Systems-wide analysis of A. fumigatus using kinetic modeling of metabolic pathways to identify putative drug targets

Aspergillosis is a major causative factor for morbidity in those with impaired immune systems, often caused by Aspergillus fumigatus. The diagnosis and treatment are difficult due to the diversity of individuals and risk factors and still pose a challenge for medical professionals. To understand the pathogenicity of any organism, it is critical to identify the significant metabolic pathways that are involved. Our work focused on developing kinetic models of critical pathways crucial for the survival of A. fumigatus using COPASI. While focusing on the folate biosynthesis, ergosterol biosynthesis and glycolytic pathway; sensitivity, time-course and steady-state analysis were performed to find the proteins/enzymes that are essential in the pathway and can be considered as potential drug targets. For further analysis of the interaction of drug targets identified, a protein-protein interaction (PPI) network was built, and hub nodes were identified using the Cytohubba package from Cytoscape. Based on the findings, dihydropteroate-synthase, dihydrofolate-reductase, 4-amino-4-deoxychorismate synthase, HMG-CoA-reductase, PG-isomerase and hexokinase could act as potential drug targets. Further, molecular docking and MM-GBSA analysis were performed with ligands chosen from DrugBank, and PubChem, and validated by experimental evidence and existing literature based on results from kinetic modeling and PPI network analysis. Based on docking scores and MM-GBSA results, molecular simulations were carried out for 1AJ2-dapsone, 1DIS-sulfamethazine, 1T02-lovastatin and 70YL-3-bromopyruvic acid complexes, which validated our findings. Our study provides a deeper insight into the mechanisms of A. fumigatus's metabolism to reveal dapsone, sulfamethazine, lovastatin and 3-bromopyruvic acid as potential drugs for the treatment of Aspergillosis.

16S rRNA female reproductive microbiome investigation reveals Dalfopristin, Clorgyline, and Hydrazine as potential therapeutics for the treatment of bacterial vaginosis

Bacterial vaginosis (BV) is a prevalent vaginal illness resulting from a disruption in the vaginal microbial equilibrium. The vaginal microbiota has been shown to have a substantial impact on the development and continuation of BV. This work utilized 16S rRNA sequence analysis of vaginal microbiome samples (Control vs BV samples) utilizing Parallel-Meta 3 to investigate the variations in microbial composition. The unique genes identified were used to determine prospective therapeutic targets and their corresponding inhibitory ligands. Further, molecular docking was conducted and then MD simulations were carried out to confirm the docking outcomes. In the BV samples, we detected several anaerobic bacteria recognized for their ability to generate biofilms, namely Acetohalobium, Anaerolineaceae, Desulfobacteraceae, and others. Furthermore, we identified Dalfopristin, Clorgyline, and Hydrazine as potential therapeutic options for the management of BV. This research provides new insights into the causes of BV and shows the potential effectiveness of novel pharmacological treatments.

Deep Inception-ResNet: A Novel Approach for Personalized Prediction of Cumulative Pregnancy Outcomes in Vitro Fertilization Treatment (IVF)

Background

Infertility is one of the major causes of socioeconomic stress worldwide due to social stigma and stressful lifestyles. Despite technological advances, couples still undergo several IVF cycles for conceiving without knowing their true prognosis which is causing a huge social and medical impact, and the live birth rate continues to be relatively low (~ 25%). A prediction model that predicts IVF prognosis accurately considering the pre-treatment parameters before starting the IVF cycle will help clinicians and patients to make better-informed choices.

Methods

In this study, clinical details of 2268 patients with 79 features who underwent IVF/ICSI procedure from January 2018 to December 2020, at the Center of IVF and Human Reproduction, Sir Ganga Ram Hospital were retrospectively collected. The machine learning model was developed considering features such as maternal age, number of IVF cycle, type of infertility, duration of infertility, AMH, indication for IVF, sperm type, BMI, embryo transfer, and β-hCG value at the end of a fresh cycle and/or one subsequent frozen embryo transfer cycle was selected as the measure of outcome.

Results

Compared to other classifiers, for an 80:20 train-test split with feature selection, the proposed Deep Inception-Residual Network architecture-based neural network gave the best accuracy (76%) and ROC-AUC score of 0.80. For tabular datasets, the applied approach has remained unexplored in previously made studies for reproductive health.

Conclusion

This model is the starting point for providing a personalized prediction of a successful outcome for an infertile couple before they enter the IVF procedure.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13224-023-01773-9.

Attaining freshwater and estuarine-water soil saturation in an ecosystem-scale coastal flooding experiment

Coastal upland forests are facing widespread mortality as sea-level rise accelerates and precipitation and storm regimes change. The loss of coastal forests has significant implications for the coastal carbon cycle; yet, predicting mortality likelihood is difficult due to our limited understanding of disturbance impacts on coastal forests. The manipulative, ecosystem-scale Terrestrial Ecosystem Manipulation to Probe the Effects of Storm Treatments (TEMPEST) experiment addresses the potential for freshwater and estuarine-water disturbance events to alter tree function, species composition, and ecosystem processes in a deciduous coastal forest in MD, USA. The experiment uses a large-unit (2000 m²), un-replicated experimental design, with three 50 m × 40 m plots serving as control, freshwater, and estuarine-water treatments. Transient saturation (5 h) of the entire soil rooting zone (0-30 cm) across a 2000 m² coastal forest was attained by delivering 300 m³ of water through a spatially distributed irrigation network at a rate just above the soil infiltration rate. Our water delivery approach also elevated the water table (typically ~ 2 m belowground) and achieved extensive, low-level inundation (~ 8 cm standing water). A TEMPEST simulation approximated a 15-cm rainfall event and based on historic records, was of comparable intensity to a 10-year storm for the area. This characterization was supported by showing that Hurricane Ida's (~ 5 cm rainfall) hydrologic impacts were shorter (40% lower duration) and less expansive (80% less coverage) than those generated through experimental manipulation. Future work will apply TEMPEST treatments to evaluate coastal forest resilience to changing hydrologic disturbance regimes and identify conditions that initiate ecosystem state transitions.

