bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Neighborhood Food Environment and Socioeconomic Status on Serum Phosphorus Level for Patients on Chronic Dialysis
Authors: Potluri Vishnu S. , Sawinski Deirdre , Tam Vicky , Shults Justine , Cohen Jordana B. , Wiebe Douglas J. , Shah Siddharth P. , Berns Jeffrey S. , Reese Peter P. 
Published: September 2020

Significance Statement
Persistently elevated blood phosphorus levels, which are common among patients with ESKD who undergo dialysis, are associated with a heightened risk of death. In this study, the authors used data from a national dialysis provider to investigate whether higher availability of healthier, low-phosphorus food choices, such as fruits and vegetables, in a patient’s neighborhood is associated with better phosphorus levels. However, they found no meaningful association between better availability of healthy food in the patients’ residential neighborhoods or in neighborhoods around the dialysis center and better phosphorus control. These findings suggest that rather than neighborhood availability of healthy food, health literacy, individual patient food preferences, and challenges in interpreting food labels might be the main determinants of diet-related phosphorus levels.

Background
Elevated blood phosphorus levels are common and associated with a greater risk of death for patients receiving chronic dialysis. Phosphorus-rich foods are prevalent in the American diet, and low-phosphorus foods, including fruits and vegetables, are often less available in areas with more poverty. The relative contributions of neighborhood food availability and socioeconomic status to phosphorus control in patients receiving dialysis are unknown.

Methods
Using longitudinal data from a national dialysis provider, we constructed hierarchical, linear mixed-effects models to evaluate the relationships between neighborhood food environment or socioeconomic status and serum phosphorus level among patients receiving incident dialysis.

Results
Our cohort included 258,510 patients receiving chronic hemodialysis in 2005–2013. Median age at dialysis initiation was 64 years, 45% were female, 32% were Black, and 15% were Hispanic. Within their residential zip code, patients had a median of 25 “less-healthy” food outlets (interquartile range, 11–40) available to them compared with a median of four “healthy” food outlets (interquartile range, 2–6). Living in a neighborhood with better availability of healthy food was not associated with a lower phosphorus level. Neighborhood income also was not associated with differences in phosphorus. Patient age, race, cause of ESKD, and mean monthly dialysis duration were most closely associated with phosphorus level.

Conclusions
Neither neighborhood availability of healthy food options nor neighborhood income was associated with phosphorus levels in patients receiving chronic dialysis. Modifying factors, such as nutrition literacy, individual-level financial resources, and adherence to diet restrictions and medications, may be more powerful contributors than food environment to elevated phosphorus.
Evaluation of 3 year surveillance of device associated infections in a neonatal intensive care unit
Authors: ÜSTÜN Nuran , ÖZÜMÜT Sibel , BULUT Özgül , ARSLANOĞLU Sertaç , OVALI Fahri 
Published: September 2020

Aim: The aim of this study was to determine the rates of healthcare associated infections (HAIs) and device associated healthcare associated infections (DA-HAIs) as well as the rates of invasive device utilization in a neonatal intensive care unit (NICU); and to compare findings with national and international reports.
Materials and methods: A total of 1984 patients who admitted to NICU between January 2016 and December 2018 were enrolled. We retrospectively analysed patient’s characteristics, etiologic pathogens and antibiotic susceptibility, mortality from medical charts and infection control committee surveillance reports. Infections were defined using the standart Centers for Disease Control and Prevention criteria.
Results: During the 3-year period, total 98 HAI cases 69 of which were DA-HAI were detected. The overall incidence of HAIs was 4.9% and rate was 3.7 per 1000 patient days. The most common HAI was blood stream infection (BSI) (n=64, 65.3%) of those 52 were central line-associated (CLA). The CLA-BSI rate was 8.6 per 1000 central line days with central line utilization ratio of 0.22. Ventilator associated pneumonia (VAP) rate was 5.1 per 1000 ventilator days with ventilator utilization ratio of 0.12. The most common pathogens were Klebsiella pneumonia. (38.9%), Staphylococcus epidermidis (22.1%) and Candida spp. (11.6%). The overall mortality rate was 3%. The HAI-related mortality rate was 9.2%.
Conclusion: Our findings highlight the importance of an surveillance approach in the NICU setting. HAI rates were lower than the rates reported from developing countries. However, with device utilization rates similar to those in developed countries our HAI rates were higher than that of the developed countries. Continous monitoring and implementation of necessary precautions are essential to decrease the rates of HAIs.
Objective sleep patterns and validity of self-reported sleep monitoring across different playing levels in rugby union
Authors: Leduc Cedric , Tee Jason , Phibbs Padraic , Read Dale , Ramirez Carlos , Thomas Sawczuk , Weaving Dan , Jones Ben 
Published: September 2020

