bluuebunny/crossref_metadata_2025_split huggingface dataset:
How do guideline developers identify, incorporate and report patient preferences? An international cross-sectional survey
Authors: Blackwood Jayden , Armstrong Melissa J. , Schaefer Corinna , Graham Ian D. , Knaapen Loes , Straus Sharon E. , Urquhart Robin , Gagliardi Anna R. 
Published: May 2020

Abstract
Background
Guidelines based on patient preferences differ from those developed solely by clinicians and may promote patient adherence to guideline recommendations. There is scant evidence on how to develop patient-informed guidelines. This study aimed to describe how guideline developers identify, incorporate and report patient preferences.

Methods
We employed a descriptive cross-sectional survey design. Eligible organizations were non-profit agencies who developed at least one guideline in the past five years and had considered patient preferences in guideline development. We identified developers through the Guidelines International Network and publicly-available guideline repositories, administered the survey online, and used summary statistics to report results.

Results
The response rate was 18.3% (52/284). Respondents included professional societies, and government, academic, charitable and healthcare delivery organizations from 18 countries with at least 1 to ≥6 years of experience generating patient-informed guidelines. Organizations most frequently identified preferences through patient panelists (86.5%) and published research (84.6%). Most organizations (48, 92.3%) used multiple approaches to identify preferences (median 3, range 1 to 5). Most often, organizations used preferences to generate recommendations (82.7%) or establish guideline questions (73.1%). Few organizations explicitly reported preferences; instead, they implicitly embedded preferences in guideline recommendations (82.7%), questions (73.1%), or point-of-care communication tools (61.5%). Most developers had little capacity to generate patient-informed guidelines. Few offered training to patients (30.8%), or had dedicated funding (28.9%), managers (9.6%) or staff (9.6%). Respondents identified numerous barriers to identifying preferences. They also identified processes, resources and clinician- and patient-strategies that can facilitate the development of patient-informed guidelines. In contrast to identifying preferences, developers noted few approaches for, or barriers or facilitators of incorporating or reporting preferences.

Conclusions
Developers emphasized the need for knowledge on how to identify, incorporate and report patient preferences in guidelines. In particular, how to use patient preferences to formulate recommendations, and transparently report patient preferences and the influence of preferences on guidelines is unknown. Still, insights from responding developers may help others who may be struggling to generate guidelines informed by patient preferences.
Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions
Authors: Stephens Timothy G. , González-Pech Raúl A. , Cheng Yuanyuan , Mohamed Amin R. , Burt David W. , Bhattacharya Debashish , Ragan Mark A. , Chan Cheong Xin 
Published: May 2020

Abstract
Background
Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking.

Results
Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates.

Conclusions
Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution.
Arthroscopic approaches to and anatomy of the shoulder joint of cattle: a cadaver study
Authors: Fadul Mahmoud , von Rotz Alois , Alsaaod Maher , Sato Reiichiro , Steiner Adrian 
Published: May 2020

