Exploring the Association of Cancer and Depression in Electronic Health Records: Combining Encoded Diagnosis and Mining Free Text Clinical Notes (Preprint)

Background

A cancer diagnosis is a source of psychological and emotional stress, which are often maintained for sustained periods of time that may lead to depressive disorders. Depression is one of the most common psychological conditions in patients with cancer. According to the Global Cancer Observatory, breast and colorectal cancers are the most prevalent cancers in both sexes and across all age groups in Spain.

Objective

This study aimed to compare the prevalence of depression in patients before and after the diagnosis of breast or colorectal cancer, as well as to assess the usefulness of the analysis of free-text clinical notes in 2 languages (Spanish or Catalan) for detecting depression in combination with encoded diagnoses.

Methods

We carried out an analysis of the electronic health records from a general hospital by considering the different sources of clinical information related to depression in patients with breast and colorectal cancer. This analysis included ICD-9-CM (International Classification of Diseases, Ninth Revision, Clinical Modification) diagnosis codes and unstructured information extracted by mining free-text clinical notes via natural language processing tools based on Systematized Nomenclature of Medicine Clinical Terms that mentions symptoms and drugs used for the treatment of depression.

Results

We observed that the percentage of patients diagnosed with depressive disorders significantly increased after cancer diagnosis in the 2 types of cancer considered—breast and colorectal cancers. We managed to identify a higher number of patients with depression by mining free-text clinical notes than the group selected exclusively on ICD-9-CM codes, increasing the number of patients diagnosed with depression by 34.8% (441/1269). In addition, the number of patients with depression who received chemotherapy was higher than those who did not receive this treatment, with significant differences (P<.001).

Conclusions

This study provides new clinical evidence of the depression-cancer comorbidity and supports the use of natural language processing for extracting and analyzing free-text clinical notes from electronic health records, contributing to the identification of additional clinical data that complements those provided by coded data to improve the management of these patients.

Unraveling COVID-19: A Large-Scale Characterization of 4.5 Million COVID-19 Cases Using CHARYBDIS

Purpose

Routinely collected real world data (RWD) have great utility in aiding the novel coronavirus disease (COVID-19) pandemic response. Here we present the international Observational Health Data Sciences and Informatics (OHDSI) Characterizing Health Associated Risks and Your Baseline Disease In SARS-COV-2 (CHARYBDIS) framework for standardisation and analysis of COVID-19 RWD.

Patients and Methods

We conducted a descriptive retrospective database study using a federated network of data partners in the United States, Europe (the Netherlands, Spain, the UK, Germany, France and Italy) and Asia (South Korea and China). The study protocol and analytical package were released on 11th June 2020 and are iteratively updated via GitHub. We identified three non-mutually exclusive cohorts of 4,537,153 individuals with a clinical COVID-19 diagnosis or positive test, 886,193 hospitalized with COVID-19, and 113,627 hospitalized with COVID-19 requiring intensive services.

Results

We aggregated over 22,000 unique characteristics describing patients with COVID-19. All comorbidities, symptoms, medications, and outcomes are described by cohort in aggregate counts and are readily available online. Globally, we observed similarities in the USA and Europe: more women diagnosed than men but more men hospitalized than women, most diagnosed cases between 25 and 60 years of age versus most hospitalized cases between 60 and 80 years of age. South Korea differed with more women than men hospitalized. Common comorbidities included type 2 diabetes, hypertension, chronic kidney disease and heart disease. Common presenting symptoms were dyspnea, cough and fever. Symptom data availability was more common in hospitalized cohorts than diagnosed.

Conclusion

We constructed a global, multi-centre view to describe trends in COVID-19 progression, management and evolution over time. By characterising baseline variability in patients and geography, our work provides critical context that may otherwise be misconstrued as data quality issues. This is important as we perform studies on adverse events of special interest in COVID-19 vaccine surveillance.

