Miracle-dz/UniFAR-FTUs huggingface dataset:
Verification of security protocols based on multicast communication

Over an insecure network, agents need means to communicate securely. To these means we often call security protocols. Security protocols, although constructed over the arrangement of simple security blocks, normally target the yielding of complex goals. They seem simple at a first glance, but hide subtleties that allow them to be exploited. One way of trying to systematically capture such subtleties is through the usage of formal methods. The maturity of some methods for protocol verification is a fact today. But these methods are still not able to capture the whole set of security protocols being designed. With the convergence to an on-line world, new security goals are proposed and new protocols need to be designed. The evolution of formal verification methods becomes a necessity to keep the pace with this ongoing development. This thesis covers the Inductive Method and its extensions. The Inductive Method is a formalism to specify and verify security protocols based on structural induction and higher-order logic proofs. The account of our extensions comes to enable the Inductive Method to reason about non-Unicast communication and threshold cryptography. We developed a new set of theories capable of representing the entire set of known message casting frameworks. Our theories enable the Inductive Method to reason about a whole new set of protocols. We also specified a basic abstraction of threshold cryptography as a way of proving the extensibility of the method regarding new cryptographic primitives. We showed the feasibility of our specifications by revisiting a classic protocol, now verified under our framework. Secrecy verification under a mixed environment of Multicast and Unicast was also done for a Byzantine security protocol.
Perfect simulation of monotone systems for rare event probability estimation

This paper deals with the estimation of rare event probabilities in finite capacity queuing networks. The traditional product form property of Markovian queueing networks usually vanishes when capacity of queues are finite and clients are blocked or rejected. A new efficient simulation method, derived from Propp & Wilson (Propp 1996), perfect simulation, is applied in the finite capacity queue context. An algorithm directly samples states of the network according to the stationary distribution. This method is adapted for simulation of rare events, typically when events are described by an increasing subset of the state space. Provided that events of the network are monotone, monotonicity techniques are used to reduce the sampling time. Moreover, a stopping mechanism has been developed to interrupt the simulation when an increasing set has been reached. Then, for the estimation of a monotonous reward function, the simulation time could be reduced drastically as in (Vincent and Marchand 2004).
Cellular Localization, Expression, and Structure of the Nuclear Dot Protein 52

Nuclear dots containing PML and Sp100 proteins (NDs) play a role in the development of acute promyelocytic leukemia, are modified after infection with various viruses, and are autoimmunogenic in patients with primary biliary cirrhosis (PBC). PML and Sp100 gene expression is strongly enhanced by interferons (IFN). Based on immunostaining with a monoclonal antibody (mAb C8A2), a third protein, nuclear dot protein 52 (NDP52), was recently localized in NDs. Here we analyzed the cellular localization, expression, and structure of NDP52 in more detail. Our NDP52-specific sera revealed mainly cytoplasmic staining but no ND pattern, neither in untreated nor in IFN-treated cells. Cells transfected with NDP52 expression vectors showed exclusively cytoplasmic staining. In subcellular fractionation experiments, NDP52 was found in cytoplasmic and nuclear fractions. Unlike as described for Sp100 and PML, NDP52 mRNA and protein levels were only marginally enhanced by IFN γ and not enhanced at all by IFN β. NDP52 homodimerization but no heterodimerization with Sp100 or PML could be demonstrated. None of the 93 PBC sera tested contained autoantibodies against NDP52. Finally, mAb C8A2 reacted not only with NDP52 but also with a conformation-dependent epitope on the Sp100 protein. These data imply that NDP52 forms homodimers but no heterodimers with Sp100 and PML, lacks autoantigenicity in PBC, localizes mainly in the cytoplasm, and is associated with the nucleus, but not with NDs. Finally, unlike Sp100 and PML, NDP52 expression is neither markedly enhanced nor localization detectably altered by type I and II IFNs.
Investigating Individual- and Area-Level Socioeconomic Gradients of Pulse Pressure among Normotensive and Hypertensive Participants