AbstractBackgroundArthroscopic surgery is described as a minimally invasive technique for diagnosis, exploration and treatment of joint disorders. It allows intraarticular structures to be assessed accurately, thereby improving the diagnostic capabilities, and it broadens the spectrum of surgical techniques feasible for treatment of articular pathologies in cattle.This study aimed to assess for cattle the described arthroscopic approaches to the shoulder joint of horses, and to describe the appearance of the corresponding intraarticular structures of the shoulder joint. Additionally, to perform histological examination where tissues were identified and assessed arthroscopically, but the tissue type was uncertain using cadaveric limbs from cattle of different age categories without any signs of orthopedic diseases of the front limbs.ResultsAn anatomic and arthroscopic investigation with 34-cadaveric forelimbs from 20-cattle was performed. The arthroscope was inserted either immediately cranial or 1-cm caudal to the tendon of the infraspinatus muscle for the cranial and caudal approaches, respectively. The shoulder joints were examined with the limbs in either horizontal non-pulled position, abducted non-pulled position using a three-pod limb holder adjustable in height, or horizontal manually pulled position. Arthroscopy was performed using a rigid 30°arthroscope (18-cm length, 4-mm outer diameter) to view the synovial pouches with their synovial villi and the following structures: cranial rim of the glenoid, cranial portion of the humeral head, incisura-glenoidalis, caudal rim of the glenoid, caudal portion of the humeral head, and cranial and caudal cul-de-sac. Abduction of the limb allowed improved visualization of the lateral portion of the joint. Pulling the limb facilitated investigation of the medial portion of the joint. Generally, the distention range was higher in younger as compared to adult cattle, and visualization of the medial portion of the joint was, therefore, facilitated in younger animals. The main complications observed were subcutaneous fluid extravasations and partial-thickness articular cartilages wear-lines.ConclusionThe described arthroscopic techniques allowed good overall visualization of the most relevant anatomical structures within the healthy cadaveric joint. Further investigations are warranted to evaluate the diagnostic and therapeutic applications of these techniques and the prognosis of arthroscopic surgery as a tool for the treatment of joint lesions.
Computed tomographic features of the prostatic gland in neutered and intact dogs
Authors: Kuhnt N. , Harder L. K. , Nolte I. , Wefstaedt P. 
Published: May 2020

AbstractBackgroundAim was to investigate age-dependent changes in the prostate of castrated dogs in computed tomographic (CT) examination.Thirty-six canine prostates were evaluated in pre- and post-contrast CT scans. Dogs were divided in groups with homogenous prostatic tissue (25/36) and with tissue alterations (11/36). Prostatic attenuation in Hounsfield Units (HU) and prostatic size were measured and a ratio of the prostatic size to the sixth lumbar vertebra was calculated. Additionally, the CT images of the prostate were compared with ultrasound examination.ResultsIn pre-contrast CT scans no significant differences were found in prostatic size between homogenous and altered prostatic tissue groups whereas prostatic attenuation differed significantly in post-contrast CT between these groups. The homogenous tissue pattern of homogeneous prostates could be confirmed in CT images and in ultrasound examination. Concerning prostates with alterations, the results differed between ultrasound and CT examination in four cases of 11 dogs with tissue alterations.ConclusionsCT is beneficial to examine the prostate of castrated dogs. The prostatic attenuation is characteristic for the prostatic morphology, which can vary due to ageing processes. Differences in attenuation and size can be found between prostates of castrated and intact dogs. Using contrast agent, CT can visualize prostatic alterations, which were not seen in ultrasound. The presented results should be considered preliminary until a study with larger sample size and histologic examination of the prostates is performed.
Critically appraised topic on adverse food reactions of companion animals (9): time to flare of cutaneous signs after a dietary challenge in dogs and cats with food allergies
Authors: Olivry Thierry , Mueller Ralf S. 
Published: May 2020

