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Abstract Background High-density oligonucleotide microarray technology enables the discovery of genes that are transcriptionally modulated in different biological samples due to physiology, disease or intervention. Methods for the identification of these so-called "differentially expressed genes" (DEG) would largely benefit from a deeper knowledge of the intrinsic measurement variability. Though it is clear that variance of repeated measures is highly dependent on the average expression level of a given gene, there is still a lack of consensus on how signal reproducibility is linked to signal intensity. The aim of this study was to empirically model the variance versus mean dependence in microarray data to improve the performance of existing methods for identifying DEG. Results In the present work we used data generated by our lab as well as publicly available data sets to show that dispersion of repeated measures depends on location of the measures themselves following a power law. This enables us to construct a power law global error model (PLGEM) that is applicable to various Affymetrix GeneChip data sets. A new DEG identification method is therefore proposed, consisting of a statistic designed to make explicit use of model-derived measurement spread estimates and a resampling-based hypothesis testing algorithm. Conclusions The new method provides a control of the false positive rate, a good sensitivity vs. specificity trade-off and consistent results with varying number of replicates and even using single samples.

Background: Avoiding interruptions and dropout in outpatient care can prevent mental illness symptom exacerbation and costly crisis services, such as emergency room visits and inpatient psychiatric hospitalization. During the COVID-19 pandemic, to attempt to maintain care continuity, telemedicine services were increasingly utilized, despite the lack of data on efficacy in patients with serious mental illness. Patients with serious mental illness are challenging to enroll and sustain in randomized controlled trials over time due to fluctuations in disease exacerbation. However, capturing and examining utilization and efficacy data in community mental health center (CMHC) patients with serious mental illness during the pandemic is a unique opportunity to inform future clinical and policy decision-making., Objective: We aimed to identify and describe the characteristics of CMHC patients with serious mental illness who experienced treatment interruptions and who utilized telemedicine during the pandemic., Methods: We conducted a retrospective observational study of treatment interruptions and telemedicine use during the period from December 2019 to June 2020 (compared to the period from December 2018 to June 2019) in New Hampshire CMHC patients. The study population included all Medicaid beneficiaries with serious mental illness engaged in treatment 3 months prior to the declaration of a state of emergency in response to the COVID-19 pandemic. We used chi-square tests of independence and logistic regression to explore associations between treatment interruptions and variables (gender, age, rurality, and diagnosis). Telemedicine utilization was categorized as low (<25%), medium (25%-75%), or high (>75%) use., Results: A total of 16,030 patients were identified. New Hampshire CMHCs demonstrated only a 4.9% increase in treatment interruptions compared with the year prior. Patients who were male (odds ratio [OR] 1.27, 95% CI 1.17-1.38; P<.001), under the age of 18 years (ages 0-12 years: OR 1.37, 95% CI 0.62-0.86, P<.001; aged 13-17 years: OR 1.49, 95% CI 0.57-0.79, P<.001), or among milder diagnostic categories, such as anxiety disorders (OR 3.77, 95% CI 3.04-4.68; P<.001) and posttraumatic stress disorder (OR 3.69, 95% CI 2.96-4.61; P<.001), were most likely to experience treatment interruptions. Patients who were female (OR 0.89, CI 0.65-0.74), 18 to 34 years old (OR 0.74, CI 0.70-0.79), or among milder diagnostic categories, such as anxiety disorder (OR 0.69, CI 0.65-0.74) or posttraumatic stress disorder (OR 0.77, CI 0.72-0.83), and with major depressive disorder (OR 0.73, CI 0.68-0.78) were less likely to be in the low telemedicine utilization group., Conclusions: The integration of telemedicine supported care continuity for most CMHC patients; yet, retention varied by subpopulation, as did telemedicine utilization. The development of policies and clinical practice guidelines requires empirical evidence on the effectiveness and limitations of telemedicine in patients with serious mental illness., (©Marcy Ainslie, Mary F Brunette, Michelle Capozzoli. Originally published in JMIR Mental Health (https://mental.jmir.org), 21.03.2022.)

