bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Effect of Cooled Haemodialysis on cognitive Function in Patients suffering with End-stage Kidney Disease (E-CHECKED): Feasibility Randomised Control Trial Protocol
Authors: Dasgupta Indranil , Odudu Aghogho , Baharani Jyoti , Fergusson Niall , Griffiths Helen , Harrison John , Maruff Paul , Thomas G Neil , Woodhall Gavin , Youssef Samir , Tadros George 
Published: September 2020

Abstract
Background: Cognitive impairment is common in haemodialysis (HD) patients and is associated independently with depression and mortality. This association is poorly understood, and no intervention is proven to slow cognitive decline. There is evidence that cooler dialysis fluid (dialysate) may slow white matter changes in the brain, but no study has investigated the effect of cooler dialysate on cognition. This study addresses whether cooler dialysate can prevent the decline in cognition and improve quality of life (QOL) in HD patients.Methods: This is a multi-site prospective randomised, double-blinded feasibility trial. Setting: Four HD units in the United Kingdom.: Participants and interventions Ninety HD patients randomised (1:1) to standard care (dialysate temperature 36.5C) or intervention (dialysate temperature 35°C) for 12 months. Primary outcome measure: Change in cognition using the Montreal Cognitive Assessment (MoCA). Secondary outcome measures: Recruitment and attrition rates, reasons for non-recruitment, frequency of intradialytic hypotension, depressive symptom scores, patient and carers burden, a detailed computerised cognitive test and QOL assessments. Analysis: mixed method approach, utilising measurement of cognition, questionnaires, physiological measurements and semi-structured interviews.Discussion: The results of this feasibility trial will inform the design of a future adequately powered substantive trial investigating the effect of dialysate cooling on prevention and/ or slowing in cognitive decline in patients undergoing haemodialysis using a computerised battery of neuro-cognitive tests. The main hypothesis that would be tested in this future trial is that patients treated with regular conventional haemodialysis will have a lesser decline in cognitive function and a better quality of life over one year by using cooler dialysis fluid at 35°C, versus a standard dialysis fluid temperature of 36.5°C. This also should reflect in improvements in their abilities for activities of daily living and therefore, reduce carers' burden. If successful, the treatment could be universally applied at no extra cost.Trial registration: ClinicalTrials.gov Identifier: NCT03645733. Registered retrospectively on August 24, 2018.
Deep Learning Accelerators: A Case Study with MAESTRO
Authors: Bolhasani Hamidreza , Jassbi Somayyeh Jafarali 
Published: September 2020

Abstract
In recent years, deep learning has become one of the most important topics in computer sciences. Deep learning is a growing trend in the edge of technology and its applications are now seen in many aspects of our life such as object detection, speech recognition, natural language processing, etc. Currently, almost all major sciences and technologies are benefiting from the advantages of deep learning such as high accuracy, speed and flexibility. Therefore, any efforts in improving performance of related techniques is valuable. Deep learning accelerators are considered as hardware architecture, which are designed and optimized for increasing speed, efficiency and accuracy of computers that are running deep learning algorithms. In this paper, after reviewing some backgrounds on deep learning, a well-known accelerator architecture named MAERI (Multiply-Accumulate Engine with Reconfigurable interconnects) is investigated. Performance of a deep learning task is measured and compared in two different data flow strategies: NLR (No Local Reuse) and NVDLA (NVIDIA Deep Learning Accelerator), using an open source tool called MAESTRO (Modeling Accelerator Efficiency via Spatio-Temporal Resource Occupancy). Measured performance indicators of novel optimized architecture, NVDLA shows higher L1 and L2 computation reuse, and lower total runtime (cycles) in comparison to the other one.
Discovery and validation of mucosal TNF expression combined with histological score - a biomarker for personalized treatment in ulcerative colitis
Authors: Florholmen Jon R. , Johnsen Kay-Martin , Renate Meyer , Olsen Trine , Moe Øystein Kittel , Tandberg Petter , Gundersen Mona D. , Kvamme Jan-Magnus , Johnsen Knut , Løitegård Terje , Raschpichler Gabriele , Vold Cecilia , Sørbye Sveinung W. , Goll Rasmus 
Published: September 2020

