Prioritizing Metabolic Gene Regulators through Multi-Omic Network Integration in Maize

Elucidating gene regulatory networks (GRNs) is a major area of study within plant systems biology. Phenotypic traits are intricately linked to specific gene expression profiles. These expression patterns arise primarily from regulatory connections between sets of transcription factors (TFs) and their target genes. In this study, we integrated publicly available co-expression networks derived from more than 6,000 RNA-seq samples, 283 protein-DNA interaction assays, and 16 million of SNPs used to identify expression quantitative loci (eQTL), to construct TF-target networks. In total, we analyzed ~4.6M interactions to generate four distinct types of TF-target networks: co-expression, protein-DNA interaction (PDI), trans-expression quantitative loci (trans-eQTL), and cis-eQTL combined with PDIs. To improve the functional annotation of TFs based on its target genes, we implemented three different strategies to integrate these four types of networks. We subsequently evaluated the effectiveness of our method through loss-of function mutant and random networks. The multi-network integration allowed us to identify transcriptional regulators of hormone-, metabolic- and development-related processes. Finally, using the topological properties of the fully integrated network, we identified potentially functional redundant TF paralogs. Our findings retrieved functions previously documented for numerous TFs and revealed novel functions that are crucial for informing the design of future experiments. The approach here-described lays the foundation for the integration of multi-omic datasets in maize and other plant systems.

Joint representation of molecular networks from multiple species improves gene classification

Network-based machine learning (ML) has the potential for predicting novel genes associated with nearly any health and disease context. However, this approach often uses network information from only the single species under consideration even though networks for most species are noisy and incomplete. While some recent methods have begun addressing this shortcoming by using networks from more than one species, they lack one or more key desirable properties: handling networks from more than two species simultaneously, incorporating many-to-many orthology information, or generating a network representation that is reusable across different types of and newly-defined prediction tasks. Here, we present GenePlexusZoo, a framework that casts molecular networks from multiple species into a single reusable feature space for network-based ML. We demonstrate that this multi-species network representation improves both gene classification within a single species and knowledge-transfer across species, even in cases where the inter-species correspondence is undetectable based on shared orthologous genes. Thus, GenePlexusZoo enables effectively leveraging the high evolutionary molecular, functional, and phenotypic conservation across species to discover novel genes associated with diverse biological contexts.

Comparative assessment of immunogenicity of recombinant insulin Aspart from BioGenomics and its originator NovoRapid® in adult patients with type 2 diabetes mellitus

OBJECTIVES

To assess and compare the immunogenicity of recombinant Insulin Aspart [manufactured by BioGenomics Limited (BGL-ASP)] with its originator NovoRapid® (manufactured by Novo Nordisk) in adult patients with type 2 diabetes mellitus.

RESEARCH DESIGN AND METHODS

BGL-IA-CTP301 study was a randomized, open label, parallel group, multicenter phase-III clinical study to compare the efficacy and safety of recombinant Insulin Aspart 100 U/mL [manufactured by BioGenomics Limited (BGL-ASP)] with its reference medicinal product (RMP); NovoRapid® [manufactured by Novo Nordisk], in adult patients with Type 2 diabetes mellitus (T2DM). The primary objective of the study was to compare the immunogenicity of BGL-ASP and RMP; NovoRapid® in patient serum samples collected from phase-III clinical study. Immunogenicity was studied as the incidence of patients positive for anti-insulin Aspart (AIA) antibodies, developed against BGL-ASP/RMP at baseline, end of 12 week and end of 24 week of the treatment period. The changes in incidence of patients positive for AIA antibodies post-baseline were also studied to assess and compare the treatment-emergent antibody response (TEAR) between the treatment groups (BGL-ASP and RMP). Statistical evaluation was done by Fisher's exact test to compare the overall incidence of patients positive for AIA antibodies and the TEAR positives observed post-baseline in both the treated groups. An in-vitro neutralizing antibody assay (Nab assay) was also performed to study the effect of AIA antibodies in neutralizing the biological activity/metabolic function of the insulin. The neutralizing potential of AIA was studied by its effect on %glucose uptake. We also evaluated the association between AIA antibody levels and its impact on biological activity by studying the correlation between them.

RESULTS

Analysis of immunogenicity data suggested that the percentage of patients positive for AIA antibodies until week 24 was similar and comparable in both the treatment groups, BGL-ASP and RMP; NovoRapid®. The changes in incidence of patients positive for AIA post-baseline in terms of TEAR positives were also similar and comparable between the treatment groups. The results of the Nab assay with confirmed positive AIA samples from BGL-ASP- and RMP-treated groups did not have any negative impact on %glucose uptake by the cells in Nab assay, confirming the absence of neutralizing antibodies in both the treatment groups. The correlation studies also showed absence of association between AIA antibody levels and percentage glucose uptake in both BGL-ASP and RMP-NovoRapid® treatment groups. CONCLUSIONS: The immunogenicity assessment based on the overall incidence of patients positive for AIA, changes in incidence of patients positive for AIA post-baseline, TEAR rates and absence of neutralizing antibodies, were found to be apparently similar and comparable in both the treatment groups (BGL-ASP and RMP). We conclude from our studies that the immunogenicity of BGL-ASP is similar and comparable to RMP and the observed immunogenicity in terms of anti-insulin Aspart antibody levels had no impact on the biological activity of insulin.

