Miracle-dz/UniFAR-FTUs huggingface dataset:
The Secure Machine: Efficient Secure Execution On Untrusted Platforms

In this work we present the Secure Machine, SeM for short, a CPU architecture extension for secure computing. SeM uses a small amount of in-chip additional hardware that monitors key communication channels inside the CPU chip, and only acts when required. SeM provides confidentiality and integrity for a secure program without trusting the platform software or any off-chip hardware. SeM supports existing binaries of single- and multi-threaded applications running on single- or multi-core, multi-CPU. The performance reduction caused by it is only few percent, most of which is due to the memory encryption layer that is commonly used in many secure architectures. We also developed SeM-Prepare, a software tool that automatically instruments existing applications (binaries) with additional instructions so they can be securely executed on our architecture without requiring any programming efforts or the availability of the desired program`s source code. To enable secure data sharing in shared memory environments, we developed Secure Distributed Shared Memory (SDSM), an efficient (time and memory) algorithm for allowing thousands of compute nodes to share data securely while running on an untrusted computing environment. SDSM shows a negligible reduction in performance, and it requires negligible and hardware resources. We developed Distributed Memory Integrity Trees, a method for enhancing single node integrity trees for preserving the integrity of a distributed application running on an untrusted computing environment. We show that our method is applicable to existing single node integrity trees such as Merkle Tree, Bonsai Merkle Tree, and Intel`s SGX memory integrity engine. All these building blocks may be used together to form a practical secure system, and some can be used in conjunction with other secure systems.
The mitochondrial genome of white Java sparrow (Padda oryzivora)

Abstract The complete mitochondrial genome of Padda oryzivora (Estrildidae, Passeriformes) was sequenced. It is 16 817 bp in length, with an AT content of 54.72%, including 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and 1 control region. Phylogenetic analysis demonstrated that the Java sparrow is a close relative of zebrafinch (Taeniopygia guttata) within the same family. These results are desired to provide molecular data for species taxonomy and further phylogenetic studies of passerines.
The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens

The human gastrointestinal tract hosts a diverse network of microorganisms, collectively known as the microbiota that plays an important role in health and disease. For instance, the intestinal microbiota can prevent invading microbes from colonizing the gastrointestinal tract, a phenomenon known as colonization resistance. Perturbations to the microbiota, such as antibiotic administration, can alter microbial composition and result in the loss of colonization resistance. Consequently, the host may be rendered susceptible to colonization by a pathogen. This is a particularly relevant concern in the hospital setting, where antibiotic use and antibiotic‐resistant pathogen exposure are more frequent. Many nosocomial infections arise from gastrointestinal colonization. Due to their resistance to antibiotics, treatment is often very challenging. However, recent studies have demonstrated that manipulating the commensal microbiota can prevent and treat various infections in the intestine. In this review, we discuss the members of the microbiota, as well as the mechanisms, that govern colonization resistance against specific pathogens. We also review the effects of antibiotics on the microbiota, as well as the unique epidemiology of immunocompromised patients that renders them a particularly high‐risk population to intestinal nosocomial infections.
A Stenotrophomonas maltophilia Strain Evades a Major Caenorhabditis elegans Defense Pathway

