A safety framework for flow decomposition problems via integer linear programming.

MOTIVATION: Many important problems in Bioinformatics (e.g. assembly or multiassembly) admit multiple solutions, while the final objective is to report only one. A common approach to deal with this uncertainty is finding "safe" partial solutions (e.g. contigs) which are common to all solutions. Previous research on safety has focused on polynomially time solvable problems, whereas many successful and natural models are NP-hard to solve, leaving a lack of "safety tools" for such problems. We propose the first method for computing all safe solutions for an NP-hard problem, "minimum flow decomposition" (MFD). We obtain our results by developing a "safety test" for paths based on a general integer linear programming (ILP) formulation. Moreover, we provide implementations with practical optimizations aimed to reduce the total ILP time, the most efficient of these being based on a recursive group-testing procedure. RESULTS: Experimental results on transcriptome datasets show that all safe paths for MFDs correctly recover up to 90% of the full RNA transcripts, which is at least 25% more than previously known safe paths. Moreover, despite the NP-hardness of the problem, we can report all safe paths for 99.8% of the over 27 000 non-trivial graphs of this dataset in only 1.5 h. Our results suggest that, on perfect data, there is less ambiguity than thought in the notoriously hard RNA assembly problem. AVAILABILITY AND IMPLEMENTATION: https://github.com/algbio/mfd-safety.

Chaining for accurate alignment of erroneous long reads to acyclic variation graphs.

MOTIVATION: Aligning reads to a variation graph is a standard task in pangenomics, with downstream applications such as improving variant calling. While the vg toolkit [Garrison et al. (Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol 2018;36:875-9)] is a popular aligner of short reads, GraphAligner [Rautiainen and Marschall (GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biol 2020;21:253-28)] is the state-of-the-art aligner of erroneous long reads. GraphAligner works by finding candidate read occurrences based on individually extending the best seeds of the read in the variation graph. However, a more principled approach recognized in the community is to co-linearly chain multiple seeds. RESULTS: We present a new algorithm to co-linearly chain a set of seeds in a string labeled acyclic graph, together with the first efficient implementation of such a co-linear chaining algorithm into a new aligner of erroneous long reads to acyclic variation graphs, GraphChainer. We run experiments aligning real and simulated PacBio CLR reads with average error rates 15% and 5%. Compared to GraphAligner, GraphChainer aligns 12-17% more reads, and 21-28% more total read length, on real PacBio CLR reads from human chromosomes 1, 22, and the whole human pangenome. On both simulated and real data, GraphChainer aligns between 95% and 99% of all reads, and of total read length. We also show that minigraph [Li et al. (The design and construction of reference pangenome graphs with minigraph. Genome Biol 2020;21:265-19.)] and minichain [Chandra and Jain (Sequence to graph alignment using gap-sensitive co-linear chaining. In: Proceedings of the 27th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2023). Springer, 2023, 58-73.)] obtain an accuracy of <60% on this setting. AVAILABILITY AND IMPLEMENTATION: GraphChainer is freely available at https://github.com/algbio/GraphChainer. The datasets and evaluation pipeline can be reached from the previous address.

CRISPR/Cas9 editing in conditionally immortalized HoxB8 cells for studying gene regulation in mouse dendritic cells.

HoxB8 multipotent progenitors (MPP) are obtained by expression of the estrogen receptor hormone binding domain (ERHBD) HoxB8 fusion gene in mouse BM cells. HoxB8 MPP generate (i) the full complement of DC subsets (cDC1, cDC2, and pDC) in vitro and in vivo and (ii) allow CRISPR/Cas9-mediated gene editing, for example, generating homozygous deletions in cis-acting DNA elements at high precision, and (iii) efficient gene repression by dCas9-KRAB for studying gene regulation in DC differentiation.

Fisher and Shannon Functionals for Hyperbolic Diffusion.