Gene expression, molecular docking, and molecular dynamics studies to identify potential antifungal compounds targeting virulence proteins/genes VelB and THR as possible drug targets against Curvularia lunata

Curvuluria lunata is a melanized fungus pathogenic to both plants and animals including humans, causing from mild, febrile to life-threatening illness if not well treated. In humans, it is an etiological agent of keratomycosis, sinusitis, and onychomycosis in immunocompromised and immunocompetent patients. The development of multiple-drug-resistant strains poses a critical treatment issue as well as public health problem. Natural products are attractive prototypes for drug discovery due to their broad-spectrum efficacy and lower side effects. The present study explores possible targets of natural antifungal compounds (α-pinene, eugenol, berberine, and curcumin) against C. lunata via gene expression analysis, molecular docking interaction, and molecular dynamics (MD) studies. Curcumin, berberine, eugenol, and α-pinene exhibited in vitro antifungal activity at 78 μg/ml, 156 μg/ml, 156 μg/ml, and 1250 μg/ml, respectively. In addition, treatment by these compounds led to the complete inhibition of conidial germination and hindered the adherence when observed on onion epidermis. Several pathogenic factors of fungi are crucial for their survival inside the host including those involved in melanin biosynthesis, hyphal growth, sporulation, and mitogen-activated protein kinase (MAPK) signalling. Relative gene expression of velB, brn1, clm1, and pks18 responsible for conidiation, melanin, and cell wall integrity was down-regulated significantly. Results of molecular docking possessed good binding affinity of compounds and have confirmed their potential targets as THR and VelB proteins. The docked structures, having good binding affinity among all, were further refined, and rescored from their docked poses through 100-ns long MD simulations. The MDS study revealed that curcumin formed a stable and energetically stabilized complex with the target protein. Therefore, the study concludes that the antifungal compounds possess significant efficacy to inhibit C. lunata growth targeting virulence proteins/genes involved in spore formation and melanin biosynthesis.

Coexistent diabetes is associated with the presence of adverse phenotypic features in patients with hypertrophic cardiomyopathy

Background

Type 2 diabetes mellitus (DM) is associated with worsened clinical outcomes in hypertrophic cardiomyopathy (HCM) patients. The reasons for this adverse prognostic association are incompletely understood. Although distinct entities both HCM and DM share common features of impaired myocardial energetics and coronary microvascular function.

Purpose

We sought to test the hypothesis that co-existent diabetes is associated with greater reductions in myocardial energetics and perfusion, and higher scar burden in HCM.

Research design and methods

Seventy-five age- and sex-matched participants with concomitant HCM and DM (HCM-DM, n=20), isolated HCM (n=20), isolated DM (n=20) and healthy volunteers (HV, n=15) underwent 31phosphorus magnetic resonance spectroscopy and cardiovascular magnetic resonance imaging. The HCM groups were matched for HCM phenotype. The DM groups were matched for diabetes treatment, duration, HbA1c, body mass index and hypertension comorbidity.

Results

ESC sudden cardiac death risk scores were comparable between the HCM groups (HCM: 2.2±1.5%, HCM-DM: 1.9±1.2%; p=NS) and sarcomeric mutations were equally common. HCM-DM had the highest NT-proBNP levels (HV: 42 ng/L [IQR: 35–66], DM: 118 ng/L [IQR: 53–187], HCM: 298 ng/L [IQR: 157–837], HCM-DM: 726 ng/L [IQR: 213–8695]; p<0.0001). Left-ventricular ejection fraction, mass and wall thickness were similar between the HCM groups. HCM-DM displayed a greater degree of fibrosis burden with higher scar percentage, and lower global longitudinal strain compared to the isolated HCM. PCr/ATP was similarly decreased in the HCM-DM and DM (HV: 2.17±0.49, DM: 1.61±0.23, HCM: 1.93±0.38, HCM-DM: 1.54±0.27; p=0.0003). HCM-DM had the lowest stress myocardial blood flow (HV: 2.06±0.42 ml/min/g, DM: 1.78±0.45 ml/min/g, HCM: 1.74±0.44 ml/min/g, HCM-DM: 1.39±0.42 ml/min/g; p=0.004).

Conclusions

We show for the first time that HCM patients with DM comorbidity display greater reductions in myocardial energetics, perfusion, contractile function and higher myocardial scar burden and serum NT-proBNP levels compared to patients with isolated HCM despite similar LV mass and wall thickness and presence of sarcomeric mutations. These adverse phenotypic features may be important components of the adverse clinical manifestation attributable to a combined presence of HCM and DM.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): Diabetes UK

Influence of sex on cardiovascular outcomes in RBM20 variant carriers

Background

Variants in the RBM20 gene cause dilated cardiomyopathy and may be associated with a poor prognosis.

Objectives

To determine disease penetrance, the risk of adverse events and the influence of sex on outcomes in RBM20 variant carriers.

Methods

Consecutive probands and relatives carrying pathogenic or likely pathogenic RBM20 variants were retrospectively recruited from 12 cardiomyopathy units. The primary endpoint was a composite of malignant ventricular arrhythmia (MVA) and end-stage heart failure (ESHF). MVA and ESHF endpoints were also analysed separately and males and females compared.

Results

Longitudinal follow-up data were available for 163 RBM20 variant carriers (82 male, median age 36.5 years, median follow-up 77.6 months). 10/163 had an MVA event at baseline. 30/153 without baseline MVA (19.6%) reached the primary endpoint with a trend towards worse outcomes in males (p=0.08). 16/153 (10.5%) had new MVA with no difference between males and females (p=0.92). 20/163 (12.2%) developed ESHF (17 males and 3 females; p<0.001).

By the end of follow-up, 114 patients (70%) had either left ventricular systolic dysfunction (LVSD) or had experienced MVA. 22 patients received a first diagnosis of LVSD during follow-up. Disease penetrance in individuals over 40 years of age was 78.5% by last evaluation.

Eleven patients that reached the MVA endpoint had a left ventricular ejection fraction (LVEF) available within 6 months of the event. Median [IQR] contemporary LVEF was 30% [23.75, 40%]. 5/11 patients had a contemporary LVEF >35%. 1/11 had a contemporary LVEF >45% (a female, 1st degree relative presenting with sustained ventricular tachycardia and an LVEF of 65%).

