Miracle-dz/UniFAR-FTUs huggingface dataset:
Automatic generation of model based tests for a class of security properties

This paper is a contribution to the problem of getting confident in the fact that an implementation correctly meets a security policy assigned to it. To do so, we compute tests that exercise security properties issued from the security policy. We proceed by model based testing. Classically, we use a functional model that formalizes the functional specification. But we also use a second model, in the shape of security properties, that formalize a part of the security policy. Tests are computed from the security properties, with the formal functional model as an oracle. We first formalize the informal security requirements as regular expressions. Then we introduce mutations in the regular expressions as to reflect the specific situations in which we intend to test the security properties. These mutated regular expression are unfolded into abstract test sequences. We present a set of four mutation rules that apply to a class of properties that we call sequencing properties, and we experiment our method on a standard in the smart card domain named IAS, for Identification, Authentication and electronic Signature.
Amplification of Galactic Magnetic Fields by the Cosmic-Ray-driven Dynamo

We present the first numerical model of the magnetohydrodynamic cosmic-ray-driven dynamo of the type proposed by Parker in 1992. The driving force of the amplification process comes from cosmic rays injected into the Galactic disk in randomly distributed spherical regions representing supernova remnants. The underlying disk is differentially rotating. An explicit resistivity is responsible for the dissipation of the small-scale magnetic field component. We obtain amplification of the large-scale magnetic field on a timescale of 250 Myr.
Vitamin A, nutrition, and health values of algae: Spirulina, Chlorella, and Dunaliella

Spirulina, chlorella, and dunalliella are unicellular algae that are commercially produced worldwide. These algae are concentrated sources of carotenoids (especially provitamin A carotenoids) and other nutrients, such as vitamin B12. Their health benefits as a complementary dietary source for macro and micro nutrients have been studied and confirmed in various populations. The safety of human consuming these algae and products derived from these algae by humans has been widely studied. It is generally concluded that these algae and its products are safe if cultivated properly in a non-contaminated environment, and if consumed in moderation.
When fathers are instant losers: homogenization of rDNA loci in recently formed Cardamine × schulzii trigenomic allopolyploid.

Recently formed allopolyploids represent an excellent system to study the impacts of hybridization and genomic duplication on genome structure and evolution. Here we explored the 35SrRNA genes (rDNA) in the Cardamine × schulzii allohexaploid that was formed by two subsequent hybridization events within the past c. 150 yr. The rDNA loci were analyzed by cloning, next generation sequencing (NGS), RT-PCR and FISH methods. The primary C. × insueta triploid hybrid derived from C. rivularis (♀) and C. amara (♂) had gene ratios highly skewed towards maternal sequences. Similarly, C. × schulzii, originating from the secondary hybridization event involving C. × insueta (♀) and C. pratensis (♂), showed a reduction in paternal rDNA homeologs despite an excess of chromosomes inherited from C. pratensis. We also identified novel rDNA loci in C. × schulzii, suggesting that lost loci might be slowly reinstalled by translocation (but not recombination) of genes from partner genomes. Prevalent clonal propagation of allopolyploids, C. × insueta and C. × schulzii, indicates that concerted evolution of rDNA may occur in the absence of extensive meiotic cycles. Adoption of NGS in rDNA variant analysis is highly informative for deciphering the evolutionary histories of allopolyploid species with ongoing homogenization processes.
Histogram Analysis of Hepatobiliary Phase MR Imaging as a Quantitative Value for Liver Cirrhosis: Preliminary Observations

