Co-linear chaining on pangenome graphs

Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topology and cycles can be challenging. The seed-chain-extend based alignment algorithms use co-linear chaining as a standard technique to identify a good cluster of exact seed matches that can be combined to form an alignment. Recent works show how the co-linear chaining problem can be efficiently solved for acyclic pangenome graphs by exploiting their small width and how incorporating gap cost in the scoring function improves alignment accuracy. However, it remains open on how to effectively generalize these techniques for general pangenome graphs which contain cycles. Here we present the first practical formulation and an exact algorithm for co-linear chaining on cyclic pangenome graphs. We rigorously prove the correctness and computational complexity of the proposed algorithm. We evaluate the empirical performance of our algorithm by aligning simulated long reads from the human genome to a cyclic pangenome graph constructed from 95 publicly available haplotype-resolved human genome assemblies. While the existing heuristic-based algorithms are faster, the proposed algorithm provides a significant advantage in terms of accuracy. Implementation ( https://github.com/at-cg/PanAligner ).

Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs

A pangenome graph can serve as a better reference for genomic studies because it allows a compact representation of multiple genomes within a species. Aligning sequences to a graph is critical for pangenome-based resequencing. The seed-chain-extend heuristic works by finding short exact matches between a sequence and a graph. In this heuristic, colinear chaining helps identify a good cluster of exact matches that can be combined to form an alignment. Colinear chaining algorithms have been extensively studied for aligning two sequences with various gap costs, including linear, concave, and convex cost functions. However, extending these algorithms for sequence-to-graph alignment presents significant challenges. Recently, Makinen et al. introduced a sparse dynamic programming framework that exploits the small path cover property of acyclic pangenome graphs, enabling efficient chaining. However, this framework does not consider gap costs, limiting its practical effectiveness. We address this limitation by developing novel problem formulations and provably good chaining algorithms that support a variety of gap cost functions. These functions are carefully designed to enable fast chaining algorithms whose time requirements are parameterized in terms of the size of the minimum path cover. Through an empirical evaluation, we demonstrate the superior performance of our algorithm compared with existing aligners. When mapping simulated long reads to a pangenome graph comprising 95 human haplotypes, we achieved 98.7% precision while leaving <2% of reads unmapped.

Comparison of Effects of Propofol and Sevoflurane on the Cerebral Vasculature Assessed by Digital Subtraction Angiographic Parameters in Patients Treated for Ruptured Cerebral Aneurysm: A Preliminary Study

BACKGROUND

Studies have evaluated the effects of volatile and intravenous anesthetic agents on the cerebral vasculature with inconsistent results. We used digital subtraction angiography to compare the effects of propofol and sevoflurane on the luminal diameter of cerebral vessels and on cerebral transit time in patients with aneurysmal subarachnoid hemorrhage (aSAH).

METHODS

This prospective preliminary study included adult patients with good-grade aSAH scheduled for endovascular coil embolization; patients were randomized to receive propofol or sevoflurane anesthesia during endovascular coiling. The primary outcome was the luminal diameter of 7 cerebral vessel segments measured on the diseased and nondiseased sides of the brain at 3 time points: awake, postinduction of anesthesia, and postcoiling. Cerebral transit time was also measured as a surrogate for cerebral blood flow.

RESULTS

Eighteen patients were included in the analysis (9 per group). Baseline and intraoperative parameters were similar between the groups. Propofol increased the diameter of 1 vessel segment at postinduction and postcoiling on the diseased side and in 1 segment at postcoiling on the nondiseased side of the brain ( P <0.05). Sevoflurane increased vessel diameter in 3 segments at postinduction and in 2 segments at postcoiling on the diseased side, and in 4 segments at postcoiling on the nondiseased side ( P <0.05). Cerebral transit time did not change compared with baseline awake state in either group and was not different between the groups.

CONCLUSIONS

Sevoflurane has cerebral vasodilating properties compared with propofol in patients with good-grade aSAH. However, sevoflurane affects cerebral transit time comparably to propofol.

Navigation guidance in neuroendoscopic management of complex hydrocephalus

Patients with multiloculated hydrocephalus have multiple, separate abnormal CSF collections with no communication between them. Causes include complications of neonatal meningitis, germinal matrix hemorrhage in neonates, head trauma, and intracranial surgery. Endoscopic fenestration with shunt insertion is a safe and less invasive technique as the initial treatment. In this video, the authors demonstrate a few cases in which electromagnetic navigation was used with a stylet inserted through the operating endoscope to guide the surgeon. Modalities such as insertion of intraventricular contrast and fluorescein may be used as adjuvants, as demonstrated. The use of navigation helps to identify distorted anatomical landmarks and guides surgery. The video can be found here: https://stream.cadmore.media/r10.3171/2023.1.FOCVID22152.

Coverage-preserving sparsification of overlap graphs for long-read assembly

MOTIVATION

Read-overlap-based graph data structures play a central role in computing de novo genome assembly. Most long-read assemblers use Myers's string graph model to sparsify overlap graphs. Graph sparsification improves assembly contiguity by removing spurious and redundant connections. However, a graph model must be coverage-preserving, i.e. it must ensure that there exist walks in the graph that spell all chromosomes, given sufficient sequencing coverage. This property becomes even more important for diploid genomes, polyploid genomes, and metagenomes where there is a risk of losing haplotype-specific information.