Background: Nurse practitioner programs increasingly incorporate distant learning. Challenges establishing workforce preparedness and clinical competency are well documented in distance education literature. An evidence gap exists establishing the efficacy of online course delivery modalities., Objective: To determine if an online clinical training program with required residencies is an effective delivery modality in nurse practitioner education., Methods: This observational, cohort research evaluates distant learning by comparing student cohort outcomes from a successful hybrid family nurse practitioner (FNP) program to student cohort outcomes from an online with residency requirement program. Mixed methods, comparative research examine a convenience sample of 98 FNP students. Quantitative measures include 5 summative simulation based experiences, national certification exam pass rates, and an indirect student survey. Statistical analyses include equivalence tests with Bonferroni corrections for multiple comparisons and Pearson Chi-square test for independence. Qualitative analysis employs a short answer question, open-coded for thematic analysis, to assess curricular model perceptions., Results: Analyses demonstrate no practical difference, broad statistical equivalency across 6 of 7 quantitative measures, and identify qualitative similarities in thematic analyses across cohorts., Conclusion: This study supports equivalency in outcomes between hybrid and online with residency course delivery models when curricular and clinical competency assessments are uniformly implemented. This research suggests the impact of curricular delivery modality is low., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Purpose: Fingolimod is the first oral drug approved for treatment of relapsing-remitting multiple sclerosis (RR-MS), and it has potential macular side effects. Despite the qualitative evidence of macular oedema under treatment, longitudinal quantitative assessment is lacking. To address this issue, we measured macular volume and central foveal thickness in a cohort of MS patients on fingolimod over 12 months of treatment., Methods: Central foveal thickness (CFT) and total macular volume (TMV) were longitudinally recorded with spectral-domain optical coherence tomography in a cohort of 23 RR-MS patients treated with fingolimod at baseline, 3, 6 and 12 months. OCT parameters were analysed considering previous history of optic neuritis (ON). Comparison of means was performed with variance analysis (ANOVA)., Results: Macular oedema occurred in none of the patients. Comparing both groups of patients (with and without previous ON), no statistically significant difference was found during the follow-up both for CFT and TMV (p = 0.99 and p = 0.96, respectively) although a slight early but not significant TMV reduction was detected., Conclusions: In our cohort, therapy with fingolimod did not cause any change in CFT and TMV in MS patients during a 12-month follow-up independent of previous ON.

The aim of the present study was to compare long-term adalimumab (ADA) and infliximab (IFX) retention rates in patients with intermediate, posterior, or panuveitis. Additional aims are as follows: (i) to identify any difference in the causes of treatment discontinuation between patients treated with ADA and IFX; (ii) to assess any impact of demographic features, concomitant treatments, and different lines of biologic therapy on ADA and IFX retention rates; and (iii) to identify any correlation between ADA and IFX treatment duration and the age at uveitis onset, the age at onset of the associated systemic diseases, and the age at the start of treatment. Clinical, therapeutic, and demographic data from patients with non-infectious intermediate, posterior, or panuveitis treated with ADA or IFX were retrospectively collected. Kaplan-Meier plot and log-rank (Mantel-Cox) test were used to assess survival curves. One hundred eight patients (188 eyes) were enrolled; in 87 (80.6%) patients, uveitis was associated with a systemic disease. ADA and IFX were administered in 62 and 46 patients, respectively. No statistically significant differences were identified between ADA and IFX retention rates (p value = 0.22). Similarly, no differences were identified between ADA and IFX retention rates in relation to gender (p value = 0.61 for males, p value = 0.09 for females), monotherapy (p value = 0.08), combination therapy with conventional disease-modifying antirheumatic drugs (log-rank p value = 0.63), and different lines of biologic therapy (p value = 0.79 for biologic-naïve patients; p value = 0.81 for subjects previously treated with other biologics). In conclusion, ADA and IFX have similar long-term retention rates in patients with non-infectious intermediate, posterior, and panuveitis. Demographic, clinical, and therapeutic features do not affect their long-term effectiveness.

