Miracle-dz/UniFAR-FTUs huggingface dataset:
Heat transfer in a conical porous cylinder with partial heating

The current work simulates the heat transfer across a porous medium fixed in an annular conical cylinder. The geometry is such that the lower part is conical annulus supporting a regular annular cylinder. The porous medium is fixed between inner and outer radius of conical annular cylinder. The inner radius until conical section is heated with constant temperature Th whereas the outer radius is cooled to isothermal temperature Tc such that Th>Tc. The heat transfer phenomenon in this case can be described by two coupled partial differential equations which are solved using finite element method by using 3-node triangular elements. The heat transfer characteristics in this case are quite different from other geometries being discussed in the literature. It is observed that the fluid flow is stronger in the conical section as compared to the cylindrical part of porous geometry. A very few isothermal lines penetrate into the cylindrical porous region as compared to that of conical section.
Seed‐specific RNAi in safflower generates a superhigh oleic oil with extended oxidative stability

Summary Vegetable oils extracted from oilseeds are an important component of foods, but are also used in a range of high value oleochemical applications. Despite being biodegradable, nontoxic and renewable current plant oils suffer from the presence of residual polyunsaturated fatty acids that are prone to free radical formation that limit their oxidative stability, and consequently shelf life and functionality. Many decades of plant breeding have been successful in raising the oleic content to ~90%, but have come at the expense of overall field performance, including poor yields. Here, we engineer superhigh oleic (SHO) safflower producing a seed oil with 93% oleic generated from seed produced in multisite field trials spanning five generations. SHO safflower oil is the result of seed‐specific hairpin‐based RNA interference of two safflower lipid biosynthetic genes, FAD2.2 and FATB, producing seed oil containing less than 1.5% polyunsaturates and only 4% saturates but with no impact on lipid profiles of leaves and roots. Transgenic SHO events were compared to non‐GM safflower in multisite trial plots with a wide range of growing season conditions, which showed no evidence of impact on seed yield. The oxidative stability of the field‐grown SHO oil produced from various sites was 50 h at 110°C compared to 13 h for conventional ~80% oleic safflower oils. SHO safflower produces a uniquely stable vegetable oil across different field conditions that can provide the scale of production that is required for meeting the global demands for high stability oils in food and the oleochemical industry.
Improving comprehensive learning particle swarm optimiser using generalised opposition-based learning

In this paper, we present an improved comprehensive learning particle swarm optimiser (CLPSO) by using a generalised opposition-based learning concept (GOBL). The proposed approach, called GOCLPSO, employs similar schemes of opposition-based differential evolution (ODE) for opposition-based population initialisation and generation jumping with GOBL. Experimental studies on 13 benchmark functions show that GOCLPSO could achieve more accurate solutions than CLPSO for the majority of test cases.
Molecular mechanism of extreme mechanostability in a pathogen adhesin

How a pathogen holds on to its host Staphylococcus epidermidis and Staphylococcus aureus are pathogens that can form biofilms on implants and medical devices. Central to biofilm formation is a very tight interaction between microbial surface proteins called adhesins and components of the extracellular matrix of the host. Milles et al. used atomic force microscopy-based single-molecule force spectroscopy combined with steered molecular dynamics to explore how the bond between staphylococcal adhesin SdrG and its target fibrinogen peptide can withstand forces greater than 2 nanonewtons (see the Perspective by Herman-Bausier and Dufrêne). The peptide is confined in a coiled geometry in a deep and rigid pocket through hydrogen bonds between SdrG and the peptide backbone. If pulled, the load is distributed over all hydrogen bonds so that all bonds must be broken at once to break the interaction. Science, this issue p. 1527; see also p. 1464 The mechanostability of a staphylococcal adhesin binding to its human target is virtually independent of peptide side chains. High resilience to mechanical stress is key when pathogens adhere to their target and initiate infection. Using atomic force microscopy–based single-molecule force spectroscopy, we explored the mechanical stability of the prototypical staphylococcal adhesin SdrG, which targets a short peptide from human fibrinogen β. Steered molecular dynamics simulations revealed, and single-molecule force spectroscopy experiments confirmed, the mechanism by which this complex withstands forces of over 2 nanonewtons, a regime previously associated with the strength of a covalent bond. The target peptide, confined in a screwlike manner in the binding pocket of SdrG, distributes forces mainly toward the peptide backbone through an intricate hydrogen bond network. Thus, these adhesins can attach to their target with exceptionally resilient mechanostability, virtually independent of peptide side chains.
Simultaneous couch and gantry dynamic arc rotation (CG‐Darc) in the treatment of breast cancer with accelerated partial breast irradiation (APBI): a feasibility study

