalonic acidemia
Authors: Zhang Chuan , Wang Xing , Hao Shengju , Zhang Qinghua , Zheng Lei , Zhou Bingbo , Liu Furong , Feng Xuan , Chen Xue , Ma Panpan , Chen Cuixia , Cao Zongfu , Ma Xu 
Published: July 2020

AbstractMethylmalonic acidemia (MMA)-affected patients may have developmental, hematological, neurological, metabolic, ophthalmological, and dermatological clinically abnormal findings. This study aimed to identify mutations in 13 Chinese MMA cases. We provided genetic counseling, treatment, and prenatal diagnosis for the families with MMA. Liquid chromatography-tandem mass spectrometry (LC–MS/MS) was performed and the results were confirmed by gas chromatography and mass spectrometry (GC/MS). Variant screening in probands was performed by targeted next-generation sequencing. Identified variants were confirmed by Sanger sequencing. Of these 13 MMA cases, seven were isolated MMA, and among them, six were caused by variants in MMUT and one was caused by a variant in MCEE. The other six cases were MMA with homocystinuria, which was caused by variants in MMACHC. We found six novel variants in three MMA-causing genes as follows: c.2008G>A, c.301_302insTA, c.984delC, and c.319A>T of MMUT; c.445T>C of MMACHC; and c.296T>C of MCEE. We provided prenatal diagnosis for two families with MMA at their next pregnancy, and one family had a healthy newborn. In conclusion, our findings expand the spectrum of genotypes in MMA. Effective genetic counseling is required to allow awareness of the patients’ families that MMA disease is treatable and a good prognosis can be obtained.
NLRP3 receptor contributes to protection against experimental antigen-mediated cholangitis
Authors: González Marisol Ibet , Vannan Danielle , Eksteen Bertus , Reyes José Luis 
Published: July 2020

Abstract
Inflammatory diseases of the bile ducts like primary sclerosing colangitis (PSC) are characterized by a robust cellular response targeting the biliary epithelium leading to chronic inflammation and fibrosis. Driving fibro-inflammatory diseases, NOD-like receptors such as NLRP3 have been identified as a central component to immune-mediated pathology. However, to date the role of NLRP3 in biliary diseases has been poorly explored. Here, we addressed the role of NLRP3 in the OVAbil mouse model of antigen-mediated cholangitis. As obesity continues to spread worldwide, we also evaluated the NLRP3 response in experimental cholangitis after high-fat diet exposure. We compared the extent of histopathological liver damage between OVAbil and OVAbilxNLRP3−/− mice after either a standard chow or a high-fat diet. Infiltrating immune cells were characterized by flow cytometry and levels of cytokines, chemokines and liver enzymes in blood samples were analyzed at the end of the experiment. We observed a more severe histopathological phenotype of cholangitis in absence of NLRP3, characterized by loss of bile ducts and larger inflammatory foci and higher levels of IL- 6 and CXCL10 as compared with NLRP3 sufficient mice. This phenotype was further exaggerated in the context of obesity, where cholangitis induced in NLRP3-deficient obese mice resulted in further exacerbated histopathology and increased levels of IL-13 and TNFα, suggesting a diet-specific profile. The absence of NLRP3 caused a supressed IL-17 response. In summary, our data suggest that activation of NLRP3 attenuates this antigen-mediated OVAbil model of cholangitis.
Construction of a novel prognostic-predicting model correlated to ovarian cancer
Authors: Tang Weichun , Li Jie , Chang Xinxia , Jia Lizhou , Tang Qi , Wang Ying , Zheng Yanli , Sun Lizhou , Feng Zhenqing 
Published: July 2020