The complexity measure for the distribution in space-time of a finite-velocity diffusion process is calculated. Numerical results are presented for the calculation of Fisher's information, Shannon's entropy, and the Cramér-Rao inequality, all of which are associated with a positively normalized solution to the telegrapher's equation. In the framework of hyperbolic diffusion, the non-local Fisher's information with the x-parameter is related to the local Fisher's information with the t-parameter. A perturbation theory is presented to calculate Shannon's entropy of the telegrapher's equation at long times, as well as a toy model to describe the system as an attenuated wave in the ballistic regime (short times).

Tenomodulin regulates matrix remodeling of mouse tendon stem/progenitor cells in an ex vivo collagen I gel model.

Tenomodulin (Tnmd) is predominantly expressed in tendon and ligament tissues. Loss of Tnmd in mice leads to a profound phenotype in vitro, characterized by reduced self-renewal but increased senescence of mouse tendon stem/progenitor cells (mTSPCs), as well as in vivo, by significantly impaired early tendon healing. Interestingly, injuried Achilles tendons from Tnmd-deficient mice showed inferior tendon repair, which was characterized by less contracted fibrovascular scars with disorganized matrix composition in comparison to wild type (WT) mice at day 8 after injury. To better understand Tnmd role in tendon repair, here we implemented an ex vivo three-dimensional (3D) collagen gel model and investigated whether Tnmd knockout affects the collagen contraction of mTSPCs. TSPCs were isolated from WT and Tnmd knockout (KO) tendons at 6, 9, 12, and 18 months of age. Adhesion assay demonstrated that loss of Tnmd in mTSPCs resulted in reduced adhesion to collagen type I. Quantitative time-dependent analysis revealed that Tnmd-deficient mTSPCs of all ages have significantly reduced capacity to contract collagen matrix in comparison to WT cells. Furthermore, 18 months old mTSPCs of both genotypes showed lower collagen contractility than cells obtained from 6, 9, and 12 months old animals, demonstrating an overall effect of organismal aging on matrix remodeling. Nevertheless, both cell types had a similar survival rate for the 5 days of cultivation within the gels. Lastly, quantitative PCR for 48 different genes revealed that the knockout of Tnmd majorly affected the gene expression profile of mTSPCs, as several transcription factors, tendon matrix, collagen cross-linking, and lineage maker genes were down-regulated. Taken together, our results clearly demonstrated that loss of Tnmd in mTSPCs led to profoundly altered gene expression profile, insufficient adhesion to collagen type I, and impaired ability to contract the extracellular matrix.

Biodegradation of benzo[α]pyrene, toluene, and formaldehyde from the gas phase by a consortium of Rhodococcus erythropolis and Fusarium solani.

Polycyclic aromatic hydrocarbons (PAHs) and volatile organic compounds (VOCs) are important indoor contaminants. Their hydrophobic nature hinders the possibility of biological abatement using biofiltration. Our aim was to establish whether the use of a consortium of Fusarium solani and Rhodococcus erythropolis shows an improved performance (in terms of mineralization rate and extent) towards the degradation of formaldehyde, as a slightly polar VOC; toluene, as hydrophobic VOC; and benzo[α]pyrene (BaP) as PAH at low concentrations compared to a single-species biofilm in serum bottles with vermiculite as solid support to mimic a biofilter and to relate the possible improvements with the surface hydrophobicity and partition coefficient of the biomass at three different temperatures. Results showed that the hydrophobicity of the surface of the biofilms was affected by the hydrophobicity of the carbon source in F. solani but it did not change in R. erythropolis. Similarly, the partition coefficients of toluene and BaP in F. solani biomass (both as pure culture and consortium) show a reduction of up to 38 times compared to its value in water, whereas this reduction was only 1.5 times in presence of R. erythropolis. Despite that increments in the accumulated CO2 and its production rate were found when F. solani or the consortium was used, the mineralization extent of toluene was below 25%. Regarding BaP degradation, the higher CO2 production rates and percent yields were obtained when a consortium of F. solani and R. erythropolis was used, despite a pure culture of R. erythropolis exhibits poor mineralization of BaP.