RESULTS

We develop a novel theoretical framework under which the coverage-preserving properties of a graph model can be analyzed. We first prove that de Bruijn graph and overlap graph models are guaranteed to be coverage-preserving. We next show that the standard string graph model lacks this guarantee. The latter result is consistent with prior work suggesting that removal of contained reads, i.e. the reads that are substrings of other reads, can lead to coverage gaps during string graph construction. Our experiments done using simulated long reads from HG002 human diploid genome show that 50 coverage gaps are introduced on average by ignoring contained reads from nanopore datasets. To remedy this, we propose practical heuristics that are well-supported by our theoretical results and are useful to decide which contained reads should be retained to avoid coverage gaps. Our method retains a small fraction of contained reads (1-2%) and closes majority of the coverage gaps.

AVAILABILITY AND IMPLEMENTATION

Source code is available through GitHub (https://github.com/at-cg/ContainX) and Zenodo with doi: 10.5281/zenodo.7687543.

Imaging Recommendations for Diagnosis, Staging, and Management of Nasopharynx Carcinoma

Nasopharyngeal carcinoma (NPC) is an epithelial carcinoma originating from lining of the nasopharyngeal mucosa usually at the fossa of Rosenmuller (pharyngeal recess). An early detection on endoscopy can be rewarding, however, often difficult as the tumor at the pharyngeal recess is hidden from the endoscopic view. Magnetic resonance imaging and positron emission tomography–computed tomography form the backbone of detection and spread of the carcinoma into local and distant regions. These modalities help further characterize the precise locoregional infiltration and lymph nodal involvement which aids in the planning of the surgery/chemoradiotherapy. They also help in the follow-up evaluation and further management strategies. Many research and treatment groups namely American Joint Committee on Cancer, National Comprehensive Cancer Network, American Society of Clinical Oncology, American College of Radiology, Radiological Society of North America, European Society of Radiology (iGuide), Indian Radiological & Imaging Association/Indian College of Radiology and Imaging, National Cancer Grid, etc. have devised guidelines for the optimal assessment and treatment of NPC. The present document aims at providing a comprehensive review of the clinicoradiological recommendations for the diagnosis and management of NPC based on these guidelines as well as personalized experience of the contributors.

Delayed Posttraumatic Tension Pneumocephalus: Case Report and Review of Literature

Delayed tension pneumocephalus is a rare entity. Twelve cases of posttraumatic delayed tension pneumocephalus have been reported. This study is a case report of a patient presenting with delayed posttraumatic tension pneumocephalus, and highlights the nuances of management.

Asymmetry in cerebral perfusion from circle of Willis arterial variations in normal population

BACKGROUND

Angiographic and cadaveric studies have evidenced variations in the circle of Willis (CoW). Age-related changes in cerebral hemodynamics may be attributable to vascular variations.

OBJECTIVES

The objective is to assess interdependence of completeness of CoW with age using non-invasive MRA and cerebral perfusion using arterial spin labeling (ASL).

METHODS

This single-center, prospective study segregated 189 subjects into three groups: ≤5, 5 to 18, and >18 years. Angiographic (complete CoW and vascular asymmetry index) using TOF and contrast-enhanced- (CE-) MRA, and perfusion (perfusion asymmetry index) data using ASL were obtained.

RESULTS

One hundred and six (56.08%) subjects showed complete CoW on TOF and 100 (52.91%) on CE-MRA. Anterior and posterior collateral pathways were more prevalent in the younger population. Completeness of CoW decreased with increasing age, group 1 (54/60, 90% TOF; 51/60, 85% CE), group 2 (39/64, 60% TOF; 37/64, 56.92% CE), and group 3 (13/65, 20.31% TOF; 12/65, 18.75% CE); p-value < .0001. A statistically significant decrease in cerebral and cerebellar perfusion with increasing age was seen. Cerebellar to frontal perfusion change was higher in group 1. Fetal posterior cerebral artery (PCA) led to ipsilateral low and contralateral hyperperfusion flow asymmetries between occipital lobes.

CONCLUSIONS

This study shows that a complete CoW is commoner in pediatrics than adults and with increasing age, the completeness of CoW decreases paralleled by decrease in cerebral and cerebellar perfusion. There is age-related shift of perfusion from hindbrain to forebrain and the regression of PCoA occurs with increasing age leading to alterations in cerebral perfusion and hemodynamics.

Critical Review on the Developments in Polymer Composite Materials for Biomedical Implants

There has been a lack of research for developing functional polymer composites for biomedical implants. Even though metals are widely used as implant materials, there is a need for developing polymer composites as implant materials because of the stress shielding effect that causes a lack of compatibility of metals with the human body. This review aims to bring out the latest developments in polymer composite materials for body implants and to emphasize the significance of polymer composites as a viable alternative to conventional materials used in the biomedical industry for ease of life. This review article explores the developments in functional polymer composites for biomedical applications and provides distinct divisions for their applications based on the part of the body where they are implanted. Each application has been covered in some detail. The various applications covered are bone transplants and bone regeneration, cardiovascular implants (stents), dental implants and restorative materials, neurological and spinal implants, and tendon and ligament replacement.