Abstract
BackgroundThere are no accurate markers that can predict clinical outcome in ulcerative colitis at time of diagnosis. The aim of this study was to explore a comprehensive data set to identify and validate predictors of clinical outcome in the first year following diagnosis. MethodsTreatment naive-patients with ulcerative colitis were included at time of initial diagnosis from 2004-2014, followed by a validation study from 2014-2018. Patients were treated according to clinical guidelines following a standard step-up regime. Patients were categorized according to the treatment level necessary to achieve clinical remission: mild, moderate and severe. The biopsies were assessed by Robarts histopathology index (RHI) and TNF gene transcripts. ResultsWe included 66 patients in the calibration cohort and 89 patients in the validation. Mucosal TNF transcripts showed high test reliability for predicting severe outcome in UC . When combined with histological activity (RHI) scores the test improved its diagnostic reliability. Based on the cut-off values of mucosal TNF and RHI scores from the calibration cohort, the combined test had still high reliability in the validation cohort (specificity 0.99, sensitivity 0.44, PPV 0.89, NPV 0.87) and a diagnostic odds-ratio (DOR) of 54.ConclusionsThe combined test using TNF transcript and histological score at debut of UC can predict severe outcome and the need for anti-TNF therapy with a high level of precision. These validated data may be of great clinical utility and contribute to a personalized medical approach with the possibility of top-down treatment for selected patients.
Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis
Authors: Su Wenxing , Guan Yi , Huang Biao , Wang Juanjuan , Wei Yuqian , Zhao Ying , Jiao Qingqing , Ji Jiiang , Yu Daojiang , Xu Longjiang 
Published: September 2020

Abstract
Background: Melanoma has the highest mortality rate of all skin tumors, and metastases are the major cause of death from it. The molecular mechanism leading to melanoma metastasis is currently unclear. Methods: With the goal of revealing the underlying mechanism, three data sets with accession numbers GSE8401, GSE46517 and GSE7956 were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the differentially expressed gene (DEG) of primary melanoma and metastatic melanoma, three kinds of analyses were performed, namely functional annotation, protein‐protein interaction (PPI) network and module construction, and co-expression and drug-gene interaction prediction analysis. Results: A total of 41 up-regulated genes and 79 down-regulated genes was selected for subsequent analyses. Results of pathway enrichment analysis showed that extracellular matrix organization and proteoglycans in cancer are closely related to melanoma metastasis. In addition, seven pivotal genes were identified from PPI network, including CXCL8, THBS1, COL3A1, TIMP3, KIT, DCN, and IGFBP5, which have all been verified in the TCGA database and clinical specimens, but only CXCL8, THBS1 and KIT had significant differences in expression. Conclusions: To conclude, CXCL8, THBS1 and KIT may be the hub genes in the metastasis of melanoma and thus may be regarded as therapeutic targets in the future.
Source model for the Mw 6.0 earthquake in Jiashi, China on 19 January 2020 from Sentinel-1A InSAR data
Authors: Yu Pengfei , Qiao Xuejun , Xiong Wei , Chen Wei , Nie Zhaosheng , Wang Dijin , Jia Zhige , Li Jie 
Published: September 2020

Abstract
On January 19, 2020, an Mw 6.0 earthquake occurred in Jiashi, Xinjiang Uygur Autonomous Region of China. The epicenter was located at the basin-mountain boundary between the southern Tian Shan and the Tarim Basin. Interferometric Synthetic Aperture Radar (InSAR) is used to obtain the coseismic deformation field from both ascending and descending Sentinel-1A satellite images of the European Space Agency. The results showed that the coseismic deformation is distributed between the Kalping fault and the Ozgertaou fault. The earthquake produced significant deformation over an area of approximately 40 km by 30 km. The maximum and minimal displacements along the line of sight (LOS) are 5.3 cm and -4.2 cm for the ascending interferogram and are 7.2 cm and -3.0 cm for the descending interferogram, respectively. The fault geometry from the Multi peak Particle Swarm Optimization computation indicates that the seismogenic fault is a shallow low-dipping planar fault that is 4.58 km depth underground. The finite slip model inverted by the Steepest Descent Method implies that the rupture is dominated by a thrust fault. The slips are concentrated in a depth of 5 ~ 7 km with a maximum slip of 0.29 m. The estimated total seismic moment is 1.688×1018 Nm, corresponding to a magnitude of Mw 6.1. The seismogenic fault is the Kalping fault which has a listric structure. The coseismic deformation only occurred on the décollement layer and did not involve the ramp segment. The coseismic Coulomb stress changes have enhanced the stress on the deep margin of the Jiashi earthquake rupture area, indicating that there is still the possibility of strong earthquakes in this region in the future.
Control of Panama disease of banana by intercropping with Chinese chive (Allium tuberosum Rottler): cultivar differences
Authors: Li Zhen-Fang , Wang Tong , He Chenlin , Cheng Kelin , Zeng Rensen , Song Yuanyuan 
Published: September 2020

