Challenges and barriers of using large language models (LLM) such as ChatGPT for diagnostic medicine with a focus on digital pathology - a recent scoping review

BACKGROUND

The integration of large language models (LLMs) like ChatGPT in diagnostic medicine, with a focus on digital pathology, has garnered significant attention. However, understanding the challenges and barriers associated with the use of LLMs in this context is crucial for their successful implementation.

METHODS

A scoping review was conducted to explore the challenges and barriers of using LLMs, in diagnostic medicine with a focus on digital pathology. A comprehensive search was conducted using electronic databases, including PubMed and Google Scholar, for relevant articles published within the past four years. The selected articles were critically analyzed to identify and summarize the challenges and barriers reported in the literature.

RESULTS

The scoping review identified several challenges and barriers associated with the use of LLMs in diagnostic medicine. These included limitations in contextual understanding and interpretability, biases in training data, ethical considerations, impact on healthcare professionals, and regulatory concerns. Contextual understanding and interpretability challenges arise due to the lack of true understanding of medical concepts and lack of these models being explicitly trained on medical records selected by trained professionals, and the black-box nature of LLMs. Biases in training data pose a risk of perpetuating disparities and inaccuracies in diagnoses. Ethical considerations include patient privacy, data security, and responsible AI use. The integration of LLMs may impact healthcare professionals' autonomy and decision-making abilities. Regulatory concerns surround the need for guidelines and frameworks to ensure safe and ethical implementation.

CONCLUSION

The scoping review highlights the challenges and barriers of using LLMs in diagnostic medicine with a focus on digital pathology. Understanding these challenges is essential for addressing the limitations and developing strategies to overcome barriers. It is critical for health professionals to be involved in the selection of data and fine tuning of the models. Further research, validation, and collaboration between AI developers, healthcare professionals, and regulatory bodies are necessary to ensure the responsible and effective integration of LLMs in diagnostic medicine.

Construction and validation of ShaMaq developmental screening tool

INTRODUCTION

The diagnosis of developmental delay and early intervention ameliorates long-term sequelae. There is a need for an appropriate, regionally adapted and reliable developmental screening tool to be used in low and middle-income countries with scarce resources.

AIM

The aim of this research is to construct and validate a screening tool for identifying developmental delay in Pakistani children.

METHOD

ShaMaq developmental screening tool (SDST) was developed consisting of five proformas to be administered at different age groups: 6-8 weeks (Group 1), 6-10 months (Group 2), 18-24 months (Group 3), 3-3.5 years (Group 4), and 4.5-5.5 years (Group 5). On an average, Groups 1-3 took 10-15 min, whereas Groups 4 and 5 took 20-25 min. We sampled children between the ages of 6 weeks to 5.5 years and tested them all within their designated age groups. Internal consistency was assessed by Cronbach's alpha. Interobserver testing was done for reliability and concurrent validity was undertaken by using the senior consultant developmental paediatrician's final diagnosis as the gold standard.

RESULTS

Out of 550 healthy children, 8-19% in the five groups were found to have some form of developmental delay using SDST. Approximately 50% of the families were in the low-to-moderate income bracket, and nearly 93% lived in a joint family system. Internal consistency of items in the five groups ranged from 0.784 to 0.940, whereas both interobserver reliability and concurrent validity ranged from 0.737 to 1.0. SDST showed 94.4% sensitivity and 92.9% specificity.

CONCLUSION

SDST is an effective tool for identifying delay in healthy children with good internal consistency, reliability, and validity.

Managers' leadership competencies and sustainable development goals in turbulent markets: the enabling role of resource commitment

Research on the sustainable development goals (SDGs) has brought attention to the significance of small and medium enterprises (SMEs) due to their substantial contributions to economic growth. However, SMEs still need to develop integrated frameworks to assess the implications of sustainable operations while managing scarce resources. In this study, we investigate how top managers of SMEs utilize leadership competencies to balance and allocate resources for SDGs in a turbulent environment. To test the model, the analysis was conducted on 254 SMEs operating in an emerging market. The findings indicate that resource commitment plays a partially mediating role between leadership competencies and SDGs, while environmental uncertainty does not moderate the relationship between leadership competencies and resource commitment. These insights suggest that SMEs with competent leaders commit resources to SDGs regardless of environmental conditions. This research recommends that SMEs focus on cultivating competent leaders to navigate resource constraints and contribute to the SDGs in a turbulent environment. Further implications are discussed.

Natural History of Visual Dysfunction in ABCA4 Retinopathy and Its Genetic Correlates

PURPOSE

To systematically assess the ability to detect change and retest reliability for a panel of visual function assessments in ABCA4 retinopathy.

DESIGN

Prospective natural history study (NCT01736293).

METHODS

Patients with at least 1 documented pathogenic ABCA4 variant and a clinical phenotype consistent with ABCA4 retinopathy were recruited from a tertiary referral center. Participants underwent longitudinal, multifaceted functional testing, including measures of function at fixation (best-corrected visual acuity, low-vision Cambridge Color Test), macular function (microperimetry), and retina-wide function (full-field electroretinography [ERG]). Two- and 5-year ability to detect change was determined based on the η2 statistic.

RESULTS

A total of 134 eyes from 67 participants with a mean follow-up of 3.65 years were included. In the 2-year interval, the microperimetry-derived perilesional sensitivity (η2 of 0.73 [0.53, 0.83]; -1.79 dB/y [-2.2, -1.37]) and mean sensitivity (η2 of 0.62 [0.38, 0.76]; -1.28 dB/y [-1.67, -0.89]) showed most change over time, but could only be recorded in 71.6% of the participants. In the 5-year interval, the dark-adapted ERG a- and b-wave amplitude showed marked change over time as well (eg, DA 30 a-wave amplitude with an η2 of 0.54 [0.34, 0.68]; -0.02 log10(µV)/y [-0.02, -0.01]). The genotype explained a large fraction of variability in the ERG-based age of disease initiation (adjusted R2 of 0.73) CONCLUSIONS: Microperimetry-based clinical outcome assessments were most sensitive to change but could only be acquired in a subset of participants. Across a 5-year interval, the ERG DA 30 a-wave amplitude was sensitive to disease progression, potentially allowing for more inclusive clinical trial designs encompassing the whole ABCA4 retinopathy spectrum.

Combined Single Gene Testing and Genome Sequencing as an Effective Diagnostic Approach for Anophthalmia and Microphthalmia Patients

Anophthalmia and microphthalmia (A/M) are among the most severe congenital developmental eye disorders. Despite the advancements in genome screening technologies, more than half of A/M patients do not receive a molecular diagnosis. We included seven consanguineous families affected with A/M from Pakistani cohort and an unknown molecular basis. Single gene testing of FOXE3 was performed, followed by genome sequencing for unsolved probands in order to establish a genetic diagnosis for these families. All seven families were provided with a genetic diagnosis. The identified variants were all homozygous, classified as (likely) pathogenic and present in an A/M-associated gene. Targeted FOXE3 sequencing revealed two previously reported pathogenic FOXE3 variants in four families. In the remaining families, genome sequencing revealed a known pathogenic PXDN variant, a novel 13bp deletion in VSX2, and one novel deep intronic splice variant in PXDN. An in vitro splice assay was performed for the PXDN splice variant which revealed a severe splicing defect. Our study confirmed the utility of genome sequencing as a diagnostic tool for A/M-affected individuals. Furthermore, the identification of a novel deep intronic pathogenic variant in PXDN highlights the role of non-coding variants in A/M-disorders and the value of genome sequencing for the identification of this type of variants.

Use of pager devices in New Zealand public hospitals as a critical communication tool: Barriers & way forward

OBJECTIVES

The aim of this study was to analyse the current use, identify challenges and barriers and propose a way forward for the use of the pager devices in the in-hospital communications.

METHODS

Initially, 447 studies were identified through database searching. After checking against the eligibility, 39 studies were included. Full-text records were retrieved and reviewed by two authors. After excluding unrelated studies and duplicate records, a total of 12 articles were selected for the final review.

RESULTS

The use of pagers often lacks standardisation, content, format, urgency level, and clarity within the message. Some studies reported that medical staff preferred in-person interactions with consults instead of communicating over the phone or pagers. Productive communication can reduce the turnaround time by up to 50%. The key challenges are; (1) data security and privacy, (2) timely acknowledgement of received communication, (3) lack of two-way communications causing issues in critical care situations and (4) there is no standard process for the in-hospital communications.

