Miracle-dz/UniFAR-FTUs huggingface dataset:
SECOS : Key Management for Scalable and Energy Efficient Crypto On Sensors

Issa Khalil, Saurabh Bagchi Dependable Computing Systems Lab School of Electrical & Computer Engineering, Purdue University 465 Northwestern Avenue, West Lafayette, IN 47907. Email: {ikhalil,sbagchi}@purdue.edu Abstract Wireless sensor networks are becoming a critical computational infrastructure, in which the communication between nodes needs to be protected from eavesdropping and tampering. Symmetric key cryptography is the fundamental technique being used. The protocols in this domain suffer from one or more of the problems of weak security guarantees if some nodes are compromised, lack of scalability, high energy overhead for key management and increased end-to-end data latency. In this paper, we propose a protocol called SECOS that mitigates these problems. SECOS divides the sensor field into control groups each with a control head. Data exchange between nodes within a control group happens through the mediation of the control head which provides the common key. The keys and the control heads are changed periodically to enhance security. SECOS enhances the survivability of the network by handling failures of control nodes. The experiments based on a simulation model show 7 times reduction in energy overhead and 50% reduction in latency compared to the stateof-the-art protocol, SPINS. We also provide an analytical derivation of the optimal control group size that operates under the resource constraints and minimizes energy consumption.
Several extracellular domains of the neural cell adhesion molecule L1 are involved in neurite outgrowth and cell body adhesion

The neural cell adhesion molecule L1 is a multidomain protein that plays important roles in cell adhesion, migration, and neurite outgrowth. To analyze structure-function relationships of L1 in neurite outgrowth and cell body adhesion, we have expressed and purified a set of different fragments of the extracellular part of this glycoprotein in CHO cells and in Escherichia coli. When neurite outgrowth from small cerebellar neurons was measured on substrate-coated L1 or L1 fragments, neurite outgrowth was promoted by the immunoglobulin-like domains I-II, III-IV, and V-VI, and by the fibronectin type III homologous repeats 1– 2, while the fibronectin type III homologous repeats 3–5 were ineffective. In contrast, cell bodies of small cerebellar neurons adhered mostly to the immunoglobulin-like domains I-II and V-VI, and to the fibronectin type III homologous repeats 3–5, but less to the immunoglobulin-like domains III-IV and fibronectin type III homologous repeats 1–2. In both assays, the neuronal cell surface receptor for all active protein fragments was identified as L1. No significant differences in functional activities were found between fragments with and without carbohydrate structures. These findings indicate that L1 uses several domains for homophilic interactions overlapping for the two functions analyzed here, but also showing some regional specialization. Furthermore, we show that a homophilic molecule uses several domains in one function, with neurite outgrowth requiring more domains than adhesion for maximal activity.
Low-Molecular-Weight Metabolites from Diatoms: Structures, Biological Roles and Biosynthesis

Diatoms are abundant and important biological components of the marine environment that biosynthesize diverse natural products. These microalgae are rich in various lipids, carotenoids, sterols and isoprenoids, some of them containing toxins and other metabolites. Several groups of diatom natural products have attracted great interest due to their potential practical application as energy sources (biofuel), valuable food constituents, and prospective materials for nanotechnology. In addition, hydrocarbons, which are used in climate reconstruction, polyamines which participate in biomineralization, new apoptotic agents against tumor cells, attractants and deterrents that regulate the biochemical communications between marine species in seawaters have also been isolated from diatoms. However, chemical studies on these microalgae are complicated by difficulties, connected with obtaining their biomass, and the influence of nutrients and contaminators in their environment as well as by seasonal and climatic factors on the biosynthesis of the corresponding natural products. Overall, the number of chemically studied diatoms is lower than that of other algae, but further studies, particularly those connected with improvements in the isolation and structure elucidation technique as well as the genomics of diatoms, promise both to increase the number of studied species with isolated biologically active natural products and to provide a clearer perception of their biosynthesis.
Tuberculosis associates with both airflow obstruction and low lung function: BOLD results