Background: Growing evidence highlights that elite rugby union players experience poor sleep quality and quantity which can be detrimental for performance.
Objectives: This study aimed to i) compare objective sleep measures of rugby union players between age categories over a one week period, and ii) compare self-reported measures of sleep to wristwatch actigraphy as the criterion.
Methods: Two hundred and fifty-three nights of sleep were recorded from 38 players representing four different age groups (i.e. under 16, under 18, senior academy, elite senior) in a professional rugby union club in the United Kingdom (UK). Linear mixed models and magnitude-based decisions were used for analysis.
Results: The analysis of sleep schedules showed that U16 players went to bed and woke up later than their older counterparts (small differences). In general, players obtained seven hours of sleep per night, with trivial or unclear differences between age groups. The validity analysis highlighted a large relationship between objective and subjective sleep measures for bedtime (r = 0.56 [0.48 to 0.63]), and get up time (r = 0.70 [0.63 to 0.75]). A large standardised typical error (1.50 [1.23 to 1.88]) was observed for total sleep time.
Conclusion: This study highlights that differences exist in sleep schedules between rugby union players in different age categories that should be considered when planning training. Additionally, self-reported measures overestimated sleep parameters. Coaches should consider these results to optimise sleep habits of their players and should be careful with self-reported sleep measures.
Analisis Mutu Fisik dan Citarasa Kopi Indikasi Geografis Arabika Gayo Berdasarkan Ketinggian Tempat
Authors: Purba Pembina , Sukartiko Anggoro Cahyo , Ainuri Makhmudun 
Published: September 2020

<em>Coffee is one of the flagship commodities in the international export market. Its function is important to the economy and encourages the development of world Agroindustries. The coffee beans physical and coffee flavor are the important components influenced by the genetic nature of plants, cultivation practices and growing environments and the interaction between these factors. The research aimed to detemine the beans physical quality and flavor of Gayo Arabica coffee Geographical Indications (GIs) based on the different altitudes. The research was conducted in Gayo Highlands, Aceh Tengah and Bener Meriah Districts. The stratified sampling method was conducted at an altitude of 1,000-1,500 masl (meter above sea level) and 1,500-1,750 masl, the land suitability classification included as S1 and S2 respectively. The variables observed were beans physical quality (weight of 100 Arabica coffee beans and value of defects) and flavor profile. Data were analyzed by independent sample t-test. The results showed that there were differences in the average weight of 100 Arabica coffee beans between S1 and S2 altitudes, but the defect value did not differ significantly. The other results showed that the coffee flavor profile of Arabica Gayo GIs in both districts and altitudes has a total score of 82.75-85.25 points and categorically as specialty coffee (excellent). In general, the S2 altitude of Gayo highland produces a physical quality of 100 Arabica coffee beans and flavor better than the S1 altitude.</em>
Assessment of choriocapillary blood flow changes in response to half-dose PDT in chronic central serous chorioretinopathy using OCTA
Authors: Liu Juejun , Chen Changzheng , Li Lu , Xu Yishuang , Yi Zuohuizi , He Lu , Zheng Hongmei 
Published: September 2020

