Confinement of knotted polymers in a slit

We investigate the effect of knot type on the properties of a ring polymer confined to a slit. For relatively wide slits, the more complex the knot, the more the force exerted by the polymer on the walls is decreased compared to an unknotted polymer of the same length. For more narrow slits the opposite is true. The crossover between these two regimes is, to first order, at smaller slit width for more complex knots. However, knot topology can affect these trends in subtle ways. Besides the force exerted by the polymers, we also study other quantities such as the monomer-density distribution across the slit and the anisotropic radius of gyration.Comment: 9 pages, 6 figures, submitted for publicatio

Electronic properties of shallow level defects in ZnO grown by pulsed laser deposition

We have used deep level transient spectroscopy (DLTS) to characterise four defects with shallow levels in ZnO grown by pulsed laser deposition (PLD). These defects all have DLTS peaks below 100 K. From DLTS measurements and Arrhenius plots we have calculated the energy levels of these defects as 31 meV, 64 meV, 100 meV and 140 meV, respectively, below the conduction band. The 100 meV defect displayed metastable behaviour: Annealing under reverse bias at temperatures of above 130 K introduced it while annealing under zero bias above 110 K removed it. The 64 meV and 140 meV defects exhibited a strong electric field assisted emission, indicating that they may be donors

The critical fugacity for surface adsorption of self-avoiding walks on the honeycomb lattice is 1+21+\sqrt{2}

In 2010, Duminil-Copin and Smirnov proved a long-standing conjecture of Nienhuis, made in 1982, that the growth constant of self-avoiding walks on the hexagonal (a.k.a. honeycomb) lattice is $\mu=\sqrt{2+\sqrt{2}}.$ A key identity used in that proof was later generalised by Smirnov so as to apply to a general O(n) loop model with $n\in [-2,2]$ (the case $n=0$ corresponding to SAWs). We modify this model by restricting to a half-plane and introducing a surface fugacity $y$ associated with boundary sites (also called surface sites), and obtain a generalisation of Smirnov's identity. The critical value of the surface fugacity was conjectured by Batchelor and Yung in 1995 to be $y_{\rm c}=1+2/\sqrt{2-n}.$ This value plays a crucial role in our generalized identity, just as the value of growth constant did in Smirnov's identity. For the case $n=0$, corresponding to \saws\ interacting with a surface, we prove the conjectured value of the critical surface fugacity. A crucial part of the proof involves demonstrating that the generating function of self-avoiding bridges of height $T$, taken at its critical point $1/\mu$, tends to 0 as $T$ increases, as predicted from SLE theory.Comment: Major revision, references updated, 25 pages, 13 figure

Electronic properties of shallow level defects in ZnO grown by pulsed laser deposition

We have used deep level transient spectroscopy (DLTS) to characterise four defects with shallow levels in ZnO grown by pulsed laser deposition (PLD). These defects all have DLTS peaks below 100 K. From DLTS measurements and Arrhenius plots we have calculated the energy levels of these defects as 31 meV, 64 meV, 100 meV and 140 meV, respectively, below the conduction band. The 100 meV defect displayed metastable behaviour: Annealing under reverse bias at temperatures of above 130 K introduced it while annealing under zero bias above 110 K removed it. The 64 meV and 140 meV defects exhibited a strong electric field assisted emission, indicating that they may be donors

A hetero-multimeric chitinase-containing plasmodium falciparum and plasmodium gallinaceum ookinete-secreted protein complex involved in mosquito midgut invasion

Malaria parasites are transmitted by Anopheles mosquitoes. During its life cycle in the mosquito vector the Plasmodium ookinete escapes the proteolytic milieu of the post-blood meal midgut by traversing the midgut wall. This process requires penetration of the chitin-containing peritrophic matrix lining the midgut epithelium, which depends in part on ookinete-secreted chitinases. Plasmodium falciparum ookinetes have one chitinase (PfCHT1), whereas ookinetes of the avian-infecting parasite, P. gallinaceum, have two, a long and a short form, PgCHT1 and PgCHT2, respectively. Published data indicates that PgCHT2 forms a high molecular weight (HMW) reduction-sensitive complex; and one binding partner is the ookinete-produced von Willebrand A-domain-containing protein, WARP. Size exclusion chromatography data reported here show that P. gallinaceum PgCHT2 and its ortholog, P. falciparum PfCHT1 are covalently-linked components of a HMW chitinase-containing complex (> 1,300 kDa). Mass spectrometry of ookinete-secreted proteins isolated using a new chitin bead pull-down method identified chitinase-associated proteins in P. falciparum and P. gallinaceum ookinete-conditioned culture media. Mass spectrometry of this complex showed the presence of several micronemal proteins including von Willebrand factor A domain-related protein (WARP), ookinete surface enolase, and secreted ookinete adhesive protein (SOAP). To test the hypothesis that ookinete-produced PfCHT1 can form a high molecular homo-multimer or, alternatively, interacts with P. berghei ookinete-produced proteins to produce an HMW hetero-multimer, we created chimeric P. berghei parasites expressing PfCHT1 to replace PbCHT1, enabling the production of large numbers of PfCHT1-expressing ookinetes. We show that chimeric P. berghei ookinetes express monomeric PfCHT1, but a HMW complex containing PfCHT1 is not present. A better understanding of the chitinase-containing HMW complex may enhance development of next-generation vaccines or drugs that target malaria transmission stages.Host-parasite interactio