Topological data analysis reveals a core gene expression backbone that defines form and function across flowering plants

Since they emerged approximately 125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests that there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function.

Observation of Single-Top-Quark Production in Association with a Photon Using the ATLAS Detector

This Letter reports the observation of single top quarks produced together with a photon, which directly probes the electroweak coupling of the top quark. The analysis uses 139  fb^{-1} of 13 TeV proton-proton collision data collected with the ATLAS detector at the Large Hadron Collider. Requiring a photon with transverse momentum larger than 20 GeV and within the detector acceptance, the fiducial cross section is measured to be 688±23(stat) _{-71}^{+75}(syst)  fb, to be compared with the standard model prediction of 515_{-42}^{+36}  fb at next-to-leading order in QCD.

Cryogenic vacuum valve with actuation times down to 50 ms

We have conceived, built, and operated a cryogenic vacuum valve with opening and closing times as short as 50 ms that can be used in strong magnetic fields and across a broad range of duty cycles. It is used to seal a cryogenic Penning trap at liquid-helium temperature for long-term storage of highly charged ions in a vacuum better than 10-15 hPa from a room-temperature ion beamline at vacuum conditions around 10-9 hPa. It will significantly improve any experiment where a volume at the most extreme vacuum conditions must be temporarily connected to a less demanding vacuum during repeated experimental cycles. We describe the design of this valve and show measurements that characterize its main features.

Observation of the γγ→ττ Process in Pb+Pb Collisions and Constraints on the τ-Lepton Anomalous Magnetic Moment with the ATLAS Detector

This Letter reports the observation of τ-lepton-pair production in ultraperipheral lead-lead collisions Pb+Pb→Pb(γγ→ττ)Pb and constraints on the τ-lepton anomalous magnetic moment a_{τ}. The dataset corresponds to an integrated luminosity of 1.44  nb^{-1} of LHC Pb+Pb collisions at sqrt[s_{NN}]=5.02  TeV recorded by the ATLAS experiment in 2018. Selected events contain one muon from a τ-lepton decay, an electron or charged-particle track(s) from the other τ-lepton decay, little additional central-detector activity, and no forward neutrons. The γγ→ττ process is observed in Pb+Pb collisions with a significance exceeding 5 standard deviations and a signal strength of μ_{ττ}=1.03_{-0.05}^{+0.06} assuming the standard model value for a_{τ}. To measure a_{τ}, a template fit to the muon transverse-momentum distribution from τ-lepton candidates is performed, using a dimuon (γγ→μμ) control sample to constrain systematic uncertainties. The observed 95% confidence-level interval for a_{τ} is -0.057 Collapse

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Strong Constraints on Jet Quenching in Centrality-Dependent p+Pb Collisions at 5.02 TeV from ATLAS

Jet quenching is the process of color-charged partons losing energy via interactions with quark-gluon plasma droplets created in heavy-ion collisions. The collective expansion of such droplets is well described by viscous hydrodynamics. Similar evidence of collectivity is consistently observed in smaller collision systems, including pp and p+Pb collisions. In contrast, while jet quenching is observed in Pb+Pb collisions, no evidence has been found in these small systems to date, raising fundamental questions about the nature of the system created in these collisions. The ATLAS experiment at the Large Hadron Collider has measured the yield of charged hadrons correlated with reconstructed jets in 0.36  nb^{-1} of p+Pb and 3.6  pb^{-1} of pp collisions at 5.02 TeV. The yields of charged hadrons with p_{T}^{ch}>0.5  GeV near and opposite in azimuth to jets with p_{T}^{jet}>30 or 60 GeV, and the ratios of these yields between p+Pb and pp collisions, I_{pPb}, are reported. The collision centrality of p+Pb events is categorized by the energy deposited by forward neutrons from the struck nucleus. The I_{pPb} values are consistent with unity within a few percent for hadrons with p_{T}^{ch}>4  GeV at all centralities. These data provide new, strong constraints that preclude almost any parton energy loss in central p+Pb collisions.