CONCLUSION

We found that the clinicians' age, experience, speciality and preferences greatly matter and influence the selection of tools and technology in healthcare. With revolutionary advances in technology, smartphones have inevitably become beneficial to healthcare, owing to multiple instant messaging applications (apps) that can streamline encrypted clinical communication between medical teams and could be safely used for in-hospital communications.

A novel variant affecting the cytoplasmic tail of the FAT1 protocadherin causing coloboma and renal failure: A case report

BACKGROUND

Variations in the protocadherin gene FAT1 have recently been associated with a syndrome that includes coloboma, facial dysmorphism, renal failure, syndactyly, and other developmental defects.

MATERIALS AND METHODS

Detailed medical and family history, physical examination, and molecular analysis.

RESULTS

This non-dysmorphic, intellectually normal 51-year-old woman presented with bilateral colobomata and renal failure of unclear etiology, and asymmetric sensorineural hearing loss. Family history was notable for multiple family members with various forms of cancer. Whole exome sequencing revealed a homozygous frame shift variant in FAT1, predicted to truncate the FAT1 protein at the furthest position in the protein structure published to date in a patient with coloboma.

CONCLUSIONS

This case provides further evidence of the pleiotropic effects of FAT1 in optic fissure closure and kidney function. Also, because this variant is in the last exon, it would be anticipated to escape nonsense-mediated decay, opening the possibility that the protein is made and expressed, but not completely functional, as its intracellular domain is truncated.

Ophthalmic Manifestations of ROSAH (Retinal Dystrophy, Optic Nerve Edema, Splenomegaly, Anhidrosis, and Headache) Syndrome, an Inherited NF κB-Mediated Autoinflammatory Disease with Retinal Dystrophy

PURPOSE

We aimed to characterize the ocular phenotype of patients with ROSAH (retinal dystrophy, optic nerve edema, splenomegaly, anhidrosis, and headache) syndrome and their response to therapy.

DESIGN

Single-center observational case study.

PARTICIPANTS

Eleven patients with a diagnosis of ROSAH syndrome and mutation in ALPK1 were included.

METHODS

Patients with molecularly confirmed ROSAH syndrome underwent ophthalmic evaluation, including visual acuity testing, slit-lamp and dilated examinations, color fundus and autofluorescence imaging, fluorescein angiography, OCT, and electrophysiologic testing.

MAIN OUTCOME MEASURES

Visual acuity, electrophysiology, fluorescein angiography, and OCT findings.

RESULTS

Eleven individuals (6 female and 5 male patients) from 7 families ranging in age from 7.3 to 60.2 years at the time of the initial evaluation were included in this study. Seven patients were followed up for a mean of 2.6 years (range, 0.33-5.0 years). Best-corrected visual acuity at baseline ranged from 20/16 to no light perception. Variable signs or sequelae of intraocular inflammation were observed in 9 patients, including keratic precipitates, band keratopathy, trace to 2+ anterior chamber cells, cystoid macular edema, and retinal vasculitis on fluorescein angiography. Ten patients were observed to show optic disc elevation and demonstrated peripapillary thickening on OCT. Seven patients showed retinal degeneration consistent with a cone-rod dystrophy, with atrophy tending to involve the posterior pole and extending peripherally. One patient with normal electroretinography findings and visual evoked potential was found to have decreased Arden ratio on electro-oculography.

CONCLUSIONS

Leveraging insights from the largest single-center ROSAH cohort described to date, this study identified 3 main factors as contributing to changes in visual function of patients with ROSAH syndrome: optic nerve involvement; intraocular inflammation, including cystoid macular edema; and retinal degeneration. More work is needed to determine how to arrest the progressive vision loss associated with ROSAH syndrome.

FINANCIAL DISCLOSURE(S)

Proprietary or commercial disclosure may be found after the references.

Hydrothermal assisted synthesis of hierarchical SnO2 micro flowers with CdO nanoparticles based membrane for energy storage applications

Hierarchical nanostructures with appropriate morphology and surface functionalities are highly desired to achieve an optimized electrochemical property for active electrode materials. This work renders the facile hydrothermal synthesis of CdO, SnO₂, and CdO-SnO₂ nanocomposite, and their capacitive performance was tested. The formation of the pure samples and their composite was committed by low-temperature Raman spectroscopy and x-ray diffraction studies which revealed the tetragonal and cubic structures of CdO and SnO₂ powder samples with good crystallinity and purity. The morphological postmortem reveals the formation of nanoparticles morphology of CdO with a highly smooth surface appearance. Besides, the SnO₂ illustrates the morphology of the micro flowers composed of ultrathin nanosheets. More specifically, the electrochemical properties indicate the pseudocapacitive charge storage mechanism based on cyclic voltammetry and chronopotentiometry analysis. The CdO-SnO₂ composite electrode displayed a higher capacitance due to additional pores/space offered for active sites and continuously allowed electrolyte ions to interact with the inner/outer surface of the electrode. These exciting findings led us to design and fabricate battery hybrid supercapacitors (BHSC) from CdO-SnO_2, and activated carbon (AC), referred to as CdO-SnO₂//AC BHSC, attains a high power delivery (5717 W/kg), and a maximum energy density of 42 Wh/kg at low discharge rate. Noteworthy, a stable cycling performance was obtained with only 91.3% retention after 8000 cycling at a large discharge current of 10 A/g, denoting the magnificent durability of the active electrode material.

An integrated multi-omic approach demonstrates distinct molecular signatures between human obesity with and without metabolic complications: a case-control study

OBJECTIVES

To examine the hypothesis that obesity complicated by the metabolic syndrome, compared to uncomplicated obesity, has distinct molecular signatures and metabolic pathways.

METHODS

We analyzed a cohort of 39 participants with obesity that included 21 with metabolic syndrome, age-matched to 18 without metabolic complications. We measured in whole blood samples 754 human microRNAs (miRNAs), 704 metabolites using unbiased mass spectrometry metabolomics, and 25,682 transcripts, which include both protein coding genes (PCGs) as well as non-coding transcripts. We then identified differentially expressed miRNAs, PCGs, and metabolites and integrated them using databases such as mirDIP (mapping between miRNA-PCG network), Human Metabolome Database (mapping between metabolite-PCG network) and tools like MetaboAnalyst (mapping between metabolite-metabolic pathway network) to determine dysregulated metabolic pathways in obesity with metabolic complications.

RESULTS

We identified 8 significantly enriched metabolic pathways comprising 8 metabolites, 25 protein coding genes and 9 microRNAs which are each differentially expressed between the subjects with obesity and those with obesity and metabolic syndrome. By performing unsupervised hierarchical clustering on the enrichment matrix of the 8 metabolic pathways, we could approximately segregate the uncomplicated obesity strata from that of obesity with metabolic syndrome.

CONCLUSIONS

The data suggest that at least 8 metabolic pathways, along with their various dysregulated elements, identified via our integrative bioinformatics pipeline, can potentially differentiate those with obesity from those with obesity and metabolic complications.

Assessment of Children with Cerebral Palsy Using Common Brief Core Set of International Classification of Functioning, Disability and Health for Children and Youth (ICF-CY)

Objective: To assess children with cerebral palsy using the Common Brief Core Set of International Classification of Functioning, Disability and Health for Children and Youth (ICF-CY). Study Design: Cross-sectional study Place and Duration of Study: Children Hospital & Institute of Child Health, Lahore Pakistan, from Nov 2020 to Jan 2021. Methodology: Fifty-nine children with cerebral palsy (CP) aged 0-18 years were included. Common Brief Core Set of International Classification of Functioning, Disability, and Health in Children and Youth (ICF-CY) was administered to children with cerebral palsy to assess their functional status. Strengths and weaknesses in body structure, body function,activity and participation and environmental factors were evaluated using the Common Brief Core Set of ICF-CY. Results: The majority of study participants were 38(64.4%), were spastic quadriplegic. Periventricular leukomalacia was noted in 36(67.9%) cases on MRI brain. Moderate to severe impairment was noted in body functions like intellectual function 46(78%). In addition, 26(44.1%) children with cerebral palsy had mild to moderate impairment in walking, while 4(6.8 %) could walk without any impairment. Social attitudes, construct, and design of buildings were the major barriers affecting the functionality of children with cerebral palsy. Conclusion: It was found that the Common Brief Core Set of ICF-CY in children with different types of cerebral palsy is a useful tool for assessing their functional level.Keywords: Cerebral Palsy, Common Brief Core Set, Disability, Health in Children and Youth (ICF-CY), International Classification of Functioning.  

