HeapMS: An Automatic Peak-Picking Pipeline for Targeted Proteomic Data Powered by 2D Heatmap Transformation and Convolutional Neural Networks.

The process of peak picking and quality assessment for multiple reaction monitoring (MRM) data demands significant human effort, especially for signals with low abundance and high interference. Although multiple peak-picking software packages are available, they often fail to detect peaks with low quality and do not report cases with low confidence. Furthermore, visual examination of all chromatograms is still necessary to identify uncertain or erroneous cases. This study introduces HeapMS, a web service that uses artificial intelligence to assist with peak picking and the quality assessment of MRM chromatograms. HeapMS applies a rule-based filter to remove chromatograms with low interference and high-confidence peak boundaries detected by Skyline. Additionally, it transforms two histograms (representing light and heavy peptides) into a single encoded heatmap and performs a two-step evaluation (quality detection and peak picking) using image convolutional neural networks. HeapMS offers three categories of peak picking: uncertain peak picking that requires manual inspection, deletion peak picking that requires removal or manual re-examination, and automatic peak picking. HeapMS acquires the chromatogram and peak-picking boundaries directly from Skyline output. The output results are imported back into Skyline for further manual inspection, facilitating integration with Skyline. HeapMS offers the benefit of detecting chromatograms that should be deleted or require human inspection. Based on defined categories, it can significantly reduce human workload and provide consistent results. Furthermore, by using heatmaps instead of histograms, HeapMS can adapt to future updates in image recognition models. The HeapMS is available at: https://github.com/ccllabe/HeapMS.

Helminth egg analysis platform (HEAP): An opened platform for microscopic helminth egg identification and quantification based on the integration of deep learning architectures.

BACKGROUND: Millions of people throughout the world suffer from parasite infections. Traditionally, technicians use manual eye inspection of microscopic specimens to perform a parasite examination. However, manual operations have limitations that hinder the ability to obtain precise egg counts and cause inefficient identification of infected parasites on co-infections. The technician requirements for handling a large number of microscopic examinations in countries that have limited medical resources are substantial. We developed the helminth egg analysis platform (HEAP) as a user-friendly microscopic helminth eggs identification and quantification platform to assist medical technicians during parasite infection examination. METHODS: Multiple deep learning strategies including SSD (Single Shot MultiBox Detector), U-net, and Faster R-CNN (Faster Region-based Convolutional Neural Network) are integrated to identify the same specimen allowing users to choose the best predictions. An image binning and egg-in-edge algorithm based on pixel density detection was developed to increase the performance. Computers with different operation systems can be gathered to lower the computation time using our easy-to-deploy software architecture. RESULTS: A user-friendly interface is provided to substantially increase the efficiency of manual validation. To adapt to low-cost computers, we architected a distributed computing structure with high flexibilities. CONCLUSIONS: HEAP serves not only as a prediction service provider but also as a parasitic egg database of microscopic helminth egg image collection, labeling data and pretrained models. All images and labeling resources are free and accessible at http://heap.cgu.edu.tw. HEAP can also be an ideal education and training resource for helminth egg examination.

Assessment of Body Weight Changes in Patients with Inflammatory Bowel Diseases Initiating Biologic Therapy: A Prospective Cohort Study.

BACKGROUND: Prior studies have inconsistently suggested that biologic therapy may be associated with weight gain in inflammatory bowel disease patients (IBD). Our aim was to compare weight gain across different biologic therapy classes with distinct mechanisms of action. METHODS: This prospective cohort study recruited patients with moderate to severe IBD initiating outpatient biologic therapy with anti-TNF (infliximab, adalimumab), vedolizumab, or ustekinumab. Weight measurements were performed at weeks 0, 14, 30, and 54. Changes in weight between baseline and each of the follow-up visits were modeled as a continuous variable, and multivariate regression assessed the independent effect of therapeutic class on this outcome. RESULTS: Our study enrolled 269 patients (163 CD, 106 UC) initiating biologic therapy [99 anti-TNF (37%), 122 vedolizumab (45%), 48 ustekinumab (18%)]. From baseline, the weight significantly increased at week 14 with a mean of 0.36 kg (± 3.8 kg, p = 0.004) and continued to increase compared to baseline with 0.96 kg (± 3.9 kg, p < 0.001) and 1.29 kg (± 4.2 kg, p < 0.001) at week 30 and 54, respectively. On univariate and multivariable analysis, no significant differences between any of the biologic therapies for weight gain were seen at any time point (weight gain anti-TNF: 0.31 kg, 1.06 kg, 1.33 kg; VDZ: 0.30 kg, 0.83 kg, 1.10 kg; UST: 0.63 kg, 1.21 kg, 2.31 kg at wk 14, wk 30, and wk 54, respectively). None of the disease activity parameters showed any statistical association with weight gain. CONCLUSION: There was no difference in weight gain among the different biologic therapeutic classes.

Safety of Recombinant Zoster Vaccine in Patients with Inflammatory Bowel Disease.

