eMPRess: a systematic cophylogeny reconciliation tool.

SUMMARY: We describe eMPRess, a software program for phylogenetic tree reconciliation under the duplication-transfer-loss model that systematically addresses the problems of choosing event costs and selecting representative solutions, enabling users to make more robust inferences. AVAILABILITY AND IMPLEMENTATION: eMPRess is freely available at http://www.cs.hmc.edu/empress. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Integrative analysis of 111 reference human epigenomes.

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Unusual Cerebral Aneurysm after Stereotactic Radiosurgery to Treat Trigeminal Neuralgia.

Stereotactic radiosurgery is a treatment option for trigeminal neuralgia. This procedure is minimally invasive, but tumor development and facial numbness have been reported. Here, we report an unusual presentation after stereotactic radiosurgery to treat trigeminal neuralgia. A 60-year-old man demonstrated typical signs for type 1 trigeminal nerve neuralgia and was treated with medication for 5 years. Owing to an intolerance to that medication, he received stereotactic radiosurgery with 66 Gy. During a 9-year follow-up exam, dizziness with a spinning sensation was reported and a right superior cerebellar thrombosed aneurysm was diagnosed. He received transarterial embolization with coiling of aneurysm and subsequently reported no complications on follow-up exams. Although stereotactic radiosurgery is a promising treatment for trigeminal neuralgia, aneurysm development may be considered a possible complication. Long-term follow-up care of these patients should be considered. To understand the relationship between radiosurgery and the potential development of a cerebral aneurysm, further research is needed.

Endoscopic transcanal transpetrosal approach to the petroclival region: a cadaveric study with comparison to the Kawase approach.

This study introduces expanded application of the endoscopic transcanal approach with anterior petrosectomy (ETAP) in reaching the petroclival region, which was compared through a quantitative analysis to the middle fossa transpetrosal-transtentorial approach (Kawase approach). Anatomical dissections were performed in five cadaveric heads. For each head, the ETAP was performed on one side with a detailed description of each step, while the Kawase approach was performed on the contralateral side. Quantitative measurements of the exposed area over the ventrolateral surface of the brainstem, and of the angles of attack to the posterior margin of the trigeminal nerve root entry zone (CN V-REZ) and porus acusticus internus (PAI) were obtained for statistical comparison. The ETAP provided significantly larger exposure over the ventrolateral surface of the pons (93.03 ± 21.87 mm2) than did the Kawase approach (34.57 ± 11.78 mm2). In contrast to the ETAP, the Kawase approach afforded greater angles of attack to the CN V-REZ and PAI in the vertical and horizontal planes. The ETAP is a feasible and minimally invasive procedure for accessing the petroclival region. In comparison to the Kawase approach, the ETAP allows for fully anterior petrosectomy and larger exposure over the ventrolateral surface of the brainstem without passing through the cranial nerves or requiring traction of the temporal lobe.

A comparative encyclopedia of DNA elements in the mouse genome.

The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types. By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization. Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases.

Comparative analysis of regulatory information and circuits across distant species.

Despite the large evolutionary distances between metazoan species, they can show remarkable commonalities in their biology, and this has helped to establish fly and worm as model organisms for human biology. Although studies of individual elements and factors have explored similarities in gene regulation, a large-scale comparative analysis of basic principles of transcriptional regulatory features is lacking. Here we map the genome-wide binding locations of 165 human, 93 worm and 52 fly transcription regulatory factors, generating a total of 1,019 data sets from diverse cell types, developmental stages, or conditions in the three species, of which 498 (48.9%) are presented here for the first time. We find that structural properties of regulatory networks are remarkably conserved and that orthologous regulatory factor families recognize similar binding motifs in vivo and show some similar co-associations. Our results suggest that gene-regulatory properties previously observed for individual factors are general principles of metazoan regulation that are remarkably well-preserved despite extensive functional divergence of individual network connections. The comparative maps of regulatory circuitry provided here will drive an improved understanding of the regulatory underpinnings of model organism biology and how these relate to human biology, development and disease.

Inferring Pareto-optimal reconciliations across multiple event costs under the duplication-loss-coalescence model.