Abstract
Background: Ovarian cancer (OC) is one of the most lethal gynecological cancers worldwide. The pathogenesis of the disease and outcomes prediction of OC patients remain largely unclear. The present study aimed to explore the key genes and biological pathways in ovarian carcinoma development, as well as construct a prognostic model to predict patients’ overall survival (OS).
Results: We identified 164 up-regulated and 80 down-regulated differentially expressed genes (DEGs) associated with OC. Gene Ontology (GO) term enrichment showed DEGs mainly correlated with spindle microtubes. For Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, cell cycle was mostly enriched for the DEGs. The protein–protein interaction (PPI) network yielded 238 nodes and 1284 edges. Top three modules and ten hub genes were further filtered and analyzed. Three candidiate drugs targeting for therapy were also selected. Thirteen OS-related genes were selected and an eight-mRNA model was present to stratify patients into high- and low-risk groups with significantly different survival.
Conclusions: The identified DEGs and biological pathways may provide new perspective on the pathogenesis and treatments of OC. The identified eight-mRNA signature has significant clinical implication for outcome prediction and tailored therapy guidance for OC patients.
Validation of the Yale Swallow Protocol in Post-Acute Care: A Prospective, Double-Blind, Multirater Study
Authors: Ward Matthew , Skelley-Ashford Michelle , Brown Karen , Ashford John , Suiter Debra 
Published: July 2020

Purpose
A systematic approach to the diagnosis and treatment of swallowing disorders relies heavily on valid and reliable screening protocols that provide clinicians with clear and objective information. The Yale Swallow Protocol (YSP) has been shown to be a useful, valid, and reliable screening tool for aspiration risk in the acute care setting. However, the YSP was not validated for use in post-acute care. This study evaluated the clinical utility of the YSP in the post-acute care setting.

Method
This prospective, double-blind, multirater study included a referred sample of 240 individuals, with varying medical diagnoses, who completed the YSP and an endoscopic evaluation of swallowing.

Results
Sensitivity for the YSP was 95.4%, specificity was 66.9%, positive predictive value was 77.6%, and negative predictive value was 92.4%.

Conclusions
The data from this prospective study appear to support the use of the YSP in post-acute care due to the ability to use the protocol on virtually all patients—regardless of diagnosis—and its high sensitivity and negative predictive value.
In Vitro Closure Times (PFA-100) Are Different Between Peritoneal Dialysis and Hemodialysis
Authors: Gokalp Cenk , Karadag Fatma Keklik , Braunisch Matthias Christoph , Schmaderer Christoph , Gunay Emrah , Kiper Hatice Demet , Tobu Mahmut , Ustün Celalettin , Demirci Meltem Sezis , Ozkahya Mehmet 
Published: July 2020

AbstractIntroduction Platelet dysfunction is not uncommon in patients with end-stage renal disease (ESRD). Type of renal replacement therapy may have an effect on platelet functions, which has not been well investigated. We evaluated in vitro closure time (CT) differences between peritoneal dialysis (PD) and hemodialysis (HD) patients using platelet function analyzer (PFA-100)and observed a significant difference between these renal replacement therapies.Methods Patients with ESRD undergoing PD (n = 24) or HD (n = 23) for more than 6 months were included. Blood samples for collagen/epinephrine (Col/EPI) and collagen/adenosine diphosphate (Col/ADP) measurements were obtained before HD at a mid-week session for HD patients and at an outpatient control time for PD patients.Results Three of 24 (12.5%) PD patients and 16 of 23 (69.5%) HD patients had prolonged PFA-100 Col/EPI, p< 0.001. Likewise, 4.2% of PD patients and 87.0% of HD patients had prolonged PFA-100 Col/ADP, p< 0.001. Moreover, the median times of PFA-Col/EPI and PFA-100 Col/ADP were significantly lower in PD patients compared with those of HD patients (p< 0.001). Multivariate analysis showed that the type of renal replacement was a risk factor for both elevated PFA-100 Col/ADP and PFA-100 Col/EPI after adjusted for platelets, hematocrit, and urea (p< 0.001).Conclusions The type of renal replacement therapy may have an effect on in vitro CTs; therefore, studies including more patients with long-term follow-up are needed to investigate if the difference has any impact on clinical outcomes.
A Tale of four measures of pragmatic knowledge in an EFL institutional context
Authors: Mohammad Hosseinpur Rasoul , Bagheri Nevisi Reza , Lowni Abdolreza 
Published: July 2020

