bluuebunny/crossref_metadata_2025_split huggingface dataset:
Consideration of risk management practices in regulatory risk assessments: evaluation of field trials with micro-dams to reduce pesticide transport via surface runoff and soil erosion
Authors: Sittig Stephan , Sur Robin , Baets Dirk , Hammel Klaus 
Published: June 2020

Abstract
Background
On sloped agricultural fields, water and sediment can be transported downhill as runoff and erosion. This process can cause losses of valuable top soil material, water resources for plant availability, and nutrients as well as transport of plant protection products (PPP) into adjacent surface water bodies. In the European and the US risk assessment for the registration of PPP, runoff and erosion are numerically calculated with the simulation model PRZM which uses the USDA runoff curve number (CN) concept for the water movement. Results from runoff field trials were used to estimate the effect of dedicated management practices in terms of mitigating runoff and erosion, i.e. creating micro-dams between the ridges of potato fields or in maize cultivation on model input parameters.

Results
Application of different cultivation and tillage techniques (micro-dams/bunds) showed a consistent decrease of the measured quantities of runoff, erosion, and PPP transport as well as of the calculated CN and predicted environmental concentrations in surface water. The results presented here support the approach to quantitatively consider in-field risk mitigation measures (if applied) in the context of regulatory surface water exposure calculations, as proposed by the SETAC MAgPIE workshop.

Conclusion
Based on these data, a robust case can be made to consider innovative runoff mitigation for risk assessment purposes by, e.g. lowering the CN in the exposure scenarios. In the assessment presented herein, an average decrease in the mean of the derived CN of 86 of 21 points (± 11, 10th percentile: 12) for potatoes could be derived. For maize, the mean calculated CN of 73 was lowered on average by 3 points.
DryMass: handling and analyzing quantitative phase microscopy images of spherical, cell-sized objects
Authors: Müller Paul , Cojoc Gheorghe , Guck Jochen 
Published: June 2020

Abstract
Background
Quantitative phase imaging (QPI) is an established tool for the marker-free classification and quantitative characterization of biological samples. For spherical objects, such as cells in suspension, microgel beads, or liquid droplets, a single QPI image is sufficient to extract the radius and the average refractive index. This technique is invaluable, as it allows the characterization of large sample populations at high measurement rates. However, until now, no universal software existed that could perform this type of analysis. Besides the choice of imaging modality and the variety in imaging software, the main difficulty has been to automate the entire analysis pipeline from raw data to ensemble statistics.

Results
We present DryMass, a powerful tool for QPI that covers all relevant steps from loading experimental data (multiple file formats supported), computing the phase data (built-in, automated hologram analysis), performing phase background corrections (offset, tilt, second order polynomial) to fitting scattering models (light projection, Rytov approximation, Mie simulations) to spherical phase objects for the extraction of dry mass, radius, and average refractive index. The major contribution of DryMass is a user-convenient, reliable, reproducible, and automated analysis pipeline for an arbitrary number of QPI datasets of arbitrary sizes.

Conclusion
DryMass is a leap forward for data analysis in QPI, as it not only makes it easier to visualize raw QPI data and reproduce previous results in the field, but it also opens up QPI analysis to users without a background in programming or phase imaging.
Biomarker roles identification of miR-106 family for predicting the risk and poor survival of colorectal cancer
Authors: Peng Qiliang , Shen Yi , Zhao Peifeng , Cheng Ming , Zhu Yaqun , Xu Bo 
Published: June 2020

Abstract
Background
Recent studies have extensively investigated the roles of miR-106 in colorectal cancer (CRC). However, the associations and molecular mechanism underlying the roles of miR-106 in CRC remain unclear. We aimed to thoroughly investigate the biomarker roles of miR-106 for predicting the risk and survival outcome in CRC.

Methods
We first conducted a comprehensive meta-analysis to quantitatively evaluate the roles of miR-106 in the diagnosis and prognosis of CRC. Then, we qualitatively explored the biomarker roles of miR-106 in CRC through an integrative bioinformatics analysis.

Results
The results indicated that miR-106 yielded a combined AUC of 0.79 (95% CI: 0.76–0.83), with a pooled sensitivity of 0.50 (95% CI: 0.32–0.68) and a pooled specificity of 0.93 (95% CI: 0.79–0.98) for discriminating CRC cases from normal controls. Moreover, patients with higher expression of miR-106 were significantly associated with shorter disease-free survival (HR: 1.73; 95%CI: 1.23–2.44) and overall survival (HR: 1.39; 95%CI: 1.09–1.77). Finally, gene ontology and pathway analysis demonstrated that miR-106 family was highly involved in the initiation and progression of CRC and indicated the potential molecular mechanism for miR-106 in CRC.