ABSTRACT Stenotrophomonas maltophilia is a ubiquitous bacterium and an emerging nosocomial pathogen. This bacterium is resistant to many antibiotics, associated with a number of infections, and a significant health risk, especially for immunocompromised patients. Given that Caenorhabditis elegans shares many conserved genetic pathways and pathway components with higher organisms, the study of its interaction with bacterial pathogens has biomedical implications. S. maltophilia has been isolated in association with nematodes from grassland soils, and it is likely that C. elegans encounters this bacterium in nature. We found that a local S. maltophilia isolate, JCMS, is more virulent than the other S. maltophilia isolates (R551-3 and K279a) tested. JCMS virulence correlates with intestinal distension and bacterial accumulation and requires the bacteria to be alive. Many of the conserved innate immune pathways that serve to protect C. elegans from various pathogenic bacteria also play a role in combating S. maltophilia JCMS. However, S. maltophilia JCMS is virulent to normally pathogen-resistant DAF-2/16 insulin-like signaling pathway mutants. Furthermore, several insulin-like signaling effector genes were not significantly differentially expressed between S. maltophilia JCMS and avirulent bacteria (Escherichia coli OP50). Taken together, these findings suggest that S. maltophilia JCMS evades the pathogen resistance conferred by the loss of DAF-2/16 pathway components. In summary, we have discovered a novel host-pathogen interaction between C. elegans and S. maltophilia and established a new animal model with which to study the mode of action of this emerging nosocomial pathogen.
Multiple Transceptors for Macro- and Micro-Nutrients Control Diverse Cellular Properties Through the PKA Pathway in Yeast: A Paradigm for the Rapidly Expanding World of Eukaryotic Nutrient Transceptors Up to Those in Human Cells

The nutrient composition of the medium has dramatic effects on many cellular properties in the yeast Saccharomyces cerevisiae. In addition to the well-known specific responses to starvation for an essential nutrient, like nitrogen or phosphate, the presence of fermentable sugar or a respirative carbon source leads to predominance of fermentation or respiration, respectively. Fermenting and respiring cells also show strong differences in other properties, like storage carbohydrate levels, general stress tolerance and cellular growth rate. However, the main glucose repression pathway, which controls the switch between respiration and fermentation, is not involved in control of these properties. They are controlled by the protein kinase A (PKA) pathway. Addition of glucose to respiring yeast cells triggers cAMP synthesis, activation of PKA and rapid modification of its targets, like storage carbohydrate levels, general stress tolerance and growth rate. However, starvation of fermenting cells in a glucose medium for any essential macro- or micro-nutrient counteracts this effect, leading to downregulation of PKA and its targets concomitant with growth arrest and entrance into G0. Re-addition of the lacking nutrient triggers rapid activation of the PKA pathway, without involvement of cAMP as second messenger. Investigation of the sensing mechanism has revealed that the specific high-affinity nutrient transporter(s) induced during starvation function as transporter-receptors or transceptors for rapid activation of PKA upon re-addition of the missing substrate. In this way, transceptors have been identified for amino acids, ammonium, phosphate, sulfate, iron, and zinc. We propose a hypothesis for regulation of PKA activity by nutrient transceptors to serve as a conceptual framework for future experimentation. Many properties of transceptors appear to be similar to those of classical receptors and nutrient transceptors may constitute intermediate forms in the development of receptors from nutrient transporters during evolution. The nutrient-sensing transceptor system in yeast for activation of the PKA pathway has served as a paradigm for similar studies on candidate nutrient transceptors in other eukaryotes and we succinctly discuss the many examples of transceptors that have already been documented in other yeast species, filamentous fungi, plants, and animals, including the examples in human cells.
Spatial False Alarms in Cognitive Radio

This letter introduces an observed spectrum sensing issue that: with certain probability, a secondary user (SU) misinterprets a non-interfered primary user (PU) is being interfered, resulting in access opportunity loss. This issue termed as spatial false alarm (SFA) problem is one of determinants on SU's medium access probability. However, it is neglected in current research related to spectrum sensing. By thoroughly study, the principle of SFA is presented to reveal the cause of this problem. Moreover, we quantify the impact of SFA by a closed-form expression to correctly evaluate the medium access probability for SU. The simulation results evidence both the importance of SFA and the validity of the derived medium access probability.
The notorious R.N.A. in the spotlight - drug or target for the treatment of disease

