Haplotype-aware sequence alignment to pangenome graphs.

Modern pangenome graphs are built using haplotype-resolved genome assemblies. When mapping reads to a pangenome graph, prioritizing alignments that are consistent with the known haplotypes improves genotyping accuracy. However, the existing rigorous formulations for co-linear chaining and alignment problems do not consider the haplotype paths in a pangenome graph. This often leads to spurious read alignments to those paths that are unlikely recombinations of the known haplotypes. In this paper, we develop novel formulations and algorithms for sequence-to-graph alignment and chaining problems. Inspired by the genotype imputation models, we assume that a query sequence is an imperfect mosaic of reference haplotypes. Accordingly, we introduce a recombination penalty in the scoring functions for each haplotype switch. First, we solve haplotype-aware sequence-to-graph alignment in O(|Q||E||H|) time, where Q is the query sequence, E is the set of edges, and H is the set of haplotypes represented in the graph. To complement our solution, we prove that an algorithm significantly faster than O(|Q||E||H|) is impossible under the Strong Exponential Time Hypothesis (SETH). Second, we propose a haplotype-aware chaining algorithm that runs in O(|H|N log|H|N) time after graph preprocessing, where N is the count of input anchors. We then establish that a chaining algorithm significantly faster than O(|H|N) is impossible under SETH. As a proof-of-concept, we implemented our chaining algorithm in the Minichain aligner. By aligning sequences sampled from the human major histocompatibility complex (MHC) to a pangenome graph of 60 MHC haplotypes, we demonstrate that our algorithm achieves better consistency with ground-truth recombinations when compared to a haplotype-agnostic algorithm.

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.

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.

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.

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.

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 ß 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 ß cells to stop or reverse disease progression. Thus, pancreatic ß 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 ß cells to enhance proliferation, redifferentiation and protection from cell death and/or enable selective killing of senescent ß 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 ß cell insulin signalling might protect and/or regenerate ß cells as an improved treatment of patients with diabetes.

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.

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.

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.

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.

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.

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.

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.