Conclusions
Our results indicated that miR-106 showed promising potential as diagnostic and prognostic biomarker for CRC. Nevertheless, the underlying molecular mechanism of miR-106 family involved in CRC requires further investigation.
SCDb: an integrated database of stomach cancer
Authors: Gu Erli , Song Wei , Liu Ajing , Wang Hong 
Published: June 2020

AbstractBackgroundStomach cancer (SC) is a type of cancer, which is derived from the stomach mucous membrane. As there are non-specific symptoms or no noticeable symptoms observed at the early stage, newly diagnosed SC cases usually reach an advanced stage and are thus difficult to cure. Therefore, in this study, we aimed to develop an integrated database of SC.MethodsSC-related genes were identified through literature mining and by analyzing the publicly available microarray datasets. Using the RNA-seq, miRNA-seq and clinical data downloaded from The Cancer Genome Atlas (TCGA), the Kaplan-Meier (KM) survival curves for all the SC-related genes were generated and analyzed. The miRNAs (miRanda, miRTarget2, PicTar, PITA and TargetScan databases), SC-related miRNAs (HMDD and miR2Disease databases), single nucleotide polymorphisms (SNPs, dbSNP database), and SC-related SNPs (ClinVar database) were also retrieved from the indicated databases. Moreover, gene_disease (OMIM and GAD databases), copy number variation (CNV, DGV database), methylation (PubMeth database), drug (WebGestalt database), and transcription factor (TF, TRANSFAC database) analyses were performed for the differentially expressed genes (DEGs).ResultsIn total, 9990 SC-related genes (including 8347 up-regulated genes and 1643 down-regulated genes) were identified, among which, 65 genes were further confirmed as SC-related genes by performing enrichment analysis. Besides this, 457 miRNAs, 20 SC-related miRNAs, 1570 SNPs, 108 SC-related SNPs, 419 TFs, 44,605 CNVs, 3404 drug-associated genes, 63 genes with methylation, and KM survival curves of 20,264 genes were obtained. By integrating these datasets, an integrated database of stomach cancer, designated as SCDb, (available athttp://www.stomachcancerdb.org/) was established.ConclusionsAs a comprehensive resource for human SC, SCDb database will be very useful for performing SC-related research in future, and will thus promote the understanding of the pathogenesis of SC.
Network pharmacology to dissect the mechanisms of Yinlai Decoction for pneumonia
Authors: Xu Jingnan , Bai Chen , Huang Ling , Liu Tiegang , Wan Yuxiang , Zheng Zian , Ma Xueyan , Gao Fei , Yu He , Gu Xiaohong 
Published: June 2020

Abstract
Background
Pneumonia is a common respiratory disorder, which brings an enormous financial burden to the medical system. However, the current treatment options for pneumonia are limited because of drug resistance and side effects. Our previous study preliminarily confirmed that Yinlai Decoction (YD), a common prescription for pneumonia in clinical practice, can regulate the expression of inflammatory factors, but the mechanisms are unknown yet.

Methods
In our work, a method named network pharmacology was applied, which investigated the underlying mechanisms of herbs based on a variety of databases. We obtained bioactive ingredients of YD on TCMSP database and collected potential targets of these ingredients by target fishing. Then the pneumonia-related targets database was built by TTD, Drugbank, HPO, OMIM, and CTD. Based on the matching targets between YD and pneumonia, the PPI network was built by STRING to analyze the interactions among these targets and then input into Cytoscape for further topological analysis. DAVID and KEGG were utilized for GO and pathway enrichment analysis. Then rat model based on LPS stimulated pneumonia was used to verify the possible mechanism of YD in treating pneumonia.

Results
Sixty-eight active ingredients, 103 potential targets and 8 related pathways, which likely exert a number of effects, were identified. Three networks were constructed using Cytoscape, which were herb-component-network, YD-pneumonia target network, and herb-component-YD target-pneumonia network. YD was verified to treat LPS-induced pneumonia by regulating the inflammatory factor IL-6, which was a predicted target.