Abstract
Panama disease (Fusarium wilt disease) caused by Fusarium oxysporum f. sp. cubense race 4 (FOC) severely threatens banana (Musa spp.) production worldwide. Intercropping of banana with Allium plants has shown a potential to reduce Panama disease. In this study, six cultivars of Chinese chive ( Allium tuberosum Rottler) were selected to compare their differences in antifungal activity and active compounds. Three cultivars Duokang Fujiu 11, Fujiuhuang 2, and Duokang Sijiqing with higher levels of antifungal compounds were further used for intercropping with banana in the pots and field to compare their effects on growth and disease incidence of banana.
The six cultivars showed significant differences in antifungal activity against FOC mycelia growth in both leaf volatiles and aqueous leachates. The aqueous leachates displayed stronger antifungal activity than the volatiles. FJH cultivar showed the best inhibitory effect among all six cultivars. Contents of three main antifungal compounds dipropyl trisulfide (DPT), dimethyl trisulfide (DMT), and 2-methyl-2-pentenal (MP) in volatiles and aqueous leachates varied considerably among cultivars. Pot and field experiments showed that intercropping with three selected Chinese chive cultivars significantly improved banana vegetative growth, increased photosynthetic characteristics and yield but decreased disease incidence of Panama disease.
Our results indicate that intercropping with Chinese chive shows potential to reduce banana Panama disease and selection of appropriate cultivars is vital for effective disease control.
Orthopaedic surgeons’ perceptions on COVID-19 related changes in practice: an international survey
Authors: Meraghni Nadhir , Bouyoucef Hichem , soal Nacim , Larbi Redouane Si , Benkaidali Riad , Kara Zoubir , Hamza Amine 
Published: September 2020

Abstract
Purpose The purpose of this study was to assess the orthopaedic surgeons’ perceptions on COVID-19 related changes in their practice.MethodsAn online survey was shared with orthopaedic surgeons practicing in different countries.ResultsThis study showed that orthopaedic surgery plan management was adapted to respond more effectively to the COVID-19 pandemic while maintaining the continuity of health care and ensuring protection of medical staff and patients. Among the introduced measures, elective surgery was postponed to free-up beds for suspected or COVID-19 positive patients requiring hospitalization. Additionally, the number of outpatient visits was considerably decreased and non-urgent visits were postponed to reduce the flow of patients in and out of hospitals and therefore minimize the risk of contamination. Interestingly, data revealed the willingness of orthopaedic surgeons to take care of COVID-19 positive patients and support their colleagues in intensive care units, if needed.ConclusionsThough, orthopaedic surgeons are not in the frontline, they have an important role to play to face the increasing pressure due to the COVID-19 pandemic. In addition to the changes imposed in their current practice, they have a role in providing support to other colleagues in the fight against this global crisis.
Frequent birth-and-death events throughout perforin-1 evolution
Authors: Araujo-Voces Miguel , Quesada Victor 
Published: September 2020

Abstract
Background Through its ability to open pores in cell membranes, perforin-1 plays a key role in the immune system. Consistent with this role, the gene encoding perforin shows hallmarks of complex evolutionary events, including amplification and pseudogenization, in multiple species. A large proportion of these events occurred in phyla for which scarce genomic data were available. However, recent large-scale genomics projects have added a wealth of information on those phyla. Using this input, we annotated perforin-1 homologs in more than eighty species including mammals, reptiles, birds, amphibians and fishes. Results We have annotated more than 400 perforin genes in all groups studied. Most mammalian species only have one perforin locus, which may contain a related pseudogene. However, we found four independent small expansions in unrelated members of this class. We could reconstruct the full-length coding sequences of only a few avian perforin genes, although we found incomplete and truncated forms of these gene in other birds. In the rest of reptilia, perforin-like genes can be found in at least three different loci containing up to twelve copies. Notably, mammals, non-avian reptiles, amphibians, and possibly teleosts share at least one perforin-1 locus as assessed by flanking genes. Finally, fish genomes contain multiple perforin loci with varying copy numbers and diverse exon/intron patterns. We have also found evidence for shorter genes with high similarity to the C2 domain of perforin in several teleosts. A preliminary analysis suggests that these genes arose at least twice during evolution from perforin-1 homologs. Conclusions The assisted annotation of new genomic assemblies shows complex patterns of birth-and-death events in the evolution of perforin. These events include duplication/pseudogenization in mammals, multiple amplifications and losses in reptiles and fishes and at least one case of partial duplication with a novel start codon in fishes.
Assessing the association between periodontitis and preterm birth : A case control study
Authors: UWAMBAYE Peace , MUNYANSHONGORE Cyprien , RULISA Stephen , Shiau Harlan J , NUHU Assuman , KERR Michael S 
Published: September 2020