Algorithms for Colinear Chaining with Overlaps and Gap Costs

Colinear chaining has proven to be a powerful heuristic for finding near-optimal alignments of long DNA sequences (e.g., long reads or a genome assembly) to a reference. It is used as an intermediate step in several alignment tools that employ a seed-chain-extend strategy. Despite this popularity, efficient subquadratic time algorithms for the general case where chains support anchor overlaps and gap costs are not currently known. We present algorithms to solve the colinear chaining problem with anchor overlaps and gap costs in Õ(n) time, where n denotes the count of anchors. The degree of the polylogarithmic factor depends on the type of anchors used (e.g., fixed-length anchors) and the type of precedence an optimal anchor chain is required to satisfy. We also establish the first theoretical connection between colinear chaining cost and edit distance. Specifically, we prove that for a fixed set of anchors under a carefully designed chaining cost function, the optimal "anchored" edit distance equals the optimal colinear chaining cost. The anchored edit distance for two sequences and a set of anchors is only a slight generalization of the standard edit distance. It adds an additional cost of one to an alignment of two matching symbols that are not supported by any anchor. Finally, we demonstrate experimentally that optimal colinear chaining cost under the proposed cost function can be computed orders of magnitude faster than edit distance, and achieves correlation coefficient >0.9 with edit distance for closely as well as distantly related sequences.

Targeting pancreatic β cells for diabetes treatment

Insulin is a life-saving drug for patients with type 1 diabetes; however, even today, no pharmacotherapy can prevent the loss or dysfunction of pancreatic insulin-producing β cells to stop or reverse disease progression. Thus, pancreatic β cells have been a main focus for cell-replacement and regenerative therapies as a curative treatment for diabetes. In this Review, we highlight recent advances toward the development of diabetes therapies that target β cells to enhance proliferation, redifferentiation and protection from cell death and/or enable selective killing of senescent β cells. We describe currently available therapies and their mode of action, as well as insufficiencies of glucagon-like peptide 1 (GLP-1) and insulin therapies. We discuss and summarize data collected over the last decades that support the notion that pharmacological targeting of β cell insulin signalling might protect and/or regenerate β cells as an improved treatment of patients with diabetes.

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Advances in long-read sequencing technologies and genome assembly methods have enabled the recent completion of the first telomere-to-telomere human genome assembly, which resolves complex segmental duplications and large tandem repeats, including centromeric satellite arrays in a complete hydatidiform mole (CHM13). Although derived from highly accurate sequences, evaluation revealed evidence of small errors and structural misassemblies in the initial draft assembly. To correct these errors, we designed a new repeat-aware polishing strategy that made accurate assembly corrections in large repeats without overcorrection, ultimately fixing 51% of the existing errors and improving the assembly quality value from 70.2 to 73.9 measured from PacBio high-fidelity and Illumina k-mers. By comparing our results to standard automated polishing tools, we outline common polishing errors and offer practical suggestions for genome projects with limited resources. We also show how sequencing biases in both high-fidelity and Oxford Nanopore Technologies reads cause signature assembly errors that can be corrected with a diverse panel of sequencing technologies.

Long-read mapping to repetitive reference sequences using Winnowmap2

Approximately 5-10% of the human genome remains inaccessible due to the presence of repetitive sequences such as segmental duplications and tandem repeat arrays. We show that existing long-read mappers often yield incorrect alignments and variant calls within long, near-identical repeats, as they remain vulnerable to allelic bias. In the presence of a nonreference allele within a repeat, a read sampled from that region could be mapped to an incorrect repeat copy. To address this limitation, we developed a new long-read mapping method, Winnowmap2, by using minimal confidently alignable substrings. Winnowmap2 computes each read mapping through a collection of confident subalignments. This approach is more tolerant of structural variation and more sensitive to paralog-specific variants within repeats. Our experiments highlight that Winnowmap2 successfully addresses the issue of allelic bias, enabling more accurate downstream variant calls in repetitive sequences.

PrecisionFDA Truth Challenge V2: Calling variants from short and long reads in difficult-to-map regions

The precisionFDA Truth Challenge V2 aimed to assess the state of the art of variant calling in challenging genomic regions. Starting with FASTQs, 20 challenge participants applied their variant-calling pipelines and submitted 64 variant call sets for one or more sequencing technologies (Illumina, PacBio HiFi, and Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with updated Genome in a Bottle benchmark sets and genome stratifications. Challenge submissions included numerous innovative methods, with graph-based and machine learning methods scoring best for short-read and long-read datasets, respectively. With machine learning approaches, combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.

A new comprehensive grading for giant pituitary adenomas: SLAP grading

AimGiant pituitary adenomas are difficult to resect due to multicompartmental extension. We developed a new grading system for giant pituitary adenomas (GPAs) considering possible extension in superior, lateral, anterior, and posterior (SLAP) directions. We also related the degree of resection to the SLAP grading.MethodsA review of case files and radiological images of patients with the GPAs defined as pituitary adenomas with a size of more than 4 cm in any dimension was done. The extent of the tumour was noted and scored as per the SLAP system. The maximum total score is 10 and represents a large tumour with maximum extensions in all directions. The subtotal resection (STR) was defined as a residual tumour volume of more than 10%. The association between individual and total score on the degree of resection was determined.ResultsA total of 103 cases of GPAs were analyzed. All patients had a suprasellar (S) extension. The lateral (L) extension was seen in 97.3% of cases. The anterior (A) extension was seen in 28 (27.2%) cases. The posterior (P) extension was seen in 45 (43.7%). Forty-eight (46.6%) had a total score of 5 or more. The STR was achieved in 64 (62.2%) cases. On regression analysis, a total score of ≥5 was associated with odds of 5.02 (1.69-14.93), p-value 0.004 for STR.ConclusionThe SLAP grading is a comprehensive grading system that can be applied easily to the GPAs and gives a complete picture of the extension of the tumour.