Conclusion
Network analysis indicated that YD could alleviate the symptoms and signs of pneumonia through regulating host immune inflammatory response, angiogenesis and vascular permeability, the barrier function of the airway epithelial cells, hormone releasing and cell growth, proliferation, and apoptosis.
Gangrenous mastitis in dromedary camels in UAE caused by Streptococcus agalactiae
Authors: El Tigani-Asil El Tigani Ahmed , Abdelwahab Ghada Elderdiri , Veedu Jayamohanan Thikkal Veedu Payyan , Khalafalla Abdelmalik Ibrahim , Mohamed Zayed Saud Abdullah , Ishag Hassan Zackaria Ali , Shah Asma Abdi Mohamed , Alhosani Mohamed Ali Abdulla , Al Muhairi Salama Suhail Mohammed 
Published: June 2020

Abstract
Background
Mastitis is a disease of economic concern that affects dairy industry worldwide. This study aimed to investigate and identify possible etiologies encountered in an episode of acute gangrenous mastitis in lactating she-camels in Al Dhafra region, Abu Dhabi Emirate, United Arab Emirates (UAE).
Beside the routine clinical examination, conventional bacteriological methods were used to isolate and identify possible aerobic/anaerobic bacterial or fungal pathogens from cultured milk samples collected from the mastitic she-camels. Moreover, quantitative real-time polymerase chain reaction (qPCR) was used for the detection of Mycoplasma agalactiae and Mycoplasma bovis strains, and the 16S rRNA gene was sequenced to confirm the isolation. The isolates were also tested for their susceptibility to antimicrobials.

Results
Acute gangrenous mastitis is reported in the dromedary camel herd with about 80% morbidity rate among lactating she-camels exhibited acute, painful hard swelling of affected teat, quarter or entire udder. About 41.7% of the infected animals were stamped out for culling due to complete or partial amputation of udder quarters. Streptococcus agalactiae was the sole isolated organism (6 isolates). The antimicrobial susceptibility testing revealed that, the Streptococcus agalactiae isolates were sensitive to both penicillin and ampicillin. Comparison of the 16S rRNA gene sequencing results by BLASTN confirmed the presence of Streptococcus agalactiae with high confidence (100% identity). Phylogenetic analysis indicated clustering of one isolate (CMAUAE accession number; MN267805.1) with Streptococcus agalactiae that infects multi-hosts including humans, while strains (CMBUAE to CMFUAE with accession numbers; MN267806.1 to MN267810.1 respectively) clustered with Streptococcus agalactiae that infects humans. No Mycoplasma spp was detected by qPCR analysis.

Conclusions
In the present study, the Streptococcus agalactiae was found to be the main cause of acute gangrenous mastitis in dromedary camels in UAE. More research should be done to investigate other possible causes of clinical or subclinical mastitis in dromedary camels in UAE.
Fatigue following radiotherapy of low-risk early breast cancer – a randomized controlled trial of intraoperative electron radiotherapy versus standard hypofractionated whole-breast radiotherapy: the COSMOPOLITAN trial (NCT03838419)
Authors: Forster Tobias , Jäkel Cornelia , Akbaba Sati , Krug David , Krempien Robert , Uhl Matthias , Häfner Matthias Felix , König Laila , Koerber Stefan Alexander , Harrabi Semi , Bernhardt Denise , Behnisch Rouven , Krisam Johannes , Hennigs Andre , Sohn Christof , Heil Jörg , Debus Jürgen , Hörner-Rieber Juliane 
Published: June 2020

Abstract
Background
Fatigue is one of the most common and distressing side-effects of breast cancer radiotherapy. According to current guidelines, accelerated partial breast irradiation (APBI) may be considered as an alternative treatment option for women with early-stage low-risk breast cancer. One method for APBI is single-dose intraoperative radiotherapy (IORT) applied directly to the tumor bed during breast conserving surgery (BCS). The COSMOPOLITAN trial therefore aims to analyze the intensity of fatigue following single-shot IORT with electrons (IOERT) compared to conventional hypofractionated whole breast irradiation (WBI) in low risk early breast cancer patients.

Methods
This trial is conducted as a multicenter, prospective, randomized, two-arm phase II study comparing the intensity of fatigue in early-stage breast cancer (cT1cN0cM0, tumor size < 2,5 cm, ER pos. Her2neu neg., age > 50 years) treated either with WBI or APBI after BCS. Secondary outcomes investigated are tumor control, overall survival (OS), disease-free survival (DFS), acute and chronic toxicity, quality of life (QoL) and cosmesis. A total of 202 patients will be randomized into two arms: Patients in arm A will receive WBI (40.05 Gy, 15 fractions) after surgical resection, while patients in arm B will receive IOERT (21 Gy to the 90%-isodose) during BCS. Fatigue will be assessed 12 weeks post surgery with the help of the Functional Assessment of Chronic Illness Therapy (FACIT) Fatigue Scale.

