Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunization with Radiation-Attenuated Plasmodium berghei Sporozoites Induces Liver cCD8α+DC that Activate CD8+T Cells against Liver-Stage Malaria

Immunization with radiation (γ)-attenuated Plasmodia sporozoites (γ-spz) confers sterile and long-lasting immunity against malaria liver-stage infection. In the P. berghei γ-spz model, protection is linked to liver CD8+ T cells that express an effector/memory (TEM) phenotype, (CD44hiCD45RBloCD62Llo ), and produce IFN-γ. However, neither the antigen presenting cells (APC) that activate these CD8+ TEM cells nor the site of their induction have been fully investigated. Because conventional (c)CD8α+ DC (a subset of CD11c+ DC) are considered the major inducers of CD8+ T cells, in this study we focused primarily on cCD8α+ DC from livers of mice immunized with Pb γ-spz and asked whether the cCD8α+ DC might be involved in the activation of CD8+ TEM cells. We demonstrate that multiple exposures of mice to Pb γ-spz lead to a progressive and nearly concurrent accumulation in the liver but not the spleen of both the CD11c+NK1.1− DC and CD8+ TEM cells. Upon adoptive transfer, liver CD11c+NK1.1− DC from Pb γ-spz-immunized mice induced protective immunity against sporozoite challenge. Moreover, in an in vitro system, liver cCD8α+ DC induced naïve CD8+ T cells to express the CD8+ TEM phenotype and to secrete IFN-γ. The in vitro induction of functional CD8+ TEM cells by cCD8α+ DC was inhibited by anti-MHC class I and anti-IL-12 mAbs. These data suggest that liver cCD8α+ DC present liver-stage antigens to activate CD8+ TEM cells, the pre-eminent effectors against pre-erythrocytic malaria. These results provide important implications towards a design of anti-malaria vaccines.
AEIPA: Docker-based system for Automated Evaluation of Image Processing Algorithms

Evaluation of an image processing algorithm (IPA) task is tedious and full of complexity. A lot of effort is spent to compare a new IPA with benchmark IPAs. Comparing with benchmark IPAs requires either implementing them from scratch or a lot of configurations. Also, setting up datasets for the evaluation consumes additional effort. Therefore, the need for a system to overcome the former overhead is imperative. In this paper, a design of a novel automated evaluation system, AEIPA, is proposed. AEIPA allows automatic evaluation of different IPAs using different datasets regardless the programming language of the IPAs. Also, automatic reporting module is provided to compare different IPAs results. The proposed system applies openness principal to enrich AEIPA with IPAs (using plugin-based concepts in Docker containers), and datasets.
Difference of Tissue Characteristics Between Early and Very Late Restenosis Lesions After Bare-Metal Stent Implantation: An Optical Coherence Tomography Study

Background— Although in-stent restenosis (ISR) after bare-metal stent (BMS) implantation peaks in the early phase, very late (VL) ISR occasionally is observed beyond a few years after BMS implantation. To date, this mechanism has not been fully clarified. Methods and Results— We compared the morphological characteristics of VL-ISR (>5 years, without restenosis within the first year) (n=43) to those of early (E) ISR (within the first year) (n=39) using optical coherence tomography (OCT). Qualitative restenotic tissue analysis included assessment of tissue structure (homogeneous or heterogeneous), presence of microvessels, disrupted intima with cavity, and intraluminal material and was performed at every 1-mm slice of the entire stent. The proportions of cross-sections with heterogeneous intima in the entire stent was significantly higher in the VL-ISR group compared to the E-ISR group (60.5±28.5% versus 5.8±11.5%, P<0.0001), with heterogeneous intima being more frequently observed at the minimum lumen area site in the VL-ISR group (90.7% versus 17.9%, P<0.0001). Disrupted intima with cavity and intraluminal material also were observed more frequently in the VL-ISR group for the entire stent (18.6% versus 0%, 20.9% versus 2.6%, P<0.03) as well as at the minimum lumen area site (13.9% versus 0%,16.2% versus 0%, P<0.03). Conclusions— The morphological characteristics of restenotic tissue in VL-ISR were different from those in E-ISR and similar to atherosclerotic plaque. In BMS, progression of the atherosclerotic process within neointima after stent implantation may be associated with VL-ISR.
Patients on weaning trials classified with support vector machines