The purpose of this study was to compare the dosimetry of CG‐Darc with three‐dimensional conformal radiation therapy (3D CRT) and volumetric‐modulated arc therapy (RapidArc) in the treatment of breast cancer with APBI. CG‐Darc plans were generated using two tangential couch arcs combined with a simultaneous noncoplanar gantry arc. The dynamic couch arc was modeled by consecutive IMRT fields at 10° intervals. RapidArc plans used a single partial arc with an avoidance sector, preventing direct beam exit into the thorax. CG‐Darc and RapidArc plans were compared with 3D CRT in 20 patients previously treated with 3D CRT (group A), and in 15 additional patients who failed the dosimetric constraints of the Canadian trial and of NSABP B‐39/RTOG 0413 for APBI (group B). CG‐Darc resulted in superior target coverage compared to 3D CRT and RapidArc (V95%: 98.2% vs. 97.1% and 95.7%). For outer breast lesions, CG‐Darc and RapidArc significantly reduced the ipsilateral breast V50% by 8% in group A and 15% in group B (p<0.05) as compared with 3D CRT. For inner and centrally located lesions, CG‐Darc resulted in significant ipsilateral lung V10% reduction when compared to 3D CRT and RapidArc (10.7% vs. 12.6% and 20.7% for group A, and 15.1% vs. 25.2% and 27.3% for group B). Similar advantage was observed in the dosimetry of contralateral breast where the percent maximum dose for CG‐Darc, 3D CRT, and RapidArc were 3.9%, 6.3%, and 5.8% for group A and 4.3%, 9.2%, and 6.3% for group B, respectively (p<0.05). CG‐Darc achieved superior target coverage while decreasing normal tissue dose even in patients failing APBI dose constraints. Consequently, this technique has the potential of expanding the use of APBI to patients currently ineligible for such treatment. Modification of the RapidArc algorithm will be necessary to link couch and gantry rotation with variable dose rate and, therefore, enable the use of CG‐Darc in clinical practice. PACS number: 80
Exclusive: How the (synced) Cookie Monster breached my encrypted VPN session

In recent years, and after the Snowden revelations, there has been a significant movement in the web from organizations, policymakers and individuals to enhance the privacy awareness among users. As a consequence, more and more publishers support TLS in their websites, and vendors provide privacy and anonymity tools, such as secure VPNs or Tor onions, to cover the need of users for privacy-preserving web browsing. But is the sporadic appliance of such tools enough to provide privacy? In this paper, we describe two privacy-breaching threats against users accessing the Internet over a secure VPN. The breaches are made possible through Cookie Synchronization, nowadays widely used by third parties for advertisement and tracking purposes. The generated privacy leaks can be used by a snooping entity such as an ISP, to re-identify a user in the web and reveal their browsing history even when users are hidden behind a VPN. By probing the top 12K Alexa sites, we find that 1 out of 13 websites expose their users to these privacy leaks.
Rapid transporter regulation prevents substrate flow traffic jams in boron transport

Nutrient uptake by roots often involves substrate-dependent regulated nutrient transporters. For robust uptake, the system requires a regulatory circuit within cells and a collective, coordinated behaviour across the tissue. A paradigm for such systems is boron uptake, known for its directional transport and homeostasis, as boron is essential for plant growth but toxic at high concentrations. In Arabidopsis thaliana, boron uptake occurs via diffusion facilitators (NIPs) and exporters (BORs), each presenting distinct polarity. Intriguingly, although boron soil concentrations are homogenous and stable, both transporters manifest strikingly swift boron-dependent regulation. Through mathematical modelling, we demonstrate that slower regulation of these transporters leads to physiologically detrimental oscillatory behaviour. Cells become periodically exposed to potentially cytotoxic boron levels, and nutrient throughput to the xylem becomes hampered. We conclude that, while maintaining homeostasis, swift transporter regulation within a polarised tissue context is critical to prevent intrinsic traffic-jam like behaviour of nutrient flow.
Deformable image registration and interobserver variation in contour propagation for radiation therapy planning