Impact of Screen Media Usage on Early Childhood Development

Objective: To see the impact of screen media usage on early childhood development. Study Design: Cross-sectional study. Place and Duration of study: Developmental Behavioural Paediatrics Department, Children’s Hospital and Institute of Child Health, Lahore Pakistan, from Oct to Dec 2020. Methodology: This study included 100 children with an age range between 15-36 months and divided into two groups. Group-1 was children with communication behaviour disorders (CBD) (n=50), and Group-2 was typically developing (TD)children (n=50). ShaMaq Developmental Screening Tool (SDST) was administered to children to screen their development.Childhood behaviours were rated on a scale of 0-10 on a Behaviour rating scale. Results: Children with CBD had poor eye contact, response to names, poor imitation, poor pointing and poor one-step command following (p<0.001) compared to typically developing children. Children with CBD had poor eating habits (p<0.01),were more restless (p<0.001), and had a developmental delay (p<0.001) on SDST as compared to the other group. In children with CBD, the extent of screen media exposure was significantly correlated with restlessness (p<0.05) and poor pointing(p<0.01). Conclusion: Exposure to screen media at an early age and prolonged use of screens can lead to adverse developmental outcomes and behaviour issues in children. This is more evident in children with CBD than in typically developing children.

Validation of Polygenic Risk Scores for Coronary Heart Disease in a Middle Eastern Cohort Using Whole Genome Sequencing

BACKGROUND

Enthusiasm for using polygenic risk scores (PRSs) in clinical practice is tempered by concerns about their portability to diverse ancestry groups, thus motivating genome-wide association studies in non-European ancestry cohorts.

METHODS

We conducted a genome-wide association study for coronary heart disease in a Middle Eastern cohort using whole genome sequencing and assessed the performance of 6 PRSs developed with methods including LDpred (PGS000296), metaGRS (PGS000018), Pruning and Thresholding (PGS000337), and an EnsemblePRS we developed. Additionally, we evaluated the burden of rare variants in lipid genes in cases and controls. Whole genome sequencing at 30× coverage was performed in 1067 coronary heart disease cases (mean age=59 years; 70.3% males) and 6170 controls (mean age=40 years; 43.5% males).

RESULTS

The majority of PRSs performed well; odds ratio (OR) per 1 SD increase (OR_1sd) was highest for PGS000337 (OR_1sd=1.81, 95% CI [1.66-1.98], P=3.07×10^-41). EnsemblePRS performed better than individual PRSs (OR_1sd=1.8, 95% CI [1.66-1.96], P=5.89×10^-44). The OR for the 10th decile versus the remaining deciles was >3.2 for PGS000337, PGS000296, PGS000018, and reached 4.58 for EnsemblePRS. Of 400 known genome-wide significant loci, 33 replicated at P<10^-4. However, the 9p21 locus did not replicate. Six suggestive (P<10^-5) new loci/genes with plausible biological function were identified (eg, CORO7, RBM47, PDE4D). The burden of rare functional variants in LDLR, APOB, PCSK9, and ANGPTL4 was greater in cases than controls.

CONCLUSIONS

Overall, we demonstrate that PRSs derived from European ancestry genome-wide association studies performed well in a Middle Eastern cohort, suggesting these could be used in the clinical setting while ancestry-specific PRSs are developed.

Investigation of the Effect of Exendin-4 on Oleic Acid-Induced Steatosis in HepG2 Cells Using Fourier Transform Infrared Spectroscopy

Non-alcoholic fatty liver disease (NAFLD) is a common liver lesion that is untreatable with medications. Glucagon-like peptide-1 receptor (GLP-1R) agonists have recently emerged as a potential NAFLD pharmacotherapy. However, the molecular mechanisms underlying these drugs’ beneficial effects are not fully understood. Using Fourier transform infrared (FTIR) spectroscopy, we sought to investigate the biochemical changes in a steatosis cell model treated or not with the GLP-1R agonist Exendin-4 (Ex-4). HepG2 cells were made steatotic with 400 µM of oleic acid and then treated with 200 nM Ex-4 in order to reduce lipid accumulation. We quantified steatosis using the Oil Red O staining method. We investigated the biochemical alterations induced by steatosis and Ex-4 treatment using Fourier transform infrared (FTIR) spectroscopy and chemometric analyses. Analysis of the Oil Red O staining showed that Ex-4 significantly reduces steatosis. This reduction was confirmed by FTIR analysis, as the phospholipid band (C=O) at 1740 cm⁻¹ in Ex-4 treated cells is significantly decreased compared to steatotic cells. The principal component analysis score plots for both the lipid and protein regions showed that the untreated and Ex-4-treated samples, while still separated, are clustered close to each other, far from the steatotic cells. The biochemical and structural changes induced by OA-induced lipotoxicity are at least partially reversed upon Ex-4 treatment. FTIR and chemometric analyses revealed that Ex-4 significantly reduces OA-induced lipid accumulation, and Ex-4 also restored the lipid and protein biochemical alterations caused by lipotoxicity-induced oxidative stress. In combination with chemometric analyses, FTIR spectroscopy may offer new approaches for investigating the mechanisms underpinning NAFLD.

Revisiting the relationship between remittances and CO2 emissions by applying a novel dynamic simulated ARDL: empirical evidence from G-20 economies

The current study looks at the causes of carbon dioxide (CO₂) emissions by considering the implications of remittances in the presence of economic growth, financial development, and energy consumption in the case of selected four G-20 economies over the period 1990-2019. This study first uses the dynamic simulated ARDL model to stimulate, estimate, and plot to predict graphs of negative and positive changes occurring in the variables along with their short-run and long-run relationships. Results of the ARDL bounds test confirm a long-term relationship among remittances, financial development, economic growth energy consumption, and CO₂ emissions. Furthermore, the error correction model (ECM) also confirms the long-run relationship among CO₂ emissions, remittances, financial development, economic growth, and energy use. The results of a novel dynamic simulated ARDL disclosed that financial development is completely connected to CO₂ emissions in Mexico and India in the long run. On the other hand, results confirm that there is a positive relationship between remittances and CO₂ emissions in the case of Australia, Germany, and India, but this relationship is insignificant with CO₂ emissions in the case of Mexico. The result further disclosed that renewable energy exerts a significant impact on CO₂ in Australia, Mexico, India, and Germany in the long run while remittances wield a significant impact on CO₂ emissions in Australia, Mexico, and India. Moreover, the findings concluded that GDP has significant nexus with CO₂ in the long run in the case of Australia, Mexico, and Germany. This study uses up new visions for the economies of G-20 countries to sustain financial and economic growth by protecting the environment from pollution through its efficient national environmental policy, fiscal policy, and monetary policy.

Dysregulated Metabolic Pathways in Subjects with Obesity and Metabolic Syndrome

Background: Obesity coexists with variable features of metabolic syndrome, which is associated with dysregulated metabolic pathways. We assessed potential associations between serum metabolites and features of metabolic syndrome in Arabic subjects with obesity. Methods: We analyzed a dataset of 39 subjects with obesity only (OBO, n = 18) age-matched to subjects with obesity and metabolic syndrome (OBM, n = 21). We measured 1069 serum metabolites and correlated them to clinical features. Results: A total of 83 metabolites, mostly lipids, were significantly different (p < 0.05) between the two groups. Among lipids, 22 sphingomyelins were decreased in OBM compared to OBO. Among non-lipids, quinolinate, kynurenine, and tryptophan were also decreased in OBM compared to OBO. Sphingomyelin is negatively correlated with glucose, HbA1C, insulin, and triglycerides but positively correlated with HDL, LDL, and cholesterol. Differentially enriched pathways include lysine degradation, amino sugar and nucleotide sugar metabolism, arginine and proline metabolism, fructose and mannose metabolism, and galactose metabolism. Conclusions: Metabolites and pathways associated with chronic inflammation are differentially expressed in subjects with obesity and metabolic syndrome compared to subjects with obesity but without the clinical features of metabolic syndrome.

Gain-of-function mutations in ALPK1 cause an NF-κB-mediated autoinflammatory disease: functional assessment, clinical phenotyping and disease course of patients with ROSAH syndrome

Objectives

To test the hypothesis that ROSAH (retinal dystrophy, optic nerve oedema, splenomegaly, anhidrosis and headache) syndrome, caused by dominant mutation in ALPK1, is an autoinflammatory disease.