Abstract
The upsurge of interest in L2 pragmatics studies has coincided with a growing interest in pragmatic assessment.
Employing the most efficient measure of pragmatics has led many researchers to examine the existing measures to pinpoint the most
useful ones. This study was an attempt to compare and contrast Written Discourse Completion Task (WDCT), Oral Discourse Completion
Task (ODCT), and Role-play with Natural methodology in an EFL institutional context to see which measure approximated Natural
methodology. To this end, data (requests) were collected from 27 intermediate–level Iranian EFL learners in a natural classroom
institutional context over 15 weeks, and then the WDCTs, ODCTs, and Role-plays with the same contextual features were selected to
elicit the intended data. The participants’ requests were transcribed and analyzed in terms of Schauer’s (2009) request head act strategy taxonomy and its internal and external modification devices. The results of
Binominal tests indicated that, in spite of some minor similarities, none of the elicitation measures could approximate the
natural data. The participants’ employment of direct, non-conventionally indirect request strategies, and internal and external
modification devices were more conspicuous in the WDCTs, ODCTs, and Role-plays than those in the Natural methodology. The study
implies that data collection methods should be selected based on researchers’ objectives and research questions.
Exploring lexical bundles in recent published papers in the field of applied linguistics
Authors: Nasrabady Peyman , Elahi Shirvan Majid , Ehsan Golparvar Seyed 
Published: July 2020

ABSTRACTMultiword units can contribute significantly to the fluency of linguistic production. Lexical bundles, as a type of multiword units, are sequences of three or more words used with high frequency in natural discourse. Primary studies regarding the introduction of structural and functional classifications of lexical bundles have been followed by other researchers to compare them across disciplines based on the primary classifications. However, no comprehensive study has been conducted to explore and investigate the structural as well as the functional characteristics of the lexical bundles in research articles in the field of applied linguistics. This study aimed at exploring lexical bundles used in a substantial number of academic papers published in this specific field through different journals since 2008 to identify all the lexical bundles and to capture all the possible structural and functional characteristics they express. To achieve this, a corpus of papers published in the field of applied linguistics was complied and investigated. A considerable number of lexical bundles identified were similar to those previously found in the literature while a reasonable number of them expressed new structural and functional characteristics. The study concludes with theoretical as well as some pedagogical implications of the findings.
Impact of Indo-Pacific warm pool Hadley circulation on the seasonal forecast performance for summer precipitation over the western North Pacific
Authors: Guo Yi-Peng , Feng Xiangbo , Klingaman Nicholas P , Tan Zhe-Min 
Published: July 2020

Abstract
The western North Pacific summer climate affects the densely populated East Asian countries, while seasonal forecasting over these regions remains challenging for dynamical models. This study evaluates the effect of the spring Indo-Pacific warm pool (IPWP) Hadley circulation on the forecast performance for summer western North Pacific (WNP) precipitation in the Met Office Global Seasonal Forecast System (GloSea5). GloSea5 skillfully predicts IPWP Hadley circulation, but has moderate forecast skill for summer WNP precipitation. Compared to observations, the significant relationship between the spring IPWP Hadley circulation and the summer WNP precipitation is overestimated in most hindcast members and in the ensemble mean. Furthermore, we confirmed that the forecast ensemble members with a stronger such regional circulation–precipitation relationship have better forecast performance for the summer WNP precipitation, suggesting the importance of such a relationship for the seasonal forecast of WNP precipitation. These results also imply the need to further investigate other important factors for the WNP precipitation, the effects of which may be suppressed by the overestimated regional circulation–precipitation relationship in GloSea5.