A finite-element model of mechanosensation by a Pacinian corpuscle cluster in human skin

The Pacinian corpuscle (PC) is the cutaneous mechanoreceptor responsible for sensation of high-frequency (20–1000 Hz) vibrations. PCs lie deep within the skin, often in multicorpuscle clusters with overlapping receptive fields. We developed a finite-element mechanical model of one or two PCs embedded within human skin, coupled to a multiphysics PC model to simulate action potentials elicited by each PC. A vibration was applied to the skin surface, and the resulting mechanical signal was analyzed using two metrics: the deformation amplitude ratio (\({\rho }_{\mathrm{1S}} \), \({\rho }_{\mathrm{2S}} )\) and the phase shift of the vibration (\({\delta }_{\mathrm{S}1}^{\mathrm{mech}} \), \({\delta }_{\mathrm{S}2}^{\mathrm{mech}} )\) between the stimulus and the PC. Our results showed that the amplitude attenuation and phase shift at a PC increased with distance from the stimulus to the PC. Differences in amplitude (\(\rho _{12} )\) and phase shift (\({\delta }_{12}^{\mathrm{mech}} )\) between the two PCs in simulated clusters directly affected the interspike interval between the action potentials elicited by each PC (\({\delta }_{12}^{\mathrm{spike}} )\). While \({\delta }_{12}^{\mathrm{mech}} \) had a linear relationship with \({\delta }_{12}^{\mathrm{spike}} \), \(\rho _{12} \)’s effect on \({\delta }_{12}^{\mathrm{spike}} \) was greater for lower values of \(\rho _{12} \). In our simulations, the separation between PCs and the distance of each PC from the stimulus location resulted in differences in amplitude and phase shift at each PC that caused \({\delta }_{12}^{\mathrm{spike}} \) to vary with PC location. Our results suggest that PCs within a cluster receive different mechanical stimuli which may enhance source localization of vibrotactile stimuli, drawing parallels to sound localization in binaural hearing.     

Towards the prediction of flow-induced shear stress distributions experienced by breast cancer cells in the lymphatics

Tumour metastasis in the lymphatics is a crucial step in the progression of breast cancer. The dynamics by which breast cancer cells (BCCs) travel in the lymphatics remains poorly understood. The goal of this work is to develop a model capable of predicting the shear stresses metastasising BCCs experience using numerical and experimental techniques. This paper models the fluidic transport of large particles (\(\eta =d_{\mathrm{p}}/W=0.1-0.4\) where \(d_{\mathrm{p}}\) is the particle diameter and W is the channel width) subjected to lymphatic flow conditions (\({ Re}=0.04\)), in a \(100\times 100\,\upmu \hbox {m}\) microchannel. The feasibility of using the dynamic fluid body interaction (DFBI) method to predict particle motion was assessed, and particle tracking experiments were performed. The experiments found that particle translational velocity decreased from the undisturbed fluid velocity with increasing particle size (5–14% velocity lag for \(\eta =0.1-0.3\)). DFBI simulations were found to better predict particle behaviour than theoretical predictions; however, mesh restrictions in the near-wall region (\(0.2\,\mathrm{W}>y>0.8\,\mathrm{W}\)) result in computationally expensive models. The simulations were in good agreement with the experiments (\(<12\%\) difference) across the channel (\(0.2\,\mathrm{W}\le y\le 0.8\,\mathrm{W}\)), with differences up to 25% in the near-wall region. Particles experience a range of shear stresses (0.002–0.12 Pa) and spatial shear gradients (\(0.004-0.137\,\hbox {Pa}/\upmu \hbox {m}\)) depending on their size and radial position. The predicted shear gradients are far in excess of values associated with BCC apoptosis (\(0.004-0.023\,\hbox {Pa}/\upmu \hbox {m}\)). Increasing our understanding of the shear stress magnitudes and gradients experienced by BCCs could be leveraged to elucidate whether a particular BCC size or location exists that encourages metastasis within the lymphatics.     