BACKGROUND: Reconciliation methods are widely used to explain incongruence between a gene tree and species tree. However, the common approach of inferring maximum parsimony reconciliations (MPRs) relies on user-defined costs for each type of event, which can be difficult to estimate. Prior work has explored the relationship between event costs and maximum parsimony reconciliations in the duplication-loss and duplication-transfer-loss models, but no studies have addressed this relationship in the more complicated duplication-loss-coalescence model. RESULTS: We provide a fixed-parameter tractable algorithm for computing Pareto-optimal reconciliations and recording all events that arise in those reconciliations, along with their frequencies. We apply this method to a case study of 16 fungi to systematically characterize the complexity of MPR space across event costs and identify events supported across this space. CONCLUSION: This work provides a new framework for studying the relationship between event costs and reconciliations that incorporates both macro-evolutionary events and population effects and is thus broadly applicable across eukaryotic species.

Reconciliation feasibility in the presence of gene duplication, loss, and coalescence with multiple individuals per species.

BACKGROUND: In phylogenetics, we often seek to reconcile gene trees with species trees within the framework of an evolutionary model. While the most popular models for eukaryotic species allow for only gene duplication and gene loss or only multispecies coalescence, recent work has combined these phenomena through a reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes the duplication-loss and coalescent history of a gene family. However, the LCT makes the simplifying assumption that only one individual is sampled per species whereas, with advances in gene sequencing, we now have access to multiple samples per species. RESULTS: We demonstrate that with these additional samples, there exist gene tree topologies that are impossible to reconcile with any species tree. In particular, the multiple samples enforce new constraints on the placement of duplications within a valid reconciliation. To model these constraints, we extend the LCT to a new structure, the partially labeled coalescent tree (PLCT) and demonstrate how to use the PLCT to evaluate the feasibility of a gene tree topology. We apply our algorithm to two clades of apes and flies to characterize possible sources of infeasibility. CONCLUSION: Going forward, we believe that this model represents a first step towards understanding reconciliations in duplication-loss-coalescence models with multiple samples per species.

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees.

Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a gene family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect the gene tree, many of the most popular reconciliation methods consider discordance only due to gene duplication and loss (and sometimes horizontal gene transfer). Methods that do model ILS are either highly parameterized or consider a restricted set of histories, thus limiting their applicability and accuracy. To address these challenges, we present a novel algorithm DLCpar for inferring a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and ILS. Our algorithm relies on a new reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes coalescent and duplication-loss history. We show that the LCT representation enables an exhaustive and efficient search over the space of reconciliations, and, for most gene families, the least common ancestor (LCA) mapping is an optimal solution for the species mapping between the gene tree and species tree in an MP LCT. Applying our algorithm to a variety of clades, including flies, fungi, and primates, as well as to simulated phylogenies, we achieve high accuracy, comparable to sophisticated probabilistic reconciliation methods, at reduced run time and with far fewer parameters. These properties enable inferences of the complex evolution of gene families across a broad range of species and large data sets.

Improved gene tree error correction in the presence of horizontal gene transfer.

MOTIVATION: The accurate inference of gene trees is a necessary step in many evolutionary studies. Although the problem of accurate gene tree inference has received considerable attention, most existing methods are only applicable to gene families unaffected by horizontal gene transfer. As a result, the accurate inference of gene trees affected by horizontal gene transfer remains a largely unaddressed problem. RESULTS: In this study, we introduce a new and highly effective method for gene tree error correction in the presence of horizontal gene transfer. Our method efficiently models horizontal gene transfers, gene duplications and losses, and uses a statistical hypothesis testing framework [Shimodaira-Hasegawa (SH) test] to balance sequence likelihood with topological information from a known species tree. Using a thorough simulation study, we show that existing phylogenetic methods yield inaccurate gene trees when applied to horizontally transferred gene families and that our method dramatically improves gene tree accuracy. We apply our method to a dataset of 11 cyanobacterial species and demonstrate the large impact of gene tree accuracy on downstream evolutionary analyses. AVAILABILITY AND IMPLEMENTATION: An implementation of our method is available at http://compbio.mit.edu/treefix-dtl/ CONTACT: : mukul@engr.uconn.edu or manoli@mit.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Highly conserved residues in the helical domain of dengue virus type 1 precursor membrane protein are involved in assembly, precursor membrane (prM) protein cleavage, and entry.

