bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of the ‘People–Processes–Paradigm’ critical analysis tool for mortality and morbidity reviews: improving understanding of systems factors
Authors: Salindera Shehnarz , Brennan Meagan 
Published: May 2020

AbstractBackgroundThe impact of systems problems and human factors on delivering safe, high‐quality patient care is well recognized. In the surgical setting, mortality and morbidity reviews (MMRs) are the key forum for reviewing and analysing adverse events in patient care yet there is a paucity of simple tools for undertaking such analyses. The aim of this study was to develop and pilot a new tool for analysing mortality and morbidity cases incorporating human factors and systems analysis.MethodsThe published literature, professional standards, guidelines and existing audit tools for MMRs were reviewed. The ‘People–Processes–Paradigm’ tool was developed and pilot testing was undertaken and stakeholder feedback was obtained.ResultsModels found for undertaking systems‐based analysis of adverse surgical events included the 3D model, SEIPS and the Queensland Health human error and patient safety (HEAPS) Incident Management Tool. Guidelines for standards in MMRs are provided by the Royal Australasian College of Surgeons, New South Wales Clinical Excellence Commission and Australia and New Zealand audit of surgical mortality (ANZASM). The People–Processes–Paradigm model incorporates these standards and evidence‐based systems analysis tools into a single effective tool. The pilot study evaluating the use of this tool demonstrated it to be practical and easily applicable to regular use by clinicians, with the ability to be tailored to individual health service use. Improvements such as electronic format and clarification of case selection processes were recommended by users.ConclusionThe People–Processes–Paradigm tool has been developed for surgeons by surgeons incorporating current professional, legal and regulatory requirements in Australasia, easily transferrable to electronic platforms. This model requires further testing for validation.
Relative contribution of ancient woodland indicator and non‐indicator species to herb layer distinctiveness in ancient semi‐natural, ancient replanted, and recent woodland
Authors: Swallow Kelly A. , Wood Matt J. , Goodenough Anne E. 
Published: May 2020

AbstractQuestionsThe floristic distinctiveness of ancient woodland relative to recent woodland is commonly measured by Ancient Woodland Indicator (AWI) species richness. However, focussing on a pre‐defined subset of species means that wider community‐level differences may be overlooked. Can ancient semi‐natural, ancient replanted, and recent woodland herb layer communities be distinguished by alpha, beta, and gamma diversity? How are any differences partitioned across AWI and non‐AWI species communities?LocationCotswolds, southwest UK.MethodsTo quantify AWI and non‐AWI responses to stand history in ancient semi‐natural, ancient replanted, and recent woodland, we conducted floristic surveys of 45 sites. Using a modelling approach, we tested the relative and additive contribution of alpha‐scale AWI and non‐AWI species richness to woodland distinctiveness. Ordination was applied to analyse beta species composition distinctiveness, and multilevel pattern analysis was used to examine which species were significant contributors to gamma‐scale richness differences.ResultsAWI species richness models significantly distinguished ancient semi‐natural woodland from both ancient replanted and recent woodland at the alpha scale. For the classification of ancient semi‐natural woodland and recent woodland, the hierarchical inclusion of non‐AWI alpha richness resulted in a superior and more significant model. AWI gamma richness was numerically similar for all three woodland categories, whereas non‐AWI was more varied. AWI and non‐AWI species composition showed significant beta diversity differences among all woodland types, with six species being significant drivers of differences.ConclusionsOur results have revealed previously undetected complexity in the contributions of AWI and non‐AWI species to floristic distinctiveness of ancient woodland. In addition to traditional AWI species, the non‐AWI assemblage also exhibited a sensitivity to habitat continuity that: (a) adds weight to the argument that ancient woodland is floristically distinct from recent woodland; and (b) provides a useful measure of success for ancient replanted woodland restoration.
FAM111B enhances proliferation of KRAS‐driven lung adenocarcinoma by degrading p16
Authors: Kawasaki Keisuke , Nojima Satoshi , Hijiki Sachiko , Tahara Shinichiro , Ohshima Kenji , Matsui Takahiro , Hori Yumiko , Kurashige Masako , Umeda Daisuke , Kiyokawa Hiroki , Kido Kansuke , Okuzaki Daisuke , Morii Eiichi 
Published: May 2020