Methods

This cohort study systematically evaluated 27 patients with ROSAH syndrome for inflammatory features and investigated the effect of ALPK1 mutations on immune signalling. Clinical, immunologic and radiographical examinations were performed, and 10 patients were empirically initiated on anticytokine therapy and monitored. Exome sequencing was used to identify a new pathogenic variant. Cytokine profiling, transcriptomics, immunoblotting and knock-in mice were used to assess the impact of ALPK1 mutations on protein function and immune signalling.

Results

The majority of the cohort carried the p.Thr237Met mutation but we also identified a new ROSAH-associated mutation, p.Tyr254Cys.

Nearly all patients exhibited at least one feature consistent with inflammation including recurrent fever, headaches with meningeal enhancement and premature basal ganglia/brainstem mineralisation on MRI, deforming arthritis and AA amyloidosis. However, there was significant phenotypic variation, even within families and some adults lacked functional visual deficits. While anti-TNF and anti-IL-1 therapies suppressed systemic inflammation and improved quality of life, anti-IL-6 (tocilizumab) was the only anticytokine therapy that improved intraocular inflammation (two of two patients).

Patients’ primary samples and in vitro assays with mutated ALPK1 constructs showed immune activation with increased NF-κB signalling, STAT1 phosphorylation and interferon gene expression signature. Knock-in mice with the Alpk1 T237M mutation exhibited subclinical inflammation.

Clinical features not conventionally attributed to inflammation were also common in the cohort and included short dental roots, enamel defects and decreased salivary flow.

Conclusion

ROSAH syndrome is an autoinflammatory disease caused by gain-of-function mutations in ALPK1 and some features of disease are amenable to immunomodulatory therapy.

Photoreceptor and Retinal Pigment Epithelium Relationships in Eyes With Vitelliform Macular Dystrophy Revealed by Multimodal Adaptive Optics Imaging

Purpose

To assess the structure of cone photoreceptors and retinal pigment epithelial (RPE) cells in vitelliform macular dystrophy (VMD) arising from various genetic etiologies.

Methods

Multimodal adaptive optics (AO) imaging was performed in 11 patients with VMD using a custom-assembled instrument. Non-confocal split detection and AO-enhanced indocyanine green were used to visualize the cone photoreceptor and RPE mosaics, respectively. Cone and RPE densities were measured and compared across BEST1-, PRPH2-, IMPG1-, and IMPG2-related VMD.

Results

Within macular lesions associated with VMD, both cone and RPE densities were reduced below normal, to 37% of normal cone density (eccentricity 0.2 mm) and to 8.4% of normal RPE density (eccentricity 0.5 mm). Outside of lesions, cone and RPE densities were slightly reduced (both to 92% of normal values), but with high degree of variability in the individual measurements. Comparison of juxtalesional cone and RPE measurements (<1 mm from the lesion edge) revealed significant differences in RPE density across the four genes (P < 0.05). Overall, cones were affected to a greater extent than RPE in patients with IMPG1 and IMPG2 pathogenic variants, but RPE was affected more than cones in BEST1 and PRPH2 VMD. This trend was observed even in contralateral eyes from a subset of five patients who presented with macular lesions in only one eye.

Conclusions

Assessment of cones and RPE in retinal locations outside of the macular lesions reveals a pattern of cone and RPE disruption that appears to be gene dependent in VMD. These findings provide insight into the cellular pathogenesis of disease in VMD.

Predominant Founder Effect among Recurrent Pathogenic Variants for an X-Linked Disorder

For disorders with X-linked inheritance, variants may be transmitted through multiple generations of carrier females before an affected male is ascertained. Pathogenic RS1 variants exclusively cause X-linked retinoschisis (XLRS). While RS1 is constrained to variation, recurrent variants are frequently observed in unrelated probands. Here, we investigate recurrent pathogenic variants to determine the relative burden of mutational hotspot and founder allele events to this phenomenon. A cohort RS1 variant analysis and standardized classification, including variant enrichment in the XLRS cohort and in RS1 functional domains, were performed on 332 unrelated XLRS probands. A total of 108 unique RS1 variants were identified. A subset of 19 recurrently observed RS1 variants were evaluated in 190 probands by a haplotype analysis, using microsatellite and single nucleotide polymorphisms. Fourteen variants had at least two probands with common variant-specific haplotypes over ~1.95 centimorgans (cM) flanking RS1. Overall, 99/190 of reportedly unrelated probands had 25 distinct shared haplotypes. Examination of this XLRS cohort for common RS1 haplotypes indicates that the founder effect plays a significant role in this disorder, including variants in mutational hotspots. This improves the accuracy of clinical variant classification and may be generalizable to other X-linked disorders.

De novo frameshift mutation in YAP1 associated with bilateral uveal coloboma and microphthalmia

BACKGROUND

Uveal colobomata are eye defects that result from failure of the optic fissure of the neuroectoderm-derived optic cup to close between weeks 5-7 of fetal life. Mutations in YAP1 have previously been linked to uveal coloboma. We present the clinical features and genetic basis of a one-year-old male with bilateral uveal colobomata.

MATERIALS AND METHODS

Clinical features were gathered from an age-appropriate evaluation and retrospectively from clinical records. DNA samples were collected from the proband, his uncle (who also had coloboma), both parents, and one sibling. Whole-genome sequencing of the coding regions and intron-exon boundaries confirmed a mutation in the proband. These genetic findings were verified using the Sanger method of DNA sequencing.

RESULTS

The proband is a male with congenital bilateral colobomata (iris/retina/nerve), reduced vision, nystagmus with null point, bilateral microcornea, right microphthalmia, possible mild right hemifacial microsomia, a tubular nose, possible spina bifida occulta, and astigmatism. Whole-genome sequencing confirmed a heterozygous YAP1 frameshift mutation NM_001130145.3:c.178dupG p.(Asp60GlyfsTer52) in the proband. This mutation was absent in all other tested family members.

CONCLUSIONS

We report a de novo mutation in YAP1 that likely results in nonsense-mediated decay. Given the association with YAP1 haploinsufficiency and colobomatous microphthalmia, this novel variant provides a molecular diagnosis for the proband. Further insight into YAP1 mutations may have implications in the prevention/treatment of uveal coloboma and other syndromic disorders.

Tissue-specific genotype-phenotype correlations among USH2A-related disorders in the RUSH2A study

We assessed genotype-phenotype correlations among the visual, auditory, and olfactory phenotypes of 127 participants with Usher syndrome (USH2) (n=80) or nonsyndromic autosomal recessive retinitis pigmentosa (ARRP) (n=47) due to USH2A variants, using clinical data and molecular diagnostics from the Rate of Progression in USH2A Related Retinal Degeneration (RUSH2A) study. USH2A truncating alleles were associated with USH2 and had a dose-dependent effect on hearing loss severity with no effect on visual loss severity within the USH2 subgroup. A group of missense alleles in an inter-fibronectin domain appeared to be hypomorphic in ARRP. These alleles were associated with later age of onset, larger visual field area, better sensitivity thresholds, and better electroretinographic responses. No effect of genotype on the severity of olfactory deficits was observed. This study unveils a unique, tissue-specific USH2A allelic hierarchy with important prognostic implications for patient counseling and treatment trial endpoints. These findings may inform clinical care or research approaches in others with allelic disorders or pleiotropic phenotypes. This article is protected by copyright. All rights reserved.

Rare and common variants in ROM1 and PRPH2 genes trans-modify Stargardt/ABCA4 disease

Over 1,500 variants in the ABCA4 locus cause phenotypes ranging from severe, early-onset retinal degeneration to very late-onset maculopathies. The resulting ABCA4/Stargardt disease is the most prevalent Mendelian eye disorder, although its underlying clinical heterogeneity, including penetrance of many alleles, are not well-understood. We hypothesized that a share of this complexity is explained by trans-modifiers, i.e., variants in unlinked loci, which are currently unknown. We sought to identify these by performing exome sequencing in a large cohort for a rare disease of 622 cases and compared variation in seven genes known to clinically phenocopy ABCA4 disease to cohorts of ethnically matched controls. We identified a significant enrichment of variants in 2 out of the 7 genes. Moderately rare, likely functional, variants, at the minor allele frequency (MAF) <0.005 and CADD>25, were enriched in ROM1, where 1.3% of 622 patients harbored a ROM1 variant compared to 0.3% of 10,865 controls (p = 2.41E04; OR 3.81 95% CI [1.77; 8.22]). More importantly, analysis of common variants (MAF>0.1) identified a frequent haplotype in PRPH2, tagged by the p.Asp338 variant with MAF = 0.21 in the matched general population that was significantly increased in the patient cohort, MAF 0.25, p = 0.0014. Significant differences were also observed between ABCA4 disease subgroups. In the late-onset subgroup, defined by the hypomorphic p.Asn1868Ile variant and including c.4253+43G>A, the allele frequency for the PRPH2 p.Asp338 variant was 0.15 vs 0.27 in the remaining cohort, p = 0.00057. Known functional data allowed suggesting a mechanism by which the PRPH2 haplotype influences the ABCA4 disease penetrance. These associations were replicated in an independent cohort of 408 patients. The association was highly statistically significant in the combined cohorts of 1,030 cases, p = 4.00E-05 for all patients and p = 0.00014 for the hypomorph subgroup, suggesting a substantial trans-modifying role in ABCA4 disease for both rare and common variants in two unlinked loci.