Socioeconomic status is a strong predictor of cardiovascular disease. Pulse pressure, the difference between systolic and diastolic blood pressure, has been identified as an important predictor of cardiovascular risk even after accounting for absolute measures of blood pressure. However, little is known about the social determinants of pulse pressure. The aim of this study was to examine individual- and area-level socioeconomic gradients of pulse pressure in a sample of 2,789 Australian adults. Using data from the North West Adelaide Health Study we estimated the association between pulse pressure and three indices of socioeconomic status (education, income and employment status) at the area and individual level for hypertensive and normotensive participants, using Generalized Estimating Equations. In normotensive individuals, area-level education (estimate: −0.106; 95% CI: −0.172, −0.041) and individual-level income (estimate: −1.204; 95% CI: −2.357, −0.050) and employment status (estimate: −1.971; 95% CI: −2.894, −1.048) were significant predictors of pulse pressure, even after accounting for the use of medication and lifestyle behaviors. In hypertensive individuals, only individual-level measures of socioeconomic status were significant predictors of pulse pressure (education estimate: −2.618; 95% CI: −4.878, −0.357; income estimate: −1.683, 95% CI: −3.743, 0.377; employment estimate: −2.023; 95% CI: −3.721, −0.326). Further research is needed to better understand how individual- and area-level socioeconomic status influences pulse pressure in normotensive and hypertensive individuals.
Tumor treating fields: concept, evidence and future

Introduction: Local control is fundamental, both for the curative as well as the palliative treatment of cancer. Tumor treating fields (TTFields) are low intensity (1 – 2 V/cm), intermediate frequency (100 – 200 kHz) alternating electric fields administered using insulated electrodes placed on the skin surrounding the region of a malignant tumor. TTFields were shown to destroy cells within the process of mitosis via apoptosis, thereby inhibiting tumor growth. TTFields have no effect on non-dividing cells. Areas covered: This article reviews in vitro and in vivo preclinical studies, demonstrating the activity of TTFields both as a monotherapy as well as in combination with several cytotoxic agents. Furthermore, it summarizes the clinical experience with TTFields, mainly in two indications: one in recurrent glioblastoma multiforme: in a large prospective randomized Phase III trial TTFields was compared with best standard care (including chemotherapy): TTFields significantly improved median overall survival (OS) compared with standard therapy (7.8 vs 6.1 months) for the patients treated per protocol. Importantly, quality of life was also better in the TTFields group. The second indication was a Phase II study in second-line non-small cell lung cancer, where TTFields was administered concomitantly with pemetrexed. This combination resulted in an excellent median OS of 13.8 months. Interestingly, the progression-free survival (PFS) within the area of the TTFields was 28, however, outside the TTFields the PFS was only 22 weeks. Expert opinion: The proof of concept of TTFields has been well demonstrated in the preclinical setting, and the clinical data seem promising in various tumor types. The side effects of TTFields were minimal and in general consisted of skin reaction to the electrodes. There are a number of ways in which TTFields could be further evaluated, for example, in combination with chemotherapy, as a maintenance treatment, or as a salvage therapy if radiotherapy or surgery is not possible. While more clinical data are clearly needed, TTFields is an emerging and promising novel treatment concept.
Stabilized Column Generation for the Rooted Delay-Constrained Steiner Tree Problem

We consider the rooted delay-constrained Steiner tree problem which arises for example in the design of centralized multicasting networks where quality of service constraints are of concern. We present a path based integer linear programming formulation which has already been considered in the literature for the spanning tree variant. Solving its linear relaxation by column generation has so far been regarded as not competitive due to long computational times needed. In this work, we show how to significantly accelerate the column generation process using two different stabilization techniques. Computational results indicate that due to the achieved speed-up our approach outperforms so-far proposed methods.
An alcohol-sensing site in the calcium- and voltage-gated, large conductance potassium (BK) channel