AbstractLung cancer is a common type of cancer that represents a health problem worldwide; lung adenocarcinoma (LUAD) is a major subtype of lung cancer. Although several treatments for LUAD have been developed, the mortality rate remains high because of uncontrollable progression. Further biological and clinicopathological studies are therefore needed. Here, we investigated the role of family with sequence similarity 111 member B (FAM111B), which is highly expressed in papillary‐predominant LUAD; however, its role in cancer is unclear. An immunohistochemical analysis confirmed that papillary‐predominant adenocarcinomas exhibited higher expression of FAM111B, compared with lepidic‐predominant adenocarcinomas. Additionally, FAM111B expression was significantly correlated with clinical progression. In vitro functional analyses using FAM111B‐knockout cells demonstrated that FAM111B plays an important role in proliferation and cell cycle progression of KRAS‐driven LUAD under serum‐starvation conditions. Furthermore, FAM111B regulated cyclin D1‐CDK4‐dependent cell cycle progression by degradation of p16. In summary, we revealed the clinical importance of FAM111B in human tumor tissues, as well as its function as a degradative enzyme. Therefore, FAM111B has potential as a clinicopathological prognostic marker for LUAD.
KinomeRun: An interactive utility for kinome target screening and interaction fingerprint analysis towards holistic visualization on kinome tree
Authors: Ansar Samdani , Vetrivel Umashankar 
Published: May 2020

AbstractKinases are key targets for many of the pathological conditions. Inverse screening of ligands serves as an essential mode to identify potential kinase targets in modern drug discovery research. Hence, we intend to develop KinomeRun, a robust pipeline for inverse screening and kinome tree visualization through the seamless integration of kinome structures, docking and kinome–drug interaction fingerprint analysis. In this pipeline, the hurdle of residue numbering in kinome is also resolved by creating a common index file with the conserved kinase pocket residues for comparative interaction analysis. KinomeRun can be used to screen the ligands of interest docked against multiple kinase structures in parallel around the kinase binding site and also to filter out the targets with unique interaction patterns. This automation is essential for prioritization of kinase targets that show specificity for a given drug and will also serve as a crucial tool kit for holistic approaches in kinase drug discovery. KinomeRun is developed using python and bash programming language and is distributed freely under the GNU GPL licence‐3.0 and can be downloaded at https://github.com/inpacdb/KinomeRun. The tutorial videos for installation, target screening and customized filtration are available at https://www.youtube.com/playlist?list=PLuIaEFtMVgQ7v__WigQH9ilGVxrfI1LKs and also be downloaded for offline viewing from the github link.
Targeting the interleukin‐7 receptor alpha by an anti‐CD127 monoclonal antibody improves allergic airway inflammation in mice
Authors: Mai Hoa Le , Nguyen Thi Van Ha , Bouchaud Grégory , Henrio Kelly , Cheminant Marie‐Aude , Magnan Antoine , Brouard Sophie 
Published: May 2020

AbstractBackgroundInterleukin‐7 (IL‐7) is the most important cytokine for T‐cell homeostasis. IL‐7 signals through the IL‐7 receptor (IL‐7R) which is composed of an alpha chain (IL‐7Rα), also called CD127 and a common gamma chain. T lymphocytes, especially T helper type 2, play a crucial role in the pathobiology of allergic asthma.ObjectiveTo study the effects of an anti‐CD127 monoclonal antibody (mAb) in a murine model of allergic airway inflammation induced by house dust mite (HDM).MethodsAllergic airway inflammation was induced in mice using a protocol comprising 4 weekly percutaneous sensitizations followed by 2 weekly intranasal challenges with total HDM extracts and treated by intraperitoneal injections of an anti‐CD127 mAb. Because CD127 is shared by both IL‐7R and the receptor for thymic stromal lymphopoietin (TSLP), a group of mice was also treated with an anti‐IL‐7 mAb to block only the IL‐7 signalling pathway.ResultsAnti‐CD127 mAb‐treated mice showed significantly lower airway resistance in response to methacholine and improvement in lung histology compared with isotype mAb‐treated animals. Anti‐CD127 mAb treatment significantly decreased the mRNA expression of Th2 cytokines (IL‐4, IL‐5, and IL‐13) and chemokines (CCL5/RANTES) in lung tissue, decreased the secretion of Th2 cytokines (IL‐4, IL‐5, and IL‐13) and chemokines (CXCL1 and CCL11/eotaxin) in bronchoalveolar lavage fluid (BALF), decreased serum HDM‐specific IgE, and reduced the number of total leucocytes and leucocyte subpopulations such as eosinophils, macrophages, lymphocytes, T lymphocytes, and ILC2 in BALF and lung tissue. Mice treated with anti‐IL‐7 mAb also showed less allergic airway inflammation as evidenced by significantly lower airway resistance and fewer leucocytes in BALF and lung tissue compared to mice treated with the corresponding isotype control mAb.Conclusion and Clinical RelevanceTargeting the IL‐7Rα by an anti‐CD127 mAb improves allergic airway inflammation in mice and presents as a potential therapeutic approach for allergic asthma.
Persistent viral shedding of SARS‐CoV‐2 in faeces – a rapid review
Authors: Gupta S. , Parker J. , Smits S. , Underwood J. , Dolwani S. 
Published: May 2020