Failure mode and effect analysis (FMEA) to identify and mitigate failures in a hospital rapid response system (RRS)

We performed FMEA on the existing RRS with the help of routine users of the RRS who acted as subject matter experts and evaluated the failures for their criticality using the Risk Priority Number approach based on their experience of the RRS. The FMEA found 35 potential failure modes and 101 failure mode effects across 13 process steps of the RRS. The afferent limb of RRS was found to be more prone to these failures (62, 61.4%) than the efferent limb of the RRS (39, 38.6%). Modification of calling criteria (12, 11.9%) and calculation of New Zealand Early Warning Scores (NZEWS) calculation (11, 10.9%) steps were found to potentially give rise to the highest number of these failures. Causes of these failures include human error and related factors (35, 34.7%), staff workload/staffing levels (30, 29.7%) and limitations due to paper-based charts and organisational factors (n = 30, 29.7%). The demonstrated electronic system was found to potentially eliminate or reduce the likelihood of 71 (70.2%) failures. The failures not eliminated by the electronic RRS require targeted corrective measures including scenario-based training and education, and revised calling criteria to include triggers for hypothermia and high systolic blood pressure.

Photoreceptor degeneration in ABCA4-associated retinopathy and its genetic correlates

BACKGROUND

Outcome measures sensitive to disease progression are needed for ATP-binding cassette, sub-family A, member 4–associated (ABCA4-associated) retinopathy. We aimed to quantify ellipsoid zone (EZ) loss and photoreceptor degeneration beyond EZ-loss in ABCA4-associated retinopathy and investigate associations between photoreceptor degeneration, genotype, and age.

METHODS

We analyzed 132 eyes from 66 patients (of 67 enrolled) with molecularly confirmed ABCA4-associated retinopathy from a prospective natural history study with a median [IQR] follow-up of 4.2 years [3.1, 5.1]. Longitudinal spectral-domain optical coherence tomography volume scans (37 B-scans, 30° × 15°) were segmented using a deep learning (DL) approach. For genotype-phenotype analysis, a model of ABCA4 variants was applied with the age of criterion EZ-loss (6.25 mm²) as the dependent variable.

RESULTS

Patients exhibited an average (square-root-transformed) EZ-loss progression rate of [95% CI] 0.09 mm/y [0.06, 0.11]. Outer nuclear layer (ONL) thinning extended beyond the area of EZ-loss. The average distance from the EZ-loss boundary to normalization of ONL thickness (to ±2 z score units) was 3.20° [2.53, 3.87]. Inner segment (IS) and outer segment (OS) thinning was less pronounced, with an average distance from the EZ-loss boundary to layer thickness normalization of 1.20° [0.91, 1.48] for the IS and 0.60° [0.49, 0.72] for the OS. An additive model of allele severity explained 52.7% of variability in the age of criterion EZ-loss.

CONCLUSION

Patients with ABCA4-associated retinopathy exhibited significant alterations of photoreceptors outside of EZ-loss. DL-based analysis of photoreceptor laminae may help monitor disease progression and estimate the severity of ABCA4 variants.

TRIAL REGISTRATION

ClinicalTrials.gov identifier: NCT01736293.

FUNDING

National Eye Institute Intramural Research Program and German Research Foundation grant PF950/1-1.

Characteristic MicroRNAs Linked to Dysregulated Metabolic Pathways in Qatari Adult Subjects With Obesity and Metabolic Syndrome

BACKGROUND

Obesity-associated dysglycemia is associated with metabolic disorders. MicroRNAs (miRNAs) are known regulators of metabolic homeostasis. We aimed to assess the relationship of circulating miRNAs with clinical features in obese Qatari individuals.

METHODS

We analyzed a dataset of 39 age-matched patients that includes 18 subjects with obesity only (OBO) and 21 subjects with obesity and metabolic syndrome (OBM). We measured 754 well-characterized human microRNAs (miRNAs) and identified differentially expressed miRNAs along with their significant associations with clinical markers in these patients.

RESULTS

A total of 64 miRNAs were differentially expressed between metabolically healthy obese (OBO) versus metabolically unhealthy obese (OBM) patients. Thirteen out of 64 miRNAs significantly correlated with at least one clinical trait of the metabolic syndrome. Six out of the thirteen demonstrated significant association with HbA1c levels; miR-331-3p, miR-452-3p, and miR-485-5p were over-expressed, whereas miR-153-3p, miR-182-5p, and miR-433-3p were under-expressed in the OBM patients with elevated HbA1c levels. We also identified, miR-106b-3p, miR-652-3p, and miR-93-5p that showed a significant association with creatinine; miR-130b-5p, miR-363-3p, and miR-636 were significantly associated with cholesterol, whereas miR-130a-3p was significantly associated with LDL. Additionally, miR-652-3p's differential expression correlated significantly with HDL and creatinine.

CONCLUSIONS

MicroRNAs associated with metabolic syndrome in obese subjects may have a pathophysiologic role and can serve as markers for obese individuals predisposed to various metabolic diseases like diabetes.

Simple risk score to screen for prediabetes: A cross-sectional study from the Qatar Biobank cohort

AIMS/INTRODUCTION

The progression from prediabetes to type 2 diabetes is preventable by lifestyle intervention and/or pharmacotherapy in a large fraction of individuals with prediabetes. Our objective was to develop a risk score to screen for prediabetes in the Middle East, where diabetes prevalence is one of the highest in the world.

MATERIALS AND METHODS

In this cross-sectional, case-control study, we used data of 4,895 controls and 2,373 prediabetic adults obtained from the Qatar Biobank cohort. Significant risk factors were identified by logistic regression and other machine learning methods. The receiver operating characteristic was used to calculate the area under curve, cut-off point, sensitivity, specificity, positive and negative predictive values. The prediabetes risk score was developed from data of Qatari citizens, as well as long-term (≥15 years) residents.

RESULTS

The significant risk factors for the Prediabetes Risk Score in Qatar were age, sex, body mass index, waist circumference and blood pressure. The risk score ranges from 0 to 45. The area under the curve of the score was 80% (95% confidence interval 78-83%), and the cut-off point of 16 yielded sensitivity and specificity of 86.2% (95% confidence interval 82.7-89.2%) and 57.9% (95% confidence interval 65.5-71.4%), respectively. Prediabetes Risk Score in Qatar performed equally in Qatari nationals and long-term residents.

CONCLUSIONS

Prediabetes Risk Score in Qatar is the first prediabetes screening score developed in a Middle Eastern population. It only uses risk factors measured non-invasively, is simple, cost-effective, and can be easily understood by the general public and health providers. Prediabetes Risk Score in Qatar is an important tool for early detection of prediabetes, and can help tremendously in curbing the diabetes epidemic in the region.

PDE6C: Novel Mutations, Atypical Phenotype, and Differences Among Children and Adults

Purpose

Genetic variation in PDE6C is associated with achromatopsia and cone dystrophy, with only a few reports of cone-rod dystrophy in the literature. We describe two pediatric and two adult patients with PDE6C related cone and cone-rod dystrophy and the first longitudinal data of a pediatric patient with PDE6C-related cone dystrophy.

Methods

This cohort of four patients underwent comprehensive ophthalmologic evaluation at the National Eye Institute's Ophthalmic Genetics clinic, including visual field testing, retinal imaging and electroretinogram (ERG). Next-generation sequencing-based genetic testing was performed and subsequent analysis of the variants was done through three-dimensional protein models generated by Phyre2 and Chimera.

Results

All cases shared decreased best-corrected visual acuity and poor color discrimination. Three of the four patients had a cone-rod dystrophy, presenting with an ERG showing decreased amplitude on both photopic and scotopic waveforms and a mild to moderately constricted visual field. One of the children was diagnosed with cone dystrophy, having a preserved peripheral field. The children had none to minor structural retinal changes, whereas the adults had clear macular dystrophy.