The complete sequence of a human genome

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Accelerating minimap2 for long-read sequencing applications on modern CPUs

Long-read sequencing is now routinely used at scale for genomics and transcriptomics applications. Mapping long reads or a draft genome assembly to a reference sequence is often one of the most time-consuming steps in these applications. Here we present techniques to accelerate minimap2, a widely used software for this task. We present multiple optimizations using single-instruction multiple-data parallelization, efficient cache utilization and a learned index data structure to accelerate the three main computational modules of minimap2: seeding, chaining and pairwise sequence alignment. These optimizations result in an up to 1.8-fold reduction of end-to-end mapping time of minimap2 while maintaining identical output.

Whole brain atlas-based diffusion kurtosis imaging parameters for evaluation of minimal hepatic encephalopathy

BACKGROUND AND PURPOSES

Minimal hepatic encephalopathy (MHE) has no recognizable clinical symptoms, but patients have cognitive and psychomotor deficits. Hyperammonemia along with neuroinflammation lead to microstructural changes in cerebral parenchyma. Changes at conventional imaging are detected usually at the overt clinical stage, but microstructural alterations by advanced magnetic resonance imaging techniques can be detected at an early stage.

MATERIALS AND METHODS

Whole brain diffusion kurtosis imaging (DKI) data acquired at 3T was analyzed to investigate microstructural parenchymal changes in 15 patients with MHE and compared with 15 age- and sex-matched controls. DKI parametric maps, namely kurtosis fractional anisotropy (kFA), mean kurtosis (MK), axial kurtosis (AK) and radial kurtosis (RK), were evaluated at 64 white matter (WM) and gray matter (GM) regions of interest (ROIs) in the whole brain and correlated with the psychometric hepatic encephalopathy score (PHES).

RESULTS

The MHE group showed a decrease in kFA and AK across the whole brain, whereas MK and RK decreased in WM ROIs but increased in several cortical and deep GM ROIs. These alterations were consistent with brain regions involved in cognitive function. Significant moderate to strong correlations (-0.52 to -0.66; 0.56) between RK, MK and kFA kurtosis metrics and PHES were observed.

CONCLUSION

DKI parameters show extensive microstructural brain abnormalities in MHE with minor correlation between the severity of tissue damage and psychometric scores.

A machine learning application for raising WASH awareness in the times of COVID-19 pandemic

The COVID-19 pandemic has revealed the power of internet disinformation in influencing global health. The deluge of information travels faster than the epidemic itself and is a threat to the health of millions across the globe. Health apps need to leverage machine learning for delivering the right information while constantly learning misinformation trends and deliver these effectively in vernacular languages in order to combat the infodemic at the grassroot levels in the general public. Our application, WashKaro, is a multi-pronged intervention that uses conversational Artificial Intelligence (AI), machine translation, and natural language processing to combat misinformation (NLP). WashKaro uses AI to provide accurate information matched against WHO recommendations and delivered in an understandable format in local languages. The primary aim of this study was to assess the use of neural models for text summarization and machine learning for delivering WHO matched COVID-19 information to mitigate the misinfodemic. The secondary aim of this study was to develop a symptom assessment tool and segmentation insights for improving the delivery of information. A total of 5026 people downloaded the app during the study window; among those, 1545 were actively engaged users. Our study shows that 3.4 times more females engaged with the App in Hindi as compared to males, the relevance of AI-filtered news content doubled within 45 days of continuous machine learning, and the prudence of integrated AI chatbot "Satya" increased thus proving the usefulness of a mHealth platform to mitigate health misinformation. We conclude that a machine learning application delivering bite-sized vernacular audios and conversational AI is a practical approach to mitigate health misinformation.

Utility of serum Galactomannan in diagnosing COVID-19 patients with suspected IPA: an observational study in resource limited settings

OBJECTIVE

To study the utility of Galactomannan (GM) antigen as a screening marker for diagnosing invasive pulmonary aspergillosis (IPA) in coronavirus disease 2019 (COVID-19) patients.

PATIENTS AND METHODS

The serum samples from patients with severe COVID-19 diseases admitted to the Critical Care Unit were collected on the 5th day of admission for GM screening. The samples were analysed by enzyme linked immune sorbent assay (ELISA) and GM index of more than 1 was considered as positive. All GM positive patients were serially followed until discharge or death.

RESULTS

The GM was raised in serum of 12 out of 38 patients, indicating an incidence of possible COVID-19 associated IPA (CAPA) in 31.57% of patients. The median age of these CAPA patients was 56.5 years, males were significantly more affected than females. The inflammatory marker serum ferritin was raised in all 12 patients (median value of 713.74 ng/ml), while IL-6 was raised in 9 patients (median value of 54.13 ng/ml). None of these patients received antifungals. Their median length of hospital stay was 20 days (IQR: 12, 34 days). All these patients succumbed to the illness.

CONCLUSIONS

The serum GM appears to be sensitive diagnostic tool to identify early IPA in COVID-19 patients and pre-emptive antifungal therapy could play a role in salvaging these patients.