Discussion
The present trial aims to evaluate treatment response to compare single-shot intraoperative electron APBI to conventional WBI following BCS in early-stage low risk breast cancer patients. Fatigue is selected as the primary, patient-reported endpoint due its major clinical relevance.

Trial registration
The study is prospectively registered on February 12th, 2019: Clinicaltrials.gov, NCT03838419. “Intraoperative Electron Radiotherapy for Low-risk Early Breast Cancer (COSMOPOLITAN)”.

Study status
Ongoing study. Start of recruitment was December 2019.
Natural outcome of hemoglobin and functional recovery after the direct anterior versus the posterolateral approach for total hip arthroplasty: a randomized study
Authors: Cao Jia , Zhou Yiqin , Xin Wei , Zhu Jun , Chen Yi , Wang Bo , Qian Qirong 
Published: June 2020

AbstractBackgroundTotal hip arthroplasty (THA) is one of the most successful orthopedic surgeries. There are many common surgical approaches for THA. The direct anterior approach (DAA) and posterolateral approach (PLA) were compared, leading to controversial results.MethodsWe report on a prospective randomized study which compared the changes of perioperative hemoglobin (Hb), the Harris hip score (HHS) and a visual analog scale (VAS) pain score following THA using DAA or PLA. A total of 130 participants were randomly divided into two groups (65 DAA versus 65 PLA). Perioperative ΔHb and other clinical outcomes were recorded.ResultsA total of 130 participants completed follow-up, while 14 patients were not recorded in blood outcomes due to blood transfusions and complications. The average Hb decrease immediately after surgery in the DAA group was greater than that in the PLA group (21.1 versus 15.8 g/L,P< .001). However, post-operative Hb descent velocity was slower in the DAA group, and the lowest point was reached earlier. No significant differences in ΔHb levels could be observed after 1 month in the two groups. When compared with the PLA group, the DAA group had a shorter incision (9.1 versus 13.5 cm,P< .001) and shorter hospital stay (4.2 versus 4.7 days,P= .004). However, the operation time of the DAA group was longer (88.0 versus 66.8 min,P< .001). The DAA group had a better HHS and VAS pain score at 6 weeks post-surgery. However, no significant differences were observed at later time points.ConclusionWe concluded that DAA performed better on enhanced recovery after surgery (ERAS) than PLA in THA, while both DAA and PLA could result in a positive, similar result after 3 months.Trial registrationThe study was registered by the Chinese Clinical Trial Registry (ChiCTR1900020770, 19 January 2019).
Modulation of inflammatory factors predicts the outcome following spinal cord injury
Authors: Yu Zepeng , Sun Xingwei , Xia Rui , Chen Qian , Wu Qin , Zheng Weiwei 
Published: June 2020

AbstractBackgroundThe correlation between inflammatory responses caused by spinal cord injury (SCI) and the prognosis of patients with SCI still remains controversial.MethodsIn the present study, we preliminary investigated the serum levels of interleukin (IL)-4, IL-10, major histocompatibility complex (MHC)-I, and inducible nitric oxide synthase (iNOS) and compared the serum IL-4 and IL-10 expression in rats of high Basso-Beattie-Bresnahan (BBB) scores with these of low BBB scores. Besides, the infiltration of macrophage and the axonal regeneration of the injured spinal cord were observed from day 10 to day 30.ResultsWe found that higher serum levels of IL-4 and IL-10 can reflect the restorability degree of SCI and could be potential biomarkers for the prognosis of SCI. The infiltration of the M2 subtype of macrophage and the axons regrowth might contribute to a better prognosis.ConclusionsThe current study demonstrates that the serum levels of IL-4 and IL-10 are preliminarily adopted as serologic markers to forecast SCI, and high serum levels of IL-4 and IL-10 may indicate a better prognosis. Moreover, the way to promote macrophage polarization from M1 to M2 may contribute to better axonal regeneration.
H1-antihistamines as antischistosomal drugs: in vitro and in vivo studies
Authors: Xavier Rogério P. , Mengarda Ana C. , Silva Marcos P. , Roquini Daniel B. , Salvadori Maria C. , Teixeira Fernanda S. , Pinto Pedro L. , Morais Thiago R. , Ferreira Leonardo L. G. , Andricopulo Adriano D. , de Moraes Josué 
Published: June 2020