Aortic wave intensity analysis of ventricular-vascular interaction during incremental dobutamine infusion in adult sheep

This study undertook a detailed examination of the ventricular-vascular interaction of the predominant beta-adrenergic agonist dobutamine using wave intensity analysis. Eight anesthetized open-chest ewes were instrumented with an aortic micromanometer to measure central aortic blood pressure (P) and an ultrasonic flow probe to obtain ascending aortic blood velocity (U). Hemodynamics were recorded during incremental dobutamine infusion (0.5, 1, 2.5, 5, 7.5, and 10 microg.kg(-1).min(-1)). Wave intensity (dI(W)) was calculated as the product of the rates of change of P and U with customized software using ensemble-averaged signals. Forward and backward components of dI(W), P, and U were determined after calculation of wave speed. As well as the typical initial forward compression wave (FCW), midsystolic backward compression wave (BCW), and late-systolic forward expansion wave (FEW(es)), two minor and previously unheralded waves were also detectable in the wave intensity profile at baseline. The first was an early systolic backward expansion wave (BEW), which reduced P but increased peak U. The second was a mid-systolic forward expansion wave (FEW(ms)), which reduced P and U. During dobutamine infusion FCW dI(W) increased 18-fold (P < 0.001), but BCW dI(W) rose 12-fold (P < 0.001) while FEW(es) dI(W) fell by 70% (P < 0.001). However, the latter changes were accompanied by a 44-fold increase in BEW dI(W) (P = 0.005) that augmented the initial aortic forward flow and a >100-fold rise in FEW(ms) dI(W) (P < 0.001) that produced earlier and enhanced aortic blood deceleration. These findings provide new insights into the ventricular-vascular interaction of dobutamine.     

Simultaneous pulmonary trunk and pulmonary arterial wave intensity analysis in fetal lambs: evidence for cyclical, midsystolic pulmonary vasoconstriction

The physiological basis of a characteristically low blood flow to the fetal lungs is incompletely understood. To determine the potential role of pulmonary vascular interaction in this phenomenon, simultaneous wave intensity analysis (WIA) was performed in the pulmonary trunk (PT) and left pulmonary artery (LPA) of 10 anesthetized late-gestation fetal sheep instrumented with PT and LPA micromanometer catheters to measure pressure (P) and transit-time flow probes to obtain blood velocity (U). Studies were performed at rest and during brief complete occlusion of the ductus arteriosus to augment pulmonary vasoconstriction (n = 4) or main pulmonary artery to abolish wave transmission from the lungs (n = 3). Wave intensity (dI(W)) was calculated as the product of the P and U rates of change. Forward and backward components of dI(W) were determined after calculation of wave speed. PT and LPA WIA displayed an early systolic forward compression wave (FCW(is)) increasing P and U, and a late systolic forward expansion wave decreasing P and U. However, a marked midsystolic fall in LPA U to near-zero was related to an extremely prominent midsystolic backward compression wave (BCW(ms)) that arose approximately 5 cm distal to the LPA, was threefold larger than the PT BCW(ms) (P < 0.001), of similar size to FCW(is) at rest (P > 0.6), larger than FCW(is) following ductal occlusion (P < 0.05) and abolished after main pulmonary artery occlusion. These findings suggest that the absence of pulmonary arterial midsystolic forward flow which accompanies a low fetal lung blood flow is due to a BCW(ms) generated in part by cyclical vasoconstriction within the pulmonary microcirculation.     

