Automating Pitted Red Blood Cell Counts Using Deep Neural Network Analysis: A New Method for Measuring Splenic Function in Sickle Cell Anaemia.

The spleen plays an important role in the body's defence against bacterial infections. Measuring splenic function is of interest in multiple conditions, including sickle cell anaemia (SCA), where spleen injury occurs early in life. Unfortunately, there is no direct and simple way of measuring splenic function, and it is rarely assessed in clinical or research settings. Manual counts of pitted red blood cells (RBCs) observed with differential interference contrast (DIC) microscopy is a well-validated surrogate biomarker of splenic function. The method, however, is both user-dependent and laborious. In this study, we propose a new automated workflow for counting pitted RBCs using deep neural network analysis. Secondly, we assess the durability of fixed RBCs for pitted RBC counts over time. We included samples from 48 children with SCA and 10 healthy controls. Cells were fixed in paraformaldehyde and examined using an oil-immersion objective, and microscopy images were recorded with a DIC setup. Manual pitted RBC counts were performed by examining a minimum of 500 RBCs for pits, expressing the proportion of pitted RBCs as a percentage (%PIT). Automated pitted RBC counts were generated by first segmenting DIC images using a Zeiss Intellesis deep learning model, recognising and segmenting cells and pits from background. Subsequently, segmented images were analysed using a small ImageJ macro language script. Selected samples were stored for 24 months, and manual pitted RBC counts performed at various time points. When comparing manual and automated pitted RBC counts, we found the two methods to yield comparable results. Although variability between the measurements increased with higher %PIT, this did not change the diagnosis of asplenia. Furthermore, we found no significant changes in %PIT after storing samples for up to 24 months and under varying temperatures and light exposures. We have shown that automated pitted RBC counts, produced using deep neural network analysis, are comparable to manual counts, and that fixed samples can be stored for long periods of time without affecting the %PIT. Automating pitted RBC counts makes the method less time consuming and results comparable across laboratories.

Validation of an abbreviated food frequency questionnaire for estimating DHA intake of pregnant women in the United States.

Docosahexaenoic acid (DHA) intake was estimated in pregnant women between 12- and 20-weeks' gestation using the National Cancer Institute's (NCI) Diet History Questionnaire-II (DHQ-II) and a 7-question screener designed to capture DHA intake (DHA Food Frequency Questionnaire, DHA-FFQ). Results from both methods were compared to red blood cell phospholipid DHA (RBC-DHA) weight percent of total fatty acids. DHA intake from the DHA-FFQ was more highly correlated with RBC-DHA (rs=0.528) than the DHQ-II (rs=0.352). Moreover, the DHA-FFQ allowed us to obtain reliable intake data from 1355 of 1400 participants. The DHQ-II provided reliable intake for only 847 of 1400, because many participants only partially completed it and it was not validated for Hispanic participants. Maternal age, parity, and socioeconomic status (SES) were also significant predictors of RBC-DHA. When included with estimated intake from the DHA-FFQ, the model accounted for 36% of the variation in RBC-DHA.

Effect of Collaborative Review of Electronic Patient-Reported Outcomes for Shared Reporting in Breast Cancer Patients: Descriptive Comparative Study.

BACKGROUND: Digital monitoring of treatment-related symptoms and self-reported patient outcomes is important for the quality of care among cancer patients. As mobile devices are ubiquitous nowadays, the collection of electronic patient-reported outcomes (ePROs) is gaining momentum. So far, data are lacking on the modalities that contribute to the quantity and quality of ePROs. OBJECTIVE: The objective of our study was to compare the utilization of two versions of a subsequently employed mobile app for electronic monitoring of PROs and to test our hypothesis that a shared review of symptoms in patient-physician collaboration has an impact on the number of data entries. METHODS: The Consilium Care app engages cancer patients to standardize reporting of well-being and treatment-related symptoms in outpatient settings. For descriptive comparison of the utilization of two slightly different app versions, data were obtained from an early breast cancer trial (version 1 of the app, n=86) and an ongoing study including patients with advanced disease (version 2 of the app, n=106). In both app versions, patients and doctors were allowed to share the information from data entries during consultations. Version 2 of the app, however, randomly selected symptoms that required a detailed and shared regular patient-doctor review in order to focus on the collection and appropriate interpretation regarding awareness and guidance for severity grading. The numbers and types of symptom entries, satisfaction with both app versions, and patients' perceived effects during consultations were included for analysis. RESULTS: Symptom severity grading was performed according to the Common Terminology Criteria for Adverse Events (CTCAE) using a horizontal slider and was indicated in descriptive terminology in both apps, while a graphical display facilitated the illustration of symptom history charts. In total, 192 patients electronically reported 11,437 data entries on well-being and 33,380 data entries on individual symptoms. Overall, 628 (of 872 intended) requested patient-doctor symptom reviews were performed in version 2 of the app. Both the amount of data entries per patient and day for well-being (version 1 vs version 2: 0.3 vs 1.0; P<.001) and symptoms (version 1 vs version 2: 1.3 vs 1.9; P=.04) appeared significantly increased in version 2 of the app. Overall satisfaction with both app versions was high, although version 2 of the app was perceived to be more helpful in general. CONCLUSIONS: Version 2 of the app showed much better results than version 1 of the app. A request for collaborative patient-doctor symptom review is likely to affect the number of digital symptom data entries. This app shows high potential to improve the patient-doctor experience. TRIAL REGISTRATION: ClinicalTrials.gov NCT02004496; https://clinicaltrials.gov/ct2/show/NCT02004496 and ClinicalTrials.gov NCT03578731; https://clinicaltrials.gov/ct2/show/NCT03578731.