Conclusions

RBM20 variants are highly penetrant. The risk of MVA in male and female RBM20 variant carriers is similar but male sex is strongly associated with ESHF. MVA events occur in patients with LVEF >35%.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): British Heart Foundation Clinical Research Training Fellowship

Identification of QTNs Associated With Flowering Time, Maturity, and Plant Height Traits in Linum usitatissimum L. Using Genome-Wide Association Study

Early flowering, maturity, and plant height are important traits for linseed to fit in rice fallows, for rainfed agriculture, and for economically viable cultivation. Here, Multi-Locus Genome-Wide Association Study (ML-GWAS) was undertaken in an association mapping panel of 131 accessions, genotyped using 68,925 SNPs identified by genotyping by sequencing approach. Phenotypic evaluation data of five environments comprising 3 years and two locations were used. GWAS was performed for three flowering time traits including days to 5%, 50%, and 95% flowering, days to maturity, and plant height by employing five ML-GWAS methods: FASTmrEMMA, FASTmrMLM, ISIS EM-BLASSO, mrMLM, and pLARmEB. A total of 335 unique QTNs have been identified for five traits across five environments. 109 QTNs were stable as observed in ≥2 methods and/or environments, explaining up to 36.6% phenotypic variance. For three flowering time traits, days to maturity, and plant height, 53, 30, and 27 stable QTNs, respectively, were identified. Candidate genes having roles in flower, pollen, embryo, seed and fruit development, and xylem/phloem histogenesis have been identified. Gene expression of candidate genes for flowering and plant height were studied using transcriptome of an early maturing variety Sharda (IC0523807). The present study unravels QTNs/candidate genes underlying complex flowering, days to maturity, and plant height traits in linseed.

Optimization of external (in air) particle induced gamma-ray emission (PIGE) methodology for rapid, non-destructive, and simultaneous quantification of fluorine, sodium, and phosphorus in nuclear waste immobilization matrices

External (in air) PIGE methodology has been optimized for rapid quantification of fluorine, sodium, and phosphorus in fluorapatite waste immobilization matrices for Molten Salt Reactor (MSR).

Proteome analysis using machine learning approaches and its applications to diseases

With the tremendous developments in the fields of biological and medical technologies, huge amounts of data are generated in the form of genomic data, images in medical databases or as data on protein sequences, and so on. Analyzing this data through different tools sheds light on the particulars of the disease and our body's reactions to it, thus, aiding our understanding of the human health. Most useful of these tools is artificial intelligence and deep learning (DL). The artificially created neural networks in DL algorithms help extract viable data from the datasets, and further, to recognize patters in these complex datasets. Therefore, as a part of machine learning, DL helps us face all the various challenges that come forth during protein prediction, protein identification and their quantification. Proteomics is the study of such proteins, their structures, features, properties and so on. As a form of data science, Proteomics has helped us progress excellently in the field of genomics technologies. One of the major techniques used in proteomics studies is mass spectrometry (MS). However, MS is efficient with analysis of large datasets only with the added help of informatics approaches for data analysis and interpretation; these mainly include machine learning and deep learning algorithms. In this chapter, we will discuss in detail the applications of deep learning and various algorithms of machine learning in proteomics.

Detrimental immediate and long-term clinical effects of right ventricular pacing in patients with myocardial fibrosis

Funding Acknowledgements

Type of funding sources: None.

Background

Long-term right ventricular (RV) pacing leads to heart failure or a decline in left ventricular (LV) function in up to a fifth of patients.

Objectives

We aimed to establish whether patients with focal fibrosis detected on late gadolinium enhancement cardiovascular magnetic resonance (CMR) have deterioration in LV function after RV pacing.

Methods

We recruited 110 patients (84 in final analysis) into two observational CMR studies. Patients (n = 34) with a dual chamber device and preserved atrioventricular (AV) conduction underwent CMR in two asynchronous pacing modes (AOO & DOO) to compare intrinsic conduction with RV pacing. Patients (n = 50) with high-grade AV block underwent CMR before and 6 months after pacemaker implantation to investigate the long-term effects of RV pacing.

Results: The three key findings were

1) Initiation of RV pacing in patients with fibrosis, compared to those without, was associated with greater immediate changes in both LV end-systolic volume index (LVESVi) (5.3 ± 3.5 vs 2.1 ± 2.4 mL/m2; p < 0.01) and LV ejection fraction (LVEF) (-5.7 ± 3.4% vs -3.2 ± 2.6%; p = 0.02); 2) Long-term RV pacing in patients with fibrosis, compared to those without, was associated with greater changes in LVESVi (8.0 ± 10.4 vs -0.6 ± 7.3 mL/m2; p = 0.008) and LVEF (-12.3 ± 7.9 vs -6.7 ± 6.2%; p = 0.012); 3) Patients with fibrosis did not experience an improvement in quality of life, biomarkers or functional class after pacemaker implantation.

Conclusions

Fibrosis detected on CMR is associated with immediate and long-term deterioration in LV function following RV pacing and could be used to identify those at risk of heart failure prior to pacemaker implantation.

Characteristics before and after pacing Study 1 No fibrosis (n = 16) Fibrosis (n = 18) AOO DOO p-value AOO DOO p-value LVEDVi - mL/m² 66 ± 13 66 ± 12 0.67 78 ± 14 79 ± 13 0.34 LVESVi - mL/m² 30 ± 10 32 ± 9 0.003 38 ± 11 43 ± 12 <0.001 LVEF - % 56 ± 6 53 ± 5 <0.001 52 ± 8 47 ± 9 <0.001 Mechanical Dyssynchrony index - ms 61 ± 17 71 ± 25 0.07 81 ± 18 89 ± 21 0.04 Study 2 No fibrosis (n = 19) Fibrosis (n = 31) Pre-PPM Post-PPM p-value Pre-PPM Post-PPM p-value LVEDVi -mL/m² 88 ± 21 73 ± 14 <0.001 90 ± 18 83 ± 21 0.007 LVESVi -mL/m² 35 ± 9 34 ± 9 0.71 41 ± 14 49 ± 21 0.001 LVEF - % 60 ± 5 54 ± 7 <0.001 56 ± 8 43 ± 12 <0.001 Mechanical Dyssynchrony index - ms 70 ± 29 81 ± 22 0.15 84 ± 30 98 ± 31 0.03 Abstract Figure. Mechanism for heart failure after pacing

PluriMetNet: A dynamic electronic model decrypting the metabolic variations in human embryonic stem cells (hESCs) at fluctuating oxygen concentrations