Toward translating near-infrared spectroscopy oxygen saturation data for the non-invasive prediction of spatial and temporal hemodynamics during exercise

Image-based computational fluid dynamics (CFD) studies conducted at rest have shown that atherosclerotic plaque in the thoracic aorta (TA) correlates with adverse wall shear stress (WSS), but there is a paucity of such data under elevated flow conditions. We developed a pedaling exercise protocol to obtain phase contrast magnetic resonance imaging (PC-MRI) blood flow measurements in the TA and brachiocephalic arteries during three-tiered supine pedaling at 130, 150, and 170 % of resting heart rate (HR), and relate these measurements to non-invasive tissue oxygen saturation \((\hbox {StO}_{2})\) acquired by near-infrared spectroscopy (NIRS) while conducting the same protocol. Local quantification of WSS indices by CFD revealed low time-averaged WSS on the outer curvature of the ascending aorta and the inner curvature of the descending aorta (dAo) that progressively increased with exercise, but that remained low on the anterior surface of brachiocephalic arteries. High oscillatory WSS observed on the inner curvature of the aorta persisted during exercise as well. Results suggest locally continuous exposure to potentially deleterious indices of WSS despite benefits of exercise. Linear relationships between flow distributions and tissue oxygen extraction calculated from \(\hbox {StO}_{2}\) were found between the left common carotid versus cerebral tissue \((r^{2}=0.96)\) and the dAo versus leg tissue \((r^{2}=0.87)\). A resulting six-step procedure is presented to use NIRS data as a surrogate for exercise PC-MRI when setting boundary conditions for future CFD studies of the TA under simulated exercise conditions. Relationships and ensemble-averaged PC-MRI inflow waveforms are provided in an online repository for this purpose.     

A Mathematical Model Supports a Key Role for Ae4 (Slc4a9) in Salivary Gland Secretion

We develop a mathematical model of a salivary gland acinar cell with the objective of investigating the role of two \(\mathrm{Cl}^-/\mathrm{HCO}_3^-\) exchangers from the solute carrier family 4 (Slc4), Ae2 (Slc4a2) and Ae4 (Slc4a9), in fluid secretion. Water transport in this type of cell is predominantly driven by \(\mathrm{Cl}^-\) movement. Here, a basolateral \(\mathrm{Na}^+/ \mathrm{K}^+\) adenosine triphosphatase pump (NaK-ATPase) and a \(\mathrm{Na}^+\)–\(\mathrm{K}^+\)–\(2 \mathrm{Cl}^-\) cotransporter (Nkcc1) are primarily responsible for concentrating the intracellular space with \(\mathrm{Cl}^-\) well above its equilibrium potential. Gustatory and olfactory stimuli induce the release of \(\mathrm{Ca}^{2+}\) ions from the internal stores of acinar cells, which triggers saliva secretion. \(\mathrm{Ca}^{2+}\)-dependent \(\mathrm{Cl}^-\) and \(\mathrm{K}^+\) channels promote ion secretion into the luminal space, thus creating an osmotic gradient that promotes water movement in the secretory direction. The current model for saliva secretion proposes that \(\mathrm{Cl}^-/ \mathrm{HCO}_3^-\) anion exchangers (Ae), coupled with a basolateral \(\mathrm{Na}^+/\hbox {proton}\) (\(\hbox {H}^+\)) (Nhe1) antiporter, regulate intracellular pH and act as a secondary \(\mathrm{Cl}^-\) uptake mechanism (Nauntofte in Am J Physiol Gastrointest Liver Physiol 263(6):G823–G837, 1992; Melvin et al. in Annu Rev Physiol 67:445–469, 2005.  https://doi.org/10.1146/annurev.physiol.67.041703.084745). Recent studies demonstrated that Ae4 deficient mice exhibit an approximate \(30\%\) decrease in gland salivation (Peña-Münzenmayer et al. in J Biol Chem 290(17):10677–10688, 2015). Surprisingly, the same study revealed that absence of Ae2 does not impair salivation, as previously suggested. These results seem to indicate that the Ae4 may be responsible for the majority of the secondary \(\mathrm{Cl}^-\) uptake and thus a key mechanism for saliva secretion. Here, by using ‘in-silico’ Ae2 and Ae4 knockout simulations, we produced mathematical support for such controversial findings. Our results suggest that the exchanger’s cotransport of monovalent cations is likely to be important in establishing the osmotic gradient necessary for optimal transepithelial fluid movement.     

