bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of DNA methylation markers for early detection of CRC indicates a role for nervous system-related genes in CRC
Authors: Rademakers Glenn , Massen Maartje , Koch Alexander , Draht Muriel X. , Buekers Nikkie , Wouters Kim A. D. , Vaes Nathalie , De Meyer Tim , Carvalho Beatriz , Meijer Gerrit A. , Herman James G. , Smits Kim M. , van Engeland Manon , Melotte Veerle 
Published: April 2021

Abstract
Purpose
Colonoscopy and the fecal immunochemical test (FIT) are currently the most widely used screening modalities for colorectal cancer (CRC), however, both with their own limitations. Here we aim to identify and validate stool-based DNA methylation markers for the early detection of CRC and investigate the biological pathways prone to DNA methylation.

Methods
DNA methylation marker discovery was performed using The Cancer Genome Atlas (TCGA) colon adenocarcinoma data set consisting of normal and primary colon adenocarcinoma tissue. The performance of the five best candidate markers and a previously identified marker, NDRG4, was evaluated on tissues and whole stool samples of healthy subjects and CRC patients using quantitative MSP assays. The results were compared and combined with FIT data. Finally, pathway and gene ontology enrichment analyses were performed using ToppFun, GOrilla and clusterProfiler.

Results
GDNF, HAND2, SLC35F3, SNAP91 and SORCS1 were ranked as the best performing markers. Gene combinations of all five markers, NDRG4 and FIT were evaluated to establish the biomarker panel with the highest diagnostic potential, resulting in the identification of GDNF/SNAP91/NDRG4/FIT as the best performing marker panel. Pathway and gene ontology enrichment analyses revealed that genes associated with the nervous system were enriched in the set of best performing CRC-specific biomarkers.

Conclusion
In silico discovery analysis using TCGA-derived data yielded a novel DNA-methylation-based assay for the early detection of CRC, potentially improving current screening modalities. Additionally, nervous system-related pathways were enriched in the identified genes, indicating an epigenetic regulation of neuronal genes in CRC.
QSAR-Co-X: an open source toolkit for multitarget QSAR modelling
Authors: Halder Amit Kumar , Dias Soeiro Cordeiro M. Natália 
Published: April 2021

AbstractQuantitative structure activity relationships (QSAR) modelling is a well-known computational tool, often used in a wide variety of applications. Yet one of the major drawbacks of conventional QSAR modelling is that models are set up based on a limited number of experimental and/or theoretical conditions. To overcome this, the so-called multitasking or multitarget QSAR (mt-QSAR) approaches have emerged as new computational tools able to integrate diverse chemical and biological data into a single model equation, thus extending and improving the reliability of this type of modelling. We have developed QSAR-Co-X, an open source python–based toolkit (available to download at https://github.com/ncordeirfcup/QSAR-Co-X) for supporting mt-QSAR modelling following the Box-Jenkins moving average approach. The new toolkit embodies several functionalities for dataset selection and curation plus computation of descriptors, for setting up linear and non-linear models, as well as for a comprehensive results analysis. The workflow within this toolkit is guided by a cohort of multiple statistical parameters and graphical outputs onwards assessing both the predictivity and the robustness of the derived mt-QSAR models. To monitor and demonstrate the functionalities of the designed toolkit, four case-studies pertaining to previously reported datasets are examined here. We believe that this new toolkit, along with our previously launched QSAR-Co code, will significantly contribute to make mt-QSAR modelling widely and routinely applicable.
Consensus for Treatment of Metastatic Castration-Sensitive Prostate Cancer: Report From the First Global Prostate Cancer Consensus Conference for Developing Countries (PCCCDC)
Authors: Maluf Fernando Cotait , Pereira Felipe Moraes Toledo , Serrano Uson Pedro Luiz , Bastos Diogo Assed , Rodrigues da Rosa Diogo Augusto , Wiermann Evanius Garcia , Schutz Fábio A. , Kater Fábio Roberto , de Oliveira Fernando Nunes Galvão , Marques Monteiro Fernando Sabino , de Pádua Fernando Vidigal , Orlandi Francisco Javier , de Almeida Saito Helena Paes , Ayadi Mouna , Boghikian Pamela Salman , Kopp Ray Manneh , de Carvalho Ricardo Saraiva , de Fogace Rodrigo Nogueira , de Araújo Cavallero Sandro Roberto , Aguiar Sergio , Souza Vinicius Carreira , Sommer Silke Gillessen 
Published: April 2021