In small studies and cases series, a history of tuberculosis has been associated with both airflow obstruction, which is characteristic of chronic obstructive pulmonary disease, and restrictive patterns on spirometry. The objective of the present study was to assess the association between a history of tuberculosis and airflow obstruction and spirometric abnormalities in adults. The study was performed in adults, aged 40 years and above, who took part in the multicentre, cross-sectional, general population-based Burden of Obstructive Lung Disease study, and had provided acceptable post-bronchodilator spirometry measurements and information on a history of tuberculosis. The associations between a history of tuberculosis and airflow obstruction and spirometric restriction were assessed within each participating centre, and estimates combined using meta-analysis. These estimates were stratified by high- and low/middle-income countries, according to gross national income. A self-reported history of tuberculosis was associated with airflow obstruction (adjusted odds ratio 2.51, 95% CI 1.83–3.42) and spirometric restriction (adjusted odds ratio 2.13, 95% CI 1.42–3.19). A history of tuberculosis was associated with both airflow obstruction and spirometric restriction, and should be considered as a potentially important cause of obstructive disease and low lung function, particularly where tuberculosis is common. Tuberculosis should be considered a potentially important risk factor for obstructive disease and low lung function http://ow.ly/Ns4vR
Class I histone deacetylase inhibitors inhibit the retention of BRCA1 and 53BP1 at the site of DNA damage

BRCA1 and 53BP1 antagonistically regulate homology‐directed repair (HDR) and non‐homologous end‐joining (NHEJ) of DNA double‐strand breaks (DSB). The histone deacetylase (HDAC) inhibitor trichostatin A directly inhibits the retention of 53BP1 at DSB sites by acetylating histone H4 (H4ac), which interferes with 53BP1 binding to dimethylated histone H4 Lys20 (H4K20me2). Conversely, we recently found that the retention of the BRCA1/BARD1 complex is also affected by another methylated histone residue, H3K9me2, which can be suppressed by the histone lysine methyltransferase (HKMT) inhibitor UNC0638. Here, we investigate the effects of the class I HDAC inhibitors MS‐275 and FK228 compared to UNC0638 on histone modifications and the DNA damage response. In addition to H4ac, the HDAC inhibitors induce H3K9ac and inhibit H3K9me2 at doses that do not affect the expression levels of DNA repair genes. By contrast, UNC0638 selectively inhibits H3K9me2 without affecting the levels of H3K9ac, H3K56ac or H4ac. Reflecting their effects on histone modifications, the HDAC inhibitors inhibit ionizing radiation‐induced foci (IRIF) formation of BRCA1 and BARD1 as well as 53BP1 and RIF1, whereas UNC0638 suppresses IRIF formation of BRCA1 and BARD1 but not 53BP1 and RIF1. Although HDAC inhibitors suppressed HDR, they did not cooperate with the poly(ADP‐ribose) polymerase inhibitor olaparib to block cancer cell growth, possibly due to simultaneous suppression of NHEJ pathway components. Collectively, these results suggest the mechanism by that HDAC inhibitors inhibit both the HDR and NHEJ pathways, whereas HKMT inhibitor inhibits only the HDR pathway; this finding may affect the chemosensitizing effects of the inhibitors.
Leveraging Sparse and Dense Feature Combinations for Sentiment Classification

Neural networks are one of the most popular approaches for many natural language processing tasks such as sentiment analysis. They often outperform traditional machine learning models and achieve the state-of-art results on most tasks. However, many existing deep learning models are complex, difficult to train and provide a limited improvement over simpler methods. We propose a simple, robust and powerful model for sentiment classification. This model outperforms many deep learning models and achieves comparable results to other deep learning models with complex architectures on sentiment analysis datasets. We publish the code online.
Host Cell Invasion by Apicomplexan Parasites: Insights from the Co-Structure of AMA1 with a RON2 Peptide

The structure of a eukaryotic pathogen adhesin bound to its receptor provides a basis for design of therapeutics. Apicomplexan parasites such as Toxoplasma gondii and Plasmodium species actively invade host cells through a moving junction (MJ) complex assembled at the parasite–host cell interface. MJ assembly is initiated by injection of parasite rhoptry neck proteins (RONs) into the host cell, where RON2 spans the membrane and functions as a receptor for apical membrane antigen 1 (AMA1) on the parasite. We have determined the structure of TgAMA1 complexed with a RON2 peptide at 1.95 angstrom resolution. A stepwise assembly mechanism results in an extensive buried surface area, enabling the MJ complex to resist the mechanical forces encountered during host cell invasion. Besides providing insights into host cell invasion by apicomplexan parasites, the structure offers a basis for designing therapeutics targeting these global pathogens.
Local delivery of paclitaxel to inhibit restenosis during angioplasty of the leg.