Stem cells are an excellent resource in translational medicine however much is known only in terms of transcriptional and epigenetic regulation of human embryonic stem cells (hESCs). Metabolic regulation of hESCs is still unexplored in many ways, particularly the role of energy metabolism, which is intrinsic to the maintenance of cell viability, however, is very little explored in the past years. Also, there exists no hESC specific core metabolic model of pluripotency as per our knowledge. Through our work, we establish such a metabolic model of hESC using combinatorial in-silico approach of genome scale model reduction and literature curation. Further, through perturbations taking oxygen as a parameter we propose that under lower levels of oxygen concentration there is a significant dynamic change in the energy metabolism of the hESC. We further investigated energy subsystem pathways and their respective reactions in order to locate the direction of energy production along with the dynamic of nutrient metabolites like glucose and glutamine. The output shows a steep increment/decrement at a certain oxygen range. These sharp increments/decrements under hypoxic conditions are termed here as a critical range for hESC metabolic pathway. The data also resonates with the previous experimental studies on hESC energy metabolism confirming the robustness of our model. The model helps to extract range for different pathways in the energy subsystem, making us a little closer in understanding the metabolism of hESC. We also demonstrated the possible range of pathway changes in hESC's energy metabolism that can serve as the crucial preliminary data for further prospective studies. The model also offers a promise in the prediction of the flux behaviour of various metabolites in hESC.Communicated by Ramaswamy H. Sarma.

VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach

Vitiligo is a disease of mysterious origins in the context of its occurrence and pathogenesis. The autoinflammatory theory is perhaps the most widely accepted theory that discusses the occurrence of Vitiligo. The theory elaborates the clinical association of vitiligo with autoimmune disorders such as Psoriasis, Multiple Sclerosis and Rheumatoid Arthritis and Diabetes. In the present work, we discuss the comprehensive set of differentially co-expressed genes involved in the crosstalk events between Vitiligo and associated autoimmune disorders (Psoriasis, Multiple Sclerosis and Rheumatoid Arthritis). We progress our previous tool, Vitiligo Information Resource (VIRdb), and incorporate into it a compendium of Vitiligo-related multi-omics datasets and present it as VIRdb 2.0. It is available as a web-resource consisting of statistically sound and manually curated information. VIRdb 2.0 is an integrative database as its datasets are connected to KEGG, STRING, GeneCards, SwissProt, NPASS. Through the present study, we communicate the major updates and expansions in the VIRdb and deliver the new version as VIRdb 2.0. VIRdb 2.0 offers the maximum user interactivity along with ease of navigation. We envision that VIRdb 2.0 will be pertinent for the researchers and clinicians engaged in drug development for vitiligo.

VIRdb 2.0: Interactive analysis of comorbidity conditions associated with vitiligo pathogenesis using co-expression network-based approach

Vitiligo is a disease of mysterious origins in the context of its occurrence and pathogenesis. The autoinflammatory theory is perhaps the most widely accepted theory that discusses the occurrence of Vitiligo. The theory elaborates the clinical association of vitiligo with autoimmune disorders such as Psoriasis, Multiple Sclerosis and Rheumatoid Arthritis and Diabetes. In the present work, we discuss the comprehensive set of differentially co-expressed genes involved in the crosstalk events between Vitiligo and associated autoimmune disorders (Psoriasis, Multiple Sclerosis and Rheumatoid Arthritis). We progress our previous tool, Vitiligo Information Resource (VIRdb), and incorporate into it a compendium of Vitiligo-related multi-omics datasets and present it as VIRdb 2.0. It is available as a web-resource consisting of statistically sound and manually curated information. VIRdb 2.0 is an integrative database as its datasets are connected to KEGG, STRING, GeneCards, SwissProt, NPASS. Through the present study, we communicate the major updates and expansions in the VIRdb and deliver the new version as VIRdb 2.0. VIRdb 2.0 offers the maximum user interactivity along with ease of navigation. We envision that VIRdb 2.0 will be pertinent for the researchers and clinicians engaged in drug development for vitiligo.

Towards optogenetic vision restoration with high resolution

In many cases of inherited retinal degenerations, ganglion cells are spared despite photoreceptor cell death, making it possible to stimulate them to restore visual function. Several studies have shown that it is possible to express an optogenetic protein in ganglion cells and make them light sensitive, a promising strategy to restore vision. However the spatial resolution of optogenetically-reactivated retinas has rarely been measured, especially in the primate. Since the optogenetic protein is also expressed in axons, it is unclear if these neurons will only be sensitive to the stimulation of a small region covering their somas and dendrites, or if they will also respond to any stimulation overlapping with their axon, dramatically impairing spatial resolution. Here we recorded responses of mouse and macaque retinas to random checkerboard patterns following an in vivo optogenetic therapy. We show that optogenetically activated ganglion cells are each sensitive to a small region of visual space. A simple model based on this small receptive field predicted accurately their responses to complex stimuli. From this model, we simulated how the entire population of light sensitive ganglion cells would respond to letters of different sizes. We then estimated the maximal acuity expected by a patient, assuming it could make an optimal use of the information delivered by this reactivated retina. The obtained acuity is above the limit of legal blindness. Our model also makes interesting predictions on how acuity might vary upon changing the therapeutic strategy, assuming an optimal use of the information present in the retinal activity. Optogenetic therapy could thus potentially lead to high resolution vision, under conditions that our model helps to determinine.

In many cases of blindness, ganglion cells, the retinal output, remain functional. A promising strategy to restore vision is to express optogenetic proteins in ganglion cells. However, it is not clear what is the resolution of this new light sensor. A major concern is that axons might become light sensitive, and a focal stimulation would activate a very broad area of the retina, dramatically impairing spatial resolution. Here we show that this is not the case. Ganglion cells are activated only by stimulations close to their soma. Using a combination of data analysis and modeling based on mouse and non-human primate retina recordings, we show that the acuity expected with this therapy could be above the level of legal blindness.