Mechanisms in fluid retention - towards a mutual concept.

Fluid retention is a common and challenging condition in daily clinical practice. The normal fluid homoeostasis in the human body is based on accurately counter-balanced physiological mechanisms. When compromised fluid retention occurs and is seen in pathophysiologically different conditions such as liver cirrhosis, heart and kidney failure, and in preeclampsia. These conditions may share pathophysiological mechanisms such as functional arterial underfilling, which seems to be a mutual element in cirrhosis, cardiac failure, cardiorenal and hepatorenal syndromes, and in pregnancy. However, there are also distinct differences and it is still unclear whether kidney dysfunction or arterial underfilling is the initiating factor of fluid retention or if they happen simultaneously. This review focuses on similarities and differences in water retaining conditions and points to areas where important knowledge is still needed.

Changes in ventilatory capacity and pulmonary gas exchange during systemic and pulmonary inflammation in humans.

The exact mechanism linking the systemic inflammatory response associated with sepsis to changes in lung function remains to be determined. In a human experimental model of inflammation, we investigated how acute systemic and local pulmonary inflammation affects ventilatory capacity and pulmonary gas exchange. Fifteen volunteers received Escherichia coli lipopolysaccharide (LPS) intravenously or endobronchially on two different study days. Blood samples were obtained hourly (t = 0-8 h) and spirometry was performed at baseline and after 8 h. Both interventions decreased ventilatory capacity compared to baseline (p < 0.01), and this was more pronounced after intravenous (forced expiratory volume in 1-s, FEV1 ; 0.6 L/12% reduction) compared to endobronchial (FEV1 ; 0.32 L/7% reduction) administration (p < 0.05). Furthermore, the alveolar-arterial oxygen difference increased after intravenous but not after endobronchial endotoxin. These findings indicate that pulmonary gas exchange is impaired to a greater extent during endotoxin-induced systemic inflammation than during endotoxin-induced local pulmonary inflammation.

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase.

UniProtKB/Swiss-Prot, a curated protein database, and dictyBase, the Model Organism Database for Dictyostelium discoideum, have established a collaboration to improve data sharing. One of the major steps in this effort was the 'Dicty annotation marathon', a week-long exercise with 30 annotators aimed at achieving a major increase in the number of D. discoideum proteins represented in UniProtKB/Swiss-Prot. The marathon led to the annotation of over 1000 D. discoideum proteins in UniProtKB/Swiss-Prot. Concomitantly, there were a large number of updates in dictyBase concerning gene symbols, protein names and gene models. This exercise demonstrates how UniProtKB/Swiss-Prot can work in very close cooperation with model organism databases and how the annotation of proteins can be accelerated through those collaborations.

Determinants of ligand binding specificity of the alpha(1)beta(1) and alpha(2)beta(1) integrins.

The alpha(1)beta(1) and alpha(2)beta(1) integrins are cell surface collagen receptors. Cells expressing the alpha(1)beta(1) integrin preferentially adhere to collagen IV, whereas cells expressing the alpha(2)beta(1) integrin preferentially adhere to collagen I. Recombinant alpha(1) and alpha(2) integrin I domains exhibit the same collagen type preferences as the intact integrins. In addition, the alpha(2) integrin I domain binds echovirus 1; the alpha(1) I domain does not. To identify the structural components of the I domains responsible for the varying ligand specificities, we have engineered several alpha(1)/alpha(2) integrin I domain chimeras and evaluated their virus and collagen binding activities. Initially, large secondary structural components of the alpha(2) I domain were replaced with corresponding regions of the alpha(1) I domain. Following analysis in echovirus 1 and collagen binding assays, chimeras with successively smaller regions of alpha(1) I were constructed and analyzed. The chimeras were analyzed by ELISA with several different alpha(2) integrin monoclonal antibodies to assess their proper folding. Three different regions of the alpha(1) I domain, when present in the alpha(2) I domain, conferred enhanced collagen IV binding activity upon the alpha(2) I domain. These include the alpha3 and alpha5 helices and a portion of the alpha6 helix. Echovirus 1 binding was lost in a chimera containing the alphaC-alpha6 loop; higher resolution mapping identified Asn(289) as playing a critical role in echovirus 1 binding. Asn(289) had not been implicated in previous echovirus 1 binding studies. Taken together, these data reveal the existence of multiple determinants of ligand binding specificities within the alpha(1) and alpha(2) integrin I domains.