Significance Alcohol (ethanol) is one of the most widely consumed psychoactive agents. Ethanol’s targets in the body include voltage/calcium-gated, large conductance potassium (BK) channels. Here we identified and characterized for the first time an alcohol-sensing site in BK channel-forming proteins. Our discovery opens new ground for rational design of tools to counteract the effects of ethanol intoxication that are mediated by BK channels. We anticipate that genetic or epigenetic modifications of the BK channel ethanol-recognition site could explain differential sensitivity to ethanol. Finally, since individuals with low sensitivity to ethanol are prone to developing heavy drinking habits, genetic, epigenetic or other mechanisms acting at the newly identified BK channel ethanol-recognition site might be considered as potential predictors for developing alcohol preference. Ethanol alters BK (slo1) channel function leading to perturbation of physiology and behavior. Site(s) and mechanism(s) of ethanol–BK channel interaction are unknown. We demonstrate that ethanol docks onto a water-accessible site that is strategically positioned between the slo1 calcium-sensors and gate. Ethanol only accesses this site in presence of calcium, the BK channel’s physiological agonist. Within the site, ethanol hydrogen-bonds with K361. Moreover, substitutions that hamper hydrogen bond formation or prevent ethanol from accessing K361 abolish alcohol action without altering basal channel function. Alcohol interacting site dimensions are approximately 10.7 × 8.6 × 7.1 Å, accommodating effective (ethanol-heptanol) but not ineffective (octanol, nonanol) channel activators. This study presents: (i) to our knowledge, the first identification and characterization of an n-alkanol recognition site in a member of the voltage-gated TM6 channel superfamily; (ii) structural insights on ethanol allosteric interactions with ligand-gated ion channels; and (iii) a first step for designing agents that antagonize BK channel-mediated alcohol actions without perturbing basal channel function.
Exaggerated Left Ventricular Dilation and Reduced Collagen Deposition After Myocardial Infarction in Mice Lacking Osteopontin

Abstract— Osteopontin (OPN), an extracellular matrix protein, is expressed in the myocardium with hypertrophy and failure. We tested the hypothesis that OPN plays a role in left ventricular (LV) remodeling after myocardial infarction (MI). Accordingly, OPN expression and LV structural and functional remodeling were determined in wild-type (WT) and OPN knockout (KO) mice 4 weeks after MI. Northern analysis showed increased OPN expression in the infarcted region, peaking 3 days after MI and gradually decreasing over the next 28 days. In the remote LV, OPN expression was biphasic, with peaks at 3 and 28 days. In situ hybridization and immunohistochemical analyses showed increased OPN mRNA and protein primarily in the interstitium. Infarct size, heart weight, and survival were similar in KO and WT mice after MI (P =NS), whereas the lung wet weight/dry weight ratio was increased in the KO mice (P <0.005 versus sham-operated mice). Peak LV developed pressure was reduced to a similar degree after MI in the KO and WT mice. The number of terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling (TUNEL)-positive myocytes was similar in KO and WT mice after MI. In contrast, post-MI LV chamber dilation was approximately twice as great in KO versus WT mice (P <0.001). Myocyte length increased after MI in WT mice (P <0.001) but not in KO mice. Electron microscopy showed increased collagen content in WT mice after MI but not in KO mice after MI. Type I collagen content was increased ≈3-fold and ≈7-fold in remote and infarcted regions, respectively, of WT hearts after MI but not in KO hearts (P <0.01 versus WT hearts). Likewise, Northern analyses showed increased collagen I(&agr;1) mRNA after MI in remote regions of WT hearts but not in KO hearts. Thus, increased OPN expression plays an important role in regulating post-MI LV remodeling, at least in part, by promoting collagen synthesis and accumulation.
Modalities and Complications Associated With the Use of High-Flow Nasal Cannula: Experience in a Pediatric ICU