Unexpected properties of the inductively coupled plasma induced defect in germanium

Inductively coupled plasma (ICP) etching of germanium introduces a single defect, the E0.31 electron trap, for a large range of argon partial pressures from 4 × 10-3 to 6.5 × 10-4mbar that correspond to ion energies of 8 to 60 eV. Ge of three crystallographic orientations, (100), (110) and (111), treated with 20 and 60 eV ICP had defect concentration profiles that were similar in appearance, with a maximum concentration of 1014 cm-3 extending more than a μm into the material, approximately three orders of magnitude deeper than what TRIM simulations predicted. All profiles were measured using Laplace deep level transient spectroscopy (L-DLTS), a technique that is sensitive to defect concentrations as low as 1011 cm-3. Isochronal annealing of samples showed concentration curves broadening after a 400 K anneal and decreasing to the 1013 cm-3 level after a 450 K anneal. Unannealed samples measured after a year exhibited similar decreases in defect concentration without broadening of their profiles. A 550 K anneal lowered the defect concentration to levels below the L-DLTS detection limit. Thereafter additional plasma treatment of the surface failed to reintroduce this defect indicating that the structure required for the formation of E0.31 was no longer present in the region under observation.http://www.elsevier.com/locate/physbhb201

The characteristics of juvenile myasthenia gravis among South Africans

OBJECTIVES: To report the characteristics of juvenile-onset (<20 years) myasthenia gravis (MG) in Africa. SUBJECTS AND METHOD: Six South African centres collected data which included acetylcholine receptor-antibody (AChR-ab) status, delay before diagnosis, MG Foundation of America grade at onset, maximum severity and severity at last visit, therapies, outcomes and complications. RESULTS: We report on 190 individuals with a 4-year median follow-up (interquartile range (IQR) 1 - 8). The median age at symptom onset was 7 years (IQR 4 - 14). Ocular MG (26%) occurred among younger children (mean 5.1 years) compared with those developing generalised MG (74%) (mean 10.2 years) (p=0.0004). Remissions were obtained in 45% of generalised and 50% of ocular MG patients, of whom the majority received immunosuppressive treatment, mainly prednisone. Children with post-pubertal onset had more severe MG, but deaths were infrequent. Thymectomies were performed in 43% of those with generalised MG who suffered greater maximum disease severity (p=0.002); there was a trend towards more remissions in the thymectomy group compared with the non-thymectomy group (p=0.057). There was no racial variation with respect to AChR-ab status, maximum severity, or use of immunosuppression. However, 23% of children of African genetic ancestry developed partial or complete ophthalmoplegia as a complication of generalised MG (p=0.002). CONCLUSION: Younger children developed ocular MG and older children generalised MG. Persistent ophthalmoplegia developing as a MG complication is not uncommon among juveniles of African genetic ancestry. A successful approach to the management of this complication that causes significant morbidity is, as yet, unclear.http://www.samj.org.z

The Flare-energy Distributions Generated by Kink-unstable Ensembles of Zero-net-current Coronal Loops

It has been proposed that the million degree temperature of the corona is due to the combined effect of barely-detectable energy releases, so called nanoflares, that occur throughout the solar atmosphere. Alas, the nanoflare density and brightness implied by this hypothesis means that conclusive verification is beyond present observational abilities. Nevertheless, we investigate the plausibility of the nanoflare hypothesis by constructing a magnetohydrodynamic (MHD) model that can derive the energy of a nanoflare from the nature of an ideal kink instability. The set of energy-releasing instabilities is captured by an instability threshold for linear kink modes. Each point on the threshold is associated with a unique energy release and so we can predict a distribution of nanoflare energies. When the linear instability threshold is crossed, the instability enters a nonlinear phase as it is driven by current sheet reconnection. As the ensuing flare erupts and declines, the field transitions to a lower energy state, which is modelled by relaxation theory, i.e., helicity is conserved and the ratio of current to field becomes invariant within the loop. We apply the model so that all the loops within an ensemble achieve instability followed by energy-releasing relaxation. The result is a nanoflare energy distribution. Furthermore, we produce different distributions by varying the loop aspect ratio, the nature of the path to instability taken by each loop and also the level of radial expansion that may accompany loop relaxation. The heating rate obtained is just sufficient for coronal heating. In addition, we also show that kink instability cannot be associated with a critical magnetic twist value for every point along the instability threshold