Search for Heavy Neutral Leptons in Decays of W Bosons Using a Dilepton Displaced Vertex in sqrt[s]=13 TeV pp Collisions with the ATLAS Detector

A search for a long-lived, heavy neutral lepton (N) in 139  fb^{-1} of sqrt[s]=13  TeV pp collision data collected by the ATLAS detector at the Large Hadron Collider is reported. The N is produced via W→Nμ or W→Ne and decays into two charged leptons and a neutrino, forming a displaced vertex. The N mass is used to discriminate between signal and background. No signal is observed, and limits are set on the squared mixing parameters of the N with the left-handed neutrino states for the N mass range 3  GeV Collapse

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Test of CP Invariance in Higgs Boson Vector-Boson-Fusion Production Using the H→γγ Channel with the ATLAS Detector

A test of CP invariance in Higgs boson production via vector-boson fusion has been performed in the H→γγ channel using 139  fb^{-1} of proton-proton collision data at sqrt[s]=13  TeV collected by the ATLAS detector at the LHC. The optimal observable method is used to probe the CP structure of interactions between the Higgs boson and electroweak gauge bosons, as described by an effective field theory. No sign of CP violation is observed in the data. Constraints are set on the parameters describing the strength of the CP-odd component in the coupling between the Higgs boson and the electroweak gauge bosons in two effective field theory bases: d[over ˜] in the HISZ basis and c_{HW[over ˜]} in the Warsaw basis. The results presented are the most stringent constraints on CP violation in the coupling between Higgs and weak bosons. The 95% C.L. constraint on d[over ˜] is derived for the first time and the 95% C.L. constraint on c_{HW[over ˜]} has been improved by a factor of 5 compared to the previous measurement.

Palliative care management committees: a model of collaborative governance for primary health care

SETTING

The community-based primary palliative care programme in Kerala, India, has received international acclaim. Programme functioning is supported through Palliative Care Management Committees (PMCs) at the local government (LG) level.

OBJECTIVE

To study the functioning of the PMCs within the decentralised governance space to identify achievements, gaps and notable innovations.

DESIGN

This qualitative study included seven key informant interviews (KIIs), 28 in-depth interviews and a review of relevant publicly available policies and documents. Major themes were recognised from the KII transcripts. Codes emerging from the document review and in-depth interview transcripts were mapped into the identified thematic areas.

RESULTS

Successful PMCs raised resources like money, human resource, equipment, had good skilled care options for symptom relief and facilitated reduced out-of-pocket expenditure by providing home care and free medicines, and improved access to interventions that addressed the social determinants of suffering like poverty. PMCs had varying managerial and technical capacities. In some LGs, the programme was weak and mostly limited to the supply of medicines, basic aids and appliances to patients' homes.

CONCLUSION

Despite varied implementation patterns, PMCs in Kerala are examples of state-supported, community-owned care initiatives, that can potentially address medical and social determinants of suffering.

Re-engineering primary healthcare in Kerala

INTRODUCTION

In the backdrop of the Sustainable Development Goals (SDGs), the state of Kerala, India, revamped its existing primary health centres (PHCs) into people-friendly family health centres (FHCs) in order to provide comprehensive primary care as part of a mission-based ('Aardram') initiative. It was envisioned that the mission's implementation and operation would make use of decentralised governance. The present study explored how the decentralised governance influenced reorganisation of primary care.

METHODS

The study adopted an exploratory approach using qualitative methods: key informant interviews (n = 8), in-depth interviews (n = 20) and document reviews. Thematic analysis was done following deductive coding and the themes that emerged were organised under a schema.

RESULTS

The results could be summarised under five overarching themes. Strong political commitment, combined with bureaucratic competence, facilitated implementation and functioning of 'Aardram' primary care. The insights developed through multi-sectoral training helped local governments (LGs) get involve and engage with the health system as a team in order to plan and implement interventions. The decentralised governance structures enabled re-engineering of PHCs by mobilisation of financial resources, provision of human resources, infrastructure modification, and enhanced community participation at various levels. Non-uniformity of commitment, sub-optimal engagement of urban LGs and issues of sustainability and monitoring were the shortcomings observed.

CONCLUSION

Decentralised governance played a positive role in the re-engineering of PHCs, which was utilised as a platform to demonstrate best practices in health governance through a participatory approach. The importance of empowering LGs through capacity building to address challenges in achieving primary care SDGs is highlighted in this study.

PyGenePlexus: a Python package for gene discovery using network-based machine learning

SUMMARY

PyGenePlexus is a Python package that enables a user to gain insight into any gene set of interest through a molecular interaction network informed supervised machine learning model. PyGenePlexus provides predictions of how associated every gene in the network is to the input gene set, offers interpretability by comparing the model trained on the input gene set to models trained on thousands of known gene sets, and returns the network connectivity of the top predicted genes.