VIRdb: a comprehensive database for interactive analysis of genes/proteins involved in the pathogenesis of vitiligo

Vitiligo is a chronic asymptomatic disorder affecting melanocytes from the basal layer of the epidermis which leads to a patchy loss of skin color. Even though it is one of the neglected disease conditions, people suffering from vitiligo are more prone to psychological disorders. As of now, various studies have been done in order to project auto-immune implications as the root cause. To understand the complexity of vitiligo, we propose the Vitiligo Information Resource (VIRdb) that integrates both the drug-target and systems approach to produce a comprehensive repository entirely devoted to vitiligo, along with curated information at both protein level and gene level along with potential therapeutics leads. These 25,041 natural compounds are curated from Natural Product Activity and Species Source Database. VIRdb is an attempt to accelerate the drug discovery process and laboratory trials for vitiligo through the computationally derived potential drugs. It is an exhaustive resource consisting of 129 differentially expressed genes, which are validated through gene ontology and pathway enrichment analysis. We also report 22 genes through enrichment analysis which are involved in the regulation of epithelial cell differentiation. At the protein level, 40 curated protein target molecules along with their natural hits that are derived through virtual screening. We also demonstrate the utility of the VIRdb by exploring the Protein-Protein Interaction Network and Gene-Gene Interaction Network of the target proteins and differentially expressed genes. For maintaining the quality and standard of the data in the VIRdb, the gold standard in bioinformatics toolkits like Cytoscape, Schrödinger's GLIDE, along with the server installation of MATLAB, are used for generating results. VIRdb can be accessed through "http://www.vitiligoinfores.com/".

0054 Metabolite Profiles of Obstructive Sleep Apnea Distinguishes Cases from Controls and Improve With CPAP

Introduction

Obstructive sleep apnea (OSA) is a common sleep breathing disorder with significant public health consequences. Despite this, no clinically available objective molecular biomarkers to diagnose, risk stratify and quantify treatment efficiency exist. To this end, high-throughput metabolomics data could serve as a valuable quantitative tool.

Methods

We designed a pilot study to investigate the metabolomic effects of OSA and CPAP treatment. Blood serum samples were collected from OSA patients and healthy controls matched with respect to age (±5 years), BMI (±2.5 kg/m2) and gender (N = 20/group). Samples from OSA patients were obtained before and after continuous positive airway pressure (CPAP) treatment. Polar metabolites were analyzed using a targeted ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) metabolomics technique.

Results

Supervised multivariate analysis using serum metabolic values of OSA patients and healthy controls showed a significantly different overall metabolic profile between the two groups (orthogonal partial least squares discriminant analysis [OPLS-DA] Q2=0.25, p=0.04). Acetylornithine, choline, cytidine, dodecenoylcarnitine, methionine sulfoxide and 3-indoxylsulfate were among the most perturbed metabolites. Major metabolic pathways altered in the OSA patients were methionine and phospholipid metabolism, as well as gut microbial co-metabolism. Lysophosphatidylcholine (16:0), a phospholipid metabolite, demonstrated significant linear association with improved oxygen saturation nadir post CPAP treatment (R2 = 0.57), suggesting the metabolic features may be used as prognostic clinical biomarkers.

Conclusion

These results suggest that OSA significantly impacts blood metabolites, which could potentially be used to establish OSA biomarkers. Moreover, specific metabolic features are associated with post CPAP improvement, such as phospholipids, suggesting a functional association of these metabolites that may help us understand the heterogeneity of OSA. Overall, these results demonstrate the potential of metabolic profiling to develop quantitative molecular markers of OSA. Further studies are underway to validate these findings and investigate the utility of metabolic profiles to objectively measure CPAP efficacy.

Support

The work was supported by the program project grant P01 HL094307.

0346 Metabolic Aging and Sleep Loss: Metabolite Signatures Link Sleep Deprivation and Aging Across Tissues

Introduction

Insufficient sleep is a hallmark of modern society, and sleep deprivation (SD) is a risk factor for neurodegenerative and cardiometabolic disorders. The interactions of aging with systemic and local metabolic alterations induced by sleep deprivation are essentially unexplored. In this study, we demonstrate a shared metabolic imprint of SD and aging in plasma, liver, and hippocampus.

Methods

Young (2 - 4 months) and aged (22 - 24 months) mice were sleep deprived (N = 10/group) for 5 hours followed by collection of blood plasma, liver and hippocampus. The samples were extracted and subjected to UPLC-MS/MS based targeted metabolomics analysis.

Results

Young animals displayed greater sensitivity to SD induced metabolic changes with >40% more metabolites perturbed in each sample type measured compared to aged animals. Enrichment analysis based on known disease-associated metabolites suggests that plasma change in young animals are of pathological relevance, but not in aged animals. A common hepatic signature of sleep-loss across the two age groups consisted of ketosis and urea cycle perturbation. Approximately 20-30% of measured metabolites exhibit similar changes when the sleep deprivation induced signature is compared with the aging metabolic imprint in a tissue-dependent manner. Central energetics, urea cycle and aromatic amino acid metabolism highlight the common pathways altered by sleep and aging in the periphery. In the hippocampus, choline and acetylcholine pools were depleted, potentially providing insight into the changes in metabolism that accompany analogous defects in memory consolidation.

Conclusion

These results support the notion that SD makes the ‘young seem old’. The results further connect neurobehavioral observations tying together aging and sleep loss, by implicating molecular mechanisms at the level of metabolism.

Support

This work was supported by NIH grant R21AG052905 (AMW, AS), P50AG017628 (TA; A.I. Pack, PI) and R01AG062398 (TA, JT). TA was supported by the Brush Family Chair in Biology at Penn and is currently supported by the Roy J. Carver Chair of Neuroscience at Iowa.

Reduced Global Efficiency and Random Network Features in Patients with Relapsing-Remitting Multiple Sclerosis with Cognitive Impairment

BACKGROUND AND PURPOSE

Graph theory uses structural similarity to analyze cortical structural connectivity. We used a voxel-based definition of cortical covariance networks to quantify and assess the relationship of network characteristics to cognition in a cohort of patients with relapsing-remitting MS with and without cognitive impairment.

MATERIALS AND METHODS

We compared subject-specific structural gray matter network properties of 18 healthy controls, 25 patients with MS with cognitive impairment, and 55 patients with MS without cognitive impairment. Network parameters were compared, and predictive value for cognition was assessed, adjusting for confounders (sex, education, gray matter volume, network size and degree, and T1 and T2 lesion load). Backward stepwise multivariable regression quantified predictive factors for 5 neurocognitive domain test scores.