BACKGROUND Drug-eluting stents reduce restenosis in coronary arteries, but clinical trials have failed to prove their efficacy in peripheral arteries. We investigated the use of paclitaxel-coated angioplasty balloons and paclitaxel dissolved in the angiographic contrast medium during angioplasty of the leg. METHODS In a small, multicenter trial, we randomly assigned 154 patients with stenosis or occlusion of a femoropopliteal artery to treatment with standard balloon catheters coated with paclitaxel, uncoated balloons with paclitaxel dissolved in the contrast medium, or uncoated balloons without paclitaxel (control). The primary end point was late lumen loss at 6 months. RESULTS The mean (+/-SD) age of the patients was 68+/-8 years, 24% were smokers, and 49% had diabetes. Twenty-seven percent of the lesions were total occlusions, and 36% were restenotic lesions. The mean lesion length was 7.4+/-6.5 cm. There were no significant differences in baseline characteristics between the groups. There were no adverse events attributable to the paclitaxel-coated balloons. At 6 months, the mean late lumen loss was 1.7+/-1.8 mm in the control group, as compared with 0.4+/-1.2 mm (P<0.001) in the group treated with paclitaxel-coated balloons and 2.2+/-1.6 mm (P=0.11) in the group treated with paclitaxel in the contrast medium. The rate of revascularization of target lesions at 6 months was 20 of 54 (37%) in the control group, 2 of 48 (4%) in the group treated with paclitaxel-coated balloons (P<0.001 vs. control), and 15 of 52 (29%) in the group treated with paclitaxel in the contrast medium (P=0.41 vs. control); at 24 months, the rates increased to 28 of 54 (52%), 7 of 48 (15%), and 21 of 52 (40%), respectively. CONCLUSIONS Use of paclitaxel-coated angioplasty balloons during percutaneous treatment of femoropopliteal disease is associated with significant reductions in late lumen loss and target-lesion revascularization. No significant benefit is seen with the use of a paclitaxel-containing contrast medium. (ClinicalTrials.gov number, NCT00156624 [ClinicalTrials.gov].).
Regulation of Receptor Tyrosine Kinase Signaling by Endocytic Trafficking

Activated receptor tyrosine kinase (RTK) receptors are rapidly internalized and eventually delivered to the lysosomes. Although ligand‐induced endocytosis was originally thought to be a mechanism of receptor inactivation, many studies suggest that receptors remain active within endosomes. This review discusses the role that internalized signaling complexes may play in different RTK systems including recent data on how ubiquitination may regulate this process. In general, it appears that some receptor systems have evolved to enhance endosomal signaling, as is the case for TrkA and NGF. In contrast, the insulin receptor system appears to limit the extent of endosomal signaling. The EGFR system is the intermediate example. In this case, some signals are specifically generated from the cell surface while others appear to be generated from within endosomes. This may act as a mechanism to produce ligand‐specific signals. Thus, trafficking could play diverse roles in receptor signaling, depending on the specific cell and tissue type.
Induction of Centrosome Amplification and Chromosome Instability in Human Bladder Cancer Cells by p53 Mutation and Cyclin E Overexpression