To identify clinical variables capable of predicting long-term treatment duration of TNF-α inhibition in patients with Behçet's disease (BD)-related uveitis. Demographic, clinical, and therapeutic data were retrospectively collected from BD patients treated with the tumor necrosis factor (TNF)-α blockers infliximab and adalimumab. Patients still continuing TNF-α inhibitors at 48-month follow-up visits were classified as long-term responders and were statistically compared to patients discontinuing treatment before the 48-month visit. Forty-five patients (75 eyes) were enrolled. Thirty-two patients continued anti-TNF-α treatment for more than 48 months; 13 patients discontinued the treatment after a mean time of 12.3 ± 10.44 months due to lack (61.5%) or loss (38.5%) of efficacy. Baseline value of BD current activity form was the only variable discriminating long- and short-term responsive patients (p = 0.048, OR = 0.656, C.I. 95% 0.433-0.996). Disease activity levels at the start of treatment predict duration of response to monoclonal TNF antagonists in ocular BD.

Background/aims: Adalimumab (ADA) has been shown to be an effective treatment for Behçet's disease (BD)-related uveitis. We aimed at evaluating the cumulative retention rate of ADA during a 48-month follow-up period in patients with BD-related uveitis, the impact of a concomitant use of disease modifying anti-rheumatic drugs (DMARDs) on ADA retention rate, and differences according to the various lines of biologic therapy (ie, first- vs second-line or more). Predictive factors of response to ADA were also investigated., Methods: We enrolled patients diagnosed with BD-related uveitis and treated with ADA between January 2009 and December 2016. Cumulative survival rates were studied using the Kaplan-Meier plot, while the log-rank (Mantel-Cox) test was used to compare survival curves. Statistical analysis was performed to identify differences according to the response to ADA., Results: 54 consecutive patients (82 eyes) were eligible for analysis. The drug retention rate at 12- and 48-month follow-up was 76.9% and 63.5%, respectively. No statistically significant differences were identified according to the use of concomitant DMARDs (p=0.27) and to the different lines of ADA treatment (p=0.37). No significant differences were found between patients continuing and discontinuing ADA in terms of age (p=0.24), age at BD onset (p=0.81), age at uveitis onset (p=0.56), overall BD duration (p=0.055), uveitis duration (p=0.46), human leucocyte antigen-B51 positivity (p=0.51), and gender (p=0.47)., Conclusions: ADA retention rate in BD-related uveitis is excellent and is not affected by the concomitant use of DMARDs or by the different lines of biological therapy. Negative prognostic factors for BD uveitis do not impact ADA efficacy., Competing Interests: Competing interests: None declared., (© Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.)

Our aim was to prospectively investigate the impact of Behçet's disease (BD), disease activity, and clinical and demographic characteristics on different aspects of quality of life (QoL) measured by the short-form (SF)-36 QoL scale. We administered the SF-36 to 37 consecutive BD patients in different moments of disease activity, and to 23 healthy controls (HC). The eight subcategories of the SF-36 underwent statistical analysis for identifying differences and correlations. Compared to HC, BD patients showed significantly lower mean scores in all SF-36 QoL subscales except mental health and role-emotional. Females showed a poorer QoL compared to males. Disease activity evaluated by the BD Current Activity Form inversely correlated with physical functioning (ρ = -0.68, p < 0.0001), bodily pain (ρ = -0.68, p < 0.0001), role-physical (ρ = -0.64, p < 0.0001), vitality (ρ = -0.64, p < 0.0001), general health (ρ = -0.64, p < 0.0001), social functioning (ρ = -0.50, p = 0.0002), mental health (ρ = -0.48, p = 0.0004), and role-emotional (ρ = -0.40, p = 0.003). Mucosal, central nervous system (CNS), musculoskeletal and ocular manifestations were the main factors that negatively affected QoL in BD. For ocular disease, physical functioning was significantly impaired in patients with panuveitis compared to other ocular manifestations (p = 0.0002). Best-corrected visual acuity was inversely correlated with social functioning (ρ = -0.53, p < 0.0001), role-physical (ρ = -0.48, p < 0.0001), bodily pain (ρ = -0.46, p = 0.02), and mental health (ρ = -0.43, p < 0.0001). Patients with BD have a poorer QoL compared to HC, particularly for women, while the decline of QoL is closely related to the overall disease activity of BD. Single organ involvements may affect independently specific SF-36 subscales, especially mucosal, CNS, musculoskeletal, and ocular manifestations.

