Darwinian Data Structure Selection

Data structure selection and tuning is laborious but can vastly improve an application's performance and memory footprint. Some data structures share a common interface and enjoy multiple implementations. We call them Darwinian Data Structures (DDS), since we can subject their implementations to survival of the fittest. We introduce ARTEMIS a multi-objective, cloud-based search-based optimisation framework that automatically finds optimal, tuned DDS modulo a test suite, then changes an application to use that DDS. ARTEMIS achieves substantial performance improvements for \emph{every} project in $5$ Java projects from DaCapo benchmark, $8$ popular projects and $30$ uniformly sampled projects from GitHub. For execution time, CPU usage, and memory consumption, ARTEMIS finds at least one solution that improves \emph{all} measures for $86\%$ ($37/43$) of the projects. The median improvement across the best solutions is $4.8\%$, $10.1\%$, $5.1\%$ for runtime, memory and CPU usage. These aggregate results understate ARTEMIS's potential impact. Some of the benchmarks it improves are libraries or utility functions. Two examples are gson, a ubiquitous Java serialization framework, and xalan, Apache's XML transformation tool. ARTEMIS improves gson by $16.5$\%, $1\%$ and $2.2\%$ for memory, runtime, and CPU; ARTEMIS improves xalan's memory consumption by $23.5$\%. \emph{Every} client of these projects will benefit from these performance improvements.Comment: 11 page

Effects of time window size and placement on the structure of aggregated networks

Complex networks are often constructed by aggregating empirical data over time, such that a link represents the existence of interactions between the endpoint nodes and the link weight represents the intensity of such interactions within the aggregation time window. The resulting networks are then often considered static. More often than not, the aggregation time window is dictated by the availability of data, and the effects of its length on the resulting networks are rarely considered. Here, we address this question by studying the structural features of networks emerging from aggregating empirical data over different time intervals, focussing on networks derived from time-stamped, anonymized mobile telephone call records. Our results show that short aggregation intervals yield networks where strong links associated with dense clusters dominate; the seeds of such clusters or communities become already visible for intervals of around one week. The degree and weight distributions are seen to become stationary around a few days and a few weeks, respectively. An aggregation interval of around 30 days results in the stablest similar networks when consecutive windows are compared. For longer intervals, the effects of weak or random links become increasingly stronger, and the average degree of the network keeps growing even for intervals up to 180 days. The placement of the time window is also seen to affect the outcome: for short windows, different behavioural patterns play a role during weekends and weekdays, and for longer windows it is seen that networks aggregated during holiday periods are significantly different.Comment: 19 pages, 11 figure

Differential cargo mobilisation within Weibel-Palade bodies after transient fusion with the plasma membrane.

Inflammatory chemokines can be selectively released from Weibel-Palade bodies (WPBs) during kiss-and-run exocytosis. Such selectivity may arise from molecular size filtering by the fusion pore, however differential intra-WPB cargo re-mobilisation following fusion-induced structural changes within the WPB may also contribute to this process. To determine whether WPB cargo molecules are differentially re-mobilised, we applied FRAP to residual post-fusion WPB structures formed after transient exocytosis in which some or all of the fluorescent cargo was retained. Transient fusion resulted in WPB collapse from a rod to a spheroid shape accompanied by substantial swelling (>2 times by surface area) and membrane mixing between the WPB and plasma membranes. Post-fusion WPBs supported cumulative WPB exocytosis. To quantify diffusion inside rounded organelles we developed a method of FRAP analysis based on image moments. FRAP analysis showed that von Willebrand factor-EGFP (VWF-EGFP) and the VWF-propolypeptide-EGFP (Pro-EGFP) were immobile in post-fusion WPBs. Because Eotaxin-3-EGFP and ssEGFP (small soluble cargo proteins) were largely depleted from post-fusion WPBs, we studied these molecules in cells preincubated in the weak base NH4Cl which caused WPB alkalinisation and rounding similar to that produced by plasma membrane fusion. In these cells we found a dramatic increase in mobilities of Eotaxin-3-EGFP and ssEGFP that exceeded the resolution of our method (∼ 2.4 µm2/s mean). In contrast, the membrane mobilities of EGFP-CD63 and EGFP-Rab27A in post-fusion WPBs were unchanged, while P-selectin-EGFP acquired mobility. Our data suggest that selective re-mobilisation of chemokines during transient fusion contributes to selective chemokine secretion during transient WPB exocytosis. Selective secretion provides a mechanism to regulate intravascular inflammatory processes with reduced risk of thrombosis