On the in vivo function of the mitral heart valve leaflet: insights into tissue–interstitial cell biomechanical coupling

There continues to be a critical need for developing data-informed computational modeling techniques that enable systematic evaluations of mitral valve (MV) function. This is important for a better understanding of MV organ-level biomechanical performance, in vivo functional tissue stresses, and the biosynthetic responses of MV interstitial cells (MVICs) in the normal, pathophysiological, and surgically repaired states. In the present study, we utilized extant ovine MV population-averaged 3D fiducial marker data to quantify the MV anterior leaflet (MVAL) deformations in various kinematic states. This approach allowed us to make the critical connection between the in vivo functional and the in vitro experimental configurations. Moreover, we incorporated the in vivo MVAL deformations and pre-strains into an enhanced inverse finite element modeling framework (Path 1) to estimate the resulting in vivo tissue prestresses \((\sigma _\mathrm{CC}\cong \sigma _\mathrm{RR}\cong \, 30\,\hbox {kPa})\) and the in vivo peak functional tissue stresses \((\sigma _\mathrm{CC}\cong 510\, \hbox {kPa}, \sigma _\mathrm{RR}\cong 740\, \hbox {kPa})\). These in vivo stress estimates were then cross-verified with the results obtained from an alternative forward modeling method (Path 2), by taking account of the changes in the in vitro and in vivo reference configurations. Moreover, by integrating the tissue-level kinematic results into a downscale MVIC microenvironment FE model, we were able to estimate, for the first time, the in vivo layer-specific MVIC deformations and deformation rates of the normal and surgically repaired MVALs. From these simulations, we determined that the placement of annuloplasty ring greatly reduces the peak MVIC deformation levels in a layer-specific manner. This suggests that the associated reductions in MVIC deformation may down-regulate MV extracellular matrix maintenance, ultimately leading to reduction in tissue mechanical integrity. These simulations provide valuable insight into MV cellular mechanobiology in response to organ- and tissue-level alternations induced by MV disease or surgical repair. They will also assist in the future development of computer simulation tools for guiding MV surgery procedure with enhanced durability and improved long-term surgical outcomes.     

Resolving the viscoelasticity and anisotropy dependence of the mechanical properties of skin from a porcine model

The mechanical response of skin to external loads is influenced by anisotropy and viscoelasticity of the tissue, but the underlying mechanisms remain unclear. Here, we report a study of the main effects of tissue orientation (TO, which is linked to anisotropy) and strain rate (SR, a measure of viscoelasticity), as well as the interaction effects between the two factors, on the tensile properties of skin from a porcine model. Tensile testing to rupture of porcine skin tissue was conducted to evaluate the sensitivity of the tissue modulus of elasticity (E) and fracture-related properties, namely maximum stress \((\sigma _{U})\) and strain \((\varepsilon _{U})\) at \(\sigma _{U}\), to varying SR and TO. Specimens were excised from the abdominal skin in two orientations, namely parallel (P) and right angle (R) to the torso midline. Each TO was investigated at three SR levels, namely 0.007–0.015 \(\hbox {s}^{-1}\) (low), 0.040 \(\hbox {s}^{-1}\) (mid) and 0.065 \(\hbox {s}^{-1}\) (high). Two-factor analysis of variance revealed that the respective parameters responded differently to varying SR and TO. Significant changes in the \(\sigma _{U}\) were observed with different TOs but not with SR. The \(\varepsilon _{U}\) decreased significantly with increasing SR, but no significant variation was observed for different TOs. Significant changes in E were observed with different TOs; E increased significantly with increasing SR. More importantly, the respective mechanical parameters were not significantly influenced by interactions between SR and TO. These findings suggest that the trends associated with the changes in the skin mechanical properties may be attributed partly to differences in the anisotropy and viscoelasticity but not through any interaction between viscoelasticity and anisotropy.     