Conclusions

PDE6C-related cone-rod dystrophy consists of a severe phenotype characterized by early-onset nystagmus, decreased best-corrected visual acuity, poor color discrimination, progressive constriction of the visual field, and night blindness. Our work contributes with valuable information toward understanding the visual prognosis and allelic heterogeneity of PDE6C-related cone and cone-rod dystrophy.

Persistent Dark Cones in Oligocone Trichromacy Revealed by Multimodal Adaptive Optics Ophthalmoscopy

Dark cone photoreceptors, defined as those with diminished or absent reflectivity when observed with adaptive optics (AO) ophthalmoscopy, are increasingly reported in retinal disorders. However, their structural and functional impact remain unclear. Here, we report a 3-year longitudinal study on a patient with oligocone trichromacy (OT) who presented with persistent, widespread dark cones within and near the macula. Diminished electroretinogram (ERG) cone but normal ERG rod responses together with normal color vision confirmed the OT diagnosis. In addition, the patient had normal to near normal visual acuity and retinal sensitivity. Occasional dark gaps in the photoreceptor layer were observed on optical coherence tomography, in agreement with reflectance AO scanning light ophthalmoscopy, which revealed that over 50% of the cones in the fovea were dark, increasing to 74% at 10° eccentricity. In addition, the cone density was 78% lower than normal histologic value at the fovea, and 20-40% lower at eccentricities of 5-15°. Interestingly, color vision testing was near normal at locations where cones were predominantly dark. These findings illustrate how a retina with predominant dark cones that persist over at least 3 years can support near normal central retinal function. Furthermore, this study adds to the growing evidence that cones can continue to survive under non-ideal conditions.

Biomolecular alterations in acute traumatic brain injury (TBI) using Fourier transform infrared (FTIR) imaging spectroscopy

Acute injury is one of the substantial stage post-traumatic brain injury (TBI) occurring at the moment of impact. Decreased metabolism, unregulated cerebral blood flow and direct tissue damage are triggered by acute injury. Understating the biochemical alterations associated with acute TBI is critical for brain plasticity and recovery. The objective of this study was to investigate the biochemical and molecular changes in hippocampus, corpus callosum and thalamus brain regions post-acute TBI in rats. Fourier Transform Infrared (FTIR) imaging spectroscopy were used to collect chemical images from control and 3 hrs post-TBI (Marmarou model was used for the TBI induction) rat brains and adjacent sections were treated by hematoxylin and eosin (H&E) staining to correlate with the disruption in tissue morphology and injured brain biochemistry. Our results revealed that the total lipid and total protein content decreased significantly in the hippocampus, corpus callosum and thalamus after brain injury. Reduction in lipid acyl chains (-CH₂) associated with an increase in methyl (-CH₃) and unsaturated lipids olefin = CH concentrations is observed. Furthermore, there is a decrease in the lipid order (disorder), which leads to an increase in acyl chain fluidity in injured rats. The results suggest acute TBI damages brain tissues mechanically rather than chemical alterations. This will help in assessing successful therapeutic strategy in order to mitigate tissue damage in acute TBI period.

A Modelling Framework for Embedding-based Predictions for Compound-Viral Protein Activity

Motivation

A global effort is underway to identify compounds for the treatment of COVID-19. Since de novo compound design is an extremely long, time-consuming, and expensive process, efforts are underway to discover existing compounds that can be repurposed for COVID-19 and new viral diseases.

Model

We propose a machine learning representation framework that uses deep learning induced vector embeddings of compounds and viral proteins as features to predict compound-viral protein activity. The prediction model in-turn uses a consensus framework to rank approved compounds against viral proteins of interest.

Results

Our consensus framework achieves a highmean Pearson correlation of 0.916, mean R2 of 0.840 and a low mean squared error of 0.313 for the task of compound-viral protein activity prediction on an independent test set. As a use case, we identify a ranked list of 47 compounds common to three main proteins of SARS-COV-2 virus (PL-PRO, 3CL-PRO and Spike protein) as potential targets including 21 antivirals, 15 anticancer, 5 antibiotics and 6 other investigationalhuman compounds.We performadditional molecular docking simulations to demonstrate thatmajority of these compounds have low binding energies and thus high binding affinity with the potential to be effective against the SARS-COV-2 virus.

Availability

All the source code and data is available at: https://github.com/raghvendra5688/Drug-Repurposing and https://dx.doi.org/10.17632/8rrwnbcgmx.3. We also implemented a web-server at: https://machinelearning-protein.qcri.org/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.

Early Detection of Prediabetes and T2DM Using Wearable Sensors and Internet-of-Things-Based Monitoring Applications

BACKGROUND

Prediabetes and type 2 diabetes mellitus (T2DM) are one of the major long-term health conditions affecting global healthcare delivery. One of the few effective approaches is to actively manage diabetes via a healthy and active lifestyle.

OBJECTIVES

This research is focused on early detection of prediabetes and T2DM using wearable technology and Internet-of-Things-based monitoring applications.

METHODS

We developed an artificial intelligence model based on adaptive neuro-fuzzy inference to detect prediabetes and T2DM via individualized monitoring. The key contributing factors to the proposed model include heart rate, heart rate variability, breathing rate, breathing volume, and activity data (steps, cadence, and calories). The data was collected using an advanced wearable body vest and combined with manual recordings of blood glucose, height, weight, age, and sex. The model analyzed the data alongside a clinical knowledgebase. Fuzzy rules were used to establish baseline values via existing interventions, clinical guidelines, and protocols.

RESULTS

The proposed model was tested and validated using Kappa analysis and achieved an overall agreement of 91%.

CONCLUSION

We also present a 2-year follow-up observation from the prediction results of the original model. Moreover, the diabetic profile of a participant using M-health applications and a wearable vest (smart shirt) improved when compared to the traditional/routine practice.

An international telemedicine program for diagnosis of genetic disorders: Partnership of pediatrician and geneticist

There is a shortage of genetics providers worldwide and access is limited to large academic centers. Telemedicine programs can facilitate access to genetic services to patients living in remote locations. The goal of this study was to improve access to genetic services in the Dominican Republic by creating a partnership model between a pediatrician and geneticist. This approach has been used within the United States but not in the setting of two different countries, healthcare system, and cultures. Patients were referred to the Centro de Obstetricia y Ginecologia program if a syndromic or genetic etiology was suspected by their local provider. Pediatrician first evaluated all patients prior to telemedicine appointment to review family and medical history. All genetic visits were scheduled within 2 weeks of referral in collaboration with telehealth program at Cincinnati Children's Hospital Medical Center. A total of 66 individuals were evaluated during a period of 5 years. Fifty-seven individuals underwent genetic studies, and a molecular diagnosis was made in 39 individuals. Exome sequencing was the most common first line test when differential diagnosis was broad (n = 40). The most common inheritance was autosomal recessive in 15 individuals, followed by 13 individuals with autosomal dominant disorders, 7 individuals X-linked disorders, and 4 individuals with chromosomal abnormalities. This study provides data to support utility of geneticist and pediatrician partnership to provide outreach telemedicine diagnostics and management services for rare diseases in an international setting.

Novel TMEM98, MFRP, PRSS56 variants in a large United States high hyperopia and nanophthalmos cohort

Nanophthalmos is a rare condition defined by a small, structurally normal eye with resultant high hyperopia. While six genes have been implicated in this hereditary condition (MFRP, PRSS56, MYRF, TMEM98, CRB1,VMD2/BEST1), the relative contribution of these to nanophthalmos or to less severe high hyperopia (≥ + 5.50 spherical equivalent) has not been fully elucidated. We collected probands and families (n = 56) with high hyperopia or nanophthalmos (≤ 21.0 mm axial length). Of 53 families that passed quality control, plausible genetic diagnoses were identified in 10/53 (18.8%) by high-throughput panel or pooled exome sequencing. These include 1 TMEM98 family (1.9%), 5 MFRP families (9.4%), and 4 PRSS56 families (7.5%), with 4 additional families having single allelic hits in MFRP or PRSS56 (7.5%). A novel deleterious TMEM98 variant (NM_015544.3, c.602G>C, p.(Arg201Pro)) segregated with disease in 4 affected members of a family. Multiple novel missense and frameshift variants in MFRP and PRSS56 were identified. PRSS56 families were more likely to have choroidal folds than other solved families, while MFRP families were more likely to have retinal degeneration. Together, this study defines the prevalence of nanophthalmos gene variants in high hyperopia and nanophthalmos and indicates that a large fraction of cases remain outside of single gene coding sequences.