AVAILABILITY AND IMPLEMENTATION

https://pypi.org/project/geneplexus/ and https://github.com/krishnanlab/PyGenePlexus.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Personalized transcranial alternating current stimulation improves sleep quality: Initial findings

Insufficient sleep is a major health issue. Inadequate sleep is associated with an array of poor health outcomes, including cardiovascular disease, diabetes, obesity, certain forms of cancer, Alzheimer's disease, depression, anxiety, and suicidality. Given concerns with typical sedative hypnotic drugs for treating sleep difficulties, there is a compelling need for alternative interventions. Here, we report results of a non-invasive electrical brain stimulation approach to optimizing sleep involving transcranial alternating current stimulation (tACS). A total of 25 participants (mean age: 46.3, S.D. ± 12.4, 15 females) were recruited for a null-stimulation controlled (Control condition), within subjects, randomized crossed design, that included two variants of an active condition involving 15 min pre-sleep tACS stimulation. To evaluate the impact on sleep quality, the two active tACS stimulation conditions were designed to modulate sleep-dependent neural activity in the theta/alpha frequency bands, with both stimulation types applied to all subjects in separate sessions. The first tACS condition used a fixed stimulation pattern across all participants, a pattern composed of stimulation at 5 and 10 Hz. The second tACS condition used a personalized stimulation approach with the stimulation frequencies determined by each individual's peak EEG frequencies in the 4-6 Hz and 9-11 Hz bands. Personalized tACS stimulation increased sleep quantity (duration) by 22 min compared to a Control condition (p = 0.04), and 19 min compared to Fixed tACS stimulation (p = 0.03). Fixed stimulation did not significantly increase sleep duration compared to Control (mean: 3 min; p = 0.75). For sleep onset, the Personalized tACS stimulation resulted in reducing the onset by 28% compared to the Fixed tACS stimulation (6 min faster, p = 0.02). For a Poor Sleep sub-group (n = 13) categorized with Clinical Insomnia and a high insomnia severity, Personalized tACS stimulation improved sleep duration by 33 min compared to Fixed stimulation (p = 0.02), and 30 min compared to Control condition (p < 0.1). Together, these results suggest that Personalized stimulation improves sleep quantity and time taken to fall asleep relative to Control and Fixed stimulation providing motivation for larger-scale trials for Personalized tACS as a sleep therapeutic, including for those with insomnia.

Accurately modeling biased random walks on weighted networks using node2vec

MOTIVATION

Accurately representing biological networks in a low-dimensional space, also known as network embedding, is a critical step in network-based machine learning and is carried out widely using node2vec, an unsupervised method based on biased random walks. However, while many networks, including functional gene interaction networks, are dense, weighted graphs, node2vec is fundamentally limited in its ability to use edge weights during the biased random walk generation process, thus under-using all the information in the network.

RESULTS

Here, we present node2vec+, a natural extension of node2vec that accounts for edge weights when calculating walk biases and reduces to node2vec in the cases of unweighted graphs or unbiased walks. Using two synthetic datasets, we empirically show that node2vec+ is more robust to additive noise than node2vec in weighted graphs. Then, using genome-scale functional gene networks to solve a wide range of gene function and disease prediction tasks, we demonstrate the superior performance of node2vec+ over node2vec in the case of weighted graphs. Notably, due to the limited amount of training data in the gene classification tasks, graph neural networks such as GCN and GraphSAGE are outperformed by both node2vec and node2vec+.

AVAILABILITY AND IMPLEMENTATION

The data and code are available on GitHub at https://github.com/krishnanlab/node2vecplus_benchmarks. All additional data underlying this article are available on Zenodo at https://doi.org/10.5281/zenodo.7007164.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Results of in situ fixation of Andersson lesion by posterior approach in 35 cases

STUDY OBJECTIVE

Due to the rarity of the Andersson lesion (AL), the literature is ambiguous regarding the type of surgical fixation, need for debridement and deformity correction. The purpose of this retrospective study is to evaluate the efficacy, feasibility and functional outcome of posterior fixation in AL.

MATERIALS AND METHODS

This study included 35 patients having thoracolumbar AL operated for in situ fixation and fusion with minimum of 24-month follow-up. VAS (Visual Analogue Score) back pain, ODI (Oswestry Disability Index), Frankel's grade were compared and analyzed. Union status was noted with complications.

RESULTS

The mean age of 35 patients was 56.34(± 11.3) years with average follow-up of 51.49 months. Two patients had AL at two levels. 27/37 AL were at discal level. Average estimated blood loss (EBL) was 276.43 ml and duration of surgery was 130.43 min. On an average, operated segments needed 7.77 screws. There were ten minor complications without long-term sequel. Neurological improvement was noted in 30 patients. Average preoperative VAS score improved from 8.69 to 3.14, ODI score improved from 68.76 to 18.77 at final follow-up which were significant (p < 0.05). There was significant improvement in Frankel's grading (Z = - 4.354, P = 0.00).

CONCLUSIONS

Surgical management of AL by posterior approach and posterior stabilization can give satisfactory results without the need of extensive anterior reconstruction, bone grafting or deformity correction procedures without added morbidity and complications.