AbstractAimIn addition to respiratory symptoms, COVID‐19 can present with gastrointestinal complaints suggesting possible faeco‐oral transmission. The primary aim of this review was to establish the incidence and timing of positive faecal samples for SARS‐CoV‐2 in patients with COVID‐19.MethodsA systematic literature review identified studies describing COVID‐19 patients tested for faecal virus. Search terms for MEDLINE included ‘clinical’, ‘faeces’, ‘gastrointestinal secretions’, ‘stool’, ‘COVID‐19’, ‘SARS‐CoV‐2’ and ‘2019‐nCoV’. Additional searches were done in the American Journal of Gastroenterology, Gastroenterology, Gut, Lancet Gastroenterology and Hepatology, the World Health Organization Database, the Centre for Evidence‐Based Medicine, New England Journal of Medicine, social media and the National Institute for Health and Care Excellence, bioRxiv and medRxiv preprints. Data were extracted concerning the type of test, number and timing of positive samples, incidence of positive faecal tests after negative nasopharyngeal swabs and evidence of viable faecal virus or faeco‐oral transmission of the virus.ResultsTwenty‐six relevant articles were identified. Combining study results demonstrated that 53.9% of those tested for faecal RNA were positive. The duration of faecal viral shedding ranged from 1 to 33 days after a negative nasopharyngeal swab with one result remaining positive 47 days after onset of symptoms. There is insufficient evidence to suggest that COVID‐19 is transmitted via faecally shed virus.ConclusionThere is a high rate of positive polymerase chain reaction tests with persistence of SARS‐CoV‐2 in faecal samples of patients with COVID‐19. Further research is needed to confirm if this virus is viable and the degree of transmission through the faeco‐oral route. This may have important implications on isolation, recommended precautions and protective equipment for interventional procedures involving the gastrointestinal tract.
The shared epitope phenomenon—A potential impediment to virtual crossmatch accuracy
Authors: Garcia‐Sanchez Cynthia , Usenko Crystal Y. , Herrera Nancy D. , Tambur Anat R. 
Published: May 2020

AbstractWith the implementation of the new kidney allocation system (KAS), there is increased reliance on a virtual crossmatch/histocompatibility risk assessment (vXM) for evaluating potential presence, as well as strength, of HLA antibodies against a potential donor. The accuracy of such an assessment depends on the precision in the identification of the recipient's antibody profile and the potential donor's HLA typing. While the development of the single antigen bead (SAB) multiplex assay has improved the sensitivity and specificity of HLA antibody detection, several limitations of the assay (specific to certain sensitized patients) can complicate accurate interpretation of results. In this report, we focus on the “shared‐epitope” phenomenon, a condition in which antibody strength can be underrepresented, or its presence completely missed, due to binding of the antibody to competing targets on multiple antigens (beads), effectively “diluting” the resulting MFI readout. Here, we provide a relevant background to understand this phenomenon and present a couple of case studies illustrating how it can be investigated, leading to a more accurate histocompatibility consultation.
Association of local complete response with prognosis after salvage photodynamic therapy for esophageal squamous cell carcinoma
Authors: Amanuma Yusuke , Horimatsu Takahiro , Ohashi Shinya , Tamaoki Masashi , Muto Manabu 
Published: May 2020