PURPOSE International guideline recommendations may not always be extrapolated to developing countries where access to resources is limited. In metastatic castration-sensitive prostate cancer (mCSPC), there have been successful drug and imaging advancements that were addressed in the Prostate Cancer Consensus Conference for Developing Countries for best-practice and limited-resource scenarios. METHODS A total of 24 out of 300 questions addressed staging, treatment, and follow-up for patients with mCSPC both in best-practice settings and resource-limited settings. Responses were compiled and presented in percentage of clinicians supporting each response. Questions had 4-8 options for response. RESULTS Recommendations for staging in mCSPC were split but there was consensus that chest x-ray, abdominal and pelvic computed tomography, and bone scan should be used where resources are limited. In both de novo and relapsed low-volume mCSPC, orchiectomy alone in limited resources was favored and in relapsed high-volume disease, androgen deprivation therapy plus docetaxel in limited resources and androgen deprivation therapy plus abiraterone in high-resource settings were consensus. A 3-weekly regimen of docetaxel was consensus among voters. When using abiraterone, a regimen of 1,000 mg plus prednisone 5 mg/d is optimal, but in limited-resource settings, half the panel agreed that abiraterone 250 mg with fatty foods plus prednisone 5 mg/d is acceptable. The panel recommended against the use of osteoclast-targeted therapy to prevent osseous complications. There was consensus that monitoring of patients undergoing systemic treatment should only be conducted in case of prostate-specific antigen elevation or progression-suggestive symptoms. CONCLUSION The treatment recommendations for most topics addressed differed between the best-practice setting and resource-limited setting, accentuating the need for high-quality evidence that contemplates the effect of limited resources on the management of mCSPC.
Incontinence-associated dermatitis: who is affected?
Authors: Pather Priscilla , Doubrovsky Anna , Jack Leanne , Coyer Fiona 
Published: April 2021

Objective: Intensive care unit (ICU) patients possess multiple risk factors for developing loss of skin integrity, particularly incontinence-associated dermatitis (IAD). IAD is an inflammatory skin condition resulting from repeated and prolonged contact with urine, faeces or both. This study aimed to measure the incidence and clinical characteristics of adult ICU patients with IAD. Method: This was a prospective observational study conducted over three months in an adult ICU. Included patients were ≥18 years who experienced faecal incontinence during their intensive care admission. Patients were excluded if they had an ileostomy or colostomy, had IAD on admission, or were continent of urine and faeces. Skin inspections were performed every second day on all recruited patients by trained research nurses. Other data were collected from patient medical records. Results: A total of 37 patients took part in the study. Incidence of IAD was 35.1%; 13 patients who had incontinence developed IAD. The mean time to onset of IAD was 3.69 days, median 3 days (SD: 1.8, range: 2–8 days). Of the 13 patients who developed IAD, 12 (92.3%) patients were initially assessed as having category 1 IAD and one (7.7%) patient was initially assessed with category 2 IAD. Of the patients with category 1 IAD, one patient (7.7%) progressed to category 2 IAD severity. Conclusion: A larger sample is recommended to fully explore ICU patient characteristics and IAD development. The incidence of IAD in ICU patients was high at 35%, indicating this condition requires due consideration in ICU patients.
In vitro modelling of disease-induced changes in the diabetic wound fibroblast
Authors: Sorooshian Parviz , Metcalfe Anthony D , Lali Ferdinand V 
Published: April 2021