Systematic tissue annotations of genomics samples by modeling unstructured metadata

There are currently >1.3 million human -omics samples that are publicly available. This valuable resource remains acutely underused because discovering particular samples from this ever-growing data collection remains a significant challenge. The major impediment is that sample attributes are routinely described using varied terminologies written in unstructured natural language. We propose a natural-language-processing-based machine learning approach (NLP-ML) to infer tissue and cell-type annotations for genomics samples based only on their free-text metadata. NLP-ML works by creating numerical representations of sample descriptions and using these representations as features in a supervised learning classifier that predicts tissue/cell-type terms. Our approach significantly outperforms an advanced graph-based reasoning annotation method (MetaSRA) and a baseline exact string matching method (TAGGER). Model similarities between related tissues demonstrate that NLP-ML models capture biologically-meaningful signals in text. Additionally, these models correctly classify tissue-associated biological processes and diseases based on their text descriptions alone. NLP-ML models are nearly as accurate as models based on gene-expression profiles in predicting sample tissue annotations but have the distinct capability to classify samples irrespective of the genomics experiment type based on their text metadata. Python NLP-ML prediction code and trained tissue models are available at https://github.com/krishnanlab/txt2onto .

A network-based approach for isolating the chronic inflammation gene signatures underlying complex diseases towards finding new treatment opportunities

Complex diseases are associated with a wide range of cellular, physiological, and clinical phenotypes. To advance our understanding of disease mechanisms and our ability to treat these diseases, it is critical to delineate the molecular basis and therapeutic avenues of specific disease phenotypes, especially those that are associated with multiple diseases. Inflammatory processes constitute one such prominent phenotype, being involved in a wide range of health problems including ischemic heart disease, stroke, cancer, diabetes mellitus, chronic kidney disease, non-alcoholic fatty liver disease, and autoimmune and neurodegenerative conditions. While hundreds of genes might play a role in the etiology of each of these diseases, isolating the genes involved in the specific phenotype (e.g., inflammation “component”) could help us understand the genes and pathways underlying this phenotype across diseases and predict potential drugs to target the phenotype. Here, we present a computational approach that integrates gene interaction networks, disease-/trait-gene associations, and drug-target information to accomplish this goal. We apply this approach to isolate gene signatures of complex diseases that correspond to chronic inflammation and use SAveRUNNER to prioritize drugs to reveal new therapeutic opportunities.

Observation of WWW Production in pp Collisions at sqrt[s]=13 TeV with the ATLAS Detector

This Letter reports the observation of WWW production and a measurement of its cross section using 139  fb^{-1} of proton-proton collision data recorded at a center-of-mass energy of 13 TeV by the ATLAS detector at the Large Hadron Collider. Events with two same-sign leptons (electrons or muons) and at least two jets, as well as events with three charged leptons, are selected. A multivariate technique is then used to discriminate between signal and background events. Events from WWW production are observed with a significance of 8.0 standard deviations, where the expectation is 5.4 standard deviations. The inclusive WWW production cross section is measured to be 820±100 (stat)±80 (syst)  fb, approximately 2.6 standard deviations from the predicted cross section of 511±18  fb calculated at next-to-leading-order QCD and leading-order electroweak accuracy.

A detailed map of Higgs boson interactions by the ATLAS experiment ten years after the discovery

The standard model of particle physics1-4 describes the known fundamental particles and forces that make up our Universe, with the exception of gravity. One of the central features of the standard model is a field that permeates all of space and interacts with fundamental particles5-9. The quantum excitation of this field, known as the Higgs field, manifests itself as the Higgs boson, the only fundamental particle with no spin. In 2012, a particle with properties consistent with the Higgs boson of the standard model was observed by the ATLAS and CMS experiments at the Large Hadron Collider at CERN10,11. Since then, more than 30 times as many Higgs bosons have been recorded by the ATLAS experiment, enabling much more precise measurements and new tests of the theory. Here, on the basis of this larger dataset, we combine an unprecedented number of production and decay processes of the Higgs boson to scrutinize its interactions with elementary particles. Interactions with gluons, photons, and W and Z bosons-the carriers of the strong, electromagnetic and weak forces-are studied in detail. Interactions with three third-generation matter particles (bottom (b) and top (t) quarks, and tau leptons (τ)) are well measured and indications of interactions with a second-generation particle (muons, μ) are emerging. These tests reveal that the Higgs boson discovered ten years ago is remarkably consistent with the predictions of the theory and provide stringent constraints on many models of new phenomena beyond the standard model.

AB0586 OCULAR ISCHEMIC SYNDROME CAUSING ACUTE BINOCULAR VISION LOSS IN THREE PATIENTS WITH TAKAYASU ARTERITIS TYPE V: A THERAPEUTIC QUANDARY

Background

Ocular Ischemic syndrome (OIS) is a rare manifestation in Takayasu Arteritis (TA) which can cause irreversible retinal ischemia and neovascular changes. Ocular Ischemic syndrome denotes hypoperfusion of both anterior and posterior segments of eye and orbital structures as a result of common/internal carotid artery occlusion1,2. Although described as a chronic phenomenon, we report three young female patients, diagnosed Takayasu Arteritis Type V (Angiographic Classification) who presented to us with acute binocular loss of vision which were managed with individually tailored approaches to restore vision.