Purpose To investigate whether histogram analysis of the hepatobiliary phase on gadoxetate enhanced-MRI could be used as a quantitative index for determination of liver cirrhosis. Materials and Methods A total of 63 patients [26 in a normal liver function (NLF) group and 37 in a cirrhotic group] underwent gadoxetate-enhanced MRI, and hepatobiliary phase images were obtained at 20 minutes after contrast injection. The signal intensity of the hepatic parenchyma was measured at four different regions of interest (ROI) of the liver, avoiding vessels and bile ducts. Standard deviation (SD), coefficient of variation (CV), and corrected CV were calculated on the histograms at the ROIs. The distributions of CVs calculated from the ROI histogram were examined and statistical analysis was carried out. Results The CV value was 0.041±0.009 (mean CV±SD) in the NLF group, while that of cirrhotic group was 0.071±0.020. There were statistically significant differences in the CVs and corrected CV values between the NLF and cirrhotic groups (p<0.001). The most accurate cut-off value among CVs for distinguishing normal from cirrhotic group was 0.052 (sensitivity 83.8% and specificity 88.5%). There was no statistically significant differences in SD between NLF and cirrhotic groups (p=0.307). Conclusion The CV of histograms of the hepatobiliary phase on gadoxetate-enhanced MRI may be useful as a quantitative value for determining the presence of liver cirrhosis.
CalFUSE v3: A Data-Reduction Pipeline for the Far Ultraviolet Spectroscopic Explorer

Since its launch in 1999, the Far Ultraviolet Spectroscopic Explorer (FUSE) has made over 4600 observations of some 2500 individual targets. The data are reduced by the Principal Investigator team at the Johns Hopkins University and archived at the Multimission Archive at Space Telescope (MAST). The data-reduction software package, called CalFUSE, has evolved considerably over the lifetime of the mission. The entire FUSE data set has recently been reprocessed with CalFUSE v3.2, the latest version of this software. This paper describes CalFUSE v3.2, the instrument calibrations upon which it is based, and the format of the resulting calibrated data files.
Differences in human and chimpanzee gene expression patterns define an evolving network of transcription factors in brain

Humans differ from other primates by marked differences in cognitive abilities and a significantly larger brain. These differences correlate with metabolic changes, as evidenced by the relative up-regulation of energy-related genes and metabolites in human brain. While the mechanisms underlying these evolutionary changes have not been elucidated, altered activities of key transcription factors (TFs) could play a pivotal role. To assess this possibility, we analyzed microarray data from five tissues from humans and chimpanzees. We identified 90 TF genes with significantly different expression levels in human and chimpanzee brain among which the rapidly evolving KRAB-zinc finger genes are markedly over-represented. The differentially expressed TFs cluster within a robust regulatory network consisting of two distinct but interlinked modules, one strongly associated with energy metabolism functions, and the other with transcription, vesicular transport, and ubiquitination. Our results suggest that concerted changes in a relatively small number of interacting TFs may coordinate major gene expression differences in human and chimpanzee brain.
Glycosylation of Recombinant Antibody Therapeutics

The adaptive immune system has the capacity to produce antibodies with a virtually infinite repertoire of specificities. Recombinant antibodies specific for human targets are established in the clinic as therapeutics and represent a major new class of drug. Therapeutic efficacy depends on the formation of complexes with target molecules and subsequent activation of downstream biologic effector mechanisms that result in elimination of the target. The activation of effector mechanisms is dependent on structural characteristics of the antibody molecule that result from posttranslational modifications, in particular, glycosylation. The production of therapeutic antibody with a consistent human glycoform profile has been and remains a considerable challenge to the biopharmaceutical industry. Recent research has shown that individual glycoforms of antibody may provide optimal efficacy for selected outcomes. Thus a further challenge will be the production of a second generation of antibody therapeutics customized for their clinical indication.
Lower value of glycated haemoglobin relative to glycaemic control in diabetic patients with end-stage renal disease not on haemodialysis