Absolute lymphocyte and neutrophil counts in neonatal ischemic brain injury

Objectives: This study aimed to identify differences in absolute neutrophils, lymphocytes, and neutrophil-to-lymphocyte ratio between neonates with two forms of ischemic brain injury, hypoxic-ischemic encephalopathy, and acute ischemic stroke, compared to controls. We also aimed to determine whether this neutrophil/lymphocyte response pattern is associated with disease severity or is a consequence of the effects of total-body cooling, an approved treatment for moderate-to-severe hypoxic-ischemic encephalopathy. Methods: A retrospective chart review of 101 neonates with hypoxic-ischemic encephalopathy+total-body cooling (n=26), hypoxic-ischemic encephalopathy (n=12), acute ischemic stroke (n=15), and transient tachypnea of the newborn (n=48) was conducted; transient tachypnea of the newborn neonates were used as the control group. Absolute neutrophil count and absolute lymphocyte count at three time-intervals (0–12, 12–36, and 36–60 h after birth) were collected, and neutrophilto-lymphocyte ratio was calculated. Results: Hypoxic-ischemic encephalopathy+total-body cooling neonates demonstrated significant time-interval-dependent changes in absolute lymphocyte count and neutrophil-to-lymphocyte ratio levels compared to transient tachypnea of the newborn and acute ischemic stroke patients. Pooled analysis of absolute lymphocyte count for neonates with acute ischemic stroke and hypoxic-ischemic encephalopathy (not hypoxic-ischemic encephalopathy+total-body cooling) revealed that absolute lymphocyte count changes occurring at 0–12h are likely due to disease progression, rather than total-body cooling treatment. Conclusion: These data suggest that the neutrophil/lymphocyte response is modulated following neonatal ischemic brain injury, representing a possible target for therapeutic intervention. However, initial severity of hypoxic-ischemic encephalopathy among these patients could also account for the observed changes in the immune response to injury. Thus, additional work to clarify the contributions of cooling therapy and disease severity to neutrophil/lymphocyte response following hypoxicischemic encephalopathy in neonates is warranted