Unraveling COVID-19: a large-scale characterization of 4.5 million COVID-19 cases using CHARYBDIS

Background: Routinely collected real world data (RWD) have great utility in aiding the novel coronavirus disease (COVID-19) pandemic response [1,2]. Here we present the international Observational Health Data Sciences and Informatics (OHDSI) [3] Characterizing Health Associated Risks, and Your Baseline Disease In SARS-COV-2 (CHARYBDIS) framework for standardisation and analysis of COVID-19 RWD. Methods: We conducted a descriptive cohort study using a federated network of data partners in the United States, Europe (the Netherlands, Spain, the UK, Germany, France and Italy) and Asia (South Korea and China). The study protocol and analytical package were released on 11 th June 2020 and are iteratively updated via GitHub [4]. Findings: We identified three non-mutually exclusive cohorts of 4,537,153 individuals with a clinical COVID-19 diagnosis or positive test, 886,193 hospitalized with COVID-19 , and 113,627 hospitalized with COVID-19 requiring intensive services . All comorbidities, symptoms, medications, and outcomes are described by cohort in aggregate counts, and are available in an interactive website: https://data.ohdsi.org/Covid19CharacterizationCharybdis/. Interpretation: CHARYBDIS findings provide benchmarks that contribute to our understanding of COVID-19 progression, management and evolution over time. This can enable timely assessment of real-world outcomes of preventative and therapeutic options as they are introduced in clinical practice.

Prescription and Integration of Accredited Mobile Apps in Catalan Health and Social Care: Protocol for the AppSalut Site Design

Background

The use of new mobile technologies in the health and social welfare sectors is already a reality. The ICT Social Health Foundation, in accordance with the technology strategy of the Catalan government’s Ministry of Health and its Ministry of Labour, Social Affairs and Families, is leading an initiative to create a public library of apps for its AppSalut Site.

Objective

The objective of this paper is to present an account of the design of the project, with a global perspective, applied to the Catalan ecosystem, which can be divided into 3 areas: the framework governing the recommendation and prescription of apps, the subset of interoperability for mobile environments, and the data storage infrastructure.

Methods

The security and credibility of the apps included in the catalog is ensured by submitting them to an accreditation process in the public domain that provides users with the guarantee that they are fit for purpose and trustworthy for the management and care of their health, while providing health care professionals with the possibility of recommending the apps in the doctor’s surgery, as well as adding the information generated by the users’ mobile devices to the information systems of the various organizations concerned.

Results

An examination of the abovementioned areas suggests possibilities for improvements in the future. The experience obtained from the development of this element has shown the heterogeneity of the vocabularies used, as expected, due to the lack of awareness on the part of the developers regarding the need to standardize the information generated by the app, requiring the foundation to take on the role of consultant.

Conclusions

The project has evolved in keeping with changes in the technological and social paradigm and responds very satisfactorily to the needs posed to it. It can be seen as a landmark experience in mobile strategies in the fields of health and welfare of any public health system. The experience has shown itself to be feasible in organizational terms, necessary in any attempt to integrate mobile technologies into public health practice, and a global pioneer in the field.

International Registered Report Identifier (IRRID)

RR1-10.2196/11414

Patient radiation doses in uterine artery embolisation using Monte Carlo simulation

This study aims at quantification of ovarian dose in uterine artery embolisation to study the level of optimisation of this dose. Individual anatomical data and all relevant exposure parameters of individual beam projections were recorded in 52 patients who underwent uterine artery embolisation in two angiography units. The recorded information was used to calculate the individual ovarian doses by Monte Carlo simulation. The mean dose-area product was 196 Gy cm(2). The corresponding mean ovarian dose was 149 mGy. The performance of the two angiography units was analysed starting from these data. Dose-area product and ovarian doses obtained in this study were compared with data from other uterine artery embolisation patient dose studies. It was concluded that although the mean dose-area product and ovarian dose are acceptable, it is possible to optimise the procedure by improving the performance of the units.