Deformable image registration (DIR) and interobserver variation inevitably introduce uncertainty into the treatment planning process. The purpose of the current work was to measure deformable image registration (DIR) errors and interobserver variability for regions of interest (ROIs) in the head and neck and pelvic regions. Measured uncertainties were combined to examine planning margin adequacy for contours propagated for adaptive therapy and to assess the trade‐off of DIR and interobserver uncertainty in atlas‐based automatic segmentation. Two experienced dosimetrists retrospectively contoured brainstem, spinal cord, anterior oral cavity, larynx, right and left parotids, optic nerves, and eyes on the planning CT (CT1) and attenuation‐correction CT of diagnostic PET/CT (CT2) for 30 patients who received radiation therapy for head and neck cancer. Two senior radiation oncology residents retrospectively contoured prostate, bladder, and rectum on the postseed‐implant CT (CT1) and planning CT (CT2) for 20 patients who received radiation therapy for prostate cancer. Interobserver variation was measured by calculating mean Hausdorff distances between the two observers' contours. CT2 was deformably registered to CT1 via commercially available multipass B‐spline DIR. CT2 contours were propagated and compared with CT1 contours via mean Hausdorff distances. These values were summed in quadrature with interobserver variation for margin analysis and compared with interobserver variation for statistical significance using two‐tailed t‐tests for independent samples (α=0.05). Combined uncertainty ranged from 1.5‐5.8 mm for head and neck structures and 3.1‐3.7 mm for pelvic structures. Conventional 5 mm margins may not be adequate to cover this additional uncertainty. DIR uncertainty was significantly less than interobserver variation for four head and neck and one pelvic ROI. DIR uncertainty was not significantly different than interobserver variation for four head and neck and one pelvic ROI. DIR uncertainty was significantly greater than interobserver variation for two head and neck and one pelvic ROI. The introduction of DIR errors may offset any reduction in interobserver variation by using atlas‐based automatic segmentation. PACS number(s): 87.57. nj, 87.55. D‐
Structure and Design of Microgrippers: A Survey

The increasing need for Microelectromechanical Systems (MEMS) leads to significant efforts devoted to the development of microgrippers that would allow the manipulation of small structures in the μm range. Various microgrippers with their targeted applications have been reported in the literature. This work presents an overview on microgripper development with the emphasis on structure design and design theories. The challenges and limitations of existing technologies and prospects for new technologies in the microgripper development are also addressed.
Caching policies under content freshness constraints

Several real-time delay-sensitive applications pose varying degrees of freshness demands on the requested content. The performance of cache replacement policies that are agnostic to these demands is likely to be sub-optimal. Motivated by this concern, in this paper, we study caching policies under a request arrival process which incorporates user freshness demands. We consider the performance metric to be the steady-state cache hit probability. We first provide a universal upper bound on the performance of any caching policy. We then analytically obtain the content-wise hit-rates for the Least Popular (LP) policy. Our key contributions are two-fold. Firstly, we develop a modified version of the LP policy which ejects cache redundancies present in the form of stale contents. Secondly, we propose a new policy which outperforms the above policies by explicitly using freshness specifications of user requests to prioritize among the cached contents. We corroborate our analytical insights with extensive simulations.
Validation of nonrigid registration in pretreatment and follow‐up PET/CT scans for quantification of tumor residue in lung cancer patients