ABSTRACT mRNA is an attractive drug target for therapeutic interventions. In this review we highlight the current state, clinical trials, and developments in antisense therapy, including the classical approaches like RNaseH-dependent oligomers, splice-switching oligomers, aptamers, and therapeutic RNA interference. Furthermore, we provide an overview on emerging concepts for using RNA in therapeutic settings including protein replacement by in-vitro-transcribed mRNAs, mRNA as vaccines and anti-allergic drugs. Finally, we give a brief outlook on early-stage RNA repair approaches that apply endogenous or engineered proteins in combination with short RNAs or chemically stabilized oligomers for the re-programming of point mutations, RNA modifications, and frame shift mutations directly on the endogenous mRNA.
The 'Greenness' of high-volume fly ash (HVFA) concrete when exposed to carbonation

With at least 50 % of the cement replaced with fly ash, the environmental benefit of High-Volume Fly Ash concrete is seemingly obvious. However, a correct evaluation of this “greenness” requires a full strength and durability assessment followed by life cycle assessment. Two exposure classes were considered: a dry (XC1) and a cyclic wet and dry (XC4) environment with carbonation. A full probabilistic service life prediction based on accelerated carbonation testing, shows that corrosion will not be a problem in both environments after 50 years if the concrete was cured at high relative humidity for at least 28 days. An environmental benefit of about 20 % can be obtained for an axially loaded HVFA column in a XC1 environment. For exposure class XC4, there is no benefit, because of the HVFA mixture‟s considerably lower strength in comparison with the reference for that environment.
A novel congestion-aware and adaptive routing algorithm in mesh-based Networks-on-Chip with segmentation

The networks on chip (NoC) have been presented as a viable and scalable solution for connecting the processor cores in a multi-core chip. In recent years, with increasing the number of cores in NoCs, the congestion has been raised as a key and bottleneck for achieving proper efficiency. In this paper, we first segment the NoC into a number of subnets and then provide a congestion-aware algorithm with three main phases based on this segmentation. The segmentation and usage of the proposed algorithm can improve the system performance compared to the previous work. This algorithm is compared with the DyXY, DyAD and CATRA algorithms and the superior results are obtained. Under SPLASH-2 traffic patterns, the average packet latencies have been improved by 13.3%, 10.6%, and 17.8%, respectively compared to DyXY, DyAD and CATRA algorithms. Moreover, in the same traffics, the proposed algorithm consumes less power compared to these algorithms. In fact, it can be whispered that the proposed scheme has not worsened in power consumption. This improvement has also been observed under synthetic traffics. In addition to present a novel algorithm, a new parameter, the variance of crossbar activity, is suggested as a parameter to assess the performance of congestion-aware routing algorithms. Compared to DyAD and CATRA, it is showed that this parameter has been enhanced in the proposed algorithm by 32.4% and 50.2%, respectively.
Hyperadherence of Pseudomonas taiwanensis VLB120ΔC increases productivity of (S)‐styrene oxide formation

The attachment strength of biofilm microbes is responsible for the adherence of the cells to surfaces and thus is a critical parameter in biofilm processes. In tubular microreactors, aqueous‐air segmented flow ensures an optimal oxygen supply and prevents excessive biofilm growth. However, organisms growing in these systems depend on an adaptation phase of several days, before mature and strong biofilms can develop. This is due to strong interfacial forces. In this study, a hyperadherent mutant of Pseudomonas taiwanensis VLB120ΔCeGFP possessing an engineered cyclic diguanylate metabolism, was applied to a continuous biofilm process for the production of (S)‐styrene oxide. Cells of the mutant P. taiwanensis VLB120ΔCeGFP Δ04710, showing the same specific activity as the wild type, adhered substantially stronger to the substratum. Adaptation to the high interfacial forces was not necessary in these cases. Thereby, 40% higher final product concentrations were achieved and the maximal volumetric productivity of the parent strain was significantly surpassed by P. taiwanensis VLB120ΔCeGFP Δ04710. Applying mutants with strong adhesion in biofilm‐based catalysis opens the door to biological process control in future applications of catalytic biofilms using other industrially relevant strains.
Pancreatic beta cells are a sensitive target of embryonic exposure to butylparaben in zebrafish (Danio rerio)