ObjectivesPhotodynamic therapy (PDT) is an effective salvage endoscopic treatment for local failure at the primary site after chemoradiotherapy (CRT) in esophageal cancer patients. However, the contribution of local control by salvage PDT to the prognosis is unclear. We investigated whether complete response at primary site by salvage PDT could improve the prognosis.MethodsBetween January 2008 and March 2016, 34 patients received salvage PDT for local failure of esophageal cancer limited to stage T1–2 after definitive CRT or radiotherapy. Local complete response (L‐CR) rate, adverse events, overall survival (OS), and progression‐free survival (PFS) were assessed retrospectively.ResultsLocal complete response rates after PDT were 68% (23/34; 95% CI, 50–83%) in all patients: 81% (17/21; 95% CI, 58–95%) for stage T1 and 46% (6/13; 95% CI, 19–75%) for stage T2 patients. Grade 3 esophageal stricture occurred in one patient. The median follow‐up was 26.0 months (range, 3.7–93.6 months); 21 patients died. The median survival times were 54.3 months in patients who achieved L‐CR after PDT (L‐CR group) and 19.8 months in those who did not (non‐CR group). The 2‐year OS rates were 79% (95% CI, 54–92%) in the L‐CR group and 40% (95% CI, 11–68%) in the non‐CR group (P = 0.0389; log‐rank test). The median PFS was 21.2 months in the L‐CR group and 1.9 months in the non‐CR group (P < 0.001; log‐rank test).ConclusionAchieving L‐CR by salvage PDT for local failure after CRT in esophageal cancer was associated with good prognosis.
Short‐term high‐dose zoledronic acid enhances crystallinity in mandibular alveolar bone in rats
Authors: Coutel Xavier , Falgayrac Guillaume , Penel Guillaume , Olejnik Cécile 
Published: May 2020

Owing to its antiresorptive properties, zoledronic acid (ZOL) is commonly used in the management of benign as well as malignant bone diseases. This molecule targets sites where bone is actively remodeling, and high concentrations have been reported in the jaw. The purpose of this study was to investigate whether treatment of male rats with ZOL, at a dosage equivalent to that used for antitumor treatment, impacts the short‐term qualitative properties of mandibular bone independent of bone remodeling. Thirty rats were randomly assigned to treatment either with ZOL or with serum‐vehicle (control) (weekly injections: 100 μg kg−1 for 6 wk, n = 15 per group). Using the tetracycline double‐labeling technique, remodeled bone areas, corresponding to the preferential site of bisphosphonate binding, were found in the alveolar bone along the alveolar bone proper. The composition of bone in these areas was characterized using Raman microspectroscopy and compared with adjacent, non‐remodeled, older bone. The ZOL‐treated group exhibited higher crystallinity in the remodeled bone areas (+2%), reflecting an early maturation of the apatite mineral after ZOL injection. Our findings highlight a direct and rapid effect of clinically relevant anti‐tumoral ZOL doses on the qualitative properties of mandibular bone, especially on mineral crystallinity in the vicinity of the teeth, namely, the alveolar bone proper.
Population expansion and breeding success of Bearded VulturesGypaetus barbatusin the French Pyrenees: results from long‐term population monitoring
Authors: Arroyo Beatriz , Lafitte Jerome , Sourp Eric , Rousseau Denis , Albert Luc , Heuacker Vadim , Terrasse Jean François , Razin Martine 
Published: May 2020

Based on monitoring of Bearded Vultures over 24 years in the French Pyrenees, we assessed factors explaining temporal and spatial variations in numbers and breeding performance. The number of territorial pairs increased throughout the study period from 16 in 1994 to 44 in 2017. No significant negative trends in mean productivity (fledglings per territorial pair) were detected with increasing population size. Colonization probability increased significantly with breeding population size the previous year and with the regular provision of supplementary food in the territory the winter when colonization occurred. Colonization of new territories simultaneously increased the distribution range and local densities, but we found no effect of number of near neighbours on productivity. Pairs having bred less than 5 years together had a much lower probability of laying clutches, and higher lay rates were observed inside or close to protected areas after accounting for pair‐bond length, so productivity of territories inside protected areas was significantly higher. Nest success decreased with advanced lay date and increased with winter food abundance. Nesting failures in the study area were frequently associated with harsh weather. Additionally, disturbance by human activities was the second most important identified cause of breeding failure. The probability of failing due to disturbance was higher in western areas (where breeding areas are more accessible to humans), outside protected areas, and has increased with time. After a failure due to disturbance, there was a significantly higher probability of not producing a clutch the following year as compared with pairs that had not failed or had failed due to other causes, indicating deferred effects of disturbance. Our results show the benefits of conservation management actions, such as implementation of protected areas or designed supplementary food programmes in winter, to help range expansion. On the other hand, we did not find a significant effect of winter supplementary food on productivity. Management of feeding sites should be adapted to more specific planning, being used only in areas where natural food availability is scarce, avoiding its use close to breeding sites when juveniles disperse, and targeted mainly to help range expansion. Our results also highlight the importance of maintaining or enhancing good populations of wild ungulates and regulating human activities around nesting sites of this threatened species.
Post‐treatment endodontic pain following occlusal reduction in mandibular posterior teeth with symptomatic irreversible pulpitis and sensitivity to percussion: a single‐centre randomized controlled trial
Authors: Ahmed Y. E. , Emara R. S. , Sarhan S. M. , El Boghdadi R. M. , El‐Bayoumi M. A. A. , El‐Far H. M. M. , Sabet N. E. , Abou El‐Nasr H. M. , Gawdat S. I. , Amin S. A. W. 
Published: May 2020