Nonrigid registrations of pre‐ and postradiotherapy (RT) PET/CT scans of NSCLC patients were performed with different algorithms and validated tracking internal landmarks. Dice overlap ratios (DR) of high FDG‐uptake areas in registered PET/CT scans were then calculated to study patterns of relapse. For 22 patients, pre‐ and post‐RT PET/CT scans were registered first rigidly and then nonrigidly. For three patients, two types (based on Demons or Morphons) of nonrigid registration algorithms each with four different parameter settings were applied and assessed using landmark validation. The two best performing methods were tested on all patients, who were then classified into three groups: large (Group 1), minor (Group 2) or insufficient improvement (Group 3) of registration accuracy. For Group 1 and 2, DRs between high FDG‐uptake areas in pre‐ and post‐RT PET scans were determined. Distances between corresponding landmarks on deformed pre‐RT and post‐RT scans decreased for all registration methods. Differences between Demons and Morphons methods were smaller than 1 mm. For Group 1, landmark distance decreased from 9.5 ± 2.1 mm to 3.8 ± 1.2 mm (mean ± 1 SD, p < 0.001), and for Group 3 from 13.6 ± 3.2 mm to 8.0 ± 2.2 mm (p=0.02). No significant change was observed for Group 2 where distances decreased from 5.6 ± 1.3 mm to 4.5 ± 1.1 mm (p=0.02). DRs of high FDG‐uptake areas improved significantly after nonrigid registration for most patients in Group 1. Landmark validation of nonrigid registration methods for follow‐up CT imaging in NSCLC is necessary. Nonrigid registration significantly improves matching between pre‐ and post‐RT CT scans for a subset of patients, although not in all patients. Hence, the quality of the registration needs to be assessed for each patient individually. Successful nonrigid registration increased the overlap between pre‐ and post‐RT high FDG‐uptake regions. PACS number: 87.57. Q‐, 87.57. C‐, 87.57. N‐, 87.57. ‐s, 87.55. ‐x, 87.55. D‐, 87.55. dh, 87.57. uk, 87.57. nj
Distributed access control in wireless networks

In mobile ad hoc networks packets are forwarded collaboratively by all nodes in the network. As intermediate nodes are not aware of local security policies at destination nodes, they typically continue forwarding unwanted packets, spending a considerable waste of bandwidth and power. The situation can be exacerbated when a particular node is under attack. Due to open network architecture, shared wireless medium, stringent resource constraints, and highly dynamic network topology deploying firewalls in a mobile wireless environment is not straight forward. In this paper, we develop a novel distributed access control scheme for mobile networks in which nodes collaboratively perform packet filtering to address resource squandering. The proposed scheme introduces techniques to distribute discarding rules suitable for both proactive and reactive routing protocols. It also proposes efficient rule placement mechanisms to maximize the number of packets discarded remotely before they reach the destination. The performed simulation show that by distributing only 1% of the rules, about 42% of the unwanted traffic is discarded before it reaches the destination, which significantly saves the network resources.
In Vitro Replication of Chelonid Herpesvirus 5 in Organotypic Skin Cultures from Hawaiian Green Turtles (Chelonia mydas)

ABSTRACT Fibropapillomatosis (FP) is a tumor disease of marine turtles associated with chelonid herpesvirus 5 (ChHV5), which has historically been refractory to growth in tissue culture. Here we show, for the first time, de novo formation of ChHV5-positive intranuclear inclusions in cultured green turtle cells, which is indicative of active lytic replication of the virus. The minimal requirements to achieve lytic replication in cultured cells included (i) either in vitro cultures of ChHV5-positive tumor biopsy specimens (plugs) or organotypic cultures (rafts) consisting of ChHV5-positive turtle fibroblasts in collagen rafts seeded with turtle keratinocytes and (ii) keratinocyte maturation induced by raising raft or biopsy cultures to the air-liquid interface. Virus growth was confirmed by detailed electron microscopic studies that revealed intranuclear sun-shaped capsid factories, tubules, various stages of capsid formation, nuclear export by budding into the perinuclear space, tegument formation, and envelopment to complete de novo virus production. Membrane synthesis was also observed as a sign of active viral replication. Interestingly, cytoplasmic particles became associated with keratin filaments, a feature not seen in conventional monolayer cell cultures, in which most studies of herpesvirus replication have been performed. Our findings draw a rich and realistic picture of ChHV5 replication in cells derived from its natural host and may be crucial not only to better understand ChHV5 circulation but also to eventually complete Koch's postulates for FP. Moreover, the principles described here may serve as a model for culture of other viruses that are resistant to replication in conventional cell culture. IMPORTANCE A major challenge in virology is the study of viruses that cannot be grown in the laboratory. One example is chelonid herpesvirus 5 (ChHV5), which is associated with fibropapillomatosis, a globally distributed, debilitating, and fatal tumor disease of endangered marine turtles. Pathological examination shows that ChHV5 is shed in skin. Here we show that ChHV5 will grow in vitro if we replicate the complex three-dimensional structure of turtle skin. Moreover, lytic virus growth requires a close interplay between fibroblasts and keratinocytes. Finally, the morphogenesis of herpesviral growth in three-dimensional cultures reveals a far richer, and likely more realistic, array of capsid morphologies than that encountered in traditional monolayer cell cultures. Our findings have applications to other viruses, including those of humans.
Staphylococcus aureus Esx Factors Control Human Dendritic Cell Functions Conditioning Th1/Th17 Response