Background Glycated haemoglobin (HbA1c) concentration is lower relative to glyacemic control in diabetic patients on haemodialysis. However, it is unknown as to whether this is also true for diabetic patients with end-stage renal disease but not on haemodialysis. Methods Correlations between HbA1c or glycated albumin (GA) and estimated glomerular filtration rate (eGFR) (determined by serum creatinine concentration, sex and age) were investigated in 86 diabetic patients with renal dysfunction not on dialysis. The mean values of HbA1c and of red blood cell (RBC) lifespan were compared among four groups of patients: Group 1 (n = 30, eGFR ≥ 60 mL/min/1.73 m2), Group 2 (n = 30, eGFR < 60 mL/min/1.73 m2 but ≥30 mL/min/1.73 m2), Group 3 (n = 13, eGFR < 30 mL/min/1.73 m2 but ≥15 mL/min/1.73 m2) and Group 4 (n = 13, eGFR < 15 mL/min/1.73 m2 without haemodialysis). RBC lifespan was determined in each subject from the difference between alveolar carbon monoxide (CO) concentration and atmospheric CO concentration. Results HbA1c was significantly correlated with eGFR (r = 0.37, P = 0.0004), but GA was not. The HbA1c values in Group 3 (6.8 ± 0.6%) and Group 4 (6.3 ± 0.5%) were significantly lower than that in Group 1 (7.4 ± 0.8%), but there was no difference between Group 2 (7.2 ± 0.7%) and Group 1. There was a significant correlation between RBC lifespan and eGFR, and the mean RBC lifespan in Group 3 (96 ± 35 d) and Group 4 (94 ± 30 d) were significantly shorter than that in Group 1 (127 ± 30 d). Conclusions Diabetic patients with stage 4 or 5 chronic kidney disease not on haemodialysis had significantly lower values of HbA1c and shorter RBC lifespan compared with diabetic patients without renal dysfunction.
Decline in HAV-associated fulminant hepatic failure and liver transplant in children in Argentina after the introduction of a universal hepatitis A vaccination program

Introduction Hepatitis A virus (HAV) infection is a vaccine-preventable disease. The most severe complication in children is fulminant hepatic failure (FHF), estimated to occur in 0.4% of cases; patients with FHF often require a liver transplant (LT). Following another outbreak of HAV infection in Argentina during 2003–2004, a one-dose HAV universal immunization (UI) program was started in 2005, resulting in a reduction in the incidence of HAV infection. We have investigated the impact of HAV UI on the trends in the occurrence of FHF and LT in children. Methods All pediatric cases of FHF admitted to four pediatric centers in Buenos Aires during March 1993–July 2005 were retrospectively reviewed, and data of cases during August 2005–December 2008 were collected. Information about demography, HAV infections and vaccination status, diagnostic data for FHF using the Pediatric Acute Liver Failure criteria, clinical laboratory results, encephalopathy, the severity of liver disease using the Pediatric End Stage Liver Disease score, assessment of patients on the LT waiting list using King’s College Criteria for LT, treatment given for FHF (pre- and post-transplant), and clinical outcome were collected using a case report form. The frequency and outcomes of HAV-associated FHF and LT cases before and after UI were analyzed. Results During the pre-immunization period, March 1993–July 2005, 54.6% (N = 165) of FHF cases were caused by HAV; HAV-associated FHF cases peaked during 2003–2004. During the post-immunization period, August 2005–December 2008, only 27.7% (N = 18) of FHF cases were caused by HAV infection; only one of these patients had received the HAV vaccine (one dose only). The number of HAV-associated FHF cases decreased from 2005, and no cases were reported from November 2006–December 2008. Multivariate analyses showed that the association of FHF with HAV infection rather than other etiologies decreased with increasing age (P = 0.03), UI against HAV (P = 0.002), and anti-actin antibodies (P = 0.002), and increased with increasing weight (P = 0.0004). Conclusions The number of children with HAV-associated FHF in Argentina has strongly decreased since the initiation of the UI program. Further monitoring is required to confirm the long-term health and economic benefits of UI against HAV infection.
Maternal care differs in mice bred for high vs. low trait anxiety: Impact of brain vasopressin and cross-fostering