RESULTS

Greater path length (r = -0.28, P < .0057) and lower normalized path length (r = 0.36, P < .0004) demonstrated a correlation with average cognition when comparing healthy controls with patients with MS. Similarly, MS with cognitive impairment demonstrated a correlation between lower normalized path length (r = 0.40, P < .001) and reduced average cognition. Increased normalized path length was associated with better performance for processing (P < .001), learning (P < .001), and executive domain function (P = .0235), while reduced path length was associated with better executive (P = .0031) and visual domains. Normalized path length improved prediction for processing (R ² = 43.6%, G² = 20.9; P < .0001) and learning (R ² = 40.4%, G² = 26.1; P < .0001) over a null model comprising confounders. Similarly, higher normalized path length improved prediction of average z scores (G² = 21.3; P < .0001) and, combined with WM volume, explained 52% of average cognition variance.

CONCLUSIONS

Patients with MS and cognitive impairment demonstrate more random network features and reduced global efficiency, impacting multiple cognitive domains. A model of normalized path length with normal-appearing white matter volume improved average cognitive z score prediction, explaining 52% of variance.

Diagnostic efficacy of cone beam computed tomography in paediatric dentistry: a systematic review

Purpose

To determine in which clinical situations it is indicated or contra-indicated to prescribe cone beam computed tomography (CBCT) for paediatric patients.

Methods

Systematic review of in vivo paediatric research studies of diagnostic efficacy using CBCT, with supplementary searches for guideline documents on CBCT and for systematic reviews permitting inclusion of ex vivo and adult studies.

Results

After screening, 190 publications were included, mostly case studies. No systematic reviews were found of in vivo paediatric research. Fourteen studies of diagnostic efficacy were identified. The supplementary searches found 18 guideline documents relevant to the review and 26 systematic reviews. The diagnostic efficacy evidence on CBCT was diverse and often of limited quality. There was ex vivo evidence for diagnostic accuracy being greater using CBCT than radiographs for root fractures. The multiplanar capabilities of CBCT are advantageous when localising dental structures for surgical planning. Patient movement during scanning is more common in children which could reduce diagnostic efficacy.

Conclusions

No strong recommendations on CBCT are possible, except that it should not be used as a primary diagnostic tool for caries. Guidelines on use of CBCT in the paediatric age group should be developed cautiously, taking into account the greater radiation risk and the higher economic costs compared with radiography. CBCT should only be used when adequate conventional radiographic examination has not answered the question for which imaging was required. Clinical research in paediatric patients is required at the higher levels of diagnostic efficacy of CBCT.

Electronic supplementary material

The online version of this article (10.1007/s40368-019-00504-x) contains supplementary material, which is available to authorized users.

Real-world Effectiveness and Safety of Vedolizumab for the Treatment of Inflammatory Bowel Disease: The Scottish Vedolizumab Cohort

BACKGROUND & AIMS

Vedolizumab is an anti-a4b7 monoclonal antibody that is licensed for the treatment of moderate to severe Crohn's disease and ulcerative colitis. The aims of this study were to establish the real-world effectiveness and safety of vedolizumab for the treatment of inflammatory bowel disease.

METHODS

This was a retrospective study involving seven NHS health boards in Scotland between June 2015 and November 2017. Inclusion criteria included: a diagnosis of ulcerative colitis or Crohn's disease with objective evidence of active inflammation at baseline (Harvey-Bradshaw Index[HBI] ≥5/Partial Mayo ≥2 plus C-reactive protein [CRP] >5 mg/L or faecal calprotectin ≥250 µg/g or inflammation on endoscopy/magnetic resonance imaging [MRI]); completion of induction; and at least one clinical follow-up by 12 months. Kaplan-Meier survival analysis was used to establish 12-month cumulative rates of clinical remission, mucosal healing, and deep remission [clinical remission plus mucosal healing]. Rates of serious adverse events were described quantitatively.

RESULTS

Our cohort consisted of 180 patients with ulcerative colitis and 260 with Crohn's disease. Combined median follow-up was 52 weeks (interquartile range [IQR] 26-52 weeks). In ulcerative colitis, 12-month cumulative rates of clinical remission, mucosal healing, and deep remission were 57.4%, 47.3%, and 38.5%, respectively. In Crohn's disease, 12-month cumulative rates of clinical remission, mucosal healing, and deep remission were 58.4%, 38.9%, and 28.3% respectively. The serious adverse event rate was 15.6 per 100 patient-years of follow-up.

CONCLUSIONS

Vedolizumab is a safe and effective treatment for achieving both clinical remission and mucosal healing in ulcerative colitis and Crohn's disease.

AN EXPERIMENTAL ANALYSIS AND VALIDATION OF ELECTRICAL IMPEDANCE TOMOGRAPHY TECHNIQUE FOR MEDICAL OR INDUSTRIAL APPLICATION

Electrical impedance tomography is a recently established technique by which impedance of an object (medical or nonmedical applications) is measured data from the surface of the object, and a numerically simulated reconstruction of the object internal shape of the image can be obtained. This imaging technique based on boundary or surface voltage is measured when the different current pattern is injected into it. For current pulse, we are creating a voltage controlled current source, which is based on the different RC circuits, according to current amplitude and frequency values. The current source used in inject the current pulse of the various phantoms. The current position and measuring voltage is controlled by the created control unit or programmable system on chip (PSOC) of the proposed EIT system. After that image reconstruction of the cross-sectional image of resistivity requires sufficient data collection from used phantoms, which is based on finite element method (FEM) method and Tikhonov regularization method with helps of graphical user interface (GUI) on MatLab. The objective of the GUI was to produce an image (2D/3D), impedance distribution graph, and the FEM mesh model according to used electrode combinations from the various phantoms. EIT system has a great potential for imaging modality, is non-invasive, radiation-free, and inexpensive for medical applications.

Construction of Discrete Model of Human Pluripotency in Predicting Lineage-Specific Outcomes and Targeted Knockdowns of Essential Genes

A network consisting of 45 core genes was developed for the genes/proteins responsible for loss/gain of function in human pluripotent stem cells. The nodes were included on the basis of literature curation. The initial network topology was further refined by constructing an inferred Boolean model from time-series RNA-seq expression data. The final Boolean network was obtained by integration of the initial topology and the inferred topology into a refined model termed as the integrated model. Expression levels were observed to be bi-modular for most of the genes involved in the mechanism of human pluripotency. Thus, single and combinatorial perturbations/knockdowns were executed using an in silico approach. The model perturbations were validated with literature studies. A number of outcomes are predicted using the knockdowns of the core pluripotency circuit and we are able to establish the minimum requirement for maintenance of pluripotency in human. The network model is able to predict lineage-specific outcomes and targeted knockdowns of essential genes involved in human pluripotency which are challenging to perform due to ethical constraints surrounding human embryonic stem cells.