The opportunistic pathogen Staphylococcus aureus (S. aureus) is a major cause of nosocomial- and community-acquired infections. In addition, many antibiotic-resistant strains are emerging worldwide, thus, there is an urgent unmet need to pinpoint novel therapeutic and prophylactic strategies. In the present study, we characterized the impact of infection with the pandemic methicillin-resistant USA300 S. aureus strain on human primary dendritic cells (DC), key initiators and regulators of immune responses. In particular, among staphylococcal virulence factors, the function of EsxA and EsxB, two small acidic dimeric proteins secreted by the type VII-like secretion system Ess (ESAT-6-like secretion system), was investigated in human DC setting. A comparative analysis of bacterial entry, replication rate as well as DC maturation, apoptosis, signaling pathway activation and cytokine production was performed by using wild type (wt) USA300 and three isogenic mutants carrying the deletion of esxA (ΔesxA), esxB (ΔesxB), or both genes (ΔesxAB). The S. aureus mutant lacking only the EsxA protein (ΔesxA) stimulated a stronger pro-apoptotic phenotype in infected DC as compared to wt USA300, ΔesxAB, and ΔesxB strains. When the mutant carrying the esxB deletion (ΔesxB) was analyzed, a higher production of both regulatory and pro-inflammatory mediators was found in the infected DC with respect to those challenged with the wt counterpart and the other esx mutants. In accordance with these data, supernatant derived from ΔesxB-infected DC promoted a stronger release of both IFN-γ and IL-17 from CD4+ T cells as compared with those conditioned with supernatants derived from wild type USA300-, ΔesxAB-, and ΔesxA-infected cultures. Although, the interaction of S. aureus with human DC is not yet fully understood, our data suggest that both cytokine production and apoptotic process are modulated by Esx factors, thus indicating a possible role of these proteins in the modulation of DC-mediated immunity to S. aureus.
Lateral condylar fractures of the humerus in children: DOES THE TYPE OF FIXATION MATTER?

Aims Displaced fractures of the lateral condyle of the humerus are frequently managed surgically with the aim of avoiding nonunion, malunion, disturbances of growth and later arthritis. The ideal method of fixation is however not known, and treatment varies between surgeons and hospitals. The aim of this study was to compare the outcome of two well‐established forms of surgical treatment, Kirschner wire (K‐wire) and screw fixation. Patients and Methods A retrospective cohort study of children who underwent surgical treatment for a fracture of the lateral condyle of the humerus between January 2005 and December 2014 at two centres was undertaken. Pre, intraoperative and postoperative characteristics were evaluated. A total of 336 children were included in the study. Their mean age at the time of injury was 5.8 years (0 to 15) with a male:female patient ratio of 3:2. A total of 243 (72%) had a Milch II fracture and the fracture was displaced by > 2 mm in 228 (68%). In all, 235 patients underwent K‐wire fixation and 101 had screw fixation. Results There was a higher rate of nonunion with K‐wire fixation (p = 0.02). There was no difference in Baumann's angle, carrying angle or the rate of major complications between the two groups. No benefit was obtained by immobilizing the elbow for more than four weeks in either group. No short‐term complications were seen when fixation crossed the lateral ossific nucleus. Conclusions Fixation of lateral condylar humeral fractures in children using either K‐wires or screws gives satisfactory results. Proponents of both techniques may find justification of their methods in our data, but prospective, randomized trials with long‐term follow‐up are required to confirm the findings, which suggest a higher rate of nonunion with K‐wire fixation.