Background: Non-infectious uveitis (NIU) leads to severe visual impairment, potentially impacting on health-related quality of life (QoL)., Objectives: To investigate the impact of NIU on QoL., Methods: Eighty NIU patients and 23 healthy controls completed the 36-item Short-Form Health Survey (SF)-36. The SF-36 values were statistically analyzed to evaluate differences between patients and healthy controls and to identify correlations between SF-36 subscores and clinical/demographic data., Results: NIU patients showed a decrease in the physical component summary score (P < 0.0001) compared to healthy controls, while no difference was highlighted in the mental component summary score (P = 0.97). NIU patients showed a decrease in physical functioning (P = 0.008), role-physical (P = 0.003), bodily pain (P = 0.0001), general health (P < 0.0001), and social functioning (P = 0.01). Physical functioning was lower in patients with acute anterior uveitis (AAU) than in those with panuveitis (P = 0.003). No differences were found between patients with bilateral or unilateral NIU, isolated NIU, or NIU associated with systemic diseases and with or without ocular activity. No correlations were identified between best-corrected visual acuity and SF-36 subscores. Physical functioning (P = 0.02), bodily pain (P = 0.004), and social functioning (P = 0.02) were reduced in males versus females., Conclusions: QoL is impaired in individuals with NIU, particularly in the physical domains, general health, and social functioning. AAU affects physical functioning more than panuveitis. NIU seems to affect per se QoL disregarding inflammatory activity, visual impairment, and presence of associated systemic diseases.

Tropical pathogens often cause febrile illnesses in humans and are responsible for considerable morbidity and mortality. The similarities in clinical symptoms provoked by these pathogens make diagnosis difficult. Thus, early, rapid and accurate diagnosis will be crucial in patient management and in the control of these diseases. In this study, a microfluidic lab-on-chip integrating multiplex molecular amplification and DNA microarray hybridization was developed for simultaneous detection and species differentiation of 26 globally important tropical pathogens. The analytical performance of the lab-on-chip for each pathogen ranged from 102 to 103 DNA or RNA copies. Assay performance was further verified with human whole blood spiked with Plasmodium falciparum and Chikungunya virus that yielded a range of detection from 200 to 4×105 parasites, and from 250 to 4×107 PFU respectively. This lab-on-chip was subsequently assessed and evaluated using 170 retrospective patient specimens in Singapore and Thailand. The lab-on-chip had a detection sensitivity of 83.1% and a specificity of 100% for P. falciparum; a sensitivity of 91.3% and a specificity of 99.3% for P. vivax; a positive 90.0% agreement and a specificity of 100% for Chikungunya virus; and a positive 85.0% agreement and a specificity of 100% for Dengue virus serotype 3 with reference methods conducted on the samples. Results suggested the practicality of an amplification microarray-based approach in a field setting for high-throughput detection and identification of tropical pathogens.