Oxidation of methane by Methylomicrobium album and Methylocystis sp. in the presence of H2S and NH 3.

Oxidation of methane by methanotrophs, Methylomicrobium album and Methylocystis sp., was measured at several initial concentrations of H2S and NH3 in the headspace of stoppered flasks, at the same initial concentration of methane as sole carbon and energy source: 15 % (v/v). No effect was observed at 0.01 % (v/v) H2S and 0.025 % (v/v) NH3 in gas phase but over 0.05 and 0.025 % (v/v), respectively, they inhibited the oxidation of methane. The effect of H2S was stronger in Methylocystis sp. and both microorganisms were similarly affected by NH3. Depending on their concentrations in gas phase, H2S and NH3 can thus affect the rate of oxidation of methane and biomass growth of both methanotrophs.

Mechanical circulatory support in cardiogenic shock following an acute myocardial infarction: a systematic review.

The significance of the utilization of mechanical circulatory support following a myocardial infarction is not well defined. We present a systematic review of this treatment alternative and suggest guidelines to be considered in the treatment of these patients.

Finding maximal exact matches in graphs.

BACKGROUND: We study the problem of finding maximal exact matches (MEMs) between a query string Q and a labeled graph G. MEMs are an important class of seeds, often used in seed-chain-extend type of practical alignment methods because of their strong connections to classical metrics. A principled way to speed up chaining is to limit the number of MEMs by considering only MEMs of length at least κ ( κ -MEMs). However, on arbitrary input graphs, the problem of finding MEMs cannot be solved in truly sub-quadratic time under SETH (Equi et al., TALG 2023) even on acyclic graphs. RESULTS: In this paper we show an O ( n · L · d L - 1 + m + M κ , L ) -time algorithm finding all κ -MEMs between Q and G spanning exactly L nodes in G, where n is the total length of node labels, d is the maximum degree of a node in G, m = | Q | , and M κ , L is the number of output MEMs. We use this algorithm to develop a κ -MEM finding solution on indexable Elastic Founder Graphs (Equi et al., Algorithmica 2022) running in time O ( n H 2 + m + M κ ) , where H is the maximum number of nodes in a block, and M κ is the total number of κ -MEMs. Our results generalize to the analysis of multiple query strings (MEMs between G and any of the strings). Additionally, we provide some experimental results showing that the number of graph MEMs is an order of magnitude smaller than the number of string MEMs of the corresponding concatenated collection. CONCLUSIONS: We show that seed-chain-extend type of alignment methods can be implemented on top of indexable Elastic Founder Graphs by providing an efficient way to produce the seeds between a set of queries and the graph. The code is available in https://github.com/algbio/efg-mems .

Intermittent Kac's flights and the generalized telegrapher's equation.

A generalized one-dimensional telegrapher equation associated with an intermittent change of sign in the velocity of a Kac's flight has been proposed. To solve this random differential equation, we used the enlarged master equation approach to obtain the exact differential equation for the evolution of a normalized positive distribution. This distribution is associated with a generalized finite-velocity diffusionlike process. We studied the robustness of the ballistic regime, the cutoff of its domain, and the time-dependent Gaussian convergence. The second moment for the evolution of the profile has been studied as a function of non-Poisson statistics (possibly intermittent) for the time intervals Δ_{ij} in the Kac's flight. Numerical results for the evolution of sharp and wide initial profiles have also been presented. In addition, for comparison with a non-Gaussian process at all times, we have revisited the non-Markov Poisson's flight with exponential pulses. A theory for generalized random flights with intermittent stochastic velocity and in the presence of a force is also presented, and the stationary distribution for two classes of potential has been obtained.

Penetration of waves in global stochastic conducting media.