Brain arginine vasopressin (AVP) not only regulates male social behavior and emotionality, but also promotes maternal behavior, as has been shown in rats. In our CD1 mice breed for high (HAB) or low (LAB) anxiety-related behavior, LAB mice have markedly less AVP mRNA expression in the hypothalamic paraventricular nucleus compared with HAB mice. Together these findings suggest that HAB and LAB mice represent a good model to assess the role of AVP in mouse maternal behavior. Therefore, we studied maternal care of HAB and LAB mouse dams and investigated the impact of maternal care on the offspring's anxiety in a cross-fostering paradigm. In comparison with HAB dams, LABs displayed less maternal care. Daily acute intracerebroventricular infusions of AVP in early lactation increased maternal care of LAB dams and acted anxiogenically. Cross-fostering on postnatal day 5 did not alter separation-induced high and low ultrasonic vocalization calling frequency, a measure of inborn anxiety, in HAB and LAB offspring, respectively. However, adult cross-fostered HAB mice displayed a trend towards decreased anxiety on the elevated plus-maze, which was still significantly higher compared with LAB mice. The low levels of depressive-like behavior, stress-reactivity, and hypothalamic AVP mRNA expression in adult LAB offspring were found to be independent of cross-fostering. In conclusion, the HAB/LAB differences in maternal care and anxiety are robust and strongly depend on differences in the AVP system. The seemingly rigid genetic predisposition to hyperanxiety can only be moderately attenuated by the received nurturing.
Systolic Binary Counter using a Cellular Automaton-based Prescaler

Counters are among the fundamental digital circuits in every computing system. For this reason, counter design is of great interest in the design of computers and embedded systems, in terms of area requirements, power dissipation and performance. Many techniques have been proposed in the past specifically to increase the counter's speed without increasing design complexity. Traditionally, it is of great concern to make a fast counter suitable for many applications, without adding to the critical path and keeping speed independent of its size. In this work, a binary counter is proposed, based on 1D Cellular Automata (CA), which is used as a prescaler in a systolic structure, that offers constant delay for counters of various bit-widths.
Blindness and poverty in India: the way forward

A few recent studies have shown that poverty is an exacerbating and often determining factor in the incidence of disabling conditions, including visual impairment. Recent estimates from the World Health Organization indicate that 90 per cent of all those affected by visual impairment live in the poorest countries of the world. India is home to one‐fifth of the world's visually impaired people and therefore, any strategies to combat avoidable blindness must take into account the socio‐economic conditions within which people live. This paper looks at the relationship between poverty and blindness in India and suggests strategies to address blindness prevention in a comprehensive manner.
Cancer-associated Cleavage of Cytokeratin 8/18 Heterotypic Complexes Exposes a Neoepitope in Human Adenocarcinomas*

The intermediate filament network in simple glandular epithelial cells predominantly consists of heterotypic complexes of cytokeratin 8 (K8) and cytokeratin 18 (K18). In contrast to other cytokeratins, K8 and K18 are persistently expressed during malignant transformation, but changes in cell morphology are accompanied by alterations in the intermediate filament network. To study molecular changes, K8 and K18 were purified from surgically removed colon cancer and normal epithelia tissues. Western blotting and amino acid sequencing revealed the presence of abundant K8 and K18 fragments, truncated at the N terminus, from cancerous, but not normal, epithelial cells. The fragmentation pattern indicates proteolysis mediated by several enzymes, including trypsin-like enzymes. The cancer-associated forms of K8 and K18 are specifically recognized by the human antibody, COU-1, cloned from the B cells of a cancer patient. We demonstrate that COU-1 recognizes a unique conformational epitope presented only by a complex between K8 and K18. The epitope is revealed after proteolytic removal of the head domain of either K8 or K18. A large panel of recombinant K8 and K18 fragments, deleted N- or C-terminally, allowed for the localization of the COU-1 epitope to the N-terminal part of the rod domains. Using surface plasmon resonance, the affinity of COU-1 for this epitope was determined to be 109 m −1, i.e.more than 2 orders of magnitude higher than for intact heterotypic K8/K18 complexes. The cellular distribution of truncated K8/K18 heterotypic complexes in viable adenocarcinomas cells was probed using COU-1 showing small fibrillar structures distinct from those of intact K8/K18 complexes. Previously we demonstrated the binding and subsequent internalization of recombinant Fab COU-1 to live cancer cells. We have thus characterized a cancer neoepitope recognized by the humoral immune system. The results have biological as well as clinical implications.
An autoradiographic study of the efferent connections of the lateral hypothalamic area in the rat