Mechanical clot dissolution technique for surgical clip-related occlusions: An emergent triple-step approach

Cerebral ischemia following clipping of cerebral aneurysms constitutes major cause of morbidity and mortality. Clip-related injury to vessel, postoperative clip rotation, prolonged temporary occlusion, intraoperative rupture, and vasospasm are some etiological factors compromising forward flow in parent or branch vessel. On suspicion of compromised forward flow, immediate intraoperative evaluation is done to detect the cause of vascular compromise and further management is done by microsurgical or endovascular means. We describe a case of ruptured distal anterior cerebral artery (ACA) aneurysm complicated by occlusion of ACA after surgical clipping. The patient was managed by endovascular means by combined technique of intra-arterial nimodipine, antiplatelet infusion, and mechanical clot disruption using J-tip microwire.

Cardiovascular adverse events are associated with usage of immune checkpoint inhibitors in real-world clinical data across the United States

Background

Immune checkpoint inhibitors (ICIs) can cause life-threatening cardiovascular adverse events (CVAEs) that may not be attributed to therapy. The outcomes of clinical trials may underestimate treatment-related adverse events due to restrictive eligibility, limited sample size, and failure to anticipate selected toxicities. We evaluated the incidence and clinical determinants of CVAEs in real-world population on ICI therapy.

Patients and methods

Among 2 687 301 patients diagnosed with cancer from 2011 to 2018, 16 574 received ICIs for any cancer. Patients in the ICI and non-ICI cohorts were matched in a 1 : 1 ratio according to age, sex, National Cancer Institute comorbidity score, and primary cancer. The non-ICI cohort was stratified into patients who received chemotherapy (N = 2875) or targeted agents (N = 4611). All CVAEs, non-cardiac immune-related adverse events occurring after treatment initiation, baseline comorbidities, and treatment details were identified and analyzed using diagnosis and billing codes.

Results

Median age was 61 and 65 years in the ICI and non-ICI cohorts, respectively (P < 0.001). ICI patients were predominantly male (P < 0.001). Lung cancer (43.1%), melanoma (30.4%), and renal cell carcinoma (9.9%) were the most common cancer types. CVAE diagnoses in our dataset by incidence proportion (ICI cohort) were stroke (4.6%), heart failure (3.5%), atrial fibrillation (2.1%), conduction disorders (1.5%), myocardial infarction (0.9%), myocarditis (0.05%), vasculitis (0.05%), and pericarditis (0.2%). Anti-cytotoxic T-lymphocyte-associated protein 4 increased the risk of heart failure [versus anti-programmed cell death protein 1; hazard ratio (HR), 1.9; 95% confidence interval (CI) 1.27-2.84] and stroke (HR, 1.7; 95% CI 1.3-2.22). Pneumonitis was associated with heart failure (HR, 2.61; 95% CI 1.23-5.52) and encephalitis with conduction disorders (HR, 4.35; 95% CI 1.6-11.87) in patients on ICIs. Advanced age, primary cancer, nephritis, and anti-cytotoxic T-lymphocyte-associated protein 4 therapy were commonly associated with CVAEs in the adjusted Cox proportional hazards model.

Conclusions

Our findings underscore the importance of risk stratification and cardiovascular monitoring for patients on ICI therapy.

•

Patient claims data across the United States were used to study cardiovascular adverse events (CVAEs) after ICI treatment.

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Patients on ICI treatment for advanced cancer have a higher incidence of CVAEs than previously reported.

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Median time to CVAE onset was significantly shorter with ICIs (~3 months) than with non-ICI systemic therapy (~8 months).

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Anti-CTLA-4 monotherapy or combination had a higher risk of heart failure and stroke than anti-PD-1 therapy (1.5-2 folds).

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Age, male sex, cancer type, nephritis, pneumonitis, and anti-CTLA-4 therapy were associated with a higher risk of CVAEs.

Real-time mapping of nanopore raw signals

Motivation

Oxford Nanopore Technologies sequencing devices support adaptive sequencing, in which undesired reads can be ejected from a pore in real time. This feature allows targeted sequencing aided by computational methods for mapping partial reads, rather than complex library preparation protocols. However, existing mapping methods either require a computationally expensive base-calling procedure before using aligners to map partial reads or work well only on small genomes.

Results

In this work, we present a new streaming method that can map nanopore raw signals for real-time selective sequencing. Rather than converting read signals to bases, we propose to convert reference genomes to signals and fully operate in the signal space. Our method features a new way to index reference genomes using k-d trees, a novel seed selection strategy and a seed chaining algorithm tailored toward the current signal characteristics. We implemented the method as a tool Sigmap. Then we evaluated it on both simulated and real data and compared it to the state-of-the-art nanopore raw signal mapper Uncalled. Our results show that Sigmap yields comparable performance on mapping yeast simulated raw signals, and better mapping accuracy on mapping yeast real raw signals with a 4.4× speedup. Moreover, our method performed well on mapping raw signals to genomes of size >100 Mbp and correctly mapped 11.49% more real raw signals of green algae, which leads to a significantly higher F₁-score (0.9354 versus 0.8660).

Availability and implementation

Sigmap code is accessible at https://github.com/haowenz/sigmap.

Supplementary information

Supplementary data are available at Bioinformatics online.

A variant selection framework for genome graphs

MOTIVATION

Variation graph representations are projected to either replace or supplement conventional single genome references due to their ability to capture population genetic diversity and reduce reference bias. Vast catalogues of genetic variants for many species now exist, and it is natural to ask which among these are crucial to circumvent reference bias during read mapping.