The attenuation in the propagation of a plane wave in conducting media has been studied. We analyzed a wave motion suffering dissipation by the Joule effect in its propagation in a medium with global disorder. We solved the stochastic telegrapher's equation in the Fourier-Laplace representation allowing us to find the space penetration length of a plane wave in a complex conducting medium. Considering fluctuations in the loss of energy, we found a critical value k_{c} for Fourier's modes, thus if |k|

Localization of plane waves in the stochastic telegrapher's equation.

From the exact solution of the stochastic telegrapher's equation, Fourier plane-wave-like modes are introduced. Then the time evolution of the plane-wave modes are analyzed when the absorption of energy in the telegrapher's equation has strong time fluctuations. We demonstrate that fluctuations in the loss of energy introduce a localized gap with a size that depends on the correlation timescale of the fluctuations. We prove that for a large time correlation the gap is strongly reduced, which means that there is delocalization in the plane-wave modes with respect to the plane waves in the ordinary telegrapher's equation. This result is of relevance in the study of the transport of electromagnetic waves in a conducting medium, and sheds light on the functional role of the fluctuations in the loss of energy in the telegrapher's dynamics.

Stochastic telegrapher's approach for solving the random Boltzmann-Lorentz gas.

The 1D random Boltzmann-Lorentz equation has been connected with a set of stochastic hyperbolic equations. Therefore, the study of the Boltzmann-Lorentz gas with disordered scattering centers has been transformed into the analysis of a set of stochastic telegrapher's equations. For global binary disorder (Markovian and non-Markovian) exact analytical results for the second moment, the velocity autocorrelation function, and the self-diffusion coefficient are presented. We have demonstrated that time-fluctuations in the lost of energy in the telegrapher's equation, can delay the entrance to the diffusive regime, this issue has been characterized by a timescale t_{c} which is a function of disorder parameters. Indeed, producing a longer ballistic dynamics in the transport process. In addition, fluctuations of the space probability distribution have been studied, showing that the mean value of a stochastic telegrapher's Fourier mode is a good statistical object to characterize the solution of the random Boltzmann-Lorentz gas. In a different context, the stochastic telegrapher's equation has also been related to the run-and-tumble model in Biophysics. Then a discussion devoted to the potential applications when swimmers' speed and tumbling rate have time fluctuations has been pointed out.

A retrospective observational study of biomarker levels and severity assessment in pediatric community-acquired pneumonia.

METHODS: A retrospective chart review was conducted on children (aged 60 days to 18 years) diagnosed with CAP, and admitted to a regional, tertiary hospital (Charleston, WV, USA) for 3 years (2015-2018). Patients were stratified into 2 severity cohorts, mild (no ICU care), and moderate/severe (required ICU care). Biomarker values were then compared between the severity cohorts and area under the curve (AUC), and cut-off values and performance characteristics were calculated. RESULTS: A total of 108 patients met inclusion criteria with 46% having moderate/severe CAP. Elevated levels of CRP (51.7 mg/L in mild vs. 104.8 mg/L in moderate/severe, P = .003, PCT (0.29 ng/ml in mild vs. 4.02 ng/mL in moderate/severe, P = .001) and band counts (8% in mild vs. 15% moderate/severe, P = .009) were associated with increased pneumonia severity. In predicting moderate/severe CAP, PCT had the highest AUC of 0.77 (P = .001) followed by bands AUC of 0.69 (P = .009) and CRP AUC of 0.67 (P = .003). Cut-off for PCT of 0.55 ng/mL had a sensitivity of 83% and a specificity of 65%. Cut-off level of 53.1 mg/L for CRP had a sensitivity of 79% and specificity of 52%. Cut off level of 12.5% bands had a sensitivity of 61% and specificity of 71%. In a multivariable model controlled for patient demographics and other biomarker levels, only PCT levels significantly predicted moderate/severe CAP (adjusted odds ratio: 1.40 [95% CI, 1.14-1.73], P = .002). CONCLUSION: Biomarkers, in particular PCT, obtained early in hospitalization may perform as possible predictors for CAP severity in children and be beneficial in guiding CAP management. However, biomarkers in pneumonia should not drive severity assessment or patient management independent of clinical presentation.