Objective:Fibroblasts have been shown to play an increasingly important role within diabetic wounds. While several in vitro models of diabetic wound fibroblasts have been reported, none replicate the natural progression of the disease over time, recapitulating the acquisition of the diseased phenotype. Therefore, this study aimed to establish an in vitro model of the diabetic wound fibroblast through sustained exposure of healthy dermal fibroblasts to hyperglycaemia.Method:Primary human fibroblasts were isolated from discarded healthy skin tissue and were either exposed to normoglycaemic (control 5.5mM glucose) media or hyperglycaemic (25mM glucose) media for four weeks. Quantitative polymerase chain reaction was performed to measure the expression of inflammatory cytokines and chemokines.Results:In the hyperglycaemia model, stromal cell-derived factor (SDF)-1 expression remained consistently downregulated across all four weeks (p<0.01), while monocyte chemoattractant protein (MCP)-1 (p<0.001), interleukin (IL)-8 (p=0.847) and chemokine (C-X-C motif) ligand 1 (CXCL1) (p=0.872) were initially downregulated at one week followed by subsequent upregulation between 2–4 weeks.Conclusion:This hyperglycaemia model may serve as a useful tool to characterise pathological changes in the diabetic wound fibroblast and help identify candidate therapeutic targets, such as SDF-1, that may reverse the pathology.
Follow-up of pressure ulcer treatment with photodynamic therapy, low level laser therapy and cellulose membrane
Authors: Rosa Luciano Pereira , Silva Francine Cristina da , Luz Suzete Carvalho Landulfo , Vieira Regiane Lima , Tanajura Beatriz Rocha , Silva Gusmão Alana Gonçalves da , de Oliveira Janeide Muritiba , Jesus Nascimento Fabiana de , dos Santos Nathalia Aparecida Campanário , Inada Natália Mayumi , Blanco Kate Cristina , Carbinatto Fernanda Mansano , Bagnato Vanderlei Salvador 
Published: April 2021

Objective: A pressure ulcer (PU) is an area of tissue trauma caused by continuous and prolonged pressure, often associated with hospitalised patients immobilised due to neurological problems, negatively affecting their quality of life, and burdening the public budget. The aim of this study was to report the follow-up, for 45 weeks, of three patients with neurological lesions due to trauma who subsequently developed PUs, and who were treated with a combination of photodynamic therapy (PDT), low level laser therapy (LLLT) and cellulose membrane (CM). Method: PDT was mediated by the photosensitiser curcumin on a 1.5% emulsion base. Blue LED light at 450 nm was delivered continuously for 12 minutes at an irradiance of 30mW/cm2 and total energy delivered to the tissue was 22J/cm2. LLLT was performed with 660 nm laser, punctuated and continuous, twice a week with parameters: spot size 0.04cm2, power of 40mW, 10 seconds per point, fluence of 10J/cm2 and irradiance of 1000mW/cm2. Results: All PUs had a significant reduction (range: 95.2–100%) of their area after 45 weeks of follow-up and two PUs had complete healing at 20 weeks and 30 weeks. All of the PUs showed a reduction in contamination with the PDT treatments in different proportions. Conclusion: From the results obtained, we conclude that the combination of PDT, LLLT and CM is a promising treatment for PU healing.
Evaluation of effectiveness of a new treatment method for healing infected wounds: an animal model
Authors: Basov Alexandr A , Fedosov Sergey R , Malyshko Vadim V , Elkina Anna A , Lyasota Oxana M , Dzhimak Stepan S 
Published: April 2021

Objective: To evaluate the effectiveness of a new treatment method in healing superficial infected wounds compared with surgical debridement with chlorhexidine solution. Method: In this animal model, two wounds were created on the back of 10 male adult rabbits. Wounds treated by Method 1 were debrided using 0.02% chlorhexidine aqueous solution and an antibiotic topical ointment. Wounds treated by Method 2 wounds were treated using a newly developed device which enabled visual monitoring of the wound as it was treated with various pharmacological solutions (including antiseptic, antiseptic oxidant and an osmotically active agent) specifically formulated for each wound healing stage. Wound area size (using digital planimetry) and time taken to clean the wound were recorded, and biopsies were taken, at the beginning of the study and at various timepoints throughout. Result: It was observed that both wound cleaning and wound healing were accelerated by treatment with method 2 compared with method 1 (by 43.8% and 36.7%, respectively). There were also a significantly smaller number of complications in these wounds [p=0.0044] due to the positive ratios of neutrophils and fibroblasts in the wound cavities (from the third to the fourteenth day after wound modelling). Conclusion: Wounds treated with the new device in method 2 had a shorter wound healing time than wounds treated with a traditional method. The automated influx–outflow of solutions removed any fragments of necrotic tissue from the wound surface. Wounds were able to be monitored without the need to remove dressings. The transparent, airtight film, which allowed for wound monitoring without the need to remove dressings, meant that suturing was not required. This resulted in no complications in the wounds treated by this new method.
Comparison of topical honey and povidone iodine-based dressings for wound healing: a systematic review and meta-analysis
Authors: Zhang Fujie , Chen Zongnan , Su Feng , Zhang Taijuan 
Published: April 2021