AbstractBackgroundSchistosomiasis is a socioeconomically devastating parasitic infection afflicting hundreds of millions of people and animals worldwide. It is the most important helminth infection, and its treatment relies solely on the drug praziquantel. Oral H1-antihistamines are available worldwide, and these agents are among the most widely used of all medications in children and adults. Given the importance of the drug repositioning strategy, we evaluated the antischistosomal properties of the H1-antihistamine drugs commonly used in clinical practices.MethodsTwenty-one antihistamine drugs were initially screened against adult schistosomesex vivo. Subsequently, we investigated the anthelmintic properties of these antihistamines in a murine model of schistosomiasis for both early and chronicS. mansoniinfections at oral dosages of 400 mg/kg single dose or 100 mg/kg daily for five consecutive days. We also demonstrated and described the ability of three antihistamines to induce tegumental damage in schistosomes through the use of scanning electron microscopy.ResultsFrom phenotypic screening, we found that desloratadine, rupatadine, promethazine, and cinnarizine kill adultS. mansoni in vitroat low concentrations (5–15 µM). These results were further supported by scanning electron microscopy analysis. In an animal model, rupatadine and cinnarizine revealed moderate worm burden reductions in mice harboring either early or chronicS. mansoniinfection. Egg production, a key mechanism for both transmission and pathogenesis, was also markedly inhibited by rupatadine and cinnarizine, and a significant reduction in hepatomegaly and splenomegaly was recorded. Although less effective, desloratadine also revealed significant activity against the adult and juvenile parasites.ConclusionsAlthough the worm burden reductions achieved are all only moderate, comparatively, treatment with any of the three antihistamines is more effective in early infection than praziquantel. On the other hand, the clinical use of H1-antihistamines for the treatment of schistosomiasis is highly unlikely.
Detection of gastrointestinal parasitism at recreational canine sites in the USA: the DOGPARCS study
Authors: Stafford Kristina , Kollasch Todd M. , Duncan Kathryn T. , Horr Stephanie , Goddu Troy , Heinz-Loomer Christine , Rumschlag Anthony J. , Ryan William G. , Sweet Sarah , Little Susan E. 
Published: June 2020

AbstractBackgroundThe rapid growth in off-leash dog parks provides opportunity for canine socialization activities but carries risk of exposure to intestinal parasites. This study assessed the prevalence of these infections in dogs visiting off-leash dog parks.MethodsFresh defecations were collected from dogs visiting parks in 30 metropolitan areas across the USA. Samples were analyzed by coproantigen immunoassay (CAI) (Fecal Dx® andGiardiaTest, IDEXX Laboratories, Inc.) and zinc sulfate centrifugal flotation (CF). Owners responded to a questionnaire on their dog’s signalment and use of heartworm/intestinal parasite control medications (HWCM).ResultsSamples were examined from 3006 dogs, 87.9% aged at least 12 months, visiting 288 parks. At least one intestinal parasite was detected in 622 (20.7%) samples, nematodes in 263 (8.8%), with hookworms, whipworms and ascarids in 7.1, 1.9 and 0.6% of samples, respectively. A sample positive for one or more intestinal parasites was found in 245 (85.1%) parks, with nematodes found in 143 (49.7%). Combined, CAI and CF detected 78.4% more intestinal nematode infections than CF alone. Hookworm and whipworm infections were detected in all age groups, but ascarids were only detected in dogs less than 4 years-old. Approximately 42% of dogs aged less than 1 year were positive for nematodes orGiardia. Based on owner reports, HWCM was current for 68.8% of dogs, dogs previously diagnosed with intestinal parasitism were more likely to be receiving a HWCM than those without such history, and a significantly lower (P = 0.0003) proportion of dogs receiving a HWCM were positive for intestinal nematodes compared with those not on such medication.ConclusionsIntestinal parasites, the most common of which wereGiardia,Ancylostoma caninumandTrichuris vulpis, were found in 20% of dogs and 85% of dog parks across the USA. Enhanced detection of canine intestinal parasitism was achieved by combining CF and CAI. Canine intestinal parasites are common across the USA and dog health can be improved by regular testing of fecal samples and routine administration of medications effective against the most common infections.