Butylparaben (butyl p‐hydroxybenzoic acid) is a common cosmetic and pharmaceutical preservative reported to induce oxidative stress and endocrine disruption. Embryonic development is sensitive to oxidative stress, with redox potentials playing critical roles in progenitor cell fate decisions. Because pancreatic beta cells have been reported to have low antioxidant gene expression, they may be sensitive targets of oxidative stress. We tested the hypotheses that butylparaben causes oxidative stress in the developing embryo, and that pancreatic beta cells are a sensitive target of butylparaben embryotoxicity.
A ROC-based feature selection method for computer-aided detection and diagnosis

Image-based computer-aided detection and diagnosis (CAD) has been a very active research topic aiming to assist physicians to detect lesions and distinguish them from benign to malignant. However, the datasets fed into a classifier usually suffer from small number of samples, as well as significantly less samples available in one class (have a disease) than the other, resulting in the classifier’s suboptimal performance. How to identifying the most characterizing features of the observed data for lesion detection is critical to improve the sensitivity and minimize false positives of a CAD system. In this study, we propose a novel feature selection method mR-FAST that combines the minimal-redundancymaximal relevance (mRMR) framework with a selection metric FAST (feature assessment by sliding thresholds) based on the area under a ROC curve (AUC) generated on optimal simple linear discriminants. With three feature datasets extracted from CAD systems for colon polyps and bladder cancer, we show that the space of candidate features selected by mR-FAST is more characterizing for lesion detection with higher AUC, enabling to find a compact subset of superior features at low cost.
Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

Restriction-site associated DNA (RAD) sequencing is a powerful new method for targeted sequencing across the genomes of many individuals. This approach has broad potential for genetic analysis of non-model organisms including genotype-phenotype association mapping, phylogeography, population genetics and scaffolding genome assemblies through linkage mapping. We constructed a RAD library using genomic DNA from a Plutella xylostella (diamondback moth) backcross that segregated for resistance to the insecticide spinosad. Sequencing of 24 individuals was performed on a single Illumina GAIIx lane (51 base paired-end reads). Taking advantage of the lack of crossing over in homologous chromosomes in female Lepidoptera, 3,177 maternally inherited RAD alleles were assigned to the 31 chromosomes, enabling identification of the spinosad resistance and W/Z sex chromosomes. Paired-end reads for each RAD allele were assembled into contigs and compared to the genome of Bombyx mori (n = 28) using BLAST, revealing 28 homologous matches plus 3 expected fusion/breakage events which account for the difference in chromosome number. A genome-wide linkage map (1292 cM) was inferred with 2,878 segregating RAD alleles inherited from the backcross father, producing chromosome and location specific sequenced RAD markers. Here we have used RAD sequencing to construct a genetic linkage map de novo for an organism that has no previous genome data. Comparative analysis of P. xyloxtella linkage groups with B. mori chromosomes shows for the first time, genetic synteny appears common beyond the Macrolepidoptera. RAD sequencing is a powerful system capable of rapidly generating chromosome specific data for non-model organisms.
Neuroprotective efficacy of hesperetin against cadmium induced oxidative stress in the brain of rats

The present study was designed to investigate the neuroprotective effect of hesperetin (Hp) against cadmium (Cd)-induced neurotoxicity in rats. Cadmium (3 mg/kg body weight (b.w.), subcutaneous) administration for 3 weeks demonstrated neurotoxicity in rats by the decreased activity of acetylcholinesterase in the brain. The oxidative stress markers (thiobarbituric acid reactive substances and protein carbonyls) were significantly increased with decreased enzymatic (superoxide dismutase, catalase, glutathione peroxidase, glutathione S-transferase) and non-enzymatic antioxidants (reduced glutathione, total sulphydryl groups and vitamin C). The proteolytic and membrane-bound enzymes (Na+ K+-ATPase, Mg2+-ATPase and Ca2+-ATPase) were also decreased with increased apoptotic markers (Bcl2 Associated X Protein (Bax), cytochrome C, caspase 3 and 9) and decreased anti-apoptotic marker (B-cell lymphoma 2 (Bcl2)) in the brain of Cd-treated rats. Moreover, Cd administration significantly decreased the mitochondrial electron transport chain complexes (I, II, III and IV) in the brain of rats. Preadministration of Hp (40 mg/kg b.w., oral) significantly attenuated the Cd-induced oxidative stress and mitochondrial dysfunction, restored the antioxidant and membrane-bound enzyme activities and decreased apoptosis in the brain of rats.
Serial Position Learning in Honeybees