Effect of microtubule-associated protein MHP1 on microtubule assembly and cell cycle progression in Saccharomyces cerevisiae.

Microtubule-associated proteins (MAPs) promote the assembly of microtubules from purified tubulin in vitro. In order to establish a model system for the investigation of the role of MAPs in microtubule assembly in vivo, we have generated Saccharomyces cerevisiae strains that permit the modulation of the expression levels of MHP1 (MAP-Homologous Protein 1) and of the alpha and beta-tubulin genes. Simultaneous overexpression of alpha and beta tubulin results in the accumulation of long aberrant microtubules in interphase, a similar phenotype as was observed in cells overexpressing MHP1. We demonstrate that overexpression of MHP1 in asynchronously growing yeast cultures leads to cell cycle arrest in G2. In cells that overexpress MHP1 and the tubulin genes, a suppression of both the MHP1 and the tubulin overexpression phenotypes can be observed. Progressive induction of alpha and beta tubulin overexpression and constitutive overexpression of MHP1 lead to the formation of long cytoplasmic microtubules more frequently than observed in cells overproducing tubulin or Mhplp individually and the increased microtubule polymerization could be correlated with the increase of a and beta tubulin expression. However, the overexpression of MHP1 did not alter the phenotypes of individual overexpression of a or beta-tubulin. These data indicate that Mhplp not only stabilizes microtubules but promotes microtubule assembly in vivo, and suggest that the role of other mammalian MAPs in the promotion of microtubule assembly could be tested in this yeast system.

Ligand binding results in divalent cation displacement from the alpha 2 beta 1 integrin I domain: evidence from terbium luminescence spectroscopy.

The alpha 2 beta 1 integrin serves as a cell surface collagen or collagen/laminin receptor. Binding of the integrin to its ligands is largely mediated by the alpha 2 subunit I domain and requires the presence of divalent cations. Terbium ion (Tb3+), a fluorescent trivalent cation that often binds divalent cation-binding sites on proteins, supported binding of the I domain to collagen with half-maximal binding occurring at 5.2 +/- 1.7 microM Tb3+. By fluorescence resonance energy transfer spectroscopy, Tb3+ showed specific and saturable binding to the recombinant I domain with a Kd of 27 +/- 4 microM. Although both Mg2+ and Mn2+ were capable of quenching Tb3+ fluorescence, Mn2+ was much more effective than Mg2+. The alpha 2 beta 1 integrin also binds the pro-alpha 1(I) collagen carboxyl-terminal propeptide in a Mg2+-dependent manner via the I domain. Recombinant propeptide was used to examine the effect of ligand on the Tb3+ binding properties of the alpha 2 integrin I domain. As propeptide bound to the I domain, Tb3+ fluorescence progressively diminished suggesting that as ligand binds to the I domain, either Tb3+ is displaced or its fluorescence is quenched. Consistent with the former possibility, little dissociation of collagen-bound I domain occurred upon the addition of EDTA and subsequent incubation. These data support a model in which (1) the divalent cation is required for initial ligand-binding activity of the I domain and (2) ligand binding results in subsequent metal ion displacement to generate a metal-free I domain-ligand complex.

Characterization of a new, highly specific, beta 3-adrenergic receptor radioligand, [3H]SB 206606.

The RR-enantiomer of the beta 3-adrenergic receptor agonist BRL 37344 was tritiated to yield a high specific activity compound, [3H]SB 206606. This new, potentially specific, beta 3-adrenergic receptor ligand was characterized by binding studies using membranes from both Chinese hamster ovary K1 cells transfected with the rat beta 3-adrenergic receptor and rat interscapular brown adipose tissue, where beta 1-, beta 2-, and beta 3-adrenergic receptor subtypes are known to coexist. [3H]SB 206606 was found to bind to a single population of binding sites in both preparations. The Kd values for [3H]SB 206606 binding to membranes from Chinese hamster ovary K1 cells and brown adipose tissue were quite comparable (58 and 38 nM, respectively). At 37 degrees, the time courses of association and dissociation of [3H]SB 206606 with membranes of brown adipose tissue were quite short. At 4 degrees, the T1/2 were found to be 13 and 40 min, respectively. The Ki values for various beta-adrenergic agonists and antagonists in brown adipose tissue membranes were similar to those obtained in Chinese hamster ovary K1 cell membranes with both [3H]SB 206606 and [125I]iodocyanopindolol. The order of binding affinity was BRL 37344 >> (-)-isoproterenol = (-)-norepinephrine > (-)-epinephrine = (+)-isoproterenol. The similarity of the Kd values and of the Ki values for various beta-adrenergic agonists and antagonists in both systems tested indicates that, in a complex membrane system, [3H]SB 206606 binds selectively to the beta 3-adrenergic receptor. The affinity of [3H]SB 206606 is 76 times higher for the beta 3-adrenergic receptor than for the beta 1/beta 2-adrenergic receptors, thus allowing, under controlled conditions, measurement of interactions only with the beta 3-adrenergic receptor in complex membrane systems.