Objectives

1.To elaborate on three patients diagnosed Takayasu Arteritis type V presenting with acute onset binocular vision loss and discuss critical aspects of management in OIS.

Methods

Case series of three patients of TA satisfying 1990 ACR classification criteria.

Results

18-year-old female presented with acute onset painless loss of vision in both eyes and severe vertigo. She appreciated hand motion on visual acuity testing. She was started on Methotrexate (MTX)and Prednisolone (PSL). In view of acute vertebrobasilar and carotid insufficiency, she underwent bilateral carotid and vertebral angioplasty. She tested 20/80 on visual acuity in both eyes and ambulated without support by two weeks after procedure.

15-year-old female presented with episodic vertigo, amaurosis fugax and claudication of both upper and lower limbs. She was kept on MTX and tapering doses of PSL and when dose of PSL reached less than 0.25mg/kg, she developed acute binocular vision loss with absent pupillary reflexes. Visual acuity testing revealed perception of hand motion in both eyes which improved to 20/40 within 2 weeks after increasing steroid dose to 0.5mg/kg and tocilizumab.

14-year-old female presented with acute binocular painless vision loss with previous history of limb claudication. Examination revealed no light perception on visual acuity testing in both eyes with absent pupillary reflexes. She was started on tapering doses of PSL and MTX. Also, she underwent a bilateral carotid and vertebral artery angioplasty. By first week, she could identify hand motion in both eyes and is continued on inpatient care.

Conclusion

We suggest that combining vascular surgical and pharmacological intervention in acute vision loss in TA may restore vision, even in active disease. Prompt follow-up and wider sample size is needed to draw insights into ocular involvement in TA.

References

[1]Peter J, David S, Joseph G, Horo S, Danda D. Hypoperfusive and hypertensive ocular manifestations in Takayasu arteritis. Clin Ophthalmol 2010;4:1173-1176.

[2]Peter J, David S, Danda D, Peter JV, Horo S, Joseph G. Ocular manifestations of Takayasu arteritis: a cross-sectional study. Retina. 2011 Jun;31(6):1170-8

Figure 1. Picture attached showing a)Fundus angiogram – increased foveal avascular zone

b)Fundus image -ischemic changes

c)CT Aortogram -Bilateral Carotid and subclavian stenosis

Table 1.

Characteristics of patients of TA with acute binocular vision loss

AgeDuration(years)Absent peripheral pulseHypertensionCRP levelsCT aortogram involvementTA typeFundus angiogram findingsFundus examination181Both brachial and radialNoHighBoth proximal subclavian arteries, common carotid, Infrarenal aorta, coeliac and superior mesenteric arteriesVcapillary non perfusion areasNormal152Both brachial, radial, right popliteal and Dorsalis pedis.YesHighBoth subclavian arteries, common carotid, renal and iliac arteries with >50% narrowing of abdominal aortaVcapillary non perfusion areasGrade II Hypertensive retinopathy144Left Brachial and radialYesNormalBoth subclavian, renal, iliac arteries and > 70% diffuse stenosis of bilateral carotidsVincreased foveal avascular zone, capillary non perfusion areasCotton wool spots, venous engorgements

Disclosure of Interests

None declared

Incidence and Outcomes of Early Cancers After Kidney Transplantation

Outcomes of early cancers after kidney transplantation are not well-understood. We included recipients of first live and deceased donor kidney transplants who developed de novo cancers in Australia and New Zealand between 1980–2016. We compared the frequency and stage of specific cancer types that developed early (≤12-months) and late (>12-months) post-transplantation. Risk factors for death were evaluated using multivariable Cox regression analyses. Of 2,759 recipients who developed de novo cancer, followed-up for 40,035 person-years, 243 (8.8%) patients were diagnosed with early cancer. Post-transplant lymphoproliferative disease, urinary cancers and melanoma were the most common cancer types (26%, 18%, and 12%) and the majority were either in-situ or locally invasive lesions (55%, 84%, and 86%). Tumors arising early from the gastrointestinal and respiratory systems were uncommon but aggressive, with 40% presenting with metastatic disease at time of diagnosis. Overall, 32% of patients with early cancers died within a median of 4.7 months (IQR:0.6–16) post-diagnosis and 91% were cancer-related deaths. Older recipient and donor age were associated with an increased risk of all-cause death. Early cancers, though infrequent in kidney transplant recipients, are associated with poor outcomes, as nearly 1 in 3 died from cancer-related death; with majority of deaths occurring within 12-months of cancer diagnosis.