AbstractBackgroundAt this time, elimination diets followed by oral food challenges (OFCs) represent the “gold standard” for diagnosing skin-manifesting food allergies (FA) in dogs and cats. Regrettably, there is no clear consensus on how long one should wait for clinical signs to flare after an OFC before diagnosing or ruling-out a FA in a dog or a cat.ResultsWe searched two databases on October 23, 2019 to look for specific information on the time for a flare of clinical signs to occur during OFCs after elimination diets in dogs and cats with skin-manifesting FAs. Altogether, we reviewed the study results of nine papers that included 234 dogs and four articles containing data from 83 cats. As multiple OFCs could be done in the same patient and not all animals included were subjected to an OFC, we were able to compile 315 and 72 times to flare (TTF) after an OFC in dogs and cats, respectively. When regrouping all cases together, about 9% of dogs and 27% of cats exhibited a flare of clinical signs in the first day after an OFC; 21% of dogs and 29% of cats had such relapse by the end of the second day. The time needed for 50 and 90% of dogs to exhibit a deterioration of clinical signs (TTF50and TTF90) was 5 and 14, respectively; in cats, these times were 4 and 7 days, respectively. By 14 days after an OFC, nearly all food-allergic patients from both species had had a relapse of clinical signs. These results are limited by the likely under-reporting of flares that occur on the first day immediately following an OFC, the time in which IgE-mediated acute allergic reactions typically develop.ConclusionVeterinary clinicians performing an OFC need to wait for 14 and 7 days for more than 90% of dogs and cats with a skin-manifesting FA to have a flare of clinical signs, respectively.
Risk stratification and prognostic factors in patients with pulmonary arterial hypertension and comorbidities a cross-sectional cohort study with survival follow-up
Authors: Xanthouli Panagiota , Koegler Maria , Marra Alberto M. , Benjamin Nicola , Fischer Lukas , Eichstaedt Christina A. , Harutyunova Satenik , Nagel Christian , Grünig Ekkehard , Egenlauf Benjamin 
Published: May 2020

Abstract
Background
The objective of this study was to analyze prognostic factors and risk stratification in patients with pulmonary arterial hypertension (PAH) and comorbidities.

Methods
Patients with invasively diagnosed PAH were included in the analysis. Comorbidities were clinically diagnosed as proposed in the 6th World Symposium of pulmonary hypertension. Uni- and multivariate analysis were employed for identification of factors predicting survival and time to first clinical worsening (TTCW). Risk stratification was based on parameters from ESC/ERS-guidelines 2015.

Results
In total 142 patients were enrolled in the study, 90 of them were diagnosed as PAH without and 52 with comorbidities. All patients received targeted PAH therapy and were followed for 3.3 ± 2.4 years. In PAH patients without comorbidities survival and TTCW were significantly associated with reduced 6-min walking distance (6MWD), elevated N-terminal pro brain natriuretic peptide (NT-proBNP), WHO-functional class (WHO-FC) and right atrial (RA) area. In the multivariate analysis, 6MWD was an independent predictor for survival (p = 0.002) and WHO-FC for TTCW (p = 0.001). In patients with PAH and comorbidities these parameters had no significant association with survival and TTCW. Average risk score was significantly associated with survival (p = 0.001) and TTCW (p = 0.013) in PAH but not in PAH with comorbidities (both p > 0.05; figure 1).

Conclusion
Risk stratification based on ESC/ERS-guidelines could only be confirmed in patients without comorbidities, but not in patients with PAH and comorbidities. The data of this study suggest, that a different risk stratification needs to be applied to PAH patients with comorbidities. Further studies are needed to confirm these results.

Trial registration
Not applicable, retrospective registry.
Nine glycolysis-related gene signature predicting the survival of patients with endometrial adenocarcinoma
Authors: Liu JinHui , Li SiYue , Feng Gao , Meng HuangYang , Nie SiPei , Sun Rui , Yang Jing , Cheng WenJun 
Published: May 2020

Abstract
Background
Endometrial cancer is the fourth most common cancer in women. The death rate for endometrial cancer has increased. Glycolysis of cellular respiration is a complex reaction and is the first step in most carbohydrate catabolism, which was proved to participate in tumors.

Methods
We analyzed the sample data of over 500 patients from TCGA database. The bioinformatic analysis included GSEA, cox and lasso regression analysis to select prognostic genes, as well as construction of a prognostic model and a nomogram for OS evaluation. The immunohistochemistry staining, survival analysis and expression level validation were also performed. Maftools package was for mutation analysis. GSEA identified Glycolysis was the most related pathway to EC. qRT-PCR verified the expression level of hub gene in clinical samples.