Evolution of mal ABC transporter operons in the Thermococcales and Thermotogales

<p>Abstract</p> <p>Background</p> <p>The <it>mal </it>genes that encode maltose transporters have undergone extensive lateral transfer among ancestors of the archaea <it>Thermococcus litoralis </it>and <it>Pyrococcus furiosus</it>. Bacterial hyperthermophiles of the order <it>Thermotogales </it>live among these archaea and so may have shared in these transfers. The genome sequence of <it>Thermotoga maritima </it>bears evidence of extensive acquisition of archaeal genes, so its ancestors clearly had the capacity to do so. We examined deep phylogenetic relationships among the <it>mal </it>genes of these hyperthermophiles and their close relatives to look for evidence of shared ancestry.</p> <p>Results</p> <p>We demonstrate that the two maltose ATP binding cassette (ABC) transporter operons now found in <it>Tc. litoralis </it>and <it>P. furiosus </it>(termed <it>mal </it>and <it>mdx </it>genes, respectively) are not closely related to one another. The <it>Tc. litoralis </it>and <it>P. furiosus mal </it>genes are most closely related to bacterial <it>mal </it>genes while their respective <it>mdx </it>genes are archaeal. The genes of the two <it>mal </it>operons in <it>Tt. maritima </it>are not related to genes in either of these archaeal operons. They are highly similar to one another and belong to a phylogenetic lineage that includes <it>mal </it>genes from the enteric bacteria. A unique domain of the enteric MalF membrane spanning proteins found also in these <it>Thermotogales </it>MalF homologs supports their relatively close relationship with these enteric proteins. Analyses of genome sequence data from other <it>Thermotogales </it>species, <it>Fervidobacterium nodosum</it>, <it>Thermosipho melanesiensis</it>, <it>Thermotoga petrophila</it>, <it>Thermotoga lettingae</it>, and <it>Thermotoga neapolitana</it>, revealed a third apparent <it>mal </it>operon, absent from the published genome sequence of <it>Tt. maritima </it>strain MSB8. This third operon, <it>mal3</it>, is more closely related to the <it>Thermococcales</it>' bacteria-derived <it>mal </it>genes than are <it>mal1 </it>and <it>mal2</it>. <it>F. nodosum</it>, <it>Ts. melanesiensis</it>, and <it>Tt. lettingae </it>have only one of the <it>mal1-mal2 </it>paralogs. The <it>mal2 </it>operon from an unknown species of <it>Thermotoga </it>appears to have been horizontally acquired by a <it>Thermotoga </it>species that had only <it>mal1</it>.</p> <p>Conclusion</p> <p>These data demonstrate that the <it>Tc. litoralis </it>and <it>P. furiosus mdx </it>maltodextrin transporter operons arose in the <it>Archaea </it>while their <it>mal </it>maltose transporter operons arose in a bacterial lineage, but not the same lineage as the two maltose transporter operons found in the published <it>Tt. maritima </it>genome sequence. These <it>Tt. maritima </it>maltose transporters are phylogenetically and structurally similar to those found in enteric bacteria and the <it>mal2 </it>operon was horizontally transferred within the <it>Thermotoga </it>lineage. Other <it>Thermotogales </it>species have a third <it>mal </it>operon that is more closely related to the bacterial <it>Thermococcales mal </it>operons, but the data do not support a recent horizontal sharing of that operon between these groups.</p

Continuous and transparent multimodal authentication: reviewing the state of the art

Individuals, businesses and governments undertake an ever-growing range of activities online and via various Internet-enabled digital devices. Unfortunately, these activities, services, information and devices are the targets of cybercrimes. Verifying the user legitimacy to use/access a digital device or service has become of the utmost importance. Authentication is the frontline countermeasure of ensuring only the authorized user is granted access; however, it has historically suffered from a range of issues related to the security and usability of the approaches. They are also still mostly functioning at the point of entry and those performing sort of re-authentication executing it in an intrusive manner. Thus, it is apparent that a more innovative, convenient and secure user authentication solution is vital. This paper reviews the authentication methods along with the current use of authentication technologies, aiming at developing a current state-of-the-art and identifying the open problems to be tackled and available solutions to be adopted. It also investigates whether these authentication technologies have the capability to fill the gap between high security and user satisfaction. This is followed by a literature review of the existing research on continuous and transparent multimodal authentication. It concludes that providing users with adequate protection and convenience requires innovative robust authentication mechanisms to be utilized in a universal level. Ultimately, a potential federated biometric authentication solution is presented; however it needs to be developed and extensively evaluated, thus operating in a transparent, continuous and user-friendly manner

OPTIMIZATION OF TOOL GEOMETRY AND CUTTING PARAMETERS FOR TURNING OPERATIONS BASED ON RESPONSE SURFACE METHODOLOGY

ABSTRACT This investigation focuses on the influence of tool geometry (nose radius) and cutting parameters (cutting speed, feed and depth of cut) on the surface finish obtained in turning of mild Steel. In order to find the effect of tool geometry and cutting parameters on the surface roughness during turning, response surface methodology (RSM) with (3 4 ) full factorial design was used and a prediction model was developed related to average surface roughness (Ra) using experimental data. The results indicated that the tool nose radius was the dominant factor on surface roughness. In addition, a good agreement between the predicted and measured surface roughness was observed. Therefore, the developed model can be effectively used to predict the surface roughness on the machining of mild steel with 95 % confidence interval within ranges of parameter studied

Lithium and GSK3-β promoter gene variants influence white matter microstructure in bipolar disorder