RESULTS

In this work, we propose a novel mathematical framework for variant selection, by casting it in terms of minimizing variation graph size subject to preserving paths of length α with at most δ differences. This framework leads to a rich set of problems based on the types of variants [e.g. single nucleotide polymorphisms (SNPs), indels or structural variants (SVs)], and whether the goal is to minimize the number of positions at which variants are listed or to minimize the total number of variants listed. We classify the computational complexity of these problems and provide efficient algorithms along with their software implementation when feasible. We empirically evaluate the magnitude of graph reduction achieved in human chromosome variation graphs using multiple α and δ parameter values corresponding to short and long-read resequencing characteristics. When our algorithm is run with parameter settings amenable to long-read mapping (α = 10 kbp, δ = 1000), 99.99% SNPs and 73% SVs can be safely excluded from human chromosome 1 variation graph. The graph size reduction can benefit downstream pan-genome analysis.

AVAILABILITY AND IMPLEMENTATION

: https://github.com/AT-CG/VF.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Mechanical Thrombectomy in Embolic Cardiac Myxoma: Case Report and Literature Review

Myxomas are the most common cardiac tumors and present clinically with cardiac manifestations, systemic constitutional symptoms, and embolic events. Posterior circulation involvement occurs in approximately 20 percent of cerebral ischemic events.The endovascular technique is an established life-saving therapy for eligible patients upto 24 hours from symptom onset. However, the role of endovascular management in embolic atrial myxoma remains unknown with no international consensus guidelines for the management of stroke in such patient population. Here, we present a case report of an embolic posterior circulation stroke in a young female treated with mechanical thrombectomy at 23 hours from symptom onset. To the best of our knowledge, this is the first thrombectomy case in posterior circulation with embolism from myxoma. Further workup confirmed an atrial myxoma which was resected. We also review the previous cases with mechanical thrombectomy done in such cases.

Horizontal Gaze Palsy, Scoliosis, and Split Pons Sign in a 6-Year-Old Girl

ABSTRACT

A 6-year-old girl presented with complaints of absent horizontal eye movements since birth. There was also associated progressive scoliosis for past 1 year. Neuroimaging revealed split pons sign, butterfly-shaped medulla, and prominent inferior olivary nuclei. The presence of congenital horizontal gaze palsy, childhood onset progressive scoliosis, and abnormal neuroimaging findings confirmed the diagnosis of horizontal gaze palsy with progressive scoliosis. This case highlights the importance of neuroimaging in a child presenting with horizontal gaze palsy and scoliosis that helped for starting early rehabilitation of the child, prevention of permanent vision loss, and parental counseling for future pregnancies.

A comprehensive evaluation of long read error correction methods

BACKGROUND

Third-generation single molecule sequencing technologies can sequence long reads, which is advancing the frontiers of genomics research. However, their high error rates prohibit accurate and efficient downstream analysis. This difficulty has motivated the development of many long read error correction tools, which tackle this problem through sampling redundancy and/or leveraging accurate short reads of the same biological samples. Existing studies to asses these tools use simulated data sets, and are not sufficiently comprehensive in the range of software covered or diversity of evaluation measures used.

RESULTS

In this paper, we present a categorization and review of long read error correction methods, and provide a comprehensive evaluation of the corresponding long read error correction tools. Leveraging recent real sequencing data, we establish benchmark data sets and set up evaluation criteria for a comparative assessment which includes quality of error correction as well as run-time and memory usage. We study how trimming and long read sequencing depth affect error correction in terms of length distribution and genome coverage post-correction, and the impact of error correction performance on an important application of long reads, genome assembly. We provide guidelines for practitioners for choosing among the available error correction tools and identify directions for future research.

CONCLUSIONS

Despite the high error rate of long reads, the state-of-the-art correction tools can achieve high correction quality. When short reads are available, the best hybrid methods outperform non-hybrid methods in terms of correction quality and computing resource usage. When choosing tools for use, practitioners are suggested to be careful with a few correction tools that discard reads, and check the effect of error correction tools on downstream analysis. Our evaluation code is available as open-source at https://github.com/haowenz/LRECE .

Isolated contralateral abducens palsy in direct carotid-cavernous fistula

Post-traumatic direct carotid-cavernous fistulas may develop in patients with a closed head injury. The classical presentation is the Dandy's triad-chemosis, pulsatile proptosis and orbital bruit. Associated findings may include orbital pain, dilated episcleral corkscrew vessels, vision deficit and cranial nerve palsies. Cranial nerves-oculomotor (III), trochlear (IV), ophthalmic (V1), and maxillary (V2) divisions of trigeminal and the abducens (VI) lie in close association of the cavernous sinus. Abducens nerve (VI) lies close to the intracavernous internal carotid artery, within the substance of the sinus and is hence easily susceptible to vascular insult. The two sinuses connect across the midline and communicate freely with each other. Back pressure changes can present with the same sided or bilateral cranial nerve palsies. We report a rare association of a long-standing left-sided carotid-cavernous fistula with right eye abduction deficit and contralateral abducens palsy.

COVID-19: Indian Society of Neuroradiology (ISNR) Consensus Statement and Recommendations for Safe Practice of Neuroimaging and Neurointerventions

The ongoing COVID-19 pandemic has forced every radiology set-up to evolve and formulate guidelines for day-to-day functioning. The sub-speciality of neuroradiology, both diagnostic and neuro-intervention, forms a very important part of any radiology or 'neuro-care' set-up. The present document is a consensus statement of the Indian Society of Neuroradiology, prepared after reviewing the available data and working experience. It scientifically tries to answer many questions faced by neuroradiologists everyday in practice. It encompasses simple things such as which patients need to be imaged, what precautions are essential, the work-flows, cleaning of radiology equipment, how to carry out neuro-interventions in COVID-suspect patients, and what procedures/tests to avoid, or their alternatives, to minimise the spread of COVID infection both to the patients and health care personnel. As radiology set-ups can be large, every sub-speciality may have certain precautions which will not be covered in general guidelines, and this document tries to answer those for neuroradiologists. Carefully evolved Standards of Operating Procedure (SOPs) and guidelines are the need of the hour to guide in providing uninterrupted and adequate services to the needy without compromising the safety of the specialised work force and facilities involved.