Centrosome amplification frequently occurs in human cancers and is a major cause of chromosome instability (CIN). In mouse cells, centrosome amplification can be readily induced by loss or mutational inactivation of p53. In human cells, however, silencing of endogenous p53 alone does not induce centrosome amplification or CIN, although high degrees of correlation between p53 mutation and CIN/centrosome amplification in human cancer can be detected, suggesting the presence of additional regulatory mechanism(s) in human cells that ensures the numeral integrity of centrosomes and genomic integrity. Cyclin E, a regulatory subunit for CDK2 that plays a key role in centrosome duplication, frequently is overexpressed in human cancers. We found that cyclin E overexpression, together with loss of p53, efficiently induces centrosome amplification and CIN in human bladder cancer cells but not by either cyclin E overexpression or loss of p53 alone. We extended these findings to bladder cancer specimens and found that centrosome amplification is strongly correlated with concomitant occurrence of cyclin E overexpression and p53 inactivation but not with either cyclin E overexpression or p53 inactivation alone. Because cyclin E expression is strictly controlled in human cells compared with mouse cells, our findings suggest that this stringent regulation of cyclin E expression plays an additional role underlying numeral homeostasis of centrosomes in human cells and that deregulation of cyclin E expression, together with inactivation of p53, results in centrosome amplification.
Documenting Contemporary Society by Preserving Relevant Information from Twitter

In recent years, Twitter has changed from a medium for posting personal updates or status information to a channel for sharing and distributing information of all kinds. Its increasingly pervasive nature is encouraging more and more people to give insights into their daily life and to stay in contact with friends. This also attracts many companies and media agencies, attempting to establish a more or less constant flow of information to their customers. The limitation to 140 characters reduces efforts, and focusses the tweet on the core information. The ease of use of Twitter and its availability on every smartphone also encourages people to act as citizen journalists and immediately report the events they witness. Twitter can thus be seen as the foremost channel for “breaking news”, where information about events appears before being distrib-
Os Circular on Qemu/kqemu/kvm/xen­hvm

OS Circular is a framework of Internet Disk Image Distributor for virtual machines. The disk images are based on QEMU­DM(device model) and boot on QEMU, KQEMU, KVM and Xen­HVM. They are distributed by the stackable virtual disk "HTTP­FUSE CLOOP". It re­constructs a virtual disk with split and compressed block files on HTTP Servers. The file name of block file is the SHA1 digest of its contents. A block file is checked when it is re­mapped to virtual disk on a client PC. Block files are cached on a local storage and they make possible disconnect operation. Trusted HTTP­FUSE CLOOP is stackable and easy to add news block files for security update. These features enable us to distribute OS images for anonymous users via Internet.
Systems With Learning and Memory Abilities

Learning and Memory at the Behavioral Level. Visual Memory in Bees (J.L. Gould). A Cognitive Action Theory of Learning (H.L. Roitblat). Developmental Change in Learning and Memory: Infantile Disposition for Unitization (N.E. Spear). Symbolic and Sub-Symbolic Models of Memory (G. Tiberghien). Neural Bases. Pharmacological Studies and Models of Learning and Memory (G. Chapouthier). A View on the Memory System of the Mammalian Brain (J. Delacour). The Organization of Memories into ``Files'' (I. Izquierdo et al.). Neuronal Organization of Memory Functions in Animals and Humans (R.P. Kesner). Long Term Memory Processing in the Human Brain: On the Influence of Individual Variations (H.J. Markowitsch). Mind and Memory: Between Metaphor and Molecule (S. Rose). EEG Research of Neural Dynamics: Implications for Models of Learning and Memory (C.A. Skarda, W.J. Freeman). Learning, Memory and Basic Biology. Conditioning of Immune Responses (R. Dantzer, F. Crestani). Learning Induced Gene Stimulation: The RNA Hypothesis for Learning and Memory (H. Hyden, A. Cupello). Molecular Memory and Sensing Chemical Signals by Enzymes (J. Ricard et al.). Learning and Memory in the Immune System: ``Know Your Self'' (M. Seman). Biology-Oriented Models. A Learning Theory Using the Hierarchic Regulators Model (P. Anizan). The Use of Neural Models Exhibiting Memory Domains Can Account for Complex Brain Phenomena (P. Anninos et al.). Correlation Principle and Physiological Interpretation of Synaptic Efficacy (G. Chauvet). Neural Networks and Visual Pattern Recognition (K. Fukushima). Mesoscales in Neocortex and in C 3 Systems (L. Ingber). Trion Model of Cortical Organization and the Search for the Code of Short-Term Memory and of Information Processing (G.L. Shaw et al.). Learning by Selection Using Energy Functions (P. Stolorz, G.W. Hoffmann). Problems in Modelling the Nervous System: Cerebellar Capacity for Pattern Recognition (J.B. Willis). Physico-Mathematical Models. Neural Networks: Learning Rules and Memory Capacity (M.B. Gordon). Independent Components Analysis in Neural Networks (J. Herault, C. Jutten). Event Horizons in Associationist Models of Memory (B.A. Huberman). Neural Networks with Self Organization (J.C.S. Levy, D. Mercier). Spin Models of Neural Networks (W.A. Little). Magnetic Domains for Memories (I.B. Puchalska, G.A. Jones). Cellular Automata and Models of Memory (P. Rujan). A Multitude of Phases in the ANNNI Model (W. Selke).
High-frequency triazole resistance found In nonculturable Aspergillus fumigatus from lungs of patients with chronic fungal disease.