The process of discontinuing mechanical ventilation is called weaning and is one of the most challenging problems in intensive care. An unnecessary delay in the discontinuation process and an early weaning trial are undesirable. This study aims to characterize the respiratory pattern through features that permit the identification of patients' conditions in weaning trials. Three groups of patients have been considered: 94 patients with successful weaning trials, who could maintain spontaneous breathing after 48 h (GSucc); 39 patients who failed the weaning trial (GFail) and 21 patients who had successful weaning trials, but required reintubation in less than 48 h (GRein). Patients are characterized by their cardiorespiratory interactions, which are described by joint symbolic dynamics (JSD) applied to the cardiac interbeat and breath durations. The most discriminating features in the classification of the different groups of patients (GSucc, GFail and GRein) are identified by support vector machines (SVMs). The SVM-based feature selection algorithm has an accuracy of 81% in classifying GSucc versus the rest of the patients, 83% in classifying GRein versus GSucc patients and 81% in classifying GRein versus the rest of the patients. Moreover, a good balance between sensitivity and specificity is achieved in all classifications.
Inspector Joins

The key idea behind Inspector Joins is that during the I/O partitioning phase of a hash-based join, we have the opportunity to look at the actual data itself and then use this knowledge in two ways: (1) to create specialized indexes, specific to the given query on the given data, for optimizing the CPU cache performance of the subsequent join phase of the algorithm, and (2) to decide which join phase algorithm best suits this specific query. We show how inspector joins, employing novel statistics and specialized indexes, match or exceed the performance of state-of-the-art cache-friendly hash join algorithms. For example, when run on eight or more processors, our experiments show that inspector joins offer 1.1-1.4X speedups over these previous algorithms, with the speedup increasing as the number of processors increases.
A new method for measuring continuity of care in family practice residencies.

Continuity of relationship between physician and patient is a fundamental aspect of the health care provided by family physicians. Measurement of continuity has proved difficult, however. Commonly applied measures, usual provider of care (UPC), continuity of care (COC), and the modified continuity index (MCI), either ignore key aspects of continuity or provide misleading results. Consequently, a new measure of continuity, the modified, modified continuity index (MMCI), with a possible range of 0 to 1, was developed to overcome these problems. It was applied to a residency model practice, in which mean MMCI was found to be 0.59 (range 0.3 to 1.0). Mean COC was . 41 and a mean MCI was . 44. Thus, unlike COC and MCI, MMCI suggests fairly good continuity of care in this practice while still implying possible improvement. The MMCI should be useful for enhancing training and practice of family medicine.
In vivo and in vitro mechanical properties of the sheep thoracic aorta in the perinatal period and adulthood.

The mammalian aorta undergoes rapid remodeling during the perinatal period and more gradual remodeling during subsequent development, but the implications of this remodeling for arterial mechanics are poorly understood. In this study in vivo and in vitro techniques were used to determine the static and viscoelastic properties of the thoracic aortas of 119-day-gestation fetal sheep (full term = 145 days), 21-day-old lambs, and adult sheep at control distending pressures and after 70% increases or 30% decreases in pressure. In the weeks surrounding birth, aortic wall tissue became substantially stiffer (static elastic modulus in vitro increased by 28%, and pressure wave velocity in vivo increased by 61%) but less viscous (pressure wave attenuation in vivo decreased by 46%, and viscoelastic phase angle in vitro decreased by 15%), whereas the wall thickness-to-radius ratio was unchanged. By contrast, modest changes in tissue viscoelasticity from neonatal to adult life were accompanied by a halving of the wall thickness-to-radius ratio from 0.19 ± 0.01 to 0.10 ± 0.01. The relative thinning of the vessel wall, combined with a doubling of blood pressure after birth, resulted in a 265% increase in aortic wall tensile stress over the period of study. We concluded that rapid remodeling in the perinatal period primarily alters the viscoelastic properties of aortic wall tissues, whereas more gradual postnatal remodeling largely affects vessel geometry.
Oxidation of cholesterol in low density and high density lipoproteins by cholesterol oxidase.