Abstract
Background: Premature delivery is among the leading causes of perinatal mortality and morbidity in developed societies which is an important problem in obstetrics. Maternal periodontitis is a prevalent condition that has been suspected to be associated with adverse pregnancy outcomes such as preterm birth. However, there are still conflicting results which this study aims to address by examining the association between periodontitis and preterm birth. This study provides necessary information to inform decisions on the screening tool to be recommended for use by nurses and midwives to screen for periodontal diseases during antenatal consultations in order to improve mothers’ and children’s health. Methods: A case control study was conducted at 12 health facilities in the Southern Province of Rwanda from February to August 2018. A total of 555 women in the postpartum period were enrolled in the study. Cases and controls were enrolled in a ratio of 1:2, each enrolled case of preterm birth was followed by 2 control cases delivered at term gestation that were next on the register. There were 185 cases of preterm deliveries and 370 controls of term delivery. Multivariate regression analysis was done and the variables were hierarchically grouped into three groups: The first group involved demographic variables that were put in the regression model as Step 1. The second group was made up of other potential factors that were put in the regression model as the second step. The third group was periodontitis, as it was hypothesized to be a major predictor variable and this constituted the the third step of the regression model. Results: Significant association was found between periodontitis and preterm birth. Women who had periodontitis had 6 times the odds of giving birth to preterm birth babies compared to women who had no periodontitis (p<0.001) (95% CI 3.9, 10.4). Conclusion: Periodontitis is a risk factor for preterm birth and preventive solutions such as having a periodontitis screening tool for nurses and midwives during antenatal care consultations is highly recommended.
Prevalence, predictors and outcome of carotid stenosis. A sub study in the Preventive Antibiotics in Stroke Study (PASS)
Authors: Velzen Twan van , Kuhrij Laurien , Westendorp Willeke , de Beek Diederik van , Nederkoorn Paul 
Published: September 2020

Abstract
Background: The prevalence of carotid artery stenosis (CAS) in acute ischaemic stroke (AIS) patients is historically reported at 15-20%, but an up-to-date estimate is lacking. We hypothesise it is lower than historically reported, due to better risk management to date. The study aims to study prevalence, predictors and survival of CAS in AIS patients. Methods: We included patients with AIS from the Preventive Antibiotics in Stroke Study (PASS), a large Dutch randomized, multicentre, open-label phase III trial that included 2538 patients with acute stroke and randomised between standard care or preventive ceftriaxone. Patients with stroke in the anterior circulation that underwent diagnostic testing of the internal carotid artery (ICA) were eligible for this sub study and used in these secondary analyses. Logistic regression analyses were performed to identify predictors for CAS ≥50%. Additionally, an ordinal regression was performed to assess the association between presence of CAS at baseline and functional outcome at three months on the modified Rankin scale (mRS). Results: 1480 patients with AIS were included; 277 had CAS (18.7%; 95%CI:17.7-19.7). Age, hypertension, smoking and male gender were found as best-fit predictors for presence of CAS. Significant shift in mRS score after 90 days for CAS ≥50% towards a higher mRS score with an OR of 1.66 (95% CI 1.30-2.10) was found.Conclusions: Current prevalence of CAS is 18.7%, which is higher than we expected. Gender, smoking and hypertension are important factors associated with CAS. Patients with CAS had a significantly higher mRs score after 90 days. Clinical Trial Registration-URL: https://doi.org/10.1186/ISRCTN66140176 Unique identifier: ISRCTN66140176
Melatonin promotes adventitious root formation in apple by promoting the function of MdWOX11
Authors: Mao Jiangping , Niu Chundong , Li Ke , Chen Shiyue , Tahir Muhammad Mobeen , Han Mingyu , Zhang Dong 
Published: September 2020

Abstract
Background: Melatonin (MT) is important for plant growth and development; however, it is not known whether MT is involved in apple adventitious root (AR) development. In this study, we treated Malus prunifolia (MP) at four different stages of AR development, and analysed the level of the endogenous hormones MT, auxin (IAA), zeatin-riboside (ZR), gibberellins (GA1+3) and abscisic acid (ABA) in all four treatment groups and in the untreated control group. The expression of genes related to MT, IAA biosynthesis, transport and signal transduction, the cell cycle, and root development was quantified by RT-qPCR, and the function of MdWOX11 was analysed in transgenic apple plants.Results: The promotion of AR development by MT was dependent on the stage of AR induction between 0–2 d in apple rootstocks. MT-treatment increased the level of IAA and crosstalk existed between MT and IAA during AR formation. The expression of MdWOX11 was induced by MT treatment and positively regulated AR formation in apple. Furthermore, transgenic lines that overexpressed MdWOX11 lines produced more ARs than ‘GL3’. Phenotypic analysis indicated that MdWOX11 overexpression lines were more sensitive to exogenous MT treatment than ‘GL3’, suggesting that MdWOX11 regulates AR formation in response to MT in apple rootstock.Conclusions: MT promotes AR formation mainly during the AR induction stage by inducing IAA levels and upregulating MdWOX11.
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 
Published: September 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.