BACKGROUND: High-flow nasal cannula (HFNC) therapy is increasingly used in pediatric ICUs as an intermediate level of support between conventional oxygen delivery and noninvasive ventilation (NIV). The safety of HFNC has seldom been studied, and some cases of barotrauma have been reported. This retrospective study aims to describe HFNC use in a tertiary care pediatric ICU, with a focus on the complications associated with this therapy. METHODS: Between January 2013 and January 2014, all children <18 y old treated with HFNC in the pediatric ICU were included. Demographic data, HFNC settings, chest radiograph reports, and blood gas values were gathered from the electronic medical records. Episodes of pneumothorax, pneumomediastinum, and significant epistaxis were noted. Pneumothorax was distinguished from chest tube-related air leak (frequent after cardiac surgery), which was defined as a small pneumothorax with no clinical impact that resolved spontaneously after chest tube removal. RESULTS: During the 1-y study period, there were 177 HFNC episodes, involving 145 subjects with a median (interquartile range) age of 8 (2–28) months. HFNC was used as primary support in 31% of episodes, after extubation in 36% and after NIV in 18%. HFNC was administered exclusively for nitric oxide delivery in 16% of episodes. Two children (1%) developed new pneumothoraces that required chest tube insertion, whereas 5 (3%) chest tube-related air leaks were noted. One (0.6%) episode of significant epistaxis was noted. Among 6 preexisting pneumothoraces, none worsened under HFNC. Failure of HFNC occurred in 32 episodes, requiring transition to NIV in 28 cases and endotracheal intubation in 5 cases. CONCLUSIONS: Support with HFNC following a clinical protocol in pediatric ICUs was associated with a relatively low rate of complications. Since HFNC use is increasing, further evidence is needed to confirm its efficacy and safety.
The Staphylococci Phages Family: An Overview

Due to their crucial role in pathogenesis and virulence, phages of Staphylococcus aureus have been extensively studied. Most of them encode and disseminate potent staphylococcal virulence factors. In addition, their movements contribute to the extraordinary versatility and adaptability of this prominent pathogen by improving genome plasticity. In addition to S. aureus, phages from coagulase-negative Staphylococci (CoNS) are gaining increasing interest. Some of these species, such as S. epidermidis, cause nosocomial infections and are therefore problematic for public health. This review provides an overview of the staphylococcal phages family extended to CoNS phages. At the morphological level, all these phages characterized so far belong to the Caudovirales order and are mainly temperate Siphoviridae. At the molecular level, comparative genomics revealed an extensive mosaicism, with genes organized into functional modules that are frequently exchanged between phages. Evolutionary relationships within this family, as well as with other families, have been highlighted. All these aspects are of crucial importance for our understanding of evolution and emergence of pathogens among bacterial species such as Staphylococci.
Hepatocellular cancer as indication for liver transplantation: pushing beyond Milan

Purpose of reviewThe Milan criteria have been considered the gold standard for the selection of patients with hepatocellular cancer (HCC) for liver transplantation. However, there is growing evidence that tumor burden is just one of many factors that predict HCC recurrence after liver transplantation. Recent findingsModest expansion beyond Milan criteria, including the University of California, San Francisco and up-to-7 criteria, appear to yield acceptable posttransplantation outcomes, but their implementation should achieve a minimal survival threshold to not harm non-HCC patients awaiting liver transplantation. Down-staging of HCC patients into Milan criteria appears to produce excellent posttransplant outcomes similar to those always within Milan criteria. Incorporating &agr;-fetoprotein into the selection scheme may further improve posttransplant outcome. Response to local regional therapy (LRT) may help identify candidates who would do well after liver transplantation even if their initial tumor burden exceeds Milan criteria. Conversely, tumor progression despite LRT is a poor prognostic factor for tumors within or beyond Milan criteria. Under the ‘ablate and wait’ principle, a sufficient length of time to observe tumor behavior is essential to avoid transplanting those with aggressive tumors too quickly, as these patients would likely do poorly after liver transplantation. SummaryTumor size and number tell only a partial tale of the characteristics that predict posttransplant outcomes. To this end, successful down-staging appears to carry equivalent posttransplantation outcomes to those always within Milan criteria. Accounting for tumor biology with &agr;-fetoprotein and response to LRT as well as assessing modifiable risk factors such as wait time is crucial to improve selection criteria and improve posttransplantation outcomes.
Docosahexaenoic acid preserves visual function by maintaining correct disc morphology in retinal photoreceptor cells