BACKGROUND Oral triazole therapy is well established for the treatment of invasive (IPA), allergic (ABPA), and chronic pulmonary (CPA) aspergillosis, and is often long-term. Triazole resistance rates are rising internationally. Microbiological diagnosis of aspergillosis is limited by poor culture yield, leading to uncertainty about the frequency of triazole resistance. METHODS Using an ultrasensitive real-time polymerase chain reaction (PCR) assay for Aspergillus spp. , we assessed respiratory fungal load in bronchoalveolar lavage (BAL) and sputum specimens. In a subset of PCR-positive, culture negative samples, we further amplified the CYP51A gene to detect key single-nucleotide polymorphisms (SNPs) associated with triazole resistance. RESULTS Aspergillus DNA was detected in BAL from normal volunteers (4/11, 36.4%) and patients with culture or microscopy confirmed IPA (21/22, 95%). Aspergillus DNA was detected in sputum in 15 of 19 (78.9%) and 30 of 42 (71.4%) patients with ABPA and CPA, compared with 0% and 16.7% by culture, respectively. In culture-negative, PCR-positive samples, we detected triazole-resistance mutations (L98H with tandem repeat [TR] and M220) within the drug target CYP51A in 55.1% of samples. Six of 8 (75%) of those with ABPA and 12 of 24 (50%) with CPA had resistance markers present, some without prior triazole treatment, and in most despite adequate plasma drug concentrations around the time of sampling. CONCLUSIONS The very low organism burdens of fungi causing infection have previously prevented direct culture and detection of antifungal resistance in clinical samples. These findings have major implications for the sustainability of triazoles for human antifungal therapy.
Elementary flux mode analysis of central carbon metabolism of Geobactersulfurreducens PCA for electricity production

Geobactersulfurreducens PCA, a delta-proteobacterium has the ability to transfer electrons directly onto the surface of electrodes, which play a crucial role in bioremediation and electricity production. Improving succinate production improves electron transfer and in turn it improves electricity generation in this organism. A pathway reconstruction was carried out for the central carbon metabolism. Elementary flux mode analysis of the reconstructed pathway was carried out and 87 modes were obtained. From the obtained modes, 8 best modes were identified and flux optimization was carried out using Linear Programming in CellNetAnalyzer. Three gene knock-outs namely 2-oxoglutarate synthase, pyruvate synthase, citrate oxaloacetate-lyase were proposed for flux optimization towards succinate. These in silico gene knock-outs yielded a seven fold increase towards succinate. This study will help in producing a better mutant for electricity production.
Systematic architecture exploration based on optimistic cycle estimation for low energy embedded processors

Systematic architecture exploration from vast solution space is a complex problem in embedded system design. It is very difficult to explore a best architecture fast and accurately because accurate evaluation usually consumes significant amount of time for point in the solution space. In this paper, we propose fast and systematic architecture exploration method for address generation unit (AGU) based on a coarse grained reconfigurable architecture model. First we prove that a set of Pareto solutions of cycle vs energy becomes a subset of Pareto solutions of cycle vs area under some practical assumptions. In addition we propose “Optimistic cycle (OC)” metric to find out promising solutions from vast solution space. Based on this metric we also propose a fast architecture exploration algorithm which only applies mapping to promising architectures. Using the proposed systematic architecture exploration method, we show that we can obtain almost the same trade-off points as the exhaustive search method and also that our method is about 164 times faster than exhaustive search.