Cleft-Related Infanticide and Abandonment: A Systematic Review of the Academic and Lay Literature

OBJECTIVE

We aimed to describe the scope of cleft-related infanticide and identify issues that might inform prevention strategies.

DESIGN

Systematic reviews of both academic (eg, PubMed, EBSCOhost) and lay literature (eg, LexisNexis Academic, Google) databases were performed to identify all primary reports of cleft-related infanticide. All languages were included. Records before 1985 were excluded. Reference lists of all included reports were screened for potentially relevant records.

MAIN OUTCOME MEASURES

Country of origin and excerpts that pertained to the concepts surrounding cleft-related infanticide were extracted. Extracted excerpts were examined using a content analysis framework.

RESULTS

Of the 1,151 records retrieved, 70 reports documented cleft-related infanticide from 27 countries. The largest number of reports was from China (14 reports; 48% of reports), followed by India (4; 14%) and Nigeria (4; 14%). However, 2 countries had 3 reports, 5 countries had 2 reports, and 17 countries had 1 report. Themes that emerged from excerpt analysis included stigma, lack of affordable cleft care, abandonment, orphanage overcrowding, and abuse and slavery.

CONCLUSIONS

Cleft-related infanticide is a global problem. Initiatives to sensitize communities to cleft lip and/or cleft palate, provide timely and affordable cleft care, and build support systems for affected families may prove beneficial. Cleft care organizations have the opportunity to advocate for these initiatives, reduce the incidence of infanticide by providing or supporting timely and affordable cleft care, and demonstrate that children with successful cleft repairs reassimilate well into their communities.

Molecular Epidemiology of Extended-Spectrum β-Lactamase-Producing Escherichia coli Pathotypes in Diarrheal Children from Low Socioeconomic Status Communities in Bihar, India: Emergence of the CTX-M Type

Background

Childhood diarrheal diseases remain highly endemic in India, but the emergence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli among children with diarrhea in Bihar remains elusive. In this study, we determine and characterize ESBL-producing E coli pathotypes among hospitalized diarrheal preschool children living in low socioeconomic level communities in Bihar, India.

Materials and methods

The stool samples were collected everyday throughout the year for 2 consecutive years. In our study, we collected stool samples randomly from every fifth patient. Stool samples were collected from a total of 633 randomly selected diarrheal children (age: 0-60 months) belonging to 17 communities and screened for identification of virulent diarrheagenic E coli (DEC) pathotype (viz, enteropathogenic E coli [EPEC], enteroaggregative E coli [EAEC], enterotoxigenic E coli [ETEC], enteroinvasive E coli [EIEC], and enterohemorrhagic E coli [EHEC]) by a multiplex polymerase chain reaction (PCR) assay. Furthermore, ESBLs were screened by conventional antibiotic resistance pattern testing and later characterized for the presence of β-lactamase (bla) genes by PCR and DNA sequencing.

Results

Diarrheagenic E coli was detected in 191 cases (30.2%) of the total 633 diarrheic children. Maximum occurrence of DEC was found in ≤12 months age group (72.7%) with prevalence of the EAEC pathotype. Most isolates were resistant to ampicillin, ciprofloxacin, piperacillin, levofloxacin, ceftazidime, cefotaxime, ceftriaxone, and gentamicin, whereas over 96% of them were sensitive to amikacin. About 37.6% of total 191 DEC isolates were ESBL producers (n = 72), being prevalent among ETEC (n = 35; 18.32%), followed by EPEC (n = 21; 10.9%), EAEC (n = 13; 6.8%), and EIEC (n = 3; 1.57%). Interestingly, the commonest β-lactamase was CTX-M type (bla_CTX-M) in 86.1% (n = 62) of the ESBL isolates, followed by bla_SHV (n = 49; 68%), bla_TEM (n = 37; 51.8%), and bla_OXA (n = 21; 29.1%) determinants. Resistance of ESBL isolates was mostly related to ampicillin (100%), ceftriaxone (98.1%), cefotaxime (92.4%), gentamicin (74.1%), and levofloxacin (73.2%), whereas best antimicrobial activities were observed for piperacillin-tazobactam, amikacin, meropenem, and imipenem.

Conclusions

This study revealed that EAEC (72.1%) is the predominant pathotype in Bihar, significantly high in ≤12 months age group children (P = .04). Moreover, the widespread prevalence of ESBLs in children, especially the CTX-M type, is of great concern, which requires monitoring of infection control measures through efficient antimicrobial management and detection of ESBL-producing isolates.

Prediction and imputation in irregularly sampled clinical time series data using hierarchical linear dynamical models

Clinical time series, comprising of repeated clinical measurements provide valuable information of the trajectory of patients' condition. Linear dynamical systems (LDS) are used extensively in science and engineering for modeling time series data. The observation and state variables in LDS are assumed to be uniformly sampled in time with a fixed sampling rate. The observation sequence for clinical time series is often irregularly sampled and LDS do not model such data well. In this paper, we develop two LDS-based models for irregularly sampled data. The key idea is to incorporate a temporal difference variable within the state equations of LDS whose parameters are estimated using observed data. Our models are evaluated on prediction and imputation tasks using real irregularly sampled clinical time series data and are found to outperform state-of-the-art techniques.

Appearance of the Retina With Full-Field Optical Coherence Tomography

PURPOSE

To interpret full-field optical coherence tomography (FFOCT) images of ex vivo retina.

METHODS

Flatmounted retinas of human, primate, pig, sheep, rat, and mouse were imaged using FFOCT. To identify retinal ganglion and amacrine cells, fixed samples immunolabeled against Tuj1 and Brn3a or live samples labeled in vitro with green fluorescent protein (GFP) were analyzed by combining FFOCT, fluorescence confocal microscopy (FCM), and fluorescence-FFOCT. To investigate postmortem tissue changes, time series were acquired over 48 hours and on fresh versus fixed tissue.