A Randomized Controlled Study to Compare Hemodynamic Effects between Clonidine and Pregabalin in Laparoscopic Cholecystectomy

Background:

Laparoscopic cholecystectomy (LC) is associated with pneumoperitoneum and hemodynamic disturbances. Pregabalin and Clonidine have been used for anesthetic effects, but a better drug for controlling hemodynamic parameters is being investigated.

Aims:

The study was done to assess and compare the efficacy of preoperative single oral dose of pregabalin and clonidine in maintaining the hemodynamic parameters in the LC.

Settings and Design:

The prospective, interventional, randomized, comparative, single-blinded study was conducted in the department of anesthesia and surgery from January 2015 to September 2016 after taking approval from the institutional ethical committee.

Materials and Methods:

The study included a total of 90 patients, aged between 18 and 56 years of both sexes scheduled for elective LC. Patients were randomized into three groups of 30 each who received oral pregabalin 150 mg, clonidine 200 ug, and placebo. The hemodynamic parameters were recorded at various time intervals along with any adverse events.

Statistical Analysis:

Quantitative variables were compared using unpaired t-test (when the data sets were not normally distributed) between the two groups. Qualitative variables were compared using Chi-square test/Fisher's exact test. P < 0.05 was considered statistically significant.

Results:

There was a significant increase in the heart rate (HR) and systolic, diastolic, and mean blood pressure during laryngoscopy and pneumoperitoneum in the control group as compared to both pregabalin and clonidine. HR was significantly lower in clonidine group after extubation and in postoperative period than both control group and pregabalin group. There was no major difference in the incidence of side effects.

Conclusion:

Both pregabalin (150 mg) and clonidine (200 ug) were effective in controlling the hemodynamic parameters during LC, with clonidine providing better hemodynamic stability than Pregabalin.

Weighted minimizer sampling improves long read mapping

MOTIVATION

In this era of exponential data growth, minimizer sampling has become a standard algorithmic technique for rapid genome sequence comparison. This technique yields a sub-linear representation of sequences, enabling their comparison in reduced space and time. A key property of the minimizer technique is that if two sequences share a substring of a specified length, then they can be guaranteed to have a matching minimizer. However, because the k-mer distribution in eukaryotic genomes is highly uneven, minimizer-based tools (e.g. Minimap2, Mashmap) opt to discard the most frequently occurring minimizers from the genome to avoid excessive false positives. By doing so, the underlying guarantee is lost and accuracy is reduced in repetitive genomic regions.

RESULTS

We introduce a novel weighted-minimizer sampling algorithm. A unique feature of the proposed algorithm is that it performs minimizer sampling while considering a weight for each k-mer; i.e. the higher the weight of a k-mer, the more likely it is to be selected. By down-weighting frequently occurring k-mers, we are able to meet both objectives: (i) avoid excessive false-positive matches and (ii) maintain the minimizer match guarantee. We tested our algorithm, Winnowmap, using both simulated and real long-read data and compared it to a state-of-the-art long read mapper, Minimap2. Our results demonstrate a reduction in the mapping error-rate from 0.14% to 0.06% in the recently finished human X chromosome (154.3 Mbp), and from 3.6% to 0% within the highly repetitive X centromere (3.1 Mbp). Winnowmap improves mapping accuracy within repeats and achieves these results with sparser sampling, leading to better index compression and competitive runtimes.

AVAILABILITY AND IMPLEMENTATION

Winnowmap is built on top of the Minimap2 codebase and is available at https://github.com/marbl/winnowmap.

Study of the Incidence, Clinicopathological Profile, and Management of Second Primary Tumors in Patients with Index Head and Neck Tumors

Introduction This study was performed to study the incidence and clinicopathological profile of second primary tumors (SPTs) in patients with squamous cell carcinoma of head and neck at our institute.

Materials and Methods In this study, we included the data of 120 patients who developed an SPT of the upper aerodigestive tract following treatment of their index tumor (IT). Since the online data of cancer patients in our cancer registry was available from January 2005, we started the study retrospectively from that time. At our institute, Rajiv Gandhi Cancer Institute and Research Centre, the incidence was found to be 8.4%. Warren and Gates criteria were followed for defining a second tumor.

Results Our study results showed an incidence of 8.4% of SPTs among patients of head and neck squamous cell carcinoma (HNSCC). The mean age of the patients was 56.47 ± 10.42 years with a male predominance. The mean period of addiction in patients was 18.48 ± 4.63 years. It was found that patients with SPT had significant history of tobacco and alcohol use. The most common location for ITs and SPT was tongue and buccal mucosa. The main modality of treatment was surgery in all patient groups. Patients were followed up at three-month intervals for the first 2 years. The SPT was diagnosed with a confirmation biopsy. Majority of patients with SPT again underwent surgery with reconstruction with either free flaps or local flaps. Recurrence after SPT treatment was seen in 16.67% cases, and primarily, it was a locoregional recurrence. Only patients with at least 6 months follow-up posttreatment of SPT were included in this study. At the end of the study, 62.5% patients were disease free, 20.83% patients were alive with disease, and 16.67% patients were dead. Some of the patients who are alive with disease developed a third primary tumor which was managed as per guidelines.