Neurobehavioural and cognitive profile of traumatic brain injury patients at risk for depression and suicide

The possibility that patients who have suffered a traumatic brain injury will commit suicide is high, and in many cases clinicians tend to underestimate this possibility. In this study, 39 consecutive patients are studied through a Rorschach technique more than 1.5 years after their hospital discharge. The data show that 48.6% of the patients fulfil the criteria that classifies them as depressive, and, of these, 65% are at clinical risk to commit suicide (33.3% of the total of TBI patients); 25.6% have not met the criteria of depression or suicidal tendencies, and another 25.6% show very low suicide tendency scores. Only 15.6% of the total patients presented only depression without risk of suicide. The neurobehavioural and cognitive profile of the TBI suicide-prone patient shows an emotional person with cognitive difficulties in how they interpret reality, the person tries to understand what is happening around them, but is unable to cope. They show concrete thoughts, although they have difficulties solving problems and have few intellectual resources to cope with their surroundings. They do not know how to distance themselves from the emotional aspects of situations.

Cloning of an ORF with homology to Mycobacterium echA1, encoding the enoyl-CoA hydratase, in Rhodococcus fascians

An open reading frame encoding a polypeptide of significant homology (55.7% identity) with the enoyl-CoA hydratase encoded by the gene echA1 from Mycobacterium tuberculosis has been found in the genome of the plant-pathogen bacteria Rhodococcus fascians strain NRRL-B-15096. Sequence alignments showed that it possesses several conserved blocks common to E. coli, M. tuberculosis and human mitochondria. One of such blocks includes a glutamate residue located at position 149, corresponding to the glutamate 139 of Escherichia coli. This glutamate was previously shown to be the catalytic residue of enoyl-CoA hydratase in the multienzyme complex of fatty acid oxidation from E. coli. Our results provide additional information on the conserved domains of this enzyme. Significant homologies in other genome regions between R. fascians and M. tuberculosis confirm their phylogenetic relationship.

Purification and characterization of limonoate dehydrogenase from Rhodococcus fascians

Limonoate dehydrogenase from Rhodococcus fascians has been purified to electrophoretic homogeneity by a procedure that consists of ion-exchange, hydrophobic, and affinity chromatography. The native enzyme has a molecular mass of around 128,000 Da and appears to be composed of four similar subunits (30,000 Da each). The isoelectric point is 4.9 as determined by isoelectric focusing. The homogeneous enzyme was used to determine the NH2-terminal amino acid sequence. The enzyme was purified from cells grown in either fructose or limonoate as a carbon source. Limonoate dehydrogenase activity was higher in limonoate-grown cultures. Additionally, the enzyme preparations differed in their affinity for limonoids but not for NAD+. In all cases limonoate dehydrogenase exhibited a higher catalytic rate and stronger affinity for limonoate A-ring lactone than for disodium limonoate, the limonoid traditionally used for in vitro activity assays. Our data confirm previous reports proposing that limonoate A-ring lactone is the physiological substrate for limonoate dehydrogenase. The increase in limonoate dehydrogenase activity observed in limonoate-grown cultures appears to be caused by a rise in protein levels, since chloramphenicol prevented such an effect.

Flask cells and flask-shaped glandular cells of amphibian skin specifically produce fucose-rich glycoproteins

A battery of horseradish peroxidase-conjugated lectins has been employed as a cytochemical tool for the labelling of specific cell types in amphibian epidermis. Among the lectins used, only Ulex europaeus I (UEA I) showed specific reaction with the cytoplasm of flask cells. In addition, UEA I stained flask-shaped secretory cells in dermal glands and a reaction on glandular ductal cells was also observed. At the electron microscopic level, lectin binding was found in granules distributed among mitochondria in the cytoplasm of flask cells and in larger mucous granules of flask-shaped glandular cells, which were released into the lumen. UEA I also stained the extracellular space above flask cells. The labelling was due mainly to a glycoprotein of mol. wt. approx. 27 kDa. Structural and cytochemical similarities between flask cells and flask-shaped cells of dermal glands could be a consequence of a common secretory role of both cell types.