Objectives: In this review and meta-analysis, we analyse the evidence to compare the efficacy of honey and povidone iodine-based dressings on the outcome of wound healing. Method: A systematic literature search was performed using PRISMA guidelines in academic databases including MEDLINE, Scopus, Embase and CENTRAL. A meta-analysis was carried out to assess the effect of honey and povidone iodine-based dressings on mean healing duration, mean hospital stay duration and visual analogue scale (VAS) score of pain. Results: From the search, 12 manuscripts with a total of 1236 participants (mean age: 40.7±11.7 years) were included. The honey-based dressings demonstrated a medium-to-large effect in reduction of mean healing duration (Hedge's g: –0.81), length of hospital stay (–3.1) and VAS score (–1.2) as compared with the povidone iodine-based dressings. We present evidence (level 1b) in favour of using honey for improvement of wound recovery as compared with povidone iodine. Conclusion: This review and meta-analysis demonstrate beneficial effects of honey-based dressings over povidone iodine-based dressings for wound recovery.
Constructed Wetlands for Water Quality Improvement: A Synthesis on Nutrient Reduction from Agricultural Effluents
Authors: Messer Tiffany L. , Moore Trisha L, , Nelson Natalie , Ahiablame Laurent , Bean Eban Z. , Boles Chelsie , Cook Sonja L. , Hall Steven G. , McMaine John , Schlea Derek 
Published: April 2021

Abstract. Excess nutrients from agricultural settings contribute to surface water and groundwater impairment. Constructed wetlands have been widely used for water quality protection in various agricultural systems. We used a synthesis approach to document the performance of constructed wetlands for nutrient removal from a range of landscapes and geographic regions with the following objectives: (1) review the current use of constructed wetlands in agricultural applications, (2) summarize the nutrient removal efficiency of constructed wetlands, and (3) identify the geographic usage and costs associated with constructed wetlands. We reviewed over 130 publications and reports to characterize nutrient removal performance for the following types of agricultural effluents: cropland surface and subsurface drainage, and wastewater from livestock production, greenhouse, aquaculture, and hydroponic systems. Data from the reviewed studies indicate that constructed wetlands are efficient in protecting water quality in agricultural production settings. However, differences in constructed wetland characteristics reported by the studies suggest that standards are needed to ensure nutrient removal goals are met based on wetland design. Researchers should consider including basic performance parameters for constructed wetlands in published reports, including influent and effluent concentrations, hydraulic retention time, hydraulic loading rate, watershed to treatment wetland ratios, and plant species and relative cover. Future studies are needed to explore cost-benefit analyses to assess the feasibility and potential promotion of wetland incentive programs in various geographic regions and watershed nonpoint-source pollution goals for using these systems in agricultural settings. Keywords: Agricultural wastewater, Agricultural water quality, Aquaculture, Cropland runoff, Greenhouse, Hydroponic, Livestock, Review, Subsurface, Treatment wetland.
Effectiveness of Denitrifying Bioreactors on Water Pollutant Reduction from Agricultural Areas
Authors: Christianson Laura E. , Cooke Richard A. , Hay Christopher H. , Helmers Matthew J. , Feyereisen Gary W. , Ranaivoson Andry Z. , McMaine John T. , McDaniel Rachel , Rosen Timothy R. , Pluer William T. , Schipper Louis A. , Dougherty Hannah , Robinson Rhianna J. , Layden Ian A. , Irvine-Brown Stuart M. , Manca Fabio , Dhaese Kris , Nelissen Victoria , von Ahnen Mathis 
Published: April 2021