GenePlexus: a web-server for gene discovery using network-based machine learning

Biomedical researchers take advantage of high-throughput, high-coverage technologies to routinely generate sets of genes of interest across a wide range of biological conditions. Although these technologies have directly shed light on the molecular underpinnings of various biological processes and diseases, the list of genes from any individual experiment is often noisy and incomplete. Additionally, interpreting these lists of genes can be challenging in terms of how they are related to each other and to other genes in the genome. In this work, we present GenePlexus (https://www.geneplexus.net/), a web-server that allows a researcher to utilize a powerful, network-based machine learning method to gain insights into their gene set of interest and additional functionally similar genes. Once a user uploads their own set of human genes and chooses between a number of different human network representations, GenePlexus provides predictions of how associated every gene in the network is to the input set. The web-server also provides interpretability through network visualization and comparison to other machine learning models trained on thousands of known process/pathway and disease gene sets. GenePlexus is free and open to all users without the need for registration.

Robust normalization and transformation techniques for constructing gene coexpression networks from RNA-seq data

BACKGROUND

Constructing gene coexpression networks is a powerful approach for analyzing high-throughput gene expression data towards module identification, gene function prediction, and disease-gene prioritization. While optimal workflows for constructing coexpression networks, including good choices for data pre-processing, normalization, and network transformation, have been developed for microarray-based expression data, such well-tested choices do not exist for RNA-seq data. Almost all studies that compare data processing and normalization methods for RNA-seq focus on the end goal of determining differential gene expression.

RESULTS

Here, we present a comprehensive benchmarking and analysis of 36 different workflows, each with a unique set of normalization and network transformation methods, for constructing coexpression networks from RNA-seq datasets. We test these workflows on both large, homogenous datasets and small, heterogeneous datasets from various labs. We analyze the workflows in terms of aggregate performance, individual method choices, and the impact of multiple dataset experimental factors. Our results demonstrate that between-sample normalization has the biggest impact, with counts adjusted by size factors producing networks that most accurately recapitulate known tissue-naive and tissue-aware gene functional relationships.

CONCLUSIONS

Based on this work, we provide concrete recommendations on robust procedures for building an accurate coexpression network from an RNA-seq dataset. In addition, researchers can examine all the results in great detail at https://krishnanlab.github.io/RNAseq_coexpression to make appropriate choices for coexpression analysis based on the experimental factors of their RNA-seq dataset.

Search for Lepton-Flavor Violation in Z-Boson Decays with τ Leptons with the ATLAS Detector

A search for lepton-flavor-violating Z→eτ and Z→μτ decays with pp collision data recorded by the ATLAS detector at the LHC is presented. This analysis uses 139  fb^{-1} of Run 2 pp collisions at sqrt[s]=13  TeV and is combined with the results of a similar ATLAS search in the final state in which the τ lepton decays hadronically, using the same data set as well as Run 1 data. The addition of leptonically decaying τ leptons significantly improves the sensitivity reach for Z→ℓτ decays. The Z→ℓτ branching fractions are constrained in this analysis to B(Z→eτ)<7.0×10^{-6} and B(Z→μτ)<7.2×10^{-6} at 95% confidence level. The combination with the previously published analyses sets the strongest constraints to date: B(Z→eτ)<5.0×10^{-6} and B(Z→μτ)<6.5×10^{-6} at 95% confidence level.

Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion

BACKGROUND

Recent studies have suggested that individual variants do not sufficiently explain the variable expressivity of phenotypes observed in complex disorders. For example, the 16p12.1 deletion is associated with developmental delay and neuropsychiatric features in affected individuals, but is inherited in > 90% of cases from a mildly-affected parent. While children with the deletion are more likely to carry additional "second-hit" variants than their parents, the mechanisms for how these variants contribute to phenotypic variability are unknown.

METHODS

We performed detailed clinical assessments, whole-genome sequencing, and RNA sequencing of lymphoblastoid cell lines for 32 individuals in five large families with multiple members carrying the 16p12.1 deletion. We identified contributions of the 16p12.1 deletion and "second-hit" variants towards a range of expression changes in deletion carriers and their family members, including differential expression, outlier expression, alternative splicing, allele-specific expression, and expression quantitative trait loci analyses.

RESULTS

We found that the deletion dysregulates multiple autism and brain development genes such as FOXP1, ANK3, and MEF2. Carrier children also showed an average of 5323 gene expression changes compared with one or both parents, which matched with 33/39 observed developmental phenotypes. We identified significant enrichments for 13/25 classes of "second-hit" variants in genes with expression changes, where 4/25 variant classes were only enriched when inherited from the noncarrier parent, including loss-of-function SNVs and large duplications. In 11 instances, including for ZEB2 and SYNJ1, gene expression was synergistically altered by both the deletion and inherited "second-hits" in carrier children. Finally, brain-specific interaction network analysis showed strong connectivity between genes carrying "second-hits" and genes with transcriptome alterations in deletion carriers.

CONCLUSIONS

Our results suggest a potential mechanism for how "second-hit" variants modulate expressivity of complex disorders such as the 16p12.1 deletion through transcriptomic perturbation of gene networks important for early development. Our work further shows that family-based assessments of transcriptome data are highly relevant towards understanding the genetic mechanisms associated with complex disorders.