Abstract
Background: To quantify blood flow changes in choriocapillaris (CC) of chronic central serous chorioretinopathy (CCSC) patients receiving half-dose photodynamic therapy (PDT) using optical coherence tomography angiography (OCTA).Methods: A total of 28 affected eyes and 24 unaffected eyes of 26 CCSC patients receiving half-dose PDT, and 40 eyes of 20 healthy gender- and age-matched subjects were retrospectively enrolled. The proportion of total areas of flow signal voids (FSV, %) in CC level of OCTA was assessed in both eyes of the CCSC patients at baseline and repeated in multiple sections at 1-week, 1-month, 3-month and 6-month intervals after PDT. In addition, CC patterns in response to PDT at early stage and their subsequent morphologic changes were qualitatively documented using OCTA. Results: For affected eyes, significant decrease in FSV was found at 6-m follow-up when compared with that at 1-m follow-up (p=0.036). When compared to normal control eyes, FSV in affected eyes was significantly higher at 1-m, 3-m and 6-m follow-up (p<0.05 for all), while FSV in unaffected eyes was significantly higher at baseline, 1-w, 1-m and 3-m follow-up (p<0.05 for all). Three CC patterns of early response to PDT were identified, including signs of recovery with more even flow signals, transient appearance of worse ischemia and secondary neovascularization within CC level.Conclusion: Abnormal CC flow attenuation remains in completely resolved eyes of CCSC patients treated with half-dose PDT.
SCC: An accurate modification method for scRNA-seq dropouts based on mixture model
Authors: zheng yan , Hu Jialu , Shang Xuequn 
Published: September 2020

Abstract
Background: Single-cell RNA sequencing (scRNA-seq) technology has advanced in past decade, which enables gene expression analysis to be carried out at higher resolution. This technology is of great significance for exploring the dynamic development process of life, studying the regulation mechanism of genes and discovering new cell types. However, there are still some limitations in scRNA-seq technology. scRNA-seq technology only detect 5-15 percent of the mRNA molecules. Therefore, low-expression genes are difficult to detect in scRNA-seq data.Method: The scRNA-seq data tend to be bimodal expression distribution because the expression is either strongly zero or high expression. In this paper, we proposal a method scRNA-seq complementation (SCC) to solve the dropouts in scRNA-seq data. Firstly, we find the nearest neighbor cells of every cell, and then use a mixture model to impute the dropouts of scRNA-seq data. The model can identifies the possibility of dropouts and estimates the reasonable gene expression value.Results: We use SCC and two existing algorithms to test performance on simulated data and three real scRNA-seq datasets (Kolod, Pollen and Usoskin). The result shows that SCC outperforms existing tools. SCC significantly reduce the intra-class distance of cells and enhance the clustering of cell subpopulation, which is significant for future research on gene expression.Conclusions: SCC is an effective tool to resolve the noise in scRNA-seq data. The code is freely accessible at the website:https://github.com/nwpuzhengyan/SCC.
Molecular characterization of Leishmania species from stray dogs and patients in Saudi Arabia
Authors: Alanazi Abdullah D , Alouffi Abdulazi S , Alyousif Mohamed S , Rahi Abdulsadah A , Ali Magda A , Abdullah Hend H.A.M. , Brayner Fabio A , Mendoza-Roldan Jairo Alfonso , Otranto Domenico 
Published: September 2020

Abstract
Background: Leishmania major and Leishmania tropica cause cutaneous leishmaniasis in humans and dogs in several parts of the world, with a large number of cases recorded in the Middle East. However, when occurring in sympatry, the role of each species of Leishmania in the epidemiology of cutaneous leishmaniasis (CL) is not clear. Methods: To determine the prevalence and to identify the species of Leishmania that infects humans and stray dogs in Riyadh and Al-Qassim (Saudi Arabia), 311 stray dogs and 27 human patients, suspected for Leishmania, were examined for CL by a nested PCR (nPCR).Results: Nested PCR (nPCR) detected seven patients (25.9%) positive for cutaneous leishmaniasis. Five patients from Riyadh were infected by L. major and two from Al-Qassim by L. tropica. In addition, five dogs (1.6%) were infected by L. tropica. Conclusions: This is one of the first molecular studies of leishmaniasis from Saudi Arabia. The relationship between the sand fly vectors and the reservoirs of both Leishmania spp. is still scarcely known in this region, and further epidemiological investigations of domestic and wild canids infected with L. major and L. tropica are needed towards a control and prevention of the infection in canine and human populations.
Untargeted metabolomics reveals the effect of lovastatin on steroid-induced necrosis of the femoral head in rabbits
Authors: Ren Xiangnan , Shao Zixing , Fan Wu , Wang Zixuan , Chen Kaiyun , Yu Xuefeng 
Published: September 2020