HighlightsDenitrifying woodchip bioreactors treat nitrate-N in a variety of applications and geographies.This review focuses on subsurface drainage bioreactors and bed-style designs (including in-ditch).Monitoring and reporting recommendations are provided to advance bioreactor science and engineering.Abstract. Denitrifying bioreactors enhance the natural process of denitrification in a practical way to treat nitrate-nitrogen (N) in a variety of N-laden water matrices. The design and construction of bioreactors for treatment of subsurface drainage in the U.S. is guided by USDA-NRCS Conservation Practice Standard 605. This review consolidates the state of the science for denitrifying bioreactors using case studies from across the globe with an emphasis on full-size bioreactor nitrate-N removal and cost-effectiveness. The focus is on bed-style bioreactors (including in-ditch modifications), although there is mention of denitrifying walls, which broaden the applicability of bioreactor technology in some areas. Subsurface drainage denitrifying bioreactors have been assessed as removing 20% to 40% of annual nitrate-N loss in the Midwest, and an evaluation across the peer-reviewed literature published over the past three years showed that bioreactors around the world have been generally consistent with that (N load reduction median: 46%; mean ±SD: 40% ±26%; n = 15). Reported N removal rates were on the order of 5.1 g N m-3 d-1 (median; mean ±SD: 7.2 ±9.6 g N m-3 d-1; n = 27). Subsurface drainage bioreactor installation costs have ranged from less than $5,000 to $27,000, with estimated cost efficiencies ranging from less than $2.50 kg-1 N year-1 to roughly $20 kg-1 N year-1 (although they can be as high as $48 kg-1 N year-1). A suggested monitoring setup is described primarily for the context of conservation practitioners and watershed groups for assessing annual nitrate-N load removal performance of subsurface drainage denitrifying bioreactors. Recommended minimum reporting measures for assessing and comparing annual N removal performance include: bioreactor dimensions and installation date; fill media size, porosity, and type; nitrate-N concentrations and water temperatures; bioreactor flow treatment details; basic drainage system and bioreactor design characteristics; and N removal rate and efficiency. Keywords: Groundwater, Nitrate, Nonpoint-source pollution, Subsurface drainage, Tile.
Review of Filter Strip Performance and Function for Improving Water Quality from Agricultural Lands
Authors: Douglas-Mankin Kyle R. , Helmers Matthew J. , Harmel R. Daren 
Published: April 2021

HighlightsFilter strip processes for water pollutant reductions were quantified from 74 studies with almost 300 data points.Regression was significant versus width (sediment, N, P), area ratio (sediment, atrazine), and Ks (N, P, atrazine, alachlor).This review discusses ten functional factors affecting FS efficiency as well as FS monitoring recommendations.Cost-effectiveness was assessed and varies considerably by influent load and treatment effectiveness.Abstract. Filter strips (FSs) are edge-of-field conservation practices commonly implemented to reduce flux of sediment, nutrients, and other constituents from agricultural fields. While various aspects of FS effectiveness have been reviewed, this study provides a comprehensive summary of FS efficiency data for sediment, nutrients, pesticides, and pathogens as part of a special collection focused on agricultural conservation practices. This analysis also fills an important gap by assessing performance-based FS costs and cost-effectiveness. Data from 74 U.S. and international studies with 294 different treatments and 3,050 replications were compiled and analyzed. Results showed that runoff reduction tended to increase with increasing FS width up to about 15 m and that sediment reduction was significantly related to the ratio of FS area to drainage area and to FS width, with reduction tending to increase with increasing width up to about 20 m. Total P reduction was significantly related to FS soil saturated hydraulic conductivity, and total N reduction was significantly related to both saturated hydraulic conductivity and width. Total P and total N reductions both tended to increase with increasing FS width up to about 20 m and with increasing FS slope up to about 10%. Annualized FS costs were estimated to range from $314 to $865 ha-1 year-1 for different FS implementations. A major component of the cost is the opportunity cost of taking land out of production. Costs per unit of sediment retained by FS systems ranged from $10.3 to $18.6 Mg-1. A comprehensive assessment of FS cost-effectiveness (cost:benefit) is needed. Monitoring equipment, approaches, and recommendations are discussed, acknowledging the challenges of implementing field-scale FS studies. This information is critical to guide on-farm and programmatic FS decisions and to increase the scientific understanding of this commonly used agricultural conservation practice. Keywords: Best management practice, Buffer strip, Nonpoint-source pollution, Riparian buffer, Vegetated filter strip.
Accurate quantitative phase imaging by the transport of intensity equation: a mixed-transfer-function approach: erratum
Authors: Lu Linpeng , Fan Yao , Sun Jiasong , Zhang Jialin , Wu Xuejuan , Chen Qian , Zuo Chao 
Published: April 2021

In this erratum, we correct Fig. 4 of our Letter [Opt. Lett.
46, 1740 (2021)OPLEDP0146-959210.1364/OL.422095]. This
does not change the scientific conclusions of the original Letter.