Purification and determination of glutamine synthetase by high-performance immunoaffinity chromatography

High-performance immunoaffinity chromatography (HPIAC) with anti-glutamine synthetase polyclonal antibodies bound to epoxy-activated silica was used to purify and determine this enzyme from the cyanobacterium Synechocystis. A single-step HPIAC procedure with cell-free extracts yielded electroporetically homogeneous glutamine synthetase. In the determination of glutamine synthetase by HPIAC a linear response in the range 10-60 micrograms of enzyme was observed. Recoveries of 70% of the loaded enzymatic activity and 100% of protein were obtained. The determination of glutamine synthetase protein by HPIAC was compared with that obtained by rocket immunoelectrophoresis. The chromatographic method is proposed as a possible alternative to other immunochemical quantitative techniques, particularly when non-limiting amounts of samples are available.

A protease with staphylolytic activity from Pseudomonas aeruginosa PAKS I

The supernatant from broth cultures of Pseudomonas aeruginosa PAKS I contains two different enzymes with staphylolytic activity. One of them, namely staphylolytic enzyme, seems to be specific for glycine-rich cross-links present in the cell wall of different Gram-positive bacteria and has been previously characterized. In addition to the staphylolytic activity, the second protein which we propose to be a staphylolytic protease, has proteolytic activity against casein. This enzyme is approximately 33 kDa, has an isoelectric point ranging from 7.3 to 8.1 and an optimum pH value of 8.0 for casein hydrolysis. Staphylolytic protease was detected in the extracellular medium after 12 h of cell growth. Immunocytochemical studies suggest that the protease is located within the periplasmic space of P. aeruginosa.

Staphylolytic enzyme from Pseudomonas aeruginosa: characterization and immunocytochemical localization

Staphylolytic enzyme, a specific peptidase produced by Pseudomonas aeruginosa, has been characterized by using immunochemical procedures. Lytic activity was detected in the extracellular medium of Pseudomonas cultures at the beginning of the stationary growth phase. No activity was detected in bacterial cells. However, lytic protein antigen was present in periplasmic and cytoplasmic fractions, suggesting that staphylolytic enzyme is synthesized as an inactive precursor which becomes active during translocation to the extracellular broth. Results obtained in immunolocalization experiments indicate the presence of the precursor in the outer part of cells. The export pathway of staphylolytic enzyme through the periplasmic space is proposed.

Role of glutamine as a direct co-repressor of glutamine synthetase in Rhodobacter capsulatus E1F1

High performance liquid chromatography (HPLC) has been used to determine the internal levels of amino acids in Rhodobacter capsulatus E1F1 cells, subjected to different treatments and nutritional conditions. Glutamine synthetase activity and enzyme concentration correlated negatively with the level of glutamine, suggesting that glutamine per se acts as a co-repressor in the enzyme synthesis. Moreover, addition of the specific inhibitor L-methionine-D,L-sulfoximine, that produced an increase in enzyme concentration, specifically promoted a depletion of intracellular glutamine.

Intracellular Localization of Nitrate Reductase in Neurospora crassa

Nitrate reductase was localized in mycelial cells of Neurospora crassa by immunohistochemical labeling with ferritin. The enzyme is found in the cell wall-plasmalemma region and in the tonoplast membranes.

Intracellular Localization of Nitrate Reductase in Neurospora crassa

Nitrate reductase was localized in mycelial cells of Neurospora crassa by immunohistochemical labeling with ferritin. The enzyme is found in the cell wall-plasmalemma region and in the tonoplast membranes.

Assimilatory nitrate reductase from Acinetobacter calcoaceticus

A soluble nitrate reductase from the bacterium Acinetobacter calcoaceticus grown on nitrate has been characterized. The reduction of nitrate to nitrite is mediated by an enzyme of 96000 molecular weight that can use as electron donors either viologen dyes chemically reduced with dithionite or enzymatically reduced with NAD(P)H, through specific diaphorases which utilize viologens as electron acceptors. Nitrate reductase activity is molybdenumdependent as shown by tungstate antagonistic experiments and is sensitive to--SH reagents and metal chelators such as KCN. The enzyme synthesis is repressed by ammonia. Moreover, nitrate reductase activity undergoes a quick inactivation either by dithionite and temperature or by dithionite in the presence of small amounts of nitrate. Cyanate prevents this inactivating process and can restore the activity once the inactivation had occurred, thus suggesting that an interconversion mechanism may participate in the regulation of Acinetobacter nitrate reductase.