Improving RNA Assembly via Safety and Completeness in Flow Decompositions.

Decomposing a network flow into weighted paths is a problem with numerous applications, ranging from networking, transportation planning, to bioinformatics. In some applications we look for a decomposition that is optimal with respect to some property, such as the number of paths used, robustness to edge deletion, or length of the longest path. However, in many bioinformatic applications, we seek a specific decomposition where the paths correspond to some underlying data that generated the flow. In these cases, no optimization criteria guarantee the identification of the correct decomposition. Therefore, we propose to instead report the safe paths, which are subpaths of at least one path in every flow decomposition. In this work, we give the first local characterization of safe paths for flow decompositions in directed acyclic graphs, leading to a practical algorithm for finding the complete set of safe paths. In addition, we evaluate our algorithm on RNA transcript data sets against a trivial safe algorithm (extended unitigs), the recently proposed safe paths for path covers (TCBB 2021) and the popular heuristic greedy-width. On the one hand, we found that besides maintaining perfect precision, our safe and complete algorithm reports a significantly higher coverage (≈50% more) compared with the other safe algorithms. On the other hand, the greedy-width algorithm although reporting a better coverage, it also reports a significantly lower precision on complex graphs (for genes expressing a large number of transcripts). Overall, our safe and complete algorithm outperforms (by ≈20%) greedy-width on a unified metric (F-score) considering both coverage and precision when the evaluated data set has a significant number of complex graphs. Moreover, it also has a superior time (4-5×) and space performance (1.2-2.2×), resulting in a better and more practical approach for bioinformatic applications of flow decomposition.

Safety in Multi-Assembly via Paths Appearing in All Path Covers of a DAG.

A multi-assembly problem asks to reconstruct multiple genomic sequences from mixed reads sequenced from all of them. Standard formulations of such problems model a solution as a path cover in a directed acyclic graph, namely a set of paths that together cover all vertices of the graph. Since multi-assembly problems admit multiple solutions in practice, we consider an approach commonly used in standard genome assembly: output only partial solutions (contigs, or safe paths), that appear in all path cover solutions. We study constrained path covers, a restriction on the path cover solution that incorporate practical constraints arising in multi-assembly problems. We give efficient algorithms finding all maximal safe paths for constrained path covers. We compute the safe paths of splicing graphs constructed from transcript annotations of different species. Our algorithms run in less than 15 seconds per species and report RNA contigs that are over 99% precise and are up to 8 times longer than unitigs. Moreover, RNA contigs cover over 70% of the transcripts and their coding sequences in most cases. With their increased length to unitigs, high precision, and fast construction time, maximal safe paths can provide a better base set of sequences for transcript assembly programs.

Random Leslie matrices in population dynamics.

We generalize the concept of the population growth rate when a Leslie matrix has random elements (correlated or not), i.e., characterizing the disorder in the vital parameters. In general, we present a perturbative formalism to deal with linear non-negative random matrix difference equations, then the non-trivial effective eigenvalue of which defines the long-time asymptotic dynamics of the mean-value population vector state is presented as the effective growth rate. This effective eigenvalue is calculated from the smallest positive root of a secular polynomial. Analytical (exact and perturbative calculations) results are presented for several models of disorder. In particular, a 3 × 3 numerical example is applied to study the effective growth rate characterizing the long-time dynamics of a biological population model. The present analysis is a perturbative method for finding the effective growth rate in cases when the vital parameters may have negative covariances across populations.

Tenomodulin knockout mice exhibit worse late healing outcomes with augmented trauma-induced heterotopic ossification of Achilles tendon.