Abstract
PURPOSE

Lovastatin is an important medicine and it shows a significant effect against glucocorticoid-induced necrosis of the femoral head. This study aimed to investigate the effect of lovastatin on preventing necrosis of the femoral head of by serum metabolomics strategy.

METHODS

Adult healthy adult Japanese white rabbits were divided into three groups: control group, model group and drug group. The pathologic changes of femoral head were assessed with magnetic resonance imaging and microscope. Metabolomics based on UHPLC-MS/MS was used to analyze the collected serum sample. Data were analyzed using principal component analysis (PCA), partial least squares-discriminate analysis (PLS-DA) and orthogonal partial least squares-discriminant analysis (OPLS-DA). All potential metabolites were identified by comparing with HMDB database, metlin database, lipid maps and chemspider database.

RESULTS

11 potential biomarkers were noted and identified as potential biomarkers. The change of biomarkers suggested that lovastatin on preventing necrosis of the femoral head may affect glycerophospholipid metabolism, linoleic acid metabolism, sphingolipid metabolism, alpha-Linolenic acid metabolism, pyrimidine metabolism, arachidonic acid metabolism.

CONCLUSION

The study suggested that lovastatin could prevent the glucocorticoid-induced necrosis of the femoral head of rabbits. The possible reasons were closely associated with adjusting the lipid metabolism, inhibiting adipogenesis and delaying the osteocyte apoptosis.
Being Pro-Active in Meeting the Needs of Suicide-Bereaved Survivors: results from an audit in Montreal
Authors: LIGIER Fabienne , Rassy Jessica , Fortin Gabrielle , Haaster Ian van , Doyon Claude , Brouillard Charlie , Séguin Monique , Lesage Alain 
Published: September 2020

Abstract
Background: Suicide is a major public health concern. In 2017, the suicide rate in Canada was 11 per 100 000 inhabitants. According to literature, 1 in 5 people have experienced a death by suicide during their lifetime. The aim of this study was to describe the met and unmet needs of suicide-bereaved survivors and to provide postvention recommendations. Methods: Further to an exploratory mixed-method audit of 39 suicides that occurred in Montreal (Canada) in 2016, suicide-bereaved survivors (n = 29) participated in semi-structured interviews and completed instruments to discuss and assess potential pathological grief, depression (PHQ-9), and anxiety (GAD-7), as well as health and social services utilization. A panel then reviewed each case and provided recommendations. The mean age of participants was 57.7 years and 23 were women.Results: Although help was offered initially, in most cases by a health professional or service provider (16/29), 22 survivors would have liked to be contacted by telephone in the first two months post suicide. Four categories of individual unmet needs (medical/pharmacological, information, support, and outreach) and one collective unmet need (suicide pre/postvention training and delivery) emerged. Conclusions: Although Quebec provincial services have been developed and offered to suicide-bereaved survivors in the past decade, many dwindled over time and none has been applied systematically. Recommendations for different stakeholders (Ministry of Health and Social Services, coroners, NGOs, and representatives of suicide-bereaved survivors) outlined in this study could be an interesting first step to help develop a suicide pre/postvention strategy.Trial registration: The research protocol was approved by the Scientific Committee of the Montreal Mental Health Institute (November 6, 2018) and the publication of results was approved by its Ethics Research Committee (February 1, 2019), project number 2019-1647.
The Effect of Plant Weight on Estimations of Stalk Lodging Resistance&nbsp;
Authors: Stubbs Christopher J , Oduntan Yusuf , Keep Tyrone , Noble Scott D , Robertson Daniel J 
Published: September 2020