BACKGROUND: Patients with inflammatory bowel disease (IBD) are at increased risk of developing herpes zoster. In October 2017, the FDA approved a two-dose adjuvanted, recombinant herpes zoster vaccine (RZV). There is a theoretical concern that vaccine adjuvants may cause flares in patients with immune-mediated diseases. We aimed to assess the rates of IBD flare and adverse reactions after administration of RZV in a cohort of patients with IBD. METHODS: We conducted a prospective observational study of patients with IBD who received RZV between February 2018 and July 2019 at a tertiary IBD referral center. IBD activity scores were collected from patients during office visit or phone call after vaccination. The primary outcome was rate of IBD flare, defined as an increase in IBD activity, resulting in escalation of medical therapy, following vaccination. The secondary outcomes were rates of local and systemic adverse reactions after vaccination. RESULTS: We identified 67 patients (28 with ulcerative colitis and 39 with Crohn's disease) who received at least one dose of RZV. The two-dose vaccine series was completed by 55 patients (82%). Median duration of follow-up after vaccination was 207 days. One case of IBD flare was identified. No cases of herpes zoster were identified. Local and systemic adverse reactions were reported in 74.6% and 56.7% of patients, respectively. CONCLUSIONS: In this cohort of 67 patients, a low rate of IBD flare (1.5%) was observed after RZV administration. Rates of local and systemic adverse reactions were comparable to those seen in the RZV clinical trials.

Infection preventionists' challenges in psychiatric clinical settings.

BACKGROUND: Infection preventionists (IPs) play an important role in preventing health care-associated infections in a health care system. However, the limitations of the clinical setting and the unique characteristics of psychiatric patients could be barriers to effective infection prevention. The purpose of this study was to understand how IPs perceived their challenges and how these challenges negatively affect their infection prevention work in psychiatric clinical settings. METHODS: A descriptive, qualitative research approach was used in this study. Thirteen Taiwanese psychiatric IPs were interviewed in semistructured interviews. Data were transcribed and then analyzed by thematic analysis. RESULTS: This analysis identified 6 themes: (1) lack of preservice training in psychiatric infection control, (2) insufficient staffing in practice, (3) working within environmental limits, (4) patient noncompliance, (5) undervaluation of the importance of infection control by professionals, and (6) involvement of hospital administrators. CONCLUSIONS: The implementation of effective infection prevention in psychiatric clinical settings may be strongly related to the factors of sufficient training and IP staffing while relying on collaboration among patients and clinical professionals and on the full support of administrators.

Relaxin Family Member Insulin-Like Peptide 6 Ameliorates Cardiac Fibrosis and Prevents Cardiac Remodeling in Murine Heart Failure Models.

BACKGROUND: The insulin/insulin-like growth factor/relaxin family represents a group of structurally related but functionally diverse proteins. The family member relaxin-2 has been evaluated in clinical trials for its efficacy in the treatment of acute heart failure. In this study, we assessed the role of insulin-like peptide 6 (INSL6), another member of this protein family, in murine heart failure models using genetic loss-of-function and protein delivery methods. METHODS AND RESULTS: Insl6-deficient and wild-type (C57BL/6N) mice were administered angiotensin II or isoproterenol via continuous infusion with an osmotic pump or via intraperitoneal injection once a day, respectively, for 2 weeks. In both models, Insl6-knockout mice exhibited greater cardiac systolic dysfunction and left ventricular dilatation. Cardiac dysfunction in the Insl6-knockout mice was associated with more extensive cardiac fibrosis and greater expression of fibrosis-associated genes. The continuous infusion of chemically synthesized INSL6 significantly attenuated left ventricular systolic dysfunction and cardiac fibrosis induced by isoproterenol infusion. Gene expression profiling suggests liver X receptor/retinoid X receptor signaling is activated in the isoproterenol-challenged hearts treated with INSL6 protein. CONCLUSIONS: Endogenous Insl6 protein inhibits cardiac systolic dysfunction and cardiac fibrosis in angiotensin II- and isoproterenol-induced cardiac stress models. The administration of recombinant INSL6 protein could have utility for the treatment of heart failure and cardiac fibrosis.

27-GAUGE NEEDLE-ASSISTED TECHNIQUE FOR REPOSITIONING A DISLOCATED INTRAOCULAR LENS.

BACKGROUND: Several techniques for the reposition of a posterior chamber intraocular lens (IOL) posterior dislocating into the vitreous cavity have been developed. However, most of these methods are complicated or include externalizing part of the IOL from a corneal or scleral wound. We here describe a 27-gauge needle-assisted technique for management of a dislocated posterior chamber IOL. METHODS: This is a retrospective, noncomparative, interventional case series that discusses the results of 27-gauge needle-assisted reposition of the posterior chamber IOL with transscleral sulcus fixation in 5 consecutive cases with an IOL dislocated into vitreous cavity. These patients underwent IOL reposition with the above-mentioned technique between April 2013 and October 2014 and were followed up for at least two months thereafter. RESULTS: The IOLs of the five cases were stable with proper centrations. The postoperative best-corrected visual acuity ranged from 20/30 to 20/20. CONCLUSION: The technique of 27-gauge needle-assisted reposition of the posterior chamber IOL with transscleral fixation is effective for reposition of a dislocated IOL. This technique provides good IOL fixation without creating a large corneal wound or scleral flap.

Candida parapsilosis keratitis treated successfully with topical and oral fluconazole.

A 73-year-old male patient presented with ocular pain, redness, and blurred vision in the left eye, which had been ongoing for more than 2 months. An oval-shaped paracentral corneal ulcer with stromal infiltration and a mild anterior chamber reaction were found. Despite treatment with empiric antibiotics, the lesion progressed and corneal thinning in the middle area was noted. The culture yielded Candida parapsilosis. We therefore prescribed topical 0.2% fluconazole (FCZ) in combination with oral FCZ as an antifungal treatment, following which the stromal infiltration gradually subsided. Complete epithelial-ization was noted on the 8th day after initiating FCZ therapy. There was no recurrent disease in the subsequent 2 years. Our case demonstrates that topical FCZ 0.2% in combination with oral FCZ can successfully treat C. parapsilosis keratitis and result in a good visual outcome.