Docosahexaenoic acid (DHA) has essential roles in photoreceptor cells in the retina and is therefore crucial to healthy vision. Although the influence of dietary DHA on visual acuity is well known and the retina has an abundance of DHA-containing phospholipids (PL-DHA), the mechanisms associated with DHA's effects on visual function are unknown. We previously identified lysophosphatidic acid acyltransferase 3 (LPAAT3) as a PL-DHA biosynthetic enzyme. Here, using comprehensive phospholipid analyses and imaging mass spectroscopy, we found that LPAAT3 is expressed in the inner segment of photoreceptor cells and that PL-DHA disappears from the outer segment in the LPAAT3-knock-out mice. Dynamic light-scattering analysis of liposomes and molecular dynamics simulations revealed that the physical characteristics of DHA reduced membrane-bending rigidity. Following loss of PL-DHA, LPAAT3-knock-out mice exhibited abnormalities in the retinal layers, such as incomplete elongation of the outer segment and decreased thickness of the outer nuclear layers and impaired visual function, as well as disordered disc morphology in photoreceptor cells. Our results indicate that PL-DHA contributes to visual function by maintaining the disc shape in photoreceptor cells and that this is a function of DHA in the retina. This study thus provides the reason why DHA is required for visual acuity and may help inform approaches for overcoming retinal disorders associated with DHA deficiency or dysfunction.
A Hybrid Approach to Build Prioritized Pairwise Interaction Test Suites

Traditional interaction testing aims to build test suites that cover all t-way interactions of inputs. But in many test scenarios, the entire test suites cannot be fully run due to the limited budget. Therefore it is necessary to take the importance of interactions into account and prioritize these tests of the test suite. In the paper, we use the hybrid approach to build prioritized pairwise interaction test suites (PITS). It adopts a one-test-at-a-time strategy to construct final test suites. But to generate a single test it firstly generates a candidate test and then applies a specific metaheuristic search strategy to enhance this test. Here we experiment four different metaheuristic search strategies. In the experiments, we compare our approach to weighted density algorithm (WDA). Meanwhile, we also analyze the effectiveness of four different search strategies and the effectiveness of the increasing iterations. Empirical results demonstrate the effectiveness of our proposed approach. Keywords-prioritized interaction test suites; greedy algorithm; metaheuristic search
Both younger and older adults have difficulty updating emotional memories.

OBJECTIVE The main purpose of the study was to examine whether emotion impairs associative memory for previously seen items in older adults, as previously observed in younger adults. METHOD Thirty-two younger adults and 32 older adults participated. The experiment consisted of 2 parts. In Part 1, participants learned picture-object associations for negative and neutral pictures. In Part 2, they learned picture-location associations for negative and neutral pictures; half of these pictures were seen in Part 1 whereas the other half were new. The dependent measure was how many locations of negative versus neutral items in the new versus old categories participants remembered in Part 2. RESULTS Both groups had more difficulty learning the locations of old negative pictures than of new negative pictures. However, this pattern was not observed for neutral items. DISCUSSION Despite the fact that older adults showed overall decline in associative memory, the impairing effect of emotion on updating associative memory was similar between younger and older adults.
Patterns of admissions for children with special needs to the paediatric assessment unit

Background: Children with special needs present a challenge to those involved in their care. Aims: To determine the role of the acute assessment unit for these children. Methods: Case notes and other records were reviewed for information on referrals, admissions, readmission within 7 and 28 days, length of stay, and management of 86 children registered for special needs. The study covered five years between January 1997 and December 2001. Results: Of the 86 children, 48 (58%) were boys; 62 children had cerebral palsy and 52 learning disability. There were 914 episodes, with 44% of these being self referrals and 35% from general practitioners; 35.5% of the episodes were managed in the assessment unit. The average length of stay in hospital was 5 days, ranging from <24 hours to 63 days; 37.5% of those admitted to the ward stayed for less than 24 hours. Respiratory tract infections and seizures were the main reasons for referral and admission. Conclusion: Children with special needs tend to have a predictable pattern of conditions requiring inpatient care. One third of the inpatients episodes did not need a prolonged stay in hospital. This latter group of children could be managed at home with support of community nurses. Integrated care pathways need to be developed to minimise disruption to their lives. Appropriate resources should be made available to achieve these goals.