Search for New Phenomena in Final States with Two Leptons and One or No b-Tagged Jets at sqrt[s]=13 TeV Using the ATLAS Detector

A search for new phenomena is presented in final states with two leptons and one or no b-tagged jets. The event selection requires the two leptons to have opposite charge, the same flavor (electrons or muons), and a large invariant mass. The analysis is based on the full run-2 proton-proton collision dataset recorded at a center-of-mass energy of sqrt[s]=13  TeV by the ATLAS experiment at the LHC, corresponding to an integrated luminosity of 139  fb^{-1}. No significant deviation from the expected background is observed in the data. Inspired by the B-meson decay anomalies, a four-fermion contact interaction between two quarks (b, s) and two leptons (ee or μμ) is used as a benchmark signal model, which is characterized by the energy scale and coupling, Λ and g_{*}, respectively. Contact interactions with Λ/g_{*} lower than 2.0 (2.4) TeV are excluded for electrons (muons) at the 95% confidence level, still far below the value that is favored by the B-meson decay anomalies. Model-independent limits are set as a function of the minimum dilepton invariant mass, which allow the results to be reinterpreted in various signal scenarios.

Search for Displaced Leptons in sqrt[s]=13 TeV pp Collisions with the ATLAS Detector

A search for charged leptons with large impact parameters using 139  fb^{-1} of sqrt[s]=13  TeV pp collision data from the ATLAS detector at the LHC is presented, addressing a long-standing gap in coverage of possible new physics signatures. Results are consistent with the background prediction. This search provides unique sensitivity to long-lived scalar supersymmetric lepton partners (sleptons). For lifetimes of 0.1 ns, selectron, smuon, and stau masses up to 720, 680, and 340  GeV, respectively, are excluded at 95% confidence level, drastically improving on the previous best limits from LEP.

Thoracic Spine Stenosis: Does Ultrasonic Osteotome Improve Outcome in Comparison to Conventional Technique?

INTRODUCTION

To investigate the efficacy of Ultrasonic Bone Scalpel (UBS) in thoracic spinal stenosis (TSS) in comparison to traditional technique.

MATERIAL AND METHODS

A total of 55 patients who had undergone conventional surgery (Group A) are compared with 45 patients of UBS (Group B) in TSS. The primary outcome measure of Modified Japanese Orthopaedic Association score (m JOA) with neurological complications and dural injury were assessed. Secondary outcome measures of total blood loss (TBL), time duration of surgery (ORT) and length of hospital stay (LHS) were analysed.

RESULTS

The pre-operative mJOA score 5.00(4.00-6.00) in the group A and 5.00(4.00-6.00) in the group B improved to 7.00(7.00-8.00) in the group A and 9.00(9.00-10.00) in the group B, respectively (P<0.001) at final average follow-up of 117.55 months for group A and 75.69 months in group B. More significant grade of myelopathy improvement and mJOA recovery rate (RR) were noted in group B. The TBL, ORT and LHS were more favourable in group B as compared to group A (p<0.0001). The group A had 9 (16.36%) neurological deficits compared to 2 (4.44%) in group B (p<0.001). Dural tears occurred in both groups (A=11, B=9). It was more frequent and not repairable in group A but without significant statistical difference.

CONCLUSION

UBS can reduce neurological deficits and improve outcomes in TSS. Secondarily, reduced blood loss, lesser surgical time and reduced LHS are significant added advantages of this new technology.

Reconciling multiple connectivity scores for drug repurposing

The basis of several recent methods for drug repurposing is the key principle that an efficacious drug will reverse the disease molecular ‘signature’ with minimal side effects. This principle was defined and popularized by the influential ‘connectivity map’ study in 2006 regarding reversal relationships between disease- and drug-induced gene expression profiles, quantified by a disease-drug ‘connectivity score.’ Over the past 15 years, several studies have proposed variations in calculating connectivity scores toward improving accuracy and robustness in light of massive growth in reference drug profiles. However, these variations have been formulated inconsistently using various notations and terminologies even though they are based on a common set of conceptual and statistical ideas. Therefore, we present a systematic reconciliation of multiple disease-drug similarity metrics (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$ES$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$css$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$Sum$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$Cosine$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$XSum$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$XCor$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$XSpe$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$XCos$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$EWCos$\end{document}) and connectivity scores (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$CS$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$RGES$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$NCS$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$WCS$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$Tau$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$CSS$\end{document}, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$EMUDRA$\end{document}) by defining them using consistent notation and terminology. In addition to providing clarity and deeper insights, this coherent definition of connectivity scores and their relationships provides a unified scheme that newer methods can adopt, enabling the computational drug-development community to compare and investigate different approaches easily. To facilitate the continuous and transparent integration of newer methods, this article will be available as a live document (https://jravilab.github.io/connectivity_scores) coupled with a GitHub repository (https://github.com/jravilab/connectivity_scores) that any researcher can build on and push changes to.