The envelope and precursor membrane (prM) proteins of dengue virus (DENV) are present on the surface of immature virions. During maturation, prM protein is cleaved by furin protease into pr peptide and membrane (M) protein. Although previous studies mainly focusing on the pr region have identified several residues important for DENV replication, the functional role of M protein, particularly the α-helical domain (MH), which is predicted to undergo a large conformational change during maturation, remains largely unknown. In this study, we investigated the role of nine highly conserved MH domain residues in the replication cycle of DENV by site-directed mutagenesis in a DENV1 prME expression construct and found that alanine substitutions introduced to four highly conserved residues at the C terminus and one at the N terminus of the MH domain greatly affect the production of both virus-like particles and replicon particles. Eight of the nine alanine mutants affected the entry of replicon particles, which correlated with the impairment in prM cleavage. Moreover, seven mutants were found to have reduced prM-E interaction at low pH, which may inhibit the formation of smooth immature particles and exposure of prM cleavage site during maturation, thus contributing to inefficient prM cleavage. Taken together, these results are the first report showing that highly conserved MH domain residues, located at 20-38 amino acids downstream from the prM cleavage site, can modulate the prM cleavage, maturation of particles, and virus entry. The highly conserved nature of these residues suggests potential targets of antiviral strategy.

Pareto-optimal phylogenetic tree reconciliation.

MOTIVATION: Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a reconciliation of minimum total cost. It is generally understood that reconciliations are sensitive to event costs, but little is understood about the relationship between event costs and solutions. Moreover, choosing appropriate event costs is a notoriously difficult problem. RESULTS: We address this problem by giving an efficient algorithm for computing Pareto-optimal sets of reconciliations, thus providing the first systematic method for understanding the relationship between event costs and reconciliations. This, in turn, results in new techniques for computing event support values and, for cophylogenetic analyses, performing robust statistical tests. We provide new software tools and demonstrate their use on a number of datasets from evolutionary genomic and cophylogenetic studies. AVAILABILITY AND IMPLEMENTATION: Our Python tools are freely available at www.cs.hmc.edu/∼hadas/xscape. .

High-avidity and potently neutralizing cross-reactive human monoclonal antibodies derived from secondary dengue virus infection.

The envelope (E) protein of dengue virus (DENV) is the major target of neutralizing antibodies (Abs) and vaccine development. Previous studies of human dengue-immune sera reported that a significant proportion of anti-E Abs, known as group-reactive (GR) Abs, were cross-reactive to all four DENV serotypes and to one or more other flaviviruses. Based on studies of mouse anti-E monoclonal antibodies (MAbs), GR MAbs were nonneutralizing or weakly neutralizing compared with type-specific MAbs; a GR response was thus not regarded as important for vaccine strategy. We investigated the epitopes, binding avidities, and neutralization potencies of 32 human GR anti-E MAbs. In addition to fusion loop (FL) residues in E protein domain II, human GR MAbs recognized an epitope involving both FL and bc loop residues in domain II. The neutralization potencies and binding avidities of GR MAbs derived from secondary DENV infection were stronger than those derived from primary infection. GR MAbs derived from primary DENV infection primarily blocked attachment, whereas those derived from secondary infection blocked DENV postattachment. Analysis of the repertoire of anti-E MAbs derived from patients with primary DENV infection revealed that the majority were GR, low-avidity, and weakly neutralizing MAbs, whereas those from secondary infection were primarily GR, high-avidity, and potently neutralizing MAbs. Our findings suggest that the weakly neutralizing GR anti-E Abs generated from primary DENV infection become potently neutralizing MAbs against the four serotypes after secondary infection. The observation that the dengue immune status of the host affects the quality of the cross-reactive Abs generated has implications for new strategies for DENV vaccination.

TreeFix: statistically informed gene tree error correction using species trees.

Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many important applications. However, sequence data alone often lack enough information to confidently support one gene tree topology over many competing alternatives. Here, we present a novel framework for combining sequence data and species tree information, and we describe an implementation of this framework in TreeFix, a new phylogenetic program for improving gene tree reconstructions. Given a gene tree (preferably computed using a maximum-likelihood phylogenetic program), TreeFix finds a "statistically equivalent" gene tree that minimizes a species tree-based cost function. We have applied TreeFix to 2 clades of 12 Drosophila and 16 fungal genomes, as well as to simulated phylogenies and show that it dramatically improves reconstructions compared with current state-of-the-art programs. Given its accuracy, speed, and simplicity, TreeFix should be applicable to a wide range of analyses and have many important implications for future investigations of gene evolution. The source code and a sample data set are available at http://compbio.mit.edu/treefix.