Cellular mechanosensitivity to substrate stiffness decreases with increasing dissimilarity to cell stiffness

Computational modelling has received increasing attention to investigate multi-scale coupled problems in micro-heterogeneous biological structures such as cells. In the current study, we investigated for a single cell the effects of (1) different cell-substrate attachment (2) and different substrate modulus \(\textit{E}_\mathrm{s}\) on intracellular deformations. A fibroblast was geometrically reconstructed from confocal micrographs. Finite element models of the cell on a planar substrate were developed. Intracellular deformations due to substrate stretch of \(\lambda =1.1\), were assessed for: (1) cell-substrate attachment implemented as full basal contact (FC) and 124 focal adhesions (FA), respectively, and \(\textit{E}_\mathrm{s}\,=\,\)140 KPa and (2) \(\textit{E}_\mathrm{s}\,=\,10\), 140, 1000, and 10,000 KPa, respectively, and FA attachment. The largest strains in cytosol, nucleus and cell membrane were higher for FC (1.35\(\text {e}^{-2}\), 0.235\(\text {e}^{-2}\) and 0.6\(\text {e}^{-2}\)) than for FA attachment (0.0952\(\text {e}^{-2}\), 0.0472\(\text {e}^{-2}\) and 0.05\(\text {e}^{-2}\)). For increasing \(\textit{E}_\mathrm{s}\), the largest maximum principal strain was 4.4\(\text {e}^{-4}\), 5\(\text {e}^{-4}\), 5.3\(\text {e}^{-4}\) and 5.3\(\text {e}^{-4}\) in the membrane, 9.5\(\text {e}^{-4}\), 1.1\(\text {e}^{-4}\), 1.2\(\text {e}^{-3}\) and 1.2\(\text {e}^{-3}\) in the cytosol, and 4.5\(\text {e}^{-4}\), 5.3\(\text {e}^{-4}\), 5.7\(\text {e}^{-4}\) and 5.7\(\text {e}^{-4}\) in the nucleus. The results show (1) the importance of representing FA in cell models and (2) higher cellular mechanical sensitivity for substrate stiffness changes in the range of cell stiffness. The latter indicates that matching substrate stiffness to cell stiffness, and moderate variation of the former is very effective for controlled variation of cell deformation. The developed methodology is useful for parametric studies on cellular mechanics to obtain quantitative data of subcellular strains and stresses that cannot easily be measured experimentally.     

Backbone resonance assignments for the SET domain of the human methyltransferase NSD2

Aberrant NSD2 methyltransferase activity is implicated as the oncogenic driver in multiple myeloma, suggesting opportunities for novel therapeutic intervention. The methyltransferase activity of NSD2 resides in its catalytic SET domain, which is conserved among most lysine methyltransferases. Here we report the backbone \(\hbox {H}^{\mathrm{N}}\), N, C\(^{\prime }\), \(\hbox {C}^\alpha\) and side-chain \(\hbox {C}^\beta\) assignments of a 25 kDa NSD2 SET domain construct, spanning residues 991–1203. A chemical shift analysis of C\(^{\prime }\), \(\hbox {C}^\alpha\) and \(\hbox {C}^\beta\) resonances predicts a secondary structural pattern that is in agreement with homology models.     

Creep and stress relaxation of human red cell membrane

In contrast to most mechanical properties of the red cell, experimental information on stress relaxation (SR) of the membrane skeleton is scarce. On the other hand, many postulates or assumptions as to the value of the characteristic time of SR \((\tau _{\mathrm{SR}})\) can be found in the literature. Here, an experiment is presented that allows measurement of \(\tau _{\mathrm{SR}}\) up to values of about 10 h. The membrane skeleton was deformed passively by changing the spontaneous curvature of the bilayer thus transforming the natively biconcave red cells into echinocytes. This shape and the concomitant deformation of the skeleton were kept up to 4 h by incubation at 37 ℃. During this period, no plastic deformation (creep) was observed. After the incubation, the spontaneous curvature was returned to normal. The resulting shape was smooth showing no remnants of the echinocytic shape. Both observations indicate \(\tau _{\mathrm{SR}}\gtrapprox \) 10 h. This result is in gross disagreement to postulates or assumptions existing in the literature.     