The efferent connections of the lateral hypothalamic area (LHA) have been analyzed in a series of 30 rat brains with injections of 3H‐amino acids into different parts of the area and the surrounding regions. Our findings indicate that all parts of the LHA contribute ascending and descending fibers to the medial forebrain bundle, and also project medially to certain of the adjoining hypothalamic nuclei. All levels of the LHA appear to send some fibers to a continuous group of structures that extends from the medial septal‐diagonal band complex rostrally, through the lateral preoptic and lateral hypothalamic areas to the mammillary complex and the ventral tegmental area caudally. In addition, it is evident that cells at different levels within the LHA may have differential projections. Thus, the anterior and lateral parts of the LHA also appear to project substantially to the anterior hypothalamic area, the ventromedial and dorsomedial hypothalamic nuclei, the parataenial and paraventricular nuclei of the thalamus, and the medial part of the lateral habenular nucleus. Similarly, cells in the tuberal and posterior parts of the LHA project to the central gray, the longest projections from the posterior region reaching as far caudally as the central tegmental field, the parabrachial nucleus, the locus coeruleus, and the superior central and dorsal nuclei of the raphe. Viewed as a whole, the LHA is therefore well‐suited to integrate inputs from the limbic system and brainstem and to relay them on the one hand to the medial zone of the hypothalamus and on the other to virtually every structure closely associated with the medical forebrain bundle and to the nuclei of origin of the major ascending monoaminergic systems.
An enhanced uplink scheduling algorithm based on voice activity for VoIP services in IEEE 802.16d/e system

An efficient uplink scheduling algorithm that can be used in IEEE 802.16d/e system for VoIP services is proposed to support as many voice users as possible. Our proposed algorithm requires no modification of the framework of IEEE 802.16d/e system. In this letter, we analyze the system throughput and the access delay of our proposed algorithm, and show, via OPNET simulation, that the throughput of our algorithm is superior to that of conventional algorithms in IEEE 802.16d/e system.
VINEA: An Architecture for Virtual Network Embedding Policy Programmability

Network virtualization has enabled new business models by allowing infrastructure providers to lease or share their physical network. A fundamental management problem that cloud providers face to support customized virtual network (VN) services is the virtual network embedding. This requires solving the (NP-hard) problem of matching constrained virtual networks onto the physical network. In this paper we present VINEA, a policy-based virtual network embedding architecture, and its system implementation. VINEA leverages our previous results on VN embedding optimality and convergence guarantees, and it is based on a network utility maximization approach that separates policies (i.e., high-level goals) from underlying embedding mechanisms: resource discovery, virtual network mapping, and allocation on the physical infrastructure. We show how VINEA can subsume existing embedding approaches, and how it can be used to design novel solutions that adapt to different scenarios, by merely instantiating different policies. We describe the VINEA architecture, as well as our object model: our VINO protocol and the API to program the embedding policies; we then analyze key representative tradeoffs among novel and existing VN embedding policy configurations, via event-driven simulations, and with our prototype implementation. Among our findings, our evaluation shows how, in contrast to existing solutions, simultaneously embedding nodes and links may lead to lower providers' revenue. We release our implementation on a testbed that uses a Linux system architecture to reserve virtual node and link capacities. Our prototype can be also used to augment existing open-source “Networking as a Service” architectures such as OpenStack Neutron, that currently lacks a VN embedding protocol, and as a policy-programmable solution to the “slice stitching” problem within wide-area virtual network testbeds.