Threatening sporadic outbreaks of avian influenza and the H1N1 pandemic of 2009 highlight the need for rapid and accurate detection and typing of influenza viruses. In this paper, we describe the validation of the VereFlu™ Lab-on-Chip Influenza Assay, which is based on the integration of two technologies: multiplex reverse transcription (RT)-PCR followed by microarray amplicon detection. This assay simultaneously detects five influenza virus subtypes, including the 2009 pandemic influenza A (H1N1), seasonal H1N1, H3N2, H5N1 and influenza B virus. The VereFlu™ assay was clinically validated in Singapore and compared against reference methods of real-time PCR, virus detection by immunofluorescence of cell cultures and sequencing. A sensitivity and specificity of 96.8% and 92.8%, respectively, was demonstrated for pandemic H1N1; 95.7% and 100%, respectively, for seasonal H1N1; 91.2% and 97.6%, respectively, for seasonal H3N2; 95.2% and 100%, respectively, for influenza B. Additional evaluations carried out at the World Health Organization (WHO) Collaborating Centre, Melbourne, Australia, confirmed that the test was able to reliably detect H5N1. This portable, fast time-to-answer (3 hours) device is particularly suited for diagnostic applications of detection, differentiation and identification of human influenza virus subtypes.

Recognition of pathogen-associated molecular patterns (PAMP) influences the response of dendritic cells (DC) and therefore development of innate and adaptive immunity. Different forms of Leishmania mexicana have distinct effects on DC, with promastigotes and amastigotes being activating and apparently neutral, respectively. We investigated whether stage-specific differences in surface composition might account for these distinct effects. Amastigotes and promastigotes lacking the lpg1 gene needed for lipophosphoglycan (LPG) biosynthesis could not activate DC in vitro. Genome-wide transcriptional profiling of DC infected with wild-type or mutant promastigotes or wild-type amastigotes revealed that wild-type promastigotes induce an inflammatory signature that is lacking in DC exposed to the other parasite forms. The proinflammatory response pattern was partly recovered by reconstitution of lpg1 expression in lpg1-/- parasites, and exposure to purified LPG increased the expression of MHC class II and CD86 on DC. Infection with wild-type but not lpg1-/- promastigotes increased the number of activated DC in draining lymph nodes, and this was correlated with lower early parasite burdens in wild-type-infected animals. These in vivo and in vitro results suggest an LPG-dependent activation of DC that contributes to host defense and agree with the notion that the parasites evolved under immune pressure to down-regulate PAMP expression in mammalian hosts.

Schistosomes are helminth parasites that display a dual impact on the immune system of their hosts. Although the larval stage, also known as schistosomulum, appears to subvert the host defenses, the egg stage induces strong inflammatory reactions. Given the pivotal role of dendritic cells (DC) in initiating and regulating immune responses, we compared the distinct transcriptional programs induced in immature mouse DC by S. mansoni eggs or schistosomula. Although SLA abrogated the transcription of many genes implicated in DC functions, eggs caused myeloid DC to produce IFN-beta. Autocrine/paracrine signaling through the type I IFN receptor in response to eggs was necessary for the induction of known IFN-responsive genes and enhanced the synthesis of key inflammatory products. Taken as a whole, our data provide molecular insights into the immune evasion mechanism of schistosomula and suggest an unexpected role for type I IFN in the innate response to helminth eggs.

Perturbation of adhesive interactions at cell-substratum and cell-cell contact sites is a critical event in the multistep process of cancer invasion. Recent studies indicate that the urokinase receptor (uPAR) is associated in large molecular complexes with other molecules, such as integrins. To test the possibility that uPAR may physically and functionally interact with vitronectin (Vn) receptors, we determined the expression level of uPAR, alpha(v)beta3, and alpha(v)beta5 Vn receptors in 10 human breast carcinomas. Here, we show the ability of uPAR to physically associate with alpha(v)beta5 in the breast carcinomas examined. The functional effects of this interaction were studied using HT1080 human fibrosarcoma and MCF-7 human breast carcinoma cell lines, both exhibiting a urokinase-dependent physical association between uPAR and alpha(v)beta5. Both cell lines respond to urokinase or to its noncatalytic amino-terminal fragment by exhibiting remarkable cytoskeletal rearrangements that are mediated by alpha(v)beta5 and require protein kinase C activity. On the contrary, binding of Vn to alpha(v)beta5 results in the protein kinase C-independent formation of F-actin containing microspike-type structures. Furthermore, alpha(v)beta5 is required for urokinase-directed, receptor-dependent MCF-7 and HT1080 cell migration. These data show that uPAR association with alpha(v)beta5 leads to a functional interaction of these receptors and suggest that uPAR directs cytoskeletal rearrangements and cell migration by altering alpha(v)beta5 signaling specificity.