RESULTS

With FFOCT, cell types and features such as nerve fiber bundles and RGC somas were resolved without use of contrast agents at 1-μm xyz resolution. Cell somas in the ganglion cell layer (GCL) in large mammals appeared predominantly bright with dark contours, while in rodents, GCL somas appeared dark with bright contours. RGC axon to soma junctions could be traced in the three-dimensional (3D) image stacks. Time series revealed undulation of retinal tissue samples over 48 hours, though no degradation of individual cells was detected, while paraformaldehyde fixation caused increased scattering and shrinkage.

CONCLUSIONS

Full-field OCT reveals micrometric morphologic detail in the retina without the use of contrast agents. We observed interspecies differences in optical properties of GCL somas. Fixation significantly alters retinal transparency hence reducing the visibility of microscopic features.

Efficacy and Safety of Mycobacterium indicus pranii as an adjunct therapy in Category II pulmonary tuberculosis in a randomized trial

Prolonged treatment of tuberculosis (TB) often leads to poor compliance, default and relapse, converting primary TB patients into category II TB (Cat IITB) cases, many of whom may convert to multi-drug resistant TB (MDR-TB). We have evaluated the immunotherapeutic potential of Mycobacterium indicus pranii (MIP) as an adjunct to Anti-Tubercular Treatment (ATT) in Cat II pulmonary TB (PTB) patients in a prospective, randomized, double blind, placebo controlled, multicentric clinical trial. 890 sputum smear positive Cat II PTB patients were randomized to receive either six intra-dermal injections (2 + 4) of heat-killed MIP at a dose of 5 × 10⁸ bacilli or placebo once in 2 weeks for 2 months. Sputum smear and culture examinations were performed at different time points. MIP was safe with no adverse effects. While sputum smear conversion did not show any statistically significant difference, significantly higher number of patients (67.1%) in the MIP group achieved sputum culture conversion at fourth week compared to the placebo (57%) group (p = 0.0002), suggesting a role of MIP in clearance of the bacilli. Since live bacteria are the major contributors for sustained incidence of TB, the potential of MIP in clearance of the bacilli has far reaching implications in controlling the spread of the disease.

Estimate of Unmet Need for Cleft Lip and/or Palate Surgery in India

IMPORTANCE

The unmet need for cleft lip and/or palate (CL/P) care in India is significant. However, estimates required for CL/P care program planning are lacking.

OBJECTIVE

To estimate the unmet need for CL/P surgery in India at the state level.

DESIGN, SETTING, AND PARTICIPANTS

To determine the proportion of individuals with CL/P who presented for care in India, data were used from patients who received care at Operation Smile programs in 12 low- and middle-income countries from June 1, 2013, to May 31, 2014. The resulting model describes the prevalent unmet need for cleft surgery in India by state and includes patients older than the surgery target ages of 1 and 2 years for cleft lip and cleft palate repair, respectively. Next, the total number of unrepaired CL/P cases in each state was estimated using state-level economic and health system indicators.

MAIN OUTCOMES AND MEASURES

Prevalent unmet need for CL/P repair.

RESULTS

In the 28 states with available data, an estimated 72 637 cases of unrepaired CL/P (uncertainty interval, 58 644-97 870 cases) were detected. The percentage of individuals with unrepaired CL/P who were older than the respective target ages ranged from 37.0% (95% CI, 30.6%-43.8%) in Goa to 65.8% (95% CI, 60.3%-70.9%) in Bihar (median, 57.9%; interquartile range, 52.6%-63.4%). The rate of unrepaired CL/Ps ranged from less than 3.5 per 100 000 population in Kerala and Goa to 10.9 per 100 000 population in Bihar (median rate, 5.9 [interquartile range, 4.6-7.3] per 100 000 population).

CONCLUSIONS AND RELEVANCE

An estimated 72 000 cases of unrepaired CL/P are found in India. Poor states with less health care infrastructure have exceptionally high rates (eg, Bihar). These estimates are useful for informing international and national CL/P care strategies, allocating resources, and advocating for individuals and families affected by CL/P more broadly.

LEVEL OF EVIDENCE

NA.

A statistical model for stroke outcome prediction and treatment planning

Stroke is a major cause of mortality and long-term disability in the world. Predictive outcome models in stroke are valuable for personalized treatment, rehabilitation planning and in controlled clinical trials. We design a new multi-class classification model to predict outcome in the short-term, the putative therapeutic window for several treatments. Our model addresses the challenges of class imbalance, where the training data is dominated by samples of a single class, and highly correlated predictor and outcome variables, which makes learning the effects of treatments on the outcome difficult. Empirically our model outperforms the best-known previous predictive models and can infer the most effective treatments in improving outcome that have been independently validated in clinical studies.

Red-shifted channelrhodopsin stimulation restores light responses in blind mice, macaque retina, and human retina

Targeting the photosensitive ion channel channelrhodopsin‐2 (ChR2) to the retinal circuitry downstream of photoreceptors holds promise in treating vision loss caused by retinal degeneration. However, the high intensity of blue light necessary to activate channelrhodopsin‐2 exceeds the safety threshold of retinal illumination because of its strong potential to induce photochemical damage. In contrast, the damage potential of red‐shifted light is vastly lower than that of blue light. Here, we show that a red‐shifted channelrhodopsin (ReaChR), delivered by AAV injections in blind rd1 mice, enables restoration of light responses at the retinal, cortical, and behavioral levels, using orange light at intensities below the safety threshold for the human retina. We further show that postmortem macaque retinae infected with AAV‐ReaChR can respond with spike trains to orange light at safe intensities. Finally, to directly address the question of translatability to human subjects, we demonstrate for the first time, AAV‐ and lentivirus‐mediated optogenetic spike responses in ganglion cells of the postmortem human retina.

Stacking dependence of carrier transport properties in multilayered black phosphorous

We present the effect of different stacking orders on carrier transport properties of multi-layer black phosphorous. We consider three different stacking orders AAA, ABA and ACA, with increasing number of layers (from 2 to 6 layers). We employ a hierarchical approach in density functional theory (DFT), with structural simulations performed with generalized gradient approximation (GGA) and the bandstructure, carrier effective masses and optical properties evaluated with the meta-generalized gradient approximation (MGGA). The carrier transmission in the various black phosphorous sheets was carried out with the non-equilibrium green's function (NEGF) approach. The results show that ACA stacking has the highest electron and hole transmission probabilities. The results show tunability for a wide range of band-gaps, carrier effective masses and transmission with a great promise for lattice engineering (stacking order and layers) in black phosphorous.