LPC$$_\mathrm{}$$: A local power controller using the frequency scheduling approach for virtualized servers

For more than a decade, the power consumption of data centers has been addressed from different perspectives. Many solutions have been proposed to reduce (or optimize) this power consumption, such as controlling the operation of the servers in data centers. However, these approaches have not yet reached their optimum goals. Existing power control solutions using CPU frequency with an ad hoc or frequency modulator approach are not sufficient. In this paper, we review the power consumption effects of different configuration settings applied to the server’s CPU. We propose our local power controller using frequency scheduling (LPC\(_\mathrm{FreqSchd}\)), which is a server-level power controller that depends on an extended gain scheduling technique. Our proposed LPC\(_\mathrm{FreqSchd}\) considers the impact of different CPU configuration settings that are typically not considered simultaneously, such as the allocated CPU credits and CPU frequency level. Through a real experimental test bed, our LPC\(_\mathrm{FreqSchd}\) exhibits effective power management of different types of machines and outperforms other existing approaches, such as ad hoc and frequency modulation, when the power budget is low. Moreover, our proposed LPC\(_\mathrm{FreqSchd}\) has a very lightweight control actuation overhead compared with other approaches: approximately \(1/10 \mathrm{th}\) of the ad hoc approach’s overhead and \(1/100 \mathrm{th}\) of the frequency modulator approach’s overhead. This lightweight control actuation overhead reduces the power consumption overhead caused by the controller, and it could be used by other controllers, such as performance or thermal controllers running on the same server.     

Pulmonary trunk, ductus arteriosus, and pulmonary arterial phasic blood flow interactions during systole and diastole in the fetus

Although the distribution of average fetal pulmonary trunk (PT) blood flow favors the ductus arteriosus (DA) over the lungs, the phasic aspects of this distribution during systole and diastole are not well understood. Accordingly, flow profile and wave intensity (WI) analyses were performed at baseline and during brief flow increases accompanying an extrasystole (ES) in 10 anesthetized late-gestation fetal sheep instrumented with PT, DA, and left pulmonary artery (PA) micromanometer catheters and transit-time flow probes. At baseline, 83% of mean PT flow crossed the DA and 17% entered the lungs. However, early systolic flow associated with a forward-running compression wave (FCW(is)) was higher in the PA and predominant DA flow only emerged in midsystole when a large PA backward-running compression wave (BCW(ms)), which reduced PA flow, was transmitted into the DA as a forward-running compression wave (FCW(ms)) that increased flow. Subsequent protodiastolic forward DA flow occurring during pulmonary valve closure was associated with substantial retrograde PA flow, but insignificant PT flow. Conversely, forward DA flow in the remainder of diastole occurred with forward PT but near-zero PA flow. These flow and WI patterns, in conjunction with the results of mathematical modeling, suggest that 1) fetal PT flow preferentially passes into the PA during early systole due to a lower PA-than-DA characteristic impedance, while DA flow predominates in mid- and late systole due to flow effects arising from the PA BCW(ms), and 2) forward DA flow is mainly sustained by reversal of PA flow in protodiastole but discharge of a more central reservoir in diastole.     