Lithium is the mainstay for the treatment of bipolar disorder (BD) and inhibits glycogen synthase kinase 3-β (GSK3-β). The less active GSK3-β promoter gene variants have been associated with less detrimental clinical features of BD. GSK3-β gene variants and lithium can influence brain gray matter structure in psychiatric conditions. Diffusion tensor imaging (DTI) measures of white matter (WM) integrity showed widespred disruption of WM structure in BD. In a sample of 70 patients affected by a major depressive episode in course of BD, we investigated the effect of ongoing long-term lithium treatment and GSK3-β promoter rs334558 polymorphism on WM microstructure, using DTI and tract-based spatial statistics with threshold-free cluster enhancement. We report that the less active GSK3-β rs334558*C gene-promoter variants, and the long-term administration of the GSK3-β inhibitor lithium, were associated with increases of DTI measures of axial diffusivity (AD) in several WM fiber tracts, including corpus callosum, forceps major, anterior and posterior cingulum bundle (bilaterally including its hippocampal part), left superior and inferior longitudinal fasciculus, left inferior fronto-occipital fasciculus, left posterior thalamic radiation, bilateral superior and posterior corona radiata, and bilateral corticospinal tract. AD reflects the integrity of axons and myelin sheaths. We suggest that GSK3-β inhibition and lithium could counteract the detrimental influences of BD on WM structure, with specific benefits resulting from effects on specific WM tracts contributing to the functional integrity of the brain and involving interhemispheric, limbic, and large frontal, parietal, and fronto-occipital connections

Retroperitoneal Perforation of the Appendix Presenting as a Right Thigh Abscess

A rare case of a retroperitoneal rupture of the appendix is being reported here. A 53-year-old male presented to us with a right sided thigh abscess. There were not any abdominal complaints at presentation. There was continuous discharge after incision and drainage from the thigh. Isolation, in culture, of an enteric bacterium from the pus prompted an evaluation of the gastrointestinal tract as a possible source. An MRI scan revealed fluid tracking from the right paracolic gutter over the psoas sheath and paraspinal muscle into the thigh. A CT scan revealed the perforation at the base of the appendix into the retroperitoneum. At laparotomy the above findings were confirmed. A segmental ileocaecal resection was done. The patient made an uneventful recovery. The absence of abdominal symptoms at presentation leads to delay in diagnosis in such cases. Nonresolving thigh and groin abscesses should lead to the evaluation of the gastrointestinal tract as origin. Diagnostic clues may also be provided by culture reports what as happened in this case

Arthroscopic Treatment of Shoulder Stiffness with Rotator Cuff Repair Yields Similar Outcomes to Isolated Rotator Cuff Repair

Purpose: To compare patient-reported and surgical outcome measures in patients with and without secondary shoulder stiffness (SSS) undergoing rotator cuff repair (RCR). Methods: Patients undergoing rotator cuff repair from 2014 to 2020 with complete patient-reported outcome measures (PROMs) by the short-form 12 survey (SF-12) were retrospectively reviewed to identify if operative intervention for SSS was performed alongside the RCR. Those patients with operative intervention for SSS were propensity matched to a group without prior intervention for stiffness by age, sex, laterality, body mass index, diabetes mellitus status, and the presence of a thyroid disorder. The groups were compared by rotator cuff tear (RCT) size, surgical outcomes, further surgical intervention, rotator cuff retear rate, postoperative range of motion (ROM), and SF-12 results at one year after surgery. Delta values were calculated for component scores of the SF-12 and ROM values by subtracting the preoperative result from the postoperative result. Results: A total of 89 patients with SSS were compared to 156 patients in the control group at final analysis. SSS group experienced a significant improvement by the delta mental health component score (MCS-12) of the SF-12 survey that was not seen in the control group (p=0.005 to p=0.539). Both groups experienced significant improvement by the delta physical health component score (PCS-12) of the SF-12 survey (SSS: 7.68, p\u3c0.001; control: 6.95, p\u3c0.001). The SSS group also experienced greater improvement of their forward flexion (25.80 vs 12.9°, p-0.005) and external rotation (7.13° vs 1.65°, p=0.031) ROM than the control group. Conclusions: Operative intervention of SSS at the time of RCR has equivalent postoperative outcomes by the SF-12 survey when compared to patients undergoing RCR without preoperative stiffness