Novel progressive acrodysostosis-like skeletal dysplasia, cerebellar atrophy, and ichthyosis

Acrodysostosis refers to a rare heterogeneous group of bone dysplasias that share skeletal features, hormone resistance, and intellectual disability. Two genes have been associated with acrodysostosis with or without hormone resistance (PRKAR1A and PDE4D). Severe intellectual disability has been reported with acrodysostosis but brain malformations and ichthyosis have not been reported in these syndromes. Here we describe a female patient with acrodysostosis, intellectual disability, cerebellar hypoplasia, and lamellar ichthyosis. The patient has an evolving distinctive facial phenotype and childhood onset ataxia. X-rays showed generalized osteopenia, shortening of middle and distal phalanges, and abnormal distal epiphysis of the ulna and radius. Brain magnetic resonance imaging showed cerebellar atrophy without other brainstem abnormalities. Genetic workup included nondiagnostic chromosomal microarray and skeletal dysplasia molecular panels. These clinical findings are different from any recognized form of acrodysostosis syndrome. Whole exome sequencing did not identify rare or predicted pathogenic variants in genes associated with known acrodysostosis, lamellar ichthyosis, and other overlapping disorders. A broader search for rare alleles absent in healthy population databases and controls identified two heterozygous truncating alleles in FBNL7 and PPM1M genes, and one missense allele in the NPEPPS gene. Identification of additional patients is required to delineate the mechanism of this unique disorder.

A genetic and clinical study of individuals with nonsyndromic retinopathy consequent upon sequence variants in HGSNAT, the gene associated with Sanfilippo C mucopolysaccharidosis

Pathogenic variants in the gene HGSNAT (heparan-α-glucosaminide N-acetyltransferase) have been reported to underlie two distinct recessive conditions, depending on the specific genotype, mucopolysaccharidosis type IIIC (MPSIIIC)-a severe childhood-onset lysosomal storage disorder, and adult-onset nonsyndromic retinitis pigmentosa (RP). Here we describe the largest cohort to-date of HGSNAT-associated nonsyndromic RP patients, and describe their retinal phenotype, leukocyte enzymatic activity, and likely pathogenic genotypes. We identified biallelic HGSNAT variants in 17 individuals (15 families) as the likely cause of their RP. None showed any other symptoms of MPSIIIC. All had a mild but significant reduction of HGSNAT enzyme activity in leukocytes. The retinal condition was generally of late-onset, showing progressive degeneration of a concentric area of paramacular retina, with preservation but reduced electroretinogram responses. Symptoms, electrophysiology, and imaging suggest the rod photoreceptor to be the cell initially compromised. HGSNAT enzymatic testing was useful in resolving diagnostic dilemmas in compatible patients. We identified seven novel sequence variants [p.(Arg239Cys); p.(Ser296Leu); p.(Phe428Cys); p.(Gly248Ala); p.(Gly418Arg), c.1543-2A>C; c.1708delA], three of which were considered to be retina-disease-specific alleles. The most prevalent retina-disease-specific allele p.(Ala615Thr) was observed heterozygously or homozygously in 8 and 5 individuals respectively (7 and 4 families). Two siblings in one family, while identical for the HGSNAT locus, but discordant for retinal disease, suggest the influence of trans-acting genetic or environmental modifying factors.

Genotype-phenotype associations in a large PRPH2-related retinopathy cohort

Molecular variant interpretation lacks disease gene-specific cohorts for determining variant enrichment in disease versus healthy populations. To address the molecular etiology of retinal degeneration, specifically the PRPH2-related retinopathies, we reviewed genotype and phenotype information obtained from 187 eyeGENE® participants from 161 families. Clinical details were provided by referring clinicians participating in the eyeGENE® Network. The cohort was sequenced for variants in PRPH2. Variant complementary DNA clusters and cohort frequency were compared to variants in public databases to help us to determine pathogenicity by current American College of Medical Genetics and Genomics/Association for Molecular Pathology interpretation criteria. The most frequent variant was c.828+3A>T, which affected 28 families (17.4%), and 25 of 79 (31.64%) variants were novel. The majority of missense variants clustered in the D2 intracellular loop of the peripherin-2 protein, constituting a hotspot. Disease enrichment was noted for 23 (29.1%) of the variants. Hotspot and disease-enrichment evidence modified variant classification for 16.5% of variants. The missense allele p.Arg172Trp was associated with a younger age of onset. To the best of our knowledge, this is the largest patient cohort review of PRPH2-related retinopathy. Large disease gene-specific cohorts permit gene modeling for hotspot and disease-enrichment analysis, providing novel variant classification evidence, including for novel missense variants.

KinVis: a visualization tool to detect cryptic relatedness in genetic datasets

MOTIVATION

It is important to characterize individual relatedness in terms of familial relationships and underlying population structure in genome-wide association studies for correct downstream analysis. The characterization of individual relatedness becomes vital if the cohort is to be used as reference panel in other studies for association tests and for identifying ethnic diversities. In this paper, we propose a kinship visualization tool to detect cryptic relatedness between subjects. We utilize multi-dimensional scaling, bar charts, heat maps and node-link visualizations to enable analysis of relatedness information.

AVAILABILITY AND IMPLEMENTATION

Available online as well as can be downloaded at http://shiny-vis.qcri.org/public/kinvis/.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Machine Learning-based Risk of Hospital Readmissions: Predicting Acute Readmissions within 30 Days of Discharge

The objective of this study was to design and develop a 30-day risk of hospital readmission predictive model using machine learning techniques. The proposed risk of readmission predictive model was then validated with the two most commonly used risk of readmission models - LACE index and patient at-risk of hospital readmission (PARR). The study cohort consisted of 180,118 admissions with 22565 (12.5%) of actual readmissions within 30-day of hospital discharge, from 01 Jan 2015 to 31 Dec 2016 from two Auckland-region hospitals. We developed a machine learning model to predict 30-day readmissions using the model types: XGBoost, Random Forests and Adaboost with decision stumps as a base learner with different feature combinations and preprocessing procedures. The proposed model achieved the F1-score (0.386 ± 0.006), sensitivity (0.598 ± 0.013), positive predictive value (PPV) (0.285 ± 0.004) and negative predictive value (NPV) (0.932 ± 0.002). When compared with LACE and PARR (NZ) models, the proposed model achieved better F1-score by 12.5% compared to LACE and 22.9% compared to PARR (NZ). The mean sensitivity of the proposed model was 6.0% higher than LACE and 42.4% higher than PARR (NZ). The mean PPV was 15.9% and 13.5% higher than LACE and PARR (NZ) respectively.

Probing the fibrillation of lysozyme by nanoscale-infrared spectroscopy

Amyloid fibrillation is the root cause of several neuro as well as non-neurological disorders. Understanding the molecular basis of amyloid aggregate formation is crucial for deciphering various neurodegenerative diseases. In our study, we have examined the lysozyme fibrillation process using nano-infrared spectroscopy (nanoIR). NanoIR enabled us to investigate both structural and chemical characteristics of lysozyme fibrillar species concurrently. The spectroscopic results indicate that lysozyme transformed into a fibrillar structure having mainly parallel β-sheets, with almost no antiparallel β-sheets. Features such as protein stiffness have a good correlation with obtained secondary structural information showing the state of the protein within the fibrillation state. The structural and chemical details were compared with transmission electron microscopy (TEM) and circular dichroism (CD). We have utilized nanoIR and measured infrared spectra to characterize lysozyme amyloid fibril structures in terms of morphology, molecular structure, secondary structure content, stability, and size of the cross-β core. We have shown that the use of nanoIR can complement other biophysical studies to analyze the aggregation process and is particularly useful for studying proteins involved in aggregation to help in designing molecules against amyloid aggregation. Specifically, the nanoIR spectra afford higher resolution information and a characteristic fingerprint for determining states of aggregation.Communicated by Ramaswamy H. Sarma.