A viscoplastic model for the active component in cardiac muscle

The HMK model (Hunter et al. in Prog Biophys Mol Biol 69:289–331, 1998) proposes mechanobiological equations for the influence of intracellular calcium concentration \(\hbox {Ca}_\mathrm{i}\) on the evolution of bound calcium concentration \(\hbox {Ca}_\mathrm{b}\) and the tropomyosin kinetics parameter z, which model processes in the active component of the tension in cardiac muscle. The inelastic response due to actin-myosin crossbridge kinetics is modeled in the HMK model with a function Q that depends on the history of the rate of total stretch of the muscle fiber. Here, an alternative model is proposed which models the active component of the muscle fiber as a viscoplastic material. In particular, an evolution equation is proposed for the elastic stretch \(\lambda _\mathrm{a} \) in the active component. Specific forms of the constitutive equations are proposed and used to match experimental data. The proposed viscoplastic formulation allows for separate modeling of three processes: the high rate deactivation of crossbridges causing rapid reduction in active tension; the high but lower rate reactivation of crossbridges causing recovery of active tension; and the low rate relaxation effects characterizing the Hill model of muscles.     

Mitochondrial signatures revealed panmixia in <Emphasis Type="Italic">Lutjanus argentimaculatus</Emphasis> (Forsskål 1775)

Mangrove red snapper, Lutjanus argentimaculatus is a commercially important fish. The genetic stock structure of L. argentimaculatus from Indian waters was identified using mitochondrial ATPase 6 and ATPase 8, and cytochrome b (Cytb) genes. A 842 bp region of ATPase 6/8 genes and 1105 bp region of Cytb gene were amplified in 120 samples from six different locations along the Indian coast and obtained 58 and 66 haplotypes, respectively. The high haplotype and low nucleotide diversity values along with mismatch distribution, Tajima’s D and Fu’s \(F_\mathrm{s}\) analysis suggested a genetic bottleneck events or founder effect, with subsequent population expansion in L. argentimaculatus. Coefficient of genetic differentiation \((F_\mathrm{ST})\) values was low and nonsignificant for both ATPase 6/8 gene and Cytb genes indicating low genetic differentiation in L. argentimaculatus which can be managed as a unit stock in Indian waters.     

An improved Four-Russians method and sparsified Four-Russians algorithm for RNA folding

Background

The basic RNA secondary structure prediction problem or single sequence folding problem (SSF) was solved 35 years ago by a now well-known \(O(n^3)\)-time dynamic programming method. Recently three methodologies—Valiant, Four-Russians, and Sparsification—have been applied to speedup RNA secondary structure prediction. The sparsification method exploits two properties of the input: the number of subsequence Z with the endpoints belonging to the optimal folding set and the maximum number base-pairs L. These sparsity properties satisfy \(0 \le L \le n / 2\) and \(n \le Z \le n^2 / 2\), and the method reduces the algorithmic running time to O(LZ). While the Four-Russians method utilizes tabling partial results.

Results

In this paper, we explore three different algorithmic speedups. We first expand the reformulate the single sequence folding Four-Russians \(\Theta \left(\frac{n^3}{\log ^2 n}\right)\)-time algorithm, to utilize an on-demand lookup table. Second, we create a framework that combines the fastest Sparsification and new fastest on-demand Four-Russians methods. This combined method has worst-case running time of \(O(\tilde{L}\tilde{Z})\), where \(\frac{{L}}{\log n} \le \tilde{L}\le min\left({L},\frac{n}{\log n}\right)\) and \(\frac{{Z}}{\log n}\le \tilde{Z} \le min\left({Z},\frac{n^2}{\log n}\right)\). Third we update the Four-Russians formulation to achieve an on-demand \(O( n^2/ \log ^2n )\)-time parallel algorithm. This then leads to an asymptotic speedup of \(O(\tilde{L}\tilde{Z_j})\) where \(\frac{{Z_j}}{\log n}\le \tilde{Z_j} \le min\left({Z_j},\frac{n}{\log n}\right)\) and \(Z_j\) the number of subsequence with the endpoint j belonging to the optimal folding set.

Conclusions

The on-demand formulation not only removes all extraneous computation and allows us to incorporate more realistic scoring schemes, but leads us to take advantage of the sparsity properties. Through asymptotic analysis and empirical testing on the base-pair maximization variant and a more biologically informative scoring scheme, we show that this Sparse Four-Russians framework is able to achieve a speedup on every problem instance, that is asymptotically never worse, and empirically better than achieved by the minimum of the two methods alone.