Abstract
Background: Stalk lodging (breaking of agricultural plant stalks prior to harvest) is a multi-billion dollar a year problem. Stalk lodging occurs when bending moments induced by a combination of external loading (e.g. wind) and self-loading (e.g. the plant’s own weight) exceed the stalk bending strength of plant stems. Previous studies have investigated external loading and self-loading of plants as separate and independent phenomena. However, these two types of loading are highly interconnected and mutually dependent. The purpose of this paper is twofold: (1) to investigate the combined effect of external loads and plant weight on the flexural response of plant stems, and (2) to provide a generalized framework for accounting for self-weight during mechanical phenotyping experiments used to predict stalk lodging resistance. Results: A mathematical methodology for properly accounting for the interconnected relationship between self-loading and external loading of plants stems is presented. The method was compared to numerous finite element models of plants stems and found to be highly accurate. The resulting interconnected set of equations from the derivation were used to produce user-friendly applications by presenting (1) simplified self-loading correction factors for common loading configurations of plants, and (2) a generalized Microsoft Excel framework that calculates the influence of self-loading on crop stems. Results indicate that ignoring the effects of self-loading when calculating stalk flexural stiffness is appropriate for large and stiff plants such as maize, bamboo, and sorghum. However, significant errors result when ignoring the effects of self-loading in smaller plants with larger relative grain sizes, such as rice (8% error) and wheat (16% error).Conclusions: Properly accounting for self-weight can be critical to determining the structural response of plant stems. Equations and tools provided herein enable researchers to properly account for the plant’s weight during mechanical phenotyping experiments used to determine stalk lodging resistance.
Differential diagnostic value of total alpha-synuclein assay in the cerebrospinal fluid between Alzheimer's disease and dementia with Lewy bodies from the prodromal stage
Authors: BOUSIGES Olivier , Philippi Nathalie , Lavaux Thomas , Perret-Liaudet Armand , Lachmann Ingolf , Schaeffer-Agalède Caroline , Anthony Pierre , Botzung Anne , Rauch Lucie , Jung Barbara , de Sousa Paulo Loureiro , Demuynck Catherine , Martin-Hunyadi Catherine , Cretin Benjamin , Blanc Frédéric 
Published: September 2020

Abstract
Background: Several studies have investigated the value of alpha-synuclein assay in the cerebrospinal fluid (CSF) of Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB) patients in the differential diagnosis of these two pathologies. However, very few studies have focused on this assay in AD and DLB patients at the MCI stage.Methods: All patients were enrolled under a hospital clinical research protocol from the tertiary Memory Clinic (CM2R) of Alsace, France, by an experienced team of clinicians. A total of 166 patients were included in this study: 21 control subjects (CS), 51 patients with DLB at the prodromal stage (pro-DLB), 16 patients with DLB at the demented stage (DLB-d), 33 AD patients at the prodromal stage (pro-AD), 32 AD patients at the demented stage (AD-d) and 13 patients with mixed pathology (AD+DLB). CSF levels of total alpha-synuclein were assessed using a commercial enzyme-linked immunosorbent assay (ELISA) for alpha-synuclein (AJ Roboscreen). Alzheimer’s biomarkers (t-Tau, P-Tau, Aβ42 and Aβ40) were also measured.Results: The alpha-synuclein assays showed a significant difference between the AD and DLB groups. Total alpha-synuclein levels were significantly higher in AD patients than in DLB patients. However, the ROC curves show a moderate discriminating power between AD and DLB (AUC = 0.78) which does not improve the discriminating power of the combination of Alzheimer biomarkers (AUC = 0.95 with or without alpha-synuclein). Interestingly, the levels appeared to be altered from the prodromal stage in both AD and DLB.Conclusions: The modification of total alpha-synuclein levels in the CSF of patients occurs early, from the prodromal stage. The adding of alpha-synuclein total to the combination of Alzheimer’s biomarker does not improve the differential diagnosis between AD and DLB.Trial registration: ClinicalTrials.gov, (AlphaLewyMa, Identifier: NCT01876459)