Arrhythmogenic mechanisms in the isolated perfused hypokalaemic murine heart

AIM: Hypokalaemia is associated with a lethal form of ventricular tachycardia (VT), torsade de pointes, through pathophysiological mechanisms requiring clarification. METHODS: Left ventricular endocardial and epicardial monophasic action potentials were compared in isolated mouse hearts paced from the right ventricular epicardium perfused with hypokalaemic (3 and 4 mm [K(+)](o)) solutions. Corresponding K(+) currents were compared in whole-cell patch-clamped epicardial and endocardial myocytes. RESULTS: Hypokalaemia prolonged epicardial action potential durations (APD) from mean APD(90)s of 37.2 ± 1.7 ms (n = 7) to 58.4 ± 4.1 ms (n =7) and 66.7 ± 2.1 ms (n = 11) at 5.2, 4 and 3 mm [K(+)](o) respectively. Endocardial APD(90)s correspondingly increased from 51.6 ± 1.9 ms (n = 7) to 62.8 ± 2.8 ms (n = 7) and 62.9 ± 5.9 ms (n = 11) giving reductions in endocardial–epicardial differences, ΔAPD(90), from 14.4 ± 2.6 to 4.4 ± 5.0 and −3.4 ± 6.0 ms respectively. Early afterdepolarizations (EADs) occurred in epicardia in three of seven spontaneously beating hearts at 4 mm [K(+)](o) with triggered beats followed by episodes of non-sustained VT in nine of 11 preparations at 3 mm. Programmed electrical stimulation never induced arrhythmic events in preparations perfused with normokalemic solutions yet induced VT in two of seven and nine of 11 preparations at 4 and 3 mm [K(+)](o) respectively. Early outward K(+) current correspondingly fell from 73.46 ± 8.45 to 61.16±6.14 pA/pF in isolated epicardial but not endocardial myocytes (n = 9) (3 mm [K(+)](o)). CONCLUSIONS: Hypokalaemic mouse hearts recapitulate the clinical arrhythmogenic phenotype, demonstrating EADs and triggered beats that might initiate VT on the one hand and reduced transmural dispersion of repolarization reflected in ΔAPD(90) suggesting arrhythmogenic substrate on the other

Deep Learning-Based Segmentation of Locally Advanced Breast Cancer on MRI in Relation to Residual Cancer Burden: A Multiinstitutional Cohort Study

Background: While several methods have been proposed for automated assessment of breast-cancer response to neoadjuvant chemotherapy on breast MRI, limited information is available about their performance across multiple institutions. Purpose: To assess the value and robustness of deep learning-derived volumes of locally advanced breast cancer (LABC) on MRI to infer the presence of residual disease after neoadjuvant chemotherapy. Study Type: Retrospective. Subjects: Training cohort: 102 consecutive female patients with LABC scheduled for neoadjuvant chemotherapy (NAC) from a single institution (age: 25–73 years). Independent testing cohort: 55 consecutive female patients with LABC from four institutions (age: 25–72 years). Field Strength/Sequence: Training cohort: single vendor 1.5 T or 3.0 T. Testing cohort: multivendor 3.0 T. Gradient echo dynamic contrast-enhanced sequences. Assessment: A convolutional neural network (nnU-Net) was trained to segment LABC. Based on resulting tumor volumes, an extremely randomized tree model was trained to assess residual cancer burden (RCB)-0/I vs. RCB-II/III. An independent model was developed using functional tumor volume (FTV). Models were tested on an independent testing cohort and response assessment performance and robustness across multiple institutions were assessed. Statistical Tests: The receiver operating characteristic (ROC) was used to calculate the area under the ROC curve (AUC). DeLong's method was used to compare AUCs. Correlations were calculated using Pearson's method. P values <0.05 were considered significant. Results: Automated segmentation resulted in a median (interquartile range [IQR]) Dice score of 0.87 (0.62–0.93), with similar volumetric measurements (R = 0.95, P < 0.05). Automated volumetric measurements were significantly correlated with FTV (R = 0.80). Tumor volume-derived from deep learning of DCE-MRI was associated with RCB, yielding an AUC of 0.76 to discriminate between RCB-0/I and RCB-II/III, performing similar to the FTV-based model (AUC = 0.77, P = 0.66). Performance was comparable across institutions (IQR AUC: 0.71–0.84). Data Conclusion: Deep learning-based segmentation estimates changes in tumor load on DCE-MRI that are associated with RCB after NAC and is robust against variations between institutions. Evidence Level: 2. Technical Efficacy: Stage 4