     

Optimal Therapy Scheduling Based on a Pair of Collaterally Sensitive Drugs

Despite major strides in the treatment of cancer, the development of drug resistance remains a major hurdle. One strategy which has been proposed to address this is the sequential application of drug therapies where resistance to one drug induces sensitivity to another drug, a concept called collateral sensitivity. The optimal timing of drug switching in these situations, however, remains unknown. To study this, we developed a dynamical model of sequential therapy on heterogeneous tumors comprised of resistant and sensitive cells. A pair of drugs (DrugA, DrugB) are utilized and are periodically switched during therapy. Assuming resistant cells to one drug are collaterally sensitive to the opposing drug, we classified cancer cells into two groups, \(A_\mathrm{R}\) and \(B_\mathrm{R}\), each of which is a subpopulation of cells resistant to the indicated drug and concurrently sensitive to the other, and we subsequently explored the resulting population dynamics. Specifically, based on a system of ordinary differential equations for \(A_\mathrm{R}\) and \(B_\mathrm{R}\), we determined that the optimal treatment strategy consists of two stages: an initial stage in which a chosen effective drug is utilized until a specific time point, T, and a second stage in which drugs are switched repeatedly, during which each drug is used for a relative duration (i.e., \(f \Delta t\)-long for DrugA and \((1-f) \Delta t\)-long for DrugB with \(0 \le f \le 1\) and \(\Delta t \ge 0\)). We prove that the optimal duration of the initial stage, in which the first drug is administered, T, is shorter than the period in which it remains effective in decreasing the total population, contrary to current clinical intuition. We further analyzed the relationship between population makeup, \(\mathcal {A/B} = A_\mathrm{R}/B_\mathrm{R}\), and the effect of each drug. We determine a critical ratio, which we term \(\mathcal {(A/B)}^{*}\), at which the two drugs are equally effective. As the first stage of the optimal strategy is applied, \(\mathcal {A/B}\) changes monotonically to \(\mathcal {(A/B)}^{*}\) and then, during the second stage, remains at \(\mathcal {(A/B)}^{*}\) thereafter. Beyond our analytic results, we explored an individual-based stochastic model and presented the distribution of extinction times for the classes of solutions found. Taken together, our results suggest opportunities to improve therapy scheduling in clinical oncology.     

White matter tract-oriented deformation predicts traumatic axonal brain injury and reveals rotational direction-specific vulnerabilities

A systematic correlation between finite element models (FEMs) and histopathology is needed to define deformation thresholds associated with traumatic brain injury (TBI). In this study, a FEM of a transected piglet brain was used to reverse engineer the range of optimal shear moduli for infant (5 days old, 553–658 Pa) and 4-week-old toddler piglet brain (692–811 Pa) from comparisons with measured in situ tissue strains. The more mature brain modulus was found to have significant strain and strain rate dependencies not observed with the infant brain. Age-appropriate FEMs were then used to simulate experimental TBI in infant (\(n=36\)) and preadolescent (\(n=17\)) piglets undergoing a range of rotational head loads. The experimental animals were evaluated for the presence of clinically significant traumatic axonal injury (TAI), which was then correlated with FEM-calculated measures of overall and white matter tract-oriented tissue deformations, and used to identify the metric with the highest sensitivity and specificity for detecting TAI. The best predictors of TAI were the tract-oriented strain (6–7 %), strain rate (38–40 s\(^{-1})\), and strain times strain rate (1.3–1.8 s\(^{-1})\) values exceeded by 90 % of the brain. These tract-oriented strain and strain rate thresholds for TAI were comparable to those found in isolated axonal stretch studies. Furthermore, we proposed that the higher degree of agreement between tissue distortion aligned with white matter tracts and TAI may be the underlying mechanism responsible for more severe TAI after horizontal and sagittal head rotations in our porcine model of nonimpact TAI than coronal plane rotations.