Early-onset Adjacent Vertebral Fractures after Balloon Kyphoplasty and SpineJack® Kyphoplasty for the Management of Single-level Thoracolumbar Vertebral Compression Fractures.

OBJECTIVE: To evaluate the risk factors contributing to early-onset adjacent level fractures (ALFs) occurring within 1 month following either balloon kyphoplasty (BKP) or SpineJack® kyphoplasty (SJ) for the treatment of thoracolumbar vertebral compression fractures (TLVCFs). MATERIALS AND METHODS: This retrospective analysis enrolled patients with single-level TLVCFs (T11-L2) who underwent either BKP or SJ between July 2013 and June 2019. We recorded the ALF occurrences within 1 month. Age, osteoporosis, severity and shape of TLVCFs, and surgical type were compared between patients with and without early-onset ALFs. RESULTS: Altogether, 106 TLVCF patients were enrolled, comprising 64 BKP and 42 SJ cases. We observed 19 early-onset ALFs, with 9 and 10 cases in the BKP and SJ, respectively. Patients with early-onset ALFs have significantly more severe TLCVFs (severe versus mild, 25% versus 0%, p = 0.055) and wedge-shaped TLVCFs (26.47% versus 2.63%, p = 0.002) and older age (81.05 versus 73.34 years, p < 0.001) and kyphoplasty performed within 1 month are risk factors of early-onset ALFs (26.92% versus 9.26%, p = 0.018). Univariable analysis showed that kyphoplasty timing within 1 month (odds ratio [OR]: 0.193, p = 0.008), wedge-shaped TLVCFs (OR: 5.358, p = 0.036), and advanced age (OR: 1.119, p = 0.001) are significant risk factors of early-onset ALFs. CONCLUSIONS: The occurrence rate of early-onset ALFs between BKP or SJ techniques in treating TLVCFs does not differ. Preoperative wedge-shaped TLVCFs, advanced age, and early treatment within 1 month are the risk factors of early-onset ALFs following kyphoplasty for TLVCFs.

Analysis of short-term ventilation weaning for patients in spontaneous supratentorial intracranial hemorrhage.

Prolonged ventilation is a complication of spontaneous supratentorial hemorrhage patients, but the predictive relationship with successful weaning in this patient cohort is not understood. Here, we evaluate the incidence and factors of ventilation weaning in case of spontaneous supratentorial hemorrhage. We retrospectively studied data from 166 patients in the same hospital from January 2015 to March 2021 and analyzed factors for ventilation weaning. The clinical data recorded included patient age, gender, timing of operation, initial Glasgow Coma Scale (GCS), Intracranial hemorrhage (ICH) score, alcohol drinking, cigarette smoking, medical comorbidity, and the blood data. Predictors of patient outcomes were determined by the Student t test, chi-square test, and logistic regression. We recruited and followed 166 patients who received operation for spontaneous supratentorial hemorrhage with cerebral herniation. The group of successful weaning had 84 patients and the group of weaning failed had 82 patients. The patient's age, type of operation, GCS on admission to the Intensive care unit (ICU), GCS at discharge from the ICU, medical comorbidity was significantly associated with successful weaning, according to Student t test and the chi-square test. According to our findings, patients with stereotaxic surgery, less history of cardiovascular or prior cerebral infarction, GCS >8 before admission to the hospital for craniotomy, and a blood albumin value >3.5 g/dL have a higher chance of being successfully weaned off the ventilator within 14 days.

Evolution at the subgene level: domain rearrangements in the Drosophila phylogeny.

Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, loss, and sometimes, horizontal transfer. However, within the Drosophila clade, we find domain rearrangements occur in 35.9% of gene families, and thus, any comprehensive study of gene evolution in these species will need to account for such events. Here, we present a new computational model and algorithm for reconstructing gene evolution at the domain level. We develop a method for detecting homologous domains between genes and present a phylogenetic algorithm for reconstructing maximum parsimony evolutionary histories that include domain generation, duplication, loss, merge (fusion), and split (fission) events. Using this method, we find that genes involved in fusion and fission are enriched in signaling and development, suggesting that domain rearrangements and reuse may be crucial in these processes. We also find that fusion is more abundant than fission, and that fusion and fission events occur predominantly alongside duplication, with 92.5% and 34.3% of fusion and fission events retaining ancestral architectures in the duplicated copies. We provide a catalog of ∼9,000 genes that undergo domain rearrangement across nine sequenced species, along with possible mechanisms for their formation. These results dramatically expand on evolution at the subgene level and offer several insights into how new genes and functions arise between species.

virDTL: Viral Recombination Analysis Through Phylogenetic Reconciliation and Its Application to Sarbecoviruses and SARS-CoV-2.

An accurate understanding of the evolutionary history of rapidly-evolving viruses like SARS-CoV-2, responsible for the COVID-19 pandemic, is crucial to tracking and preventing the spread of emerging pathogens. However, viruses undergo frequent recombination, which makes it difficult to trace their evolutionary history using traditional phylogenetic methods. In this study, we present a phylogenetic workflow, virDTL, for analyzing viral evolution in the presence of recombination. Our approach leverages reconciliation methods developed for inferring horizontal gene transfer in prokaryotes and, compared to existing tools, is uniquely able to identify ancestral recombinations while accounting for several sources of inference uncertainty, including in the construction of a strain tree, estimation and rooting of gene family trees, and reconciliation itself. We apply this workflow to the Sarbecovirus subgenus and demonstrate how a principled analysis of predicted recombination gives insight into the evolution of SARS-CoV-2. In addition to providing confirming evidence for the horseshoe bat as its zoonotic origin, we identify several ancestral recombination events that merit further study.

Corrigendum: Case report: Ruptured internal carotid artery fusiform aneurysm mimicking pituitary apoplexy after stereotactic radiosurgery.

[This corrects the article DOI: 10.3389/fneur.2023.1219372.].

Topping-off Surgery Versus Transforaminal Lumbar Intervertebral Fusion for Combined One-level Spondylolisthesis and Adjacent Lumbar Disc Herniation: A Comparative Study of Clinical Efficacy and Radiographic Outcomes With a Two-year Follow-up.

BACKGROUND/AIM: To investigate the radiographic and clinical outcomes in patients diagnosed with multilevel lumbar spine degeneration, undergoing hybrid stabilization with an interspinous device (IPD) adjacent to spine fusion, as compared with those experiencing three-segment or two-segment transforaminal lumbar interbody fusion (TLIF) via minimally invasive surgery (MIS). PATIENTS AND METHODS: Between 2015-2017, 51 consecutive patients who received three-segment TLIF, interspinous dynamic stabilization combined with two-segment TLIF (topping-off surgery), and two-segment TLIF coupled with adjacent level lumbar discectomy (two-segment TLIF+discectomy) were studied. These three operative procedures were performed by one neurosurgeon at the same hospital. Post-operative analysis of the two-year analysis was conducted by another neurosurgeon. Radiographic and clinical outcomes were compared among the three groups. RESULTS: Duration of surgery was significantly shorter in the topping-off surgery and TLIF+discectomy compared to three-segment TLIF group. Although there was no difference in hospital stay among the three groups, visual analogue scale (VAS) and Oswestry disability index (ODI) were less in the topping-off group than in the three-segment TLIF or two-segment TLIF+discectomy groups after one week and three months follow-up, respectively. Disc high index (DHI) in adjacent segment decreased from before the operation to two years follow-up postoperatively in the two-segment TLIF+discectomy group. In contrast, DHI in the segment adjacent to spondylolisthesis increased from before the operation to last follow-up post-operatively in the three-segment TLIF group. Compared with the two-segment TLIF+discectomy group, the topping-off group showed higher foramen high index at the IPD level. While there was no difference in segment range of motion among the three groups, the topping-off group showed preserved total range of motion at a two-year follow-up, as compared with the three-segment TLIF group. CONCLUSION: Under strict indications, topping-off surgery is an acceptable alternative to fusion surgery for spondylolisthesis combined with adjacent disc degeneration.