Expanding the genotypic spectrum of Jalili syndrome: Novel CNNM4 variants and uniparental isodisomy in a north American patient cohort

Jalili syndrome is a rare multisystem disorder with the most prominent features consisting of cone-rod dystrophy and amelogenesis imperfecta. Few cases have been reported in the Americas. Here we describe a case series of patients with Jalili syndrome examined at the National Eye Institute’s Ophthalmic Genetics clinic between 2016 and 2018. Three unrelated sporadic cases were systematically evaluated for ocular phenotype and determined to have cone-rod dystrophy with bull’s eye maculopathy, photophobia, and nystagmus. All patients had amelogenesis imperfecta. Two of these patients had Guatemalan ancestry and the same novel homozygous CNNM4 variant (p.Arg236Trp c.706C > T) without evidence of consanguinity. This variant met likely pathogenic criteria by the American College of Medical Genetics guidelines. An additional patient had a homozygous deleterious variant in CNNM4 (c.279delC p.Phe93Leufs*31), which resulted from paternal uniparental isodisomy for chromosome 2p22–2q37. This individual had additional syndromic features including developmental delay and spastic diplegia, likely related to mutations at other loci. Our work highlights the genotypic variability of Jalili syndrome and expands the genotypic spectrum of this condition by describing the first series of patients seen in the United States.

Towards scaling elementary flux mode computation

While elementary flux mode (EFM) analysis is now recognized as a cornerstone computational technique for cellular pathway analysis and engineering, EFM application to genome-scale models remains computationally prohibitive. This article provides a review of aspects of EFM computation that elucidates bottlenecks in scaling EFM computation. First, algorithms for computing EFMs are reviewed. Next, the impact of redundant constraints, sensitivity to constraint ordering and network compression are evaluated. Then, the advantages and limitations of recent parallelization and GPU-based efforts are highlighted. The article then reviews alternative pathway analysis approaches that aim to reduce the EFM solution space. Despite advances in EFM computation, our review concludes that continued scaling of EFM computation is necessary to apply EFM to genome-scale models. Further, our review concludes that pathway analysis methods that target specific pathway properties can provide powerful alternatives to EFM analysis.

Clinical Decision Support for Early Detection of Prediabetes and Type 2 Diabetes Mellitus Using Wearable Technology

Worldwide spending on long-term and chronic care conditions is increasing to a point that requires immediate interventions and advancements to reduce the burden of the healthcare cost. This research is focused on early detection of prediabetes and type 2 diabetes mellitus (T2DM) using wearable technology. An artificial intelligence model was developed based on adaptive-neuro fuzzy interference to detect prediabetes and T2DM via individualized monitoring. The key contributing factors to the proposed model include heart rate, heart rate variability, breathing rate, breathing volume, and activity data (steps, cadence and calories). The data was collected using an advanced wearable body vest. The real-time data was combined with manual recordings of blood glucose, height, weight, age and sex. The model analyzed the data alongside a clinical knowledge-base. Fuzzy rules were used to establish baseline values via existing interventions, clinical guidelines and protocols. The proposed model was tested and validated using Kappa analysis and achieved an overall agreement of 91%.

Investigation of Biochemical Alterations in Ischemic Stroke Using Fourier Transform Infrared Imaging Spectroscopy-A Preliminary Study

Objective: Brain damage, long-term disability and death are the dreadful consequences of ischemic stroke. It causes imbalance in the biochemical constituents that distorts the brain dynamics. Understanding the sub-cellular alterations associated with the stroke will contribute to deeper molecular understanding of brain plasticity and recovery. Current routine approaches examining lipid and protein biochemical changes post stoke can be difficult. Fourier Transform Infrared (FTIR) imaging spectroscopy can play a vital role in detecting these molecular alterations on a sub-cellular level due to its high spatial resolution, accuracy and sensitivity. This study investigates the biochemical and molecular changes in peri-infract zone (PIZ) (contiguous area not completely damaged by stroke) and ipsi-lesional white matter (WM) (right below the stroke and PIZ regions) nine weeks post photothrombotic ischemic stroke in rats. Materials and Methods: FTIR imaging spectroscopy and transmission electron microscopy (TEM) techniques were applied to investigate brain tissue samples while hematoxylin and eosin (H&E) stained images of adjacent sections were prepared for comparison and examination the morphological changes post stroke. Results: TEM results revealed shearing of myelin sheaths and loss of cell membrane, structure and integrity after ischemic stroke. FTIR results showed that ipsi-lesional PIZ and WM experienced reduction in total protein and total lipid content compared to contra-lesional hemisphere. The lipid/protein ratio reduced in PIZ and adjacent WM indicated lipid peroxidation, which results in lipid chain fragmentation and an increase in olefinic content. Protein structural change is observed in PIZ due to the shift from random coli and α-helical structures to β-sheet conformation. Conclusion: FTIR imaging bio-spectroscopy provide novel biochemical information at sub-cellular levels that be difficult to be obtained by routine approaches. The results suggest that successful therapeutic strategy that is based on administration of anti-oxidant therapy, which could reduce and prevent neurotoxicity by scavenging the lipid peroxidation products. This approach will mitigate tissue damage in chronic ischemic period. FTIR imaging bio-spectroscopy can be used as a powerful tool and offer new approach in stroke and neurodegenerative diseases research.

Quality Management: Institution of Incident Reporting in the Clinical Laboratory

Introduction

Risk assessment is a critical part of quality management for a clinical laboratory. As a part of risk management, it is important to track any deviances from standard operating procedures (SOPs) and document equipment or assay failures consistently.

Methods

Our laboratory instituted an incident reporting system for reporting any deviances from protocol or equipment failures to track recurrent issues and determine if changes to protocols were necessitated. A guidance for completing the form was used so that the forms were completed in a standardized manner. Each incident is given a unique ID for tracking and identifies who discovered the incident and a secondary person that the incident was reported to at the time of occurrence. The incident is classified as Process, Instrument, Personnel, or Other and could be grouped into more than one category. The Other category includes incidents such as those involving reagent or equipment malfunctions. Incident reports are reviewed and discussed during the weekly lab meeting to determine the most appropriate category(s) for classification. Further, a fixed decision-making algorithm was applied to intervene specifically if the incident (a) was recurring, (b) required an SOP investigation or additional personnel training, and (c) needed to be reported to the institutional review board (IRB). Incidents are tracked until corrective action has been completed and reviewed periodically by the laboratory director. We reviewed the data after our first year of incident reporting to evaluate trends in incident categories.

Results and Conclusion

Forty-nine incidents were reported December 2017-2018. The highest classification categories included Other and a dual category, Process and Personnel, with 10 reports in each (40.8% overall). Twelve incidents were considered Recurring, 16 prompted SOP updates, and 1 was reported to the IRB. Through incident reporting, we were able to identify and resolve key risk areas in our procedures, which improved our operations and overall quality.

Investigation of the Effect of PD-L1 Blockade on Triple Negative Breast Cancer Cells Using Fourier Transform Infrared Spectroscopy

Interactions between programmed death-1 (PD-1) with its ligand PD-L1 on tumor cells can antagonize T cell responses. Inhibiting these interactions using immune checkpoint inhibitors has shown promise in cancer immunotherapy. MDA-MB-231 is a triple negative breast cancer cell line that expresses PD-L1. In this study, we investigated the biochemical changes in MDA-MB-231 cells following treatment with atezolizumab, a specific PD-L1 blocker. Our readouts were Fourier Transform Infrared (FTIR) spectroscopy and flow cytometric analyses. Chemometrical analysis, such as principal component analysis (PCA), was applied to delineate the spectral differences. We were able to identify the chemical alterations in both protein and lipid structure of the treated cells. We found that there was a shift from random coil and α-helical structure to β-sheet conformation of PD-L1 on tumor cells due to atezolizumab treatment, which could hinder binding with its receptors on immune cells, ensuring sustained T cell activation for potent immune responses. This work provides novel information about the effects of atezolizumab at molecular and cellular levels. FTIR bio-spectroscopy, in combination with chemometric analyses, may expedite research and offer new approaches for cancer immunology.

Predicting Patients at Risk of 30-Day Unplanned Hospital Readmission

We developed a machine learning model to predict 30-day readmissions using the model types; XGBoost, Random Forests and Adaboost with decision stumps as a base learner with different feature combinations and preprocessing procedures. The proposed model achieved the F1-score (0.386 ± 0.006), sensitivity (0.598 ± 0.013), positive predictive value (PPV) (0.285 ± 0.004) and negative predictive value (NPV) (0.932 ± 0.002). When compared with LACE and PARR (NZ) models, the proposed model achieved better F1-score by 12.5% compared to LACE and 22.9% compared to PARR (NZ). The mean sensitivity of the proposed model was 6.0% higher than LACE and 42.4% higher than PARR (NZ). The mean PPV was 15.9% and 13.5% higher than LACE and PARR (NZ) respectively.