Learning of stimulus sequences is considered as a characteristic feature of episodic memory since it contains not only a particular item but also the experience of preceding and following events. In sensorimotor tasks resembling navigational performance, the serial order of objects is intimately connected with spatial order. Mammals and birds develop episodic(-like) memory in serial spatio-temporal tasks, and the honeybee learns spatio-temporal order when navigating between the nest and a food source. Here I examine the structure of the bees’ memory for a combined spatio-temporal task. I ask whether discrimination and generalization are based solely on simple forms of stimulus-reward learning or whether they require sequential configurations. Animals were trained to fly either left or right in a continuous T-maze. The correct choice was signaled by the sequence of colors (blue, yellow) at four positions in the access arm. If only one of the possible 4 signals is shown (either blue or yellow), the rank order of position salience is 1, 2 and 3 (numbered from T-junction). No learning is found if the signal appears at position 4. If two signals are shown, differences at positions 1 and 2 are learned best, those at position 3 at a low level, and those at position 4 not at all. If three or more signals are shown these results are corroborated. This salience rank order again appeared in transfer tests, but additional configural phenomena emerged. Most of the results can be explained with a simple model based on the assumption that the four positions are equipped with different salience scores and that these add up independently. However, deviations from the model are interpreted by assuming stimulus configuration of sequential patterns. It is concluded that, under the conditions chosen, bees rely most strongly on memories developed during simple forms of associative reward learning, but memories of configural serial patterns contribute, too.
Snf1-Dependent Transcription Confers Glucose-Induced Decay upon the mRNA Product

ABSTRACT In the yeast Saccharomyces cerevisiae, the switch from respiratory metabolism to fermentation causes rapid decay of transcripts encoding proteins uniquely required for aerobic metabolism. Snf1, the yeast ortholog of AMP-activated protein kinase, has been implicated in this process because inhibiting Snf1 mimics the addition of glucose. In this study, we show that the SNF1-dependent ADH2 promoter, or just the major transcription factor binding site, is sufficient to confer glucose-induced mRNA decay upon heterologous transcripts. SNF1-independent expression from the ADH2 promoter prevented glucose-induced mRNA decay without altering the start site of transcription. SNF1-dependent transcripts are enriched for the binding motif of the RNA binding protein Vts1, an important mediator of mRNA decay and mRNA repression whose expression is correlated with decreased abundance of SNF1-dependent transcripts during the yeast metabolic cycle. However, deletion of VTS1 did not slow the rate of glucose-induced mRNA decay. ADH2 mRNA rapidly dissociated from polysomes after glucose repletion, and sequences bound by RNA binding proteins were enriched in the transcripts from repressed cells. Inhibiting the protein kinase A pathway did not affect glucose-induced decay of ADH2 mRNA. Our results suggest that Snf1 may influence mRNA stability by altering the recruitment activity of the transcription factor Adr1.
Two Strong Baselines for the BioNLP 2009 Event Extraction Task

This paper presents two strong baselines for the BioNLP 2009 shared task on event extraction. First we re-implement a rule-based approach which allows us to explore the task and the effect of domain-adapted parsing on it. We then replace the rule-based component with support vector machine classifiers and achieve performance near the state-of-the-art without using any external resources. The good performances achieved and the relative simplicity of both approaches make them reproducible baselines. We conclude with suggestions for future work with respect to the task representation.