AbstractAimThis randomized, prospective, controlled trial assessed the effect of occlusal reduction on post‐treatment endodontic pain and medication intake following root canal treatment of mandibular posterior teeth with symptomatic irreversible pulpitis with sensitivity to percussion treated in two visits.MethodologyThree hundred and eight patients were randomly assigned into two equal groups according to whether occlusal reduction was done or not (n = 154). For all patients, root canal treatment was carried out in two visits without intracanal medication. Patients assessed their pain using the 0–10 numerical rating scale (NRS) 6, 12, 24 and 48 h after the first visit (post‐instrumentation) and 6 and 12 h following root canal filling (post‐obturation). Patients, also, recorded their medication intake (sham or analgesic), post‐instrumentation and post‐obturation; patients initially received a sham capsule, but, if pain persisted, an analgesic was prescribed. Data were analysed using Mann–Whitney U‐test, Friedman’s test, Wilcoxon’s rank test and chi‐square (χ2) test. The relative risk (RR) and its 95% confidence interval (CI) were calculated for binary data.ResultsOcclusal reduction was associated with lower pain intensity than no occlusal reduction at 12 and 24 h post‐instrumentation (P < 0.05). Pain intensity significantly and gradually decreased with both groups at all post‐instrumentation and post‐obturation time‐points compared to preoperative pain (P < 0.05). The RR of moderate‐to‐severe pain was 0.61 (95% CI: 0.41, 0.91) 12 h post‐instrumentation, and the RR of pain incidence, regardless of its level, was 0.75 (95% CI: 0.61, 0.92) 24 h post‐instrumentation. There was no significant difference in medication intake (sham or analgesic) between groups (P > 0.05).ConclusionsOcclusal reduction was effective in reducing the intensity of postoperative pain 12 h and 24 h after root canal instrumentation in the first visit in patients with symptomatic irreversible pulpitis with sensitivity to percussion. Occlusal reduction lowered the risk of moderate‐to‐severe pain by about 40% 12 h post‐instrumentation and the overall risk of pain by 25% 24 h post‐instrumentation; yet, it did not affect medication intake.
Properties of C/C‐SiC composites produced via transfer moulding and inner siliconization
Authors: Ahmad Husam , Stiller Jonas , Päßler Erik , Nestler Daisy , Kroll Lothar , Wagner Guntram 
Published: May 2020

AbstractShort carbon fiber reinforced polymers (CFRP) are successfully prepared by transfer moulding technology. For this purpose, compounds on the basis of novolac/urotropin with different 6 mm chopped carbon fibers and silicon powder contents are produced utilizing a laboratory tempered sigma‐blade kneader. These compounds are then shaped into 46 × 8 × 3 mm3CFRP specimens using a transfer moulding machine. Depending on the material composition, the conversion to C/C‐SiC composites is performed through liquid silicon infiltration (LSI) process or inner siliconization. First, the short fiber content is varied between 30 and 50 wt% and its influence on the process and properties of the composites is studied. Second, an investigation of the inner siliconization through the co‐mixing of silicon powder (1‐23 wt% in CFRPs) during the compound production as well as a comparison with the external silicon infiltration process are presented and discussed. According to the results, the best mechanical properties are achieved at a fiber content of 40 wt% in the case of the external silicon infiltration and at silicon content below 14 wt% for composites produced by the inner siliconization process.