Heterotopic ossification (HO) represents a common problem after tendon injury with no effective treatment yet being developed. Tenomodulin (Tnmd), the best-known mature marker for tendon lineage cells, has important effects in tendon tissue aging and function. We have reported that loss of Tnmd leads to inferior early tendon repair characterized by fibrovascular scaring and therefore hypothesized that its lack will persistently cause deficient repair during later stages. Tnmd knockout (Tnmd-/-) and wild-type (WT) animals were subjected to complete Achilles tendon surgical transection followed by end-to-end suture. Lineage tracing revealed a reduction in tendon-lineage cells marked by ScleraxisGFP, but an increase in alpha smooth muscle actin myofibroblasts in Tnmd-/- tendon scars. At the proliferative stage, more pro-inflammatory M1 macrophages and larger collagen II cartilaginous template were detected in this group. At the remodeling stage, histological scoring revealed lower repair quality in the injured Tnmd-/- tendons, which was coupled with higher HO quantified by micro-CT. Tendon biomechanical properties were compromised in both groups upon injury, however we identified an abnormal stiffening of non-injured Tnmd-/- tendons, which possessed higher static and dynamic E-moduli. Pathologically thicker and abnormally shaped collagen fibrils were observed by TEM in Tnmd-/- tendons and this, together with augmented HO, resulted in diminished running capacity of Tnmd-/- mice. These novel findings demonstrate that Tnmd plays a protecting role against trauma-induced endochondral HO and can inspire the generation of novel therapeutics to accelerate repair.

Tenomodulin and Chondromodulin-1 Are Both Required to Maintain Biomechanical Function and Prevent Intervertebral Disc Degeneration.

OBJECTIVE: The underlying mechanisms and molecular factors influencing intervertebral disc (IVD) homeostasis and degeneration remain clinically relevant. Tenomodulin (Tnmd) and chondromodulin (Chm1) are antiangiogenic transmembrane glycoproteins, with cleavable C-terminus, expressed by IVD cells that are implicated in the onset of degenerative processes. We evaluate the organ-level biomechanical impact of knocking out Tnmd alone, and Tnmd and Chm1, simultaneously. DESIGN: Caudal (c5-8) and lumbar vertebrae (L1-4) of skeletally mature male and female 9-month-old wildtype (WT), Tnmd knockout (Tnmd-/-), and Tnmd/Chm1 double knockout (Tnmd-/-/Chm-/-) mice were used (n = 9-13 per group). Disc height index (DHI), histomorphological changes, and axial, torsional, creep, and failure biomechanical properties were evaluated. Differences were assessed by one-way ANOVA with post hoc Bonferroni-corrected comparisons (P < 0.05). RESULTS: Tnmd-/-/Chm1-/- IVDs displayed increased DHI and histomorphological scores that indicated increased IVD degeneration compared to the WT and Tnmd-/- groups. Double knockout IVDs required significantly less torque and energy to initiate torsional failure. Creep parameters were comparable between all groups, except for the slow time constant, which indicated faster outward fluid flow. Tnmd-/- IVDs lost fluid faster than the WT group, and this effect was amplified in the double knockout IVDs. CONCLUSION: Knocking out Tnmd and Chm1 affects IVD fluid flow and organ-level biomechanical function and therefore may play a role in contributing to IVD degeneration. Larger effects of the Tnmd and Chm1 double knockout mice compared to the Tnmd single mutant suggest that Chm1 may play a compensatory role in the Tnmd single mutant IVDs.

Emergence of stationary multimodality under two-timescaled dichotomic noise.

We study a linear Langevin dynamics driven by an additive non-Markovian symmetrical dichotomic noise. It is shown that when the statistics of the time intervals between noise transitions is characterized by two well differentiated timescales, the stationary distribution may develop multimodality (bi- and trimodality). The underlying effects that lead to a probability concentration in different points include intermittence and also a dynamical locking of realizations. Our results are supported by numerical simulations as well as by an exact treatment obtained from a Markovian embedding of the full dynamics, which leads to a third-order differential equation for the stationary distribution.