Results
According to the prognostic model using the train set, 9 glycolysis-related genes including B3GALT6, PAM, LCT, GMPPB, GLCE, DCN, CAPN5, GYS2 and FBP2 were identified as prognosis-related genes. Based on nine gene signature, the EC patients could be classified into high and low risk subgroups, and patients with high risk score showed shorter survival time. Time-dependent ROC analysis and Cox regression suggested that the risk score predicted EC prognosis accurately and independently. Analysis of test and train sets yielded consistent results A nomogram which incorporated the 9-mRNA signature and clinical features was also built for prognostic prediction. Immunohistochemistry staining and TCGA validation showed that expression levels of these genes do differ between EC and normal tissue samples. GSEA revealed that the samples of the low-risk group were mainly concentrated on Bile Acid Metabolism. Patients in the low-risk group displayed obvious mutation signatures compared with those in the high-risk group. The expression levels of B3GALT6, DCN, FBP2 and GYS2 are lower in tumor samples and higher in normal tissue samples. The expression of CAPN5 and LCT in clinical sample tissues is just the opposite.

Conclusion
This study found that the Glycolysis pathway is associated with EC and screened for hub genes on the Glycolysis pathway, which may serve as new target for the treatment of EC.
Genomic characterization of a newly established esophageal squamous cell carcinoma cell line from China and published esophageal squamous cell carcinoma cell lines
Authors: Li Xiang , Tian Dongping , Guo Yi , Qiu Shiyue , Xu Zexin , Deng Wen , Su Min 
Published: May 2020

Abstract
Background
Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent malignancies and a major cause of cancer related death worldwide, especially in China. Cell lines are widely used disease models for basic medical research, however, well characterized ESCC cell models from China were seldom reported. Misidentifying and cross-contaminations of cell lines also hamper the way of producing solid and reproductive data.

Methods
CSEC216 was originated from a 45-year-old male ESCC patient from Chaoshan littoral, China. Specimens were minced into fragments and seeded in T-25 flask for primary culture. Immunoflourescence staining was performed for identifying the origination and proliferation activity. In vitro migration and invasion abilities was tested by transwell assay. DNA Short Tandem Repeats profiling was implemented for cell authorization. Karyotype was investigated by spectrum karyotyping. Whole genome sequencing was utilized to investigate genomic alterations. Background information and genomic mutation data of published ESCC cell lines were obtained from online databases.

Results
CSEC216 was an uncontaminated cell line, exhibited epithelial cell features with polygonal morphology and adherent growth as monolayer. Immuno staining demonstrated its epithelial origination and high proliferation rate. The Population Doubling time was 29.7 h. The karyotype demonstrated tumor cell patterns with aneuploidy and complex chromosomal aberrations. Mutation signatures, genes with SNA or CNA of CSEC216 and published ESCC cell lines were similar with the mutation spectrum of original ESCC tumors.

Conclusions
ESCC cell line CSEC216 from high incidence region in China was established with no cross-contamination. Biological features were studied. Genomic mutation features of CSEC216 and 28 ESCC cell lines were characterized which provided thorough cytogenetic background that facilitated future usage.
Purification and production of Plasmodium falciparum zygotes from in vitro culture using magnetic column and Percoll density gradient
Authors: Zhou Yaxian , Grieser Alexis M. , Do Julie , Itsara Leslie S. , Vaughan Ashley M. , Ghosh Anil K. 
Published: May 2020