Conclusion The incidence of SPTs is 8.4% in our institute. This study adds to the theory of field cancerization proposed by Slaughter et al. We found a significant history of tobacco chewing in our patients who developed SPT. The clinical significance of this study is identifying the features of SPT in patients with HNSCC and allowing for a rational follow-up schedule. The most important part of treatment although still lies with the patient by quitting use of alcohol and tobacco.

Aseptic orbital cellulitis: A master masquerade of intraocular malignancy

Sudden and extensive growth of intraocular tumors like retinoblastoma and choroidal melanoma may result in the clinical presentation of sterile or aseptic orbital cellulitis. In such masquerading situations, ocular and orbital imaging plays a significant role. The treatment with steroids may provide a rapid recovery from the aggressive orbital inflammation. However, a high index of suspicion is vital for apt diagnosis and timely management.

Longevity in response to lowered insulin signaling requires glycine N-methyltransferase-dependent spermidine production

Reduced insulin/IGF signaling (IIS) extends lifespan in multiple organisms. Different processes in different tissues mediate this lifespan extension, with a set of interplays that remain unclear. We here show that, in Drosophila, reduced IIS activity modulates methionine metabolism, through tissue-specific regulation of glycine N-methyltransferase (Gnmt), and that this regulation is required for full IIS-mediated longevity. Furthermore, fat body-specific expression of Gnmt was sufficient to extend lifespan. Targeted metabolomics showed that reducing IIS activity led to a Gnmt-dependent increase in spermidine levels. We also show that both spermidine treatment and reduced IIS activity are sufficient to extend the lifespan of Drosophila, but only in the presence of Gnmt. This extension of lifespan was associated with increased levels of autophagy. Finally, we found that increased expression of Gnmt occurs in the liver of liver-specific IRS1 KO mice and is thus an evolutionarily conserved response to reduced IIS. The discovery of Gnmt and spermidine as tissue-specific modulators of IIS-mediated longevity may aid in developing future therapeutic treatments to ameliorate aging and prevent disease.

Osteoid osteoma of the calcaneus misdiagnosed as subtalar sprain

Osteoid osteoma of foot and ankle account for ten percent of benign bone tumors and commonly involve the talus and metatarsals. Its occurrence in calcaneus is extremely rare and can mimic ankle instability, subtalar arthritis, osteochondritis or plantar fasciitis leading to delay in diagnosis. We present the case of a 17 year old boy with periarticular osteoid osteoma in the calcaneum, who presented following an ankle sprain. He was successfully treated with CT guided percutaneous radiofrequency ablation and we feel that it is a safe, precise and effective treatment option for even periarticular osteoid osteoma in the foot and ankle region.

Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps

Metagenomic sequence classification should be fast, accurate and information-rich. Emerging long-read sequencing technologies promise to improve the balance between these factors but most existing methods were designed for short reads. MetaMaps is a new method, specifically developed for long reads, capable of mapping a long-read metagenome to a comprehensive RefSeq database with >12,000 genomes in <16 GB or RAM on a laptop computer. Integrating approximate mapping with probabilistic scoring and EM-based estimation of sample composition, MetaMaps achieves >94% accuracy for species-level read assignment and r² > 0.97 for the estimation of sample composition on both simulated and real data when the sample genomes or close relatives are present in the classification database. To address novel species and genera, which are comparatively harder to predict, MetaMaps outputs mapping locations and qualities for all classified reads, enabling functional studies (e.g. gene presence/absence) and detection of incongruities between sample and reference genomes.

Sequencing platforms, such as Oxford Nanopore or Pacific Biosciences generate long-read data that preserve long-range genomic information but have high error rates. Here, the authors develop MetaMaps, a computational tool for strain-level metagenomic assignment and compositional estimation using long reads.

Kmerind: A Flexible Parallel Library for K-mer Indexing of Biological Sequences on Distributed Memory Systems

Counting and indexing fixed length substrings, or $k$k-mers, in biological sequences is a key step in many bioinformatics tasks including genome alignment and mapping, genome assembly, and error correction. While advances in next generation sequencing technologies have dramatically reduced the cost and improved latency and throughput, few bioinformatics tools can efficiently process the datasets at the current generation rate of 1.8 terabases per 3-day experiment from a single sequencer. We present Kmerind, a high performance parallel $k$k-mer indexing library for distributed memory environments. The Kmerind library provides a set of simple and consistent APIs with sequential semantics and parallel implementations that are designed to be flexible and extensible. Kmerind's $k$k-mer counter performs similarly or better than the best existing $k$k-mer counting tools even on shared memory systems. In a distributed memory environment, Kmerind counts $k$k-mers in a 120 GB sequence read dataset in less than 13 seconds on 1024 Xeon CPU cores, and fully indexes their positions in approximately 17 seconds. Querying for 1 percent of the $k$k-mers in these indices can be completed in 0.23 seconds and 28 seconds, respectively. Kmerind is the first $k$k-mer indexing library for distributed memory environments, and the first extensible library for general $k$k-mer indexing and counting. Kmerind is available at https://github.com/ParBLiSS/kmerind.