Miracle-dz/UniFAR-FTUs huggingface dataset:
Modified clonal selection algorithm for learning qualitative compartmental models of metabolic systems

In this paper, a modified Clonal Selection Algorithm (CSA)is proposed to learn qualitative compartmental models. Different from traditional AI search algorithm, this population based approach employs antibody repertoire to perform random search, which is suitable for the ragged and multi-modal landscape of qualitative model space. Experimental result shows that this algorithm can obtain the same kernel sets and learning reliability as previous work for learning the two compartment model, and it can also search out the target model when learning the more complex three-compartment model. Although this algorithm does not succeed in learning the four-compartment model, promising result is still obtained.
Hypoxic marker CA IX and adhesion mediator β-catenin are downregulated by lymphocytic choriomeningitis virus persistent infection

Renal cell carcinoma is one of the most frequent cancer diseases with high resistance to radio- and chemotherapy. Mutation of VHL gene is frequent in these tumors leading to simulation of hypoxic conditions. Lymphocytic choriomeningitis virus, belonging to RNA viruses, is a neglected human pathogen and teratogen. We have found that infection of renal cell carcinoma cells by lymphocytic choriomeningitis virus strain MX causes a decrease of carbonic anhydrase IX protein and RNA level. Lower expression of carbonic anhydrase IX on the cell surface provides less target for carbonic anhydrase IX-targeted immunotherapy. What more, reduced levels of adhesion mediating protein β-catenin as well as E-cadherin, as a consequence of infection, suggest a possible increase in metastatic potential of cells infected by lymphocytic choriomeningitis virus strain MX. These results might help elucidate differences in patients susceptibility to immunotherapy directed against carbonic anhydrase IX or in developing new therapeutical strategies. Our data indicate that presence of infection can significantly affect patient response to cancer therapy.
Response-Time-Optimized Distributed Cloud Resource Allocation

A current trend in networking and cloud computing is to provide compute resources over widely dispersed places exemplified by initiatives like Network Function Virtualisation. This paves the way for a widespread service deployment and can improve service quality; a nearby server can reduce the user-perceived response times. But always using the nearest server is a bad decision if that server is already highly utilized. This paper investigates the optimal assignment of users to widespread resources -- a convex capacitated facility location problem with integrated queuing systems. We determine the response times depending on the number of used resources. This enables service providers to balance between resource costs and the corresponding service quality. We also present a linear problem reformulation showing small optimality gaps and faster solving times; this speed-up enables a swift reaction to demand changes. Finally, we compare solutions by either considering or ignoring queuing systems and discuss the response time reduction by using the more complex model. Our investigations are backed by large-scale numerical evaluations.
Pathology of Second-Generation Everolimus-Eluting Stents Versus First-Generation Sirolimus- and Paclitaxel-Eluting Stents in Humans

Background— Clinical trials have demonstrated that the second-generation cobalt-chromium everolimus-eluting stent (CoCr-EES) is superior to the first-generation paclitaxel-eluting stent (PES) and is noninferior or superior to the sirolimus-eluting stent (SES) in terms of safety and efficacy. It remains unclear whether vascular responses to CoCr-EES are different from those to SES and PES because the pathology of CoCr-EES has not been described in humans. Methods and Results— A total of 204 lesions (SES=73; PES=85; CoCr-EES=46) from 149 autopsy cases with duration of implantation >30 days and ⩽3 years were pathologically analyzed, and comparison of vascular responses was corrected for duration of implantation. