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1.
Background
Telepathology may play an important role in pathology consultation and quality control for cancer diagnosis in China, as the country has the largest population of cancer patients worldwide. In 2011, the Pathology Quality Control Center of China and Ministry of Health developed and implemented a nationwide telepathology consultation and quality control program for cancer diagnosis in China. We here report the results of the two-year implementation and experiences.Methods
the program built an Internet based telepathology platform to connect participating hospitals and expert consultants. The hardware and software used for the platform were validated in previous validation studies in China. The program had three regional centers consisting of Peking Union Medical College, Huasi Medical College of Sichuan and 2nd affiliated hospital of Zhejiang University. It also had 20 provincial consultation centers based in the provincial referral hospitals. 80 provincial or national pathologists served as expert consultants for the program, providing telepathology consultation for cancer diagnosis for more than 60 participating hospitals.Results
from 2011 to July 2013, 16,247 pathology cases were submitted to the platform for consultation. Among them, 84% were due to diagnostic difficulty and 16% were due to request by patients. The preliminary diagnosis provided by submitting pathologists were in agreement with expert opinion in 59.8% of cases but was in disagreement with expert opinion in 24.2% of cases. 16.0% of cases were not provided with preliminary diagnosis. The distribution of pathology cases by system or organ were: digestive system, 17.3%; gynecologic system, 16.7%; head and neck, 15.7%; bone and soft tissue, 10.4%; lung and mediastinum, 8.6%; breast, 7.6%; urinary system, 7.5%; hematopathology, 6.4%; skin, 5.2%; neuropathology, 2.5% and cytopathology, 1.3%. Expert consultants also provided assessment of quality of slide preparation and staining, online lectures and guidance for pathology quality control.Conclusion
our results of two years' implementation indicated that telepathology could solve the problem of uneven distribution of pathology resources and provide a solution for countrywide pathology quality control in China. Telepathology could play an important role in improving pathology diagnosis in China.2.
3.
Rodríguez JE 《Diagnostic pathology》2008,3(Z1):S8
Background
The application of Information and Communication Technologies (ICTs) in the field of university education can play an important role in order to fulfil the objectives of the European Space for Higher Education (ESHE). In the absence of an infrastructure that allows virtual preparations, the high definition video may become an alternative for many PC users and telepathology enthusiasts.Methods
We have begun a video biopsy discontinuous recording pilot programme, also known as interval cinematography, in order to give our students pathological images to gather documentary evidence to follow their clinical cases. We have a working post available with a ZEISS Axioshop 2 microscope connected to a JVC digital camera with a double output for video, a PVM_14N1MDE Sony Triniton colour monitor and a LG RH199 HDD-DVD recorder.Results
Pathologists can easily produce videos lasting between 45" and 5' according to the case. Later those videos are assessed all together and given to the student and/or the doctor who requested the case study.Conclusion
Better follow-up studies of the cases can be achieved using Discontinuous video recording of biopsies. This approach has also clinical benefits since it contributes to the enrichment of integral patient care.4.
Satomi Okano Ryosuke Tanaka Akie Okayama Etsushi Tsuchida Fumikatsu Nohara Nao Suzuki Toshio Okamoto Ken Nagaya Satoru Takahashi Hiroshi Azuma 《Journal of medical case reports》2017,11(1):359
Background
Basal meningoceles are rare congenital defects and often clinically occult until they result in life-threatening complications. Therefore, it is important to know the diagnostic clues to early diagnosis.Case presentation
We describe three cases of congenital basal meningocele in a 3-year-old Japanese boy, a 1-month-old Japanese baby boy, and a 10-month-old Japanese baby girl. One of our patients died of sepsis due to traumatic rupture of the meningocele during nasal suction. His meningocele remained undiagnosed until it resulted in the fatal complication. The other patients underwent surgical repair without any complications. Their meningoceles were complicated by midfacial anomalies including cleft palate and hypertelorism, or a sign of nasal obstruction such as snoring.Conclusions
These clinical features may be a clue to the early diagnosis of congenital basal meningocele, which enables its safe preoperative management and provides an opportunity for surgical repair before the condition results in serious complications.5.
Background
This paper examines how the adoption of a subject-specific library service has changed the way in which its users interact with a digital library. The LitMiner text-analysis application was developed to enable biologists to explore gene relationships in the published literature. The application features a suite of interfaces that enable users to search PubMed as well as local databases, to view document abstracts, to filter terms, to select gene name aliases, and to visualize the co-occurrences of genes in the literature. At each of these stages, LitMiner offers the functionality of a digital library. Documents that are accessible online are identified by an icon. Users can also order documents from their institution's library collection from within the application. In so doing, LitMiner aims to integrate digital library services into the research process of its users.Methods
Case studyResults
This integration of digital library services into the research process of biologists results in increased access to the published literature.Conclusion
In order to make better use of their collections, digital libraries should customize their services to suit the research needs of their patrons.6.
Benoît Plancoulaine Myriam Oger Nicolas Elie Philippe Belhomme Paulette Herlin Abir Nasri Célia Augé Mylène Brécin Jacques Marnay Catherine Bor-Angelier 《Diagnostic pathology》2014,9(Z1):S9
Background
Currently available microscope slide scanners produce whole slide images at various resolutions from histological sections. Nevertheless, acquisition area and so visualization of large tissue samples are limited by the standardized size of glass slides, used daily in pathology departments. The proposed solution has been developed to build composite virtual slides from images of large tumor fragments.Materials and methods
Images of HES or immunostained histological sections of carefully labeled fragments from a representative slice of breast carcinoma were acquired with a digital slide scanner at a magnification of 20×. The tiling program involves three steps: the straightening of tissue fragment images using polynomial interpolation method, and the building and assembling of strips of contiguous tissue sample whole slide images in × and y directions. The final image is saved in a pyramidal BigTiff file format. The program has been tested on several tumor slices. A correlation quality control has been done on five images artificially cut.Results
Sixty tumor slices from twenty surgical specimens, cut into two to twenty six pieces, were reconstructed. A median of 98.71% is obtained by computing the correlation coefficients between native and reconstructed images for quality control.Conclusions
The proposed method is efficient and able to adapt itself to daily work conditions of classical pathology laboratories.7.
Miriam Banas Sindy Neumann Johannes Eiglsperger Eric Schiffer Franz Josef Putz Simone Reichelt-Wurm Bernhard Karl Krämer Philipp Pagel Bernhard Banas 《Metabolomics : Official journal of the Metabolomic Society》2018,14(9):116
Introduction
Allograft rejection is still an important complication after kidney transplantation. Currently, monitoring of these patients mostly relies on the measurement of serum creatinine and clinical evaluation. The gold standard for diagnosing allograft rejection, i.e. performing a renal biopsy is invasive and expensive. So far no adequate biomarkers are available for routine use.Objectives
We aimed to develop a urine metabolite constellation that is characteristic for acute renal allograft rejection.Methods
NMR-Spectroscopy was applied to a training cohort of transplant recipients with and without acute rejection.Results
We obtained a metabolite constellation of four metabolites that shows promising performance to detect renal allograft rejection in the cohorts used (AUC of 0.72 and 0.74, respectively).Conclusion
A metabolite constellation was defined with the potential for further development of an in-vitro diagnostic test that can support physicians in their clinical assessment of a kidney transplant patient.8.
Background
The purpose of this study was to determing which psychological traits of Japanese type 2 diabetes patients would provide reliability and validity to the Japanese version of the Acceptance and Action Diabetes Questionnaire (AADQ-J).Methods
Various questionnaires were administered to type 2 diabetes patients who were registered on the database of the research service provider; data from a total of 600 patients (mean?±?SD age was 57.50?±?9.87 years, female 21.83%) were analyzed.Results
Three items were excluded because of psychometric concerns related to the original 11-item AADQ. Confirmation factor analyses revealed that the eight-item version demonstrated the best indicators of a goodness of fit. The questionnaire showed adequate internal consistency. The questionnaire demonstrated high measurement accuracy in broad trait values by the test information function of Item Response Theory. The questionnaire showed stronger positive correlations with self-care activities and HbA1c than with diabetes distress and depressive mood.Conclusions
The eight-item Japanese version of AADQ has reliability and validity for type 2 diabetes patients.9.
N. Cesbron A.-L. Royer Y. Guitton A. Sydor B. Le Bizec G. Dervilly-Pinel 《Metabolomics : Official journal of the Metabolomic Society》2017,13(8):99
Introduction
Collecting feces is easy. It offers direct outcome to endogenous and microbial metabolites.Objectives
In a context of lack of consensus about fecal sample preparation, especially in animal species, we developed a robust protocol allowing untargeted LC-HRMS fingerprinting.Methods
The conditions of extraction (quantity, preparation, solvents, dilutions) were investigated in bovine feces.Results
A rapid and simple protocol involving feces extraction with methanol (1/3, M/V) followed by centrifugation and a step filtration (10 kDa) was developed.Conclusion
The workflow generated repeatable and informative fingerprints for robust metabolome characterization.10.
Objective
To examine the activities of residual enzymes in dried shiitake mushrooms, which are a traditional foodstuff in Japanese cuisine, for possible applications in food processing.Results
Polysaccharide-degrading enzymes remained intact in dried shiitake mushrooms and the activities of amylase, β-glucosidase and pectinase were high. A potato digestion was tested using dried shiitake powder. The enzymes reacted with potato tuber specimens to solubilize sugars even under a heterogeneous solid-state condition and that their reaction modes were different at 38 and 50 °C.Conclusion
Dried shiitake mushrooms have a potential use in food processing as an enzyme preparation.11.
Rachel A. Spicer Christoph Steinbeck 《Metabolomics : Official journal of the Metabolomic Society》2018,14(1):16
Introduction
Data sharing is being increasingly required by journals and has been heralded as a solution to the ‘replication crisis’.Objectives
(i) Review data sharing policies of journals publishing the most metabolomics papers associated with open data and (ii) compare these journals’ policies to those that publish the most metabolomics papers.Methods
A PubMed search was used to identify metabolomics papers. Metabolomics data repositories were manually searched for linked publications.Results
Journals that support data sharing are not necessarily those with the most papers associated to open metabolomics data.Conclusion
Further efforts are required to improve data sharing in metabolomics.12.
Introduction
Untargeted metabolomics is a powerful tool for biological discoveries. To analyze the complex raw data, significant advances in computational approaches have been made, yet it is not clear how exhaustive and reliable the data analysis results are.Objectives
Assessment of the quality of raw data processing in untargeted metabolomics.Methods
Five published untargeted metabolomics studies, were reanalyzed.Results
Omissions of at least 50 relevant compounds from the original results as well as examples of representative mistakes were reported for each study.Conclusion
Incomplete raw data processing shows unexplored potential of current and legacy data.13.
Michael Safioleas Michael Stamatakos Panagiotis Safioleas Anastasios Smyrnis Constantinos Revenas Constantinos Safioleas 《International Seminars in Surgical Oncology : ISSO》2008,5(1):12
Purpose
Mirizzi syndrome is a rare complication of long standing cholelithiasis. The purpose of this study is to retrospectively estimate the diagnostic and treatment methods applied in patients with Mirizzi syndrome.Materials and methods
Our experience with 27 cases with Mirizzi syndrome is presented. They were diagnosed either by imaging techniques, or during surgical operation. All of the patients were managed surgically.Results
8 patients were diagnosed preoperatively and the rest intraoperatively. Morbidity rate after surgery was 18,5%, and mortality rate was zero. The patients presented free of symptoms three months after surgery during the follow-up.Conclusion
Mirizzi syndrome is rarely diagnosed preoperatively and US proved inadequate for this purpose. Surgery is the only therapy and usually provides additionally definitive diagnosis.14.
Egidio Imbalzano Sebastiano Quartuccio Eleonora Di Salvo Teresa Crea Marco Casciaro Sebastiano Gangemi 《Clinical and molecular allergy : CMA》2017,15(1):12
Background
Recently, some studies demonstrated that HMGB1, as proinflammatory mediator belonging to the alarmin family, has a key role in different acute and chronic immune disorders. Asthma is a complex disease characterised by recurrent and reversible airflow obstruction associated to airway hyper-responsiveness and airway inflammation.Objective
This literature review aims to analyse advances on HMGB1 role, employment and potential diagnostic application in asthma.Methods
We reviewed experimental studies that investigated the pathogenetic role of HMGB in bronchial airway hyper-responsiveness, inflammation and the correlation between HMGB1 level and asthma.Results
A total of 19 studies assessing the association between HMGB1 and asthma were identified.Conclusions
What emerged from this literature review was the confirmation of HMGB-1 involvement in diseases characterised by chronic inflammation, especially in pulmonary pathologies. Findings reported suggest a potential role of the alarmin in being a stadiation method and a marker of therapeutic efficacy; finally, inhibiting HMGB1 in humans in order to contrast inflammation should be the aim for future further studies.15.
Ferran Casbas Pinto Srinivarao Ravipati David A. Barrett T. Charles Hodgman 《Metabolomics : Official journal of the Metabolomic Society》2017,13(7):81
Introduction
It is difficult to elucidate the metabolic and regulatory factors causing lipidome perturbations.Objectives
This work simplifies this process.Methods
A method has been developed to query an online holistic lipid metabolic network (of 7923 metabolites) to extract the pathways that connect the input list of lipids.Results
The output enables pathway visualisation and the querying of other databases to identify potential regulators. When used to a study a plasma lipidome dataset of polycystic ovary syndrome, 14 enzymes were identified, of which 3 are linked to ELAVL1—an mRNA stabiliser.Conclusion
This method provides a simplified approach to identifying potential regulators causing lipid-profile perturbations.16.
Sonia Liggi Christine Hinz Zoe Hall Maria Laura Santoru Simone Poddighe John Fjeldsted Luigi Atzori Julian L. Griffin 《Metabolomics : Official journal of the Metabolomic Society》2018,14(4):52
Introduction
Data processing is one of the biggest problems in metabolomics, given the high number of samples analyzed and the need of multiple software packages for each step of the processing workflow.Objectives
Merge in the same platform the steps required for metabolomics data processing.Methods
KniMet is a workflow for the processing of mass spectrometry-metabolomics data based on the KNIME Analytics platform.Results
The approach includes key steps to follow in metabolomics data processing: feature filtering, missing value imputation, normalization, batch correction and annotation.Conclusion
KniMet provides the user with a local, modular and customizable workflow for the processing of both GC–MS and LC–MS open profiling data.17.
Eriko Tomitsuka Katsura Igai Kiyoshi Tadokoro Ayako Morita Jun Baba Wataru Suda Andrew R. Greenhill Paul F. Horwood Kevin W. Soli Peter M. Siba Shingo Odani Kazumi Natsuhara Hidetoshi Morita Masahiro Umezaki 《Metabolomics : Official journal of the Metabolomic Society》2017,13(9):105
Introduction
Adequate amount of proteins from foods are normally needed to maintain muscle mass of the human body. Although protein intakes of Papua New Guinea (PNG) highlanders are less than biologically adequate, protein deficiency related disorders have rarely been reported. It has been postulated that gut microbiota play a role in such low-protein-adaptation.Objective
To explore underlying biological mechanisms of low-protein adaptation among PNG highlanders by investigating metabolomic profiles of faecal water and urine.Methods
We performed metabolome analysis using faecal water extracted from faecal samples of PNG highlanders, PNG non-highlanders and Japanese subjects. We paid special attention to amino acids and other metabolites produced by gut microbiota, as well as to metabolites involved in nitrogen recycling in the human gut.Results
Our results indicated that amino acid levels were higher in faecal water from PNG highlanders than PNG non-highlanders, but amino acid levels did not differ between PNG highlanders and Japanese subjects. Among PNG highlander samples, amino acid levels tended to be higher in those who consumed less protein.Conclusion
We speculated that a greater proportion of urea was excreted to the intestine among the PNG highlanders than other groups, and that the urea was used for nitrogen salvage. Intestinal bacteria are essential for producing ammonia from urea and also for producing amino acids from ammonia, which is a key process in low-protein adaptation. Profiling the gut microbiota of PNG highlanders is an important avenue for further research into the mechanisms of low-protein adaptation.18.
Background
In recent years the visualization of biomagnetic measurement data by so-called pseudo current density maps or Hosaka-Cohen (HC) transformations became popular.Methods
The physical basis of these intuitive maps is clarified by means of analytically solvable problems.Results
Examples in magnetocardiography, magnetoencephalography and magnetoneurography demonstrate the usefulness of this method.Conclusion
Hardware realizations of the HC-transformation and some similar transformations are discussed which could advantageously support cross-platform comparability of biomagnetic measurements.19.
Matteo Brunelli Serena Beccari Romano Colombari Stefano Gobbo Luca Giobelli Andrea Pellegrini Marco Chilosi Maria Lunardi Guido Martignoni Aldo Scarpa Albino Eccher 《Diagnostic pathology》2014,9(Z1):S12
Background
Validation of digital whole slide images is crucial to ensure that diagnostic performance is at least equivalent to that of glass slides and light microscopy. The College of American Pathologists Pathology and Laboratory Quality Center recently developed recommendations for internal digital pathology system validation. Following these guidelines we sought to validate the performance of a digital approach for routine diagnosis by using an iPad and digital control widescreen-assisted workstation through a pilot study.Methods
From January 2014, 61 histopathological slides were scanned by ScanScope Digital Slides Scanner (Aperio, Vista, CA). Two independent pathologists performed diagnosis on virtual slides in front of a widescreen by using two computer devices (ImageScope viewing software) located to different Health Institutions (AOUI Verona) connected by local network and a remote image server using an iPad tablet (Aperio, Vista, CA), after uploading the Citrix receiver for iPad. Quality indicators related to image characters and work-flow of the e-health cockpit enterprise system were scored based on subjective (high vs poor) perception. The images were re-evaluated two weeks apart.Results
The whole glass slides encountered 10 liver: hepatocarcinoma, 10 renal carcinoma, 10 gastric carcinoma and 10 prostate biopsies: adenocarcinoma, 5 excisional skin biopsies: melanoma, 5 lymph-nodes: lymphoma. 6 immuno- and 5 special stains were available for intra- and internet remote viewing. Scan times averaged two minutes and 54 seconds per slide (standard deviation 2 minutes 34 seconds). Megabytes ranged from 256 to 680 (mean 390) per slide storage. Reliance on glass slide, image quality (resolution and color fidelity), slide navigation time, simultaneous viewers in geographically remote locations were considered of high performance score. Side by side comparisons between diagnosis performed on tissue glass slides versus widescreen were excellent showing an almost perfect concordance (0.81, kappa index).Conclusions
We validated our institutional digital pathology system for routine diagnostic facing with whole slide images in a cockpit enterprise digital system or iPad tablet. Computer widescreens are better for diagnosing scanned glass slide that iPad. For urgent requests, iPad may be used. Legal aspects have to be soon faced with to permit the clinical use of this technology in a manner that does not compromise patient care.20.
Marta Michalczuk Beata Urban Tadeusz Porowski Anna Wasilewska Alina Bakunowicz-Łazarczyk 《Metabolomics : Official journal of the Metabolomic Society》2018,14(6):82