AbstractBackgroundPlasmodium falciparumzygotes develop in the mosquito midgut after an infectious blood meal containing mature male and female gametocytes. Studies of mosquito-producedP. falciparumzygotes to elucidate their biology and development have been hampered by high levels of contaminating mosquito proteins and macromolecules present in zygote preparations. Thus, no zygote-specific surface markers have been identified to date. Here, a methodology is developed to obtain large quantities of highly purified zygotes using in vitro culture, including purification methods that include magnetic column cell separation (MACS) followed by Percoll density gradient centrifugation. This straightforward and effective approach provides ample material for studies to enhance understanding of zygote biology and identify novel zygote surface marker candidates that can be tested as transmission blocking vaccine (TBV) candidates.MethodsPlasmodium falciparumgametocyte cultures were established and maintained from asexual cultures. Gametocytes were matured for 14 days, then transferred into zygote media for 6 h at 27 ± 2 °C to promote gamete formation and fertilization. Zygotes were then purified using a combination of MACS column separation and Percoll density gradient centrifugation. Purity of the zygotes was determined through morphological studies: the parasite body and nuclear diameter were measured, and zygotes were further transformed into ookinetes. Immunofluorescence assays (IFA) were also performed using the ookinete surface marker, Pfs28.ResultsAfter stimulation, the culture consisted of transformed zygotes and a large number of uninfected red blood cells (RBCs), as well as infected RBCs with parasites at earlier developmental stages, including gametes, gametocytes, and asexual stages. The use of two MACS columns removed the vast majority of the RBCs and gametocytes. Subsequent use of two Percoll density gradients enabled isolation of a pure population of zygotes. These zygotes transformed into viable ookinetes that expressed Pfs28.ConclusionThe combined approach of using two MACS columns and two Percoll density gradients yielded zygotes with very high purity (45-fold enrichment and a pure population of zygotes [approximately 100%]) that was devoid of contamination by other parasite stages and uninfected RBCs. These enriched zygotes, free from earlier parasites stages and mosquito-derived macromolecules, can be used to further elucidate the biology and developmental processes ofPlasmodium.
Monitoring the durability of the long-lasting insecticidal nets Olyset® and PermaNet® 2.0 in similar use environments in Zanzibar
Authors: Haji Khamis Ameir , Khatib Bakari Omar , Obi Emmanuel , Dimoso Kanuth , Koenker Hannah , Babalola Stella , Greer George , Serbantez Naomi , Abbas Faiza , Ali Abdullah , Blaufuss Sean , Olapeju Bolanle , Kilian Albert 
Published: May 2020

Abstract
Background
Malaria transmission in Zanzibar has dramatically reduced in recent years but vector control interventions such as long-lasting insecticidal nets (LLIN) must continue to reach malaria elimination. To achieve this, the Zanzibar Malaria Elimination Programme needs actionable evidence of the durability of the LLIN brands distributed. This study compared physical and insecticidal durability of two LLIN brands: Olyset® and PermaNet© 2.0 in two similar districts on the islands of Unguja and Pemba.

Methods
This was a prospective cohort study of representative samples of households from two districts, recruited at baseline 4 months after the mass campaign. All campaign nets in these households were labelled and followed up over a period of 33 months. Primary outcome was the “proportion of nets surviving in serviceable condition” based on attrition and integrity measures and the median survival in years. The outcome for insecticidal durability was determined by bio-assay from sub-samples of campaign nets.

Results
A total of 834 campaign nets (121% of target) from 299 households were included in the study. Definite outcomes could be determined for 86% of the cohort nets in Unguja (PermaNet® 2.0) and 89% in Pemba (Olyset®). After 33 months, physical survival in serviceable condition was 55% in Unguja and 51% in Pemba. Estimated median survival was lower in Pemba at all time points with 2.3–2.7 years compared to 3.1–3.3 yeas in Unguja. Multivariable Cox proportionate hazard models confirmed the difference between brands (p < 0.0001) and identified household net-care attitude (p = 0.007) and folding of hanging nets during the day (p < 0.0001) as significant determinants, in addition to exclusive use of nets by adults (p = 0.03) and use only over a finished bedframe (p = 0.01). Optimal insecticidal effectiveness was 80% or higher for both brands at all time points when both cone bio-assays and tunnel tests were applied.

Conclusions
After 3 years of follow-up, Olyset® LLIN showed significantly lower physical survival compared to PermaNet® 2.0 LLIN even after adjusting for other variables of net-use environment and net handling. This suggests that the differences were driven by the textile characteristics of the LLIN brands.