Purpose: To determine the maximum-tolerated dose of paclitaxel with carboplatin with and without filgrastim support in patients with metastatic non-small-cell lung cancer (NSCLC) and to investigate the pharmacokinetics of paclitaxel and carboplatin and correlate these with the pharmacodynamic effects., Patients and Methods: Thirty-six chemotherapy-naive patients with metastatic NSCLC were entered into this phase I dose-escalation and pharmacokinetic study. Paclitaxel was initially administered as a 24-hour infusion at a fixed dose of 135 mg/m2, and the carboplatin dose was escalated in cohorts of three patients, using Calvert's formula [dose(mg) = area under the concentration time curve (glomerular filtration rate + 25)], to target areas under the concentration time curve (AUCs) of 5, 7, 9, and 11 mg/mL x minute. A measured 24-hour urinary creatinine clearance was substituted for the glomerular filtration rate. Once the maximum-tolerated AUC (MTAUC) of carboplatin was reached, the paclitaxel dose was escalated to 175, 200, and 225 mg/m2. When the paclitaxel dose escalation began, the AUC of carboplatin was reduced to one level below the MTAUC., Results: Myelosuppression was the major dose-limiting toxicity. Thrombocytopenia was observed at a carboplatin AUC of 11 mg/mL x minute after course 2 and thereafter. End-of-infusion plasma paclitaxel concentrations and median duration of time above 0.05 microM were similar in course 1 versus course 2 at the 135 and 175 mg/m2 dose levels. The neutropenia experienced by patients was consistent with that observed in patients who had received paclitaxel alone. Measured carboplatin AUCs were approximately 12% (20% v 3% with course 1 v course 2, respectively) below the desired target, with a standard deviation of 34% at all dose levels. A sigmoid-maximum effect model describing the relationship between relative thrombocytopenia and measured free platinum exposure indicated that patients who received the combination of carboplatin with paclitaxel experienced less severe thrombocytopenia than would be expected from carboplatin alone. Of the 36 patients entered onto the study, one experienced a complete response and 17 had partial responses, for an overall response rate of 50%. The recommended doses of paclitaxel (24-hour infusion) and carboplatin for future phase II studies of this combination are (1) paclitaxel 135 mg/m2 with a carboplatin dose targeted to achieve an AUC of 7 mg/mL x minute without filgrastim support; (2) paclitaxel 135 mg/m2 with a carboplatin dose targeted to achieve an AUC of 9 mg/mL x minute with filgrastim support; and (3) paclitaxel 225 mg/m2 with a carboplatin dose targeted to achieve an AUC of 7 mg/mL x minute with filgrastim support., Conclusion: The regimen of paclitaxel and carboplatin is well-tolerated and has promising activity in the treatment of NSCLC. There is no pharmacokinetic interaction between paclitaxel and carboplatin, but there is a pharmacodynamic, platelet-sparing effect on this dose-limiting toxicity of carboplatin.

In 3 studies, the authors explored age changes and individual differences in preschool children's sustained attention in several different contexts--watching a videotape, playing with toys, and performing reaction time tasks. Various indexes of attention increased from 30 months to 54 months, whereas inattention decreased. Changes tended to occur earlier for play and television viewing than for the reaction time task. Together, the results also provide evidence for individual differences in measures of attention and inattention through high internal consistency and stability over time within situations. Correlations across situations, however, were low to modest. These results suggest that children have stable tendencies to focus and sustain attention in particular contexts but that their attention varies with the demands of the task and their ability or interest in meeting those demands.