The cholesterol oxidase-catalyzed oxidation of cholesterol in native low density (LDL) and high density lipoproteins (HDL3) as well as in monolayers prepared from surface lipids of these particles, has been examined. The objective of the study was to compare the oxidizability of cholesterol, and to examine the effects of lipid packing on oxidation rates. When [3H]cholesterol-labeled lipoproteins were exposed to cholesterol oxidase (Streptomyces sp.), it was observed that LDL [3H]cholesterol was oxidized much faster than HDL3 [3H]cholesterol. This was true both at equal cholesterol concentration per enzyme unit, and at equal amounts of lipoprotein particles per enzyme unit. About 95% of lipoprotein [3H]cholesterol was available for oxidation. The complete degradation of lipoprotein sphingomyelin by sphingomyelinase (Staphylococcus aureus) resulted in a 10-fold increase in the rate of LDL [3H]cholesterol oxidation, whereas the effects on rates of HDL3 [3H]cholesterol oxidation were less dramatic. A monolayer study with LDL surface lipids indicated that degradation of sphingomyelin loosened the lipid packing, because the ceramide formed occupied a smaller surface area than the parent sphingomyelin, and since the condensing effect of cholesterol on sphingomyelin packing was lost. The effects of sphingomyelin degradation on lipid packing in monolayers of HDL3-derived surface lipids were difficult to determine from monolayer experiments. Based on the finding that cholesterol oxidases are surface pressure-sensitive with regard to their catalytic activity, these were used to estimate the surface pressure of intact LDL and HDL3. The cut-off surface pressure of a Brevibacterium enzyme was 25 mN/m and 20 mN/m in monolayers of LDL and HDL3-derived surface lipids, respectively. (ABSTRACT TRUNCATED AT 250 WORDS)
RobotCub: an open framework for research in embodied cognition

We describe a research initiative in embodied cognition that will create and exploit a 54 degree-of-freedom humanoid robot. This humanoid - RobotCub is currently being designed and the final system will be made freely available to the scientific community through an open systems GNU-like general public license. In addition, we describe a research agenda in cognitive systems that is based on the co-developmental learning through embodied physical interaction: exploration, manipulation, imitation, and communication. This agenda borrows heavily from experience in developmental psychology and cognitive neuroscience. All cognitive software associated with RobotCub will also be available under the open systems license.
An integrated model of the human cardiopulmonary system

We have developed a mathematical model of the human cardiopulmonary system that is able to simulate the normal functions of the cardiovascular and pulmonary systems, as well as their coupled interactions. Included in the model are descriptions of atrial and ventricular mechanics, the hemodynamics of the systemic and pulmonic circulations, baroreflex control of arterial pressure, airway and lung mechanics, as well as, gas transport at alveolar-capillary membrane. With the suitable parameter set, the integrated cardiopulmonary model yielded pressure, volume and flow waveforms that agree well with published data. In addition, The model demonstrated stability under large amplitude perturbations of the physiological variables, such as Valsalva Maneuver.
Control of Acid Resistance Pathways of Enterohemorrhagic Escherichia coli Strain EDL933 by PsrB, a Prophage-Encoded AraC-Like Regulator

ABSTRACT Enterohemorrhagic Escherichia coli (EHEC) O157:H7 causes bloody diarrhea and hemolytic-uremic syndrome (HUS) and is the most prevalent E. coli serotype associated with food-borne illness worldwide. This pathogen is transmitted via the fecal-oral route and has a low infectious dose that has been estimated to be between 10 and 100 cells. We and others have previously identified three prophage-encoded AraC-like transcriptional regulators, PatE, PsrA, and PsrB in the EHEC O157:H7 EDL933 strain. Our analysis showed that PatE plays an important role in facilitating survival of EHEC under a number of acidic conditions, but the contribution of PsrA and PsrB to acid resistance (AR) was unknown. Here, we investigated the involvement of PsrA and PsrB in the survival of E. coli O157:H7 in acid. Our results showed that PsrB, but not PsrA, enhanced the survival of strain EDL933 under various acidic conditions. Transcriptional analysis using promoter-lacZ reporters and electrophoretic mobility shift assays demonstrated that PsrB activates transcription of the hdeA operon, which encodes a major acid stress chaperone, by interacting with its promoter region. Furthermore, using a mouse model, we showed that expression of PsrB significantly enhanced the ability of strain EDL933 to overcome the acidic barrier of the mouse stomach. Taken together, our results indicate that EDL933 acquired enhanced acid tolerance via horizontally acquired regulatory genes encoding transcriptional regulators that activate its AR machinery.
Analysis of Privacy in Online Social Networks from the Graph Theory Perspective

The extremely widespread adoption of Online Social Networks (OSNs) raises many questions on privacy and access control. Regardless of the particular centralized or de-centralized nature of the OSN, the achievable security and privacy degree strongly depends on the graph-theoretical properties of the social graph representing the real friendship relations between the users. In this paper, we analyze the relationship between the social network graph topology and the achievable privacy. We observe three metrics, namely degree distribution, clustering coefficient and mixing time, and show that they give fundamental insights on the privacy degree of the OSN. We propose how to exploit these insight for the design of future privacy-friendly OSN.
Using MDE for the formal verification of embedded systems modeled by UML sequence diagrams

This work presents a formal verification methodology that adopts concepts from Model Driven Engineering (MDE) for the automatic generation of a network of timed automata from the functional specification of an embedded application described using UML class and sequence diagrams. By means of transformations on the UML model of the embedded system, a MOF-based representation for the network of timed automata is automatically obtained, which can be used as input to model checking tools, as Uppaal, in order to validate desired functional and temporal properties of the embedded system specification. Since the network of timed automata is automatically generated, the methodology can be very useful for the designer, making easier the debugging and formal validation of the system specification. The paper describes the defined transformations between models, which generate the network of timed automata as well as the textual input to the Uppaal model checker, and illustrates the use of the methodology with a case study to show the effectiveness of the approach.
Spatially adaptive super-resolution sharpening-demosaicking for a single solid-state color image sensor

We previously presented a demosaicking method that simultaneously removes image blurs caused by an optical low-pass filter used in a digital color camera with the Bayer's RGB color filter array. Our prototypal sharpening-demosaicking method restored only spatial frequency components lower than the Nyquist frequency corresponding to the mosaicking pattern, but it often produced ringing artifacts near color edges. To overcome this difficulty, afterward we introduced the super-resolution into the prototypal method. We formulated the recovery problem in the DFT domain, and then introduced the super-resolution by the total-variation (TV) image regularization into the sharpening-demosaicking approach. The TV-based super-resolution effectively demosaiced sharp color images while preserving such image structures as intensity values are almost constant along edges, without producing ringing artifacts. However, the TV image regularization works as the smoothing, and it tends to suppress small intensity variations excessively. Hence, the TV-based super-resolution sharpening-demosaicking approach tends to crash texture details in texture image regions. To remedy the drawback, in this paper we introduce a spatially adaptive technique that controls the TV image regularization according to the saliency of color edges around a pixel.
An interactive algorithm for asking and incorporating feature feedback into support vector machines

Standard machine learning techniques typically require ample training data in the form of labeled instances. In many situations it may be too tedious or costly to obtain sufficient labeled data for adequate classifier performance. However, in text classification, humans can easily guess the relevance of features, that is, words that are indicative of a topic, thereby enabling the classifier to focus its feature weights more appropriately in the absence of sufficient labeled data. We will describe an algorithm for tandem learning that begins with a couple of labeled instances, and then at each iteration recommends features and instances for a human to label. Tandem learning using an "oracle" results in much better performance than learning on only features or only instances. We find that humans can emulate the oracle to an extent that results in performance (accuracy) comparable to that of the oracle. Our unique experimental design helps factor out system error from human error, leading to a better understanding of when and why interactive feature selection works.
90Y-edotreotide for metastatic carcinoid refractory to octreotide.

PURPOSE Metastatic carcinoid is an incurable malignancy whose symptoms, such as diarrhea and flushing, can be debilitating and occasionally life-threatening. Although symptom relief is available with octreotide, the disease eventually becomes refractory to octreotide, leaving no proven treatment options. The goal of this study was to evaluate the clinical effect of using (90)Y-edotreotide to treat symptomatic patients with carcinoid tumors. PATIENTS AND METHODS Patients enrolled had metastatic carcinoid, at least one sign/symptom refractory to octreotide, and at least one measurable lesion. Study treatment consisted of three cycles of 4.4 GBq (120 mCi) (90)Y-edotreotide each, once every 6 weeks. RESULTS Ninety patients were enrolled in the study. Using Southwest Oncology Group tumor response criteria, 67 (74.%) of 90 patients (95% CI, 65.4% to 83.4%) were objectively stable or responded. A statistically significant linear trend toward improvement was demonstrated across all 12 symptoms assessed. Median progression-free survival was significantly greater (P = .03) for the 38 patients who had durable diarrhea improvement than the 18 patients who did not (18.2 v 7.9 months, respectively). Adverse events (AEs) were reported in 96.7% (87 of 90) of patients. These AEs consisted primarily of reversible GI events (76 of 90), which could be caused in part by concomitant administration of amino acid solution given to reduce radiation exposure to the kidneys. There was one case each of grade 3 oliguria and grade 4 renal failure, each lasting 6 days. CONCLUSION (90)Y-edotreotide treatment improved symptoms associated with malignant carcinoid among subjects with no treatment alternatives. Treatment was well-tolerated and had an acceptable expected AE profile.
The atypical development of metaphor and metonymy comprehension in children with autism

One of the most noticeable problems in autism involves the social use of language such as metaphor and metonymy, both of which are very common in daily language use. The present study is the first to investigate the development of metaphor and metonymy comprehension in autism. Eleven children with autism were compared to 17 typically developing children in a metaphor-metonymy comprehension task. Cross-sectional trajectory analyses were used to compare the development of metaphor and metonymy comprehension using a child-friendly story picture task. Trajectories were constructed linking task performance either to chronological age or to measures of mental age. Children with autism showed an impaired metaphor comprehension in relation to both chronological and mental age, whereas performance on metonymy was delayed and in line with their receptive vocabulary. Our results suggest that understanding of metaphors and metonyms are severely affected at all ages examined in the current study.
Galactinol and Raffinose Constitute a Novel Function to Protect Plants from Oxidative Damage1[W][OA]

Galactinol synthase (GolS) is a key enzyme in the synthesis of raffinose family oligosaccharides that function as osmoprotectants in plant cells. In leaves of Arabidopsis (Arabidopsis thaliana) plants overexpressing heat shock transcription factor A2 (HsfA2), the transcription of GolS1, -2, and -4 and raffinose synthase 2 (RS2) was highly induced; thus, levels of galactinol and raffinose increased compared with those in wild-type plants under control growth conditions. In leaves of the wild-type plants, treatment with 50 μm methylviologen (MV) increased the transcript levels of not only HsfA2, but also GolS1, -2, -3, -4, and -8 and RS2, -4, -5, and -6, the total activities of GolS isoenzymes, and the levels of galactinol and raffinose. GolS1- or GolS2-overexpressing Arabidopsis plants (Ox-GolS1-11, Ox-GolS2-8, and Ox-GolS2-29) had increased levels of galactinol and raffinose in the leaves compared with wild-type plants under control growth conditions. High intracellular levels of galactinol and raffinose in the transgenic plants were correlated with increased tolerance to MV treatment and salinity or chilling stress. Galactinol and raffinose effectively protected salicylate from attack by hydroxyl radicals in vitro. These findings suggest the possibility that galactinol and raffinose scavenge hydroxyl radicals as a novel function to protect plant cells from oxidative damage caused by MV treatment, salinity, or chilling.
Analysis of the SPV secure routing protocol: weaknesses and lessons

We analyze a secure routing protocol, Secure Path Vector (SPV), proposed in SIGCOMM 2004. SPV aims to provide authenticity for route announcements in the Border Gateway Protocol (BGP) using an efficient alternative to ordinary digital signatures, called constant-time signatures. Today, SPV is often considered the best cryptographic defense for BGP. We find subtle flaws in the design of SPV which lead to attacks that can be mounted by 60% of Autonomous Systems in the Internet. In addition, we study several of SPV's design decisions and assumptions and highlight the requirements for security of routing protocols. In light of our analysis, we reexamine the need for constant-time signatures and find that certain standard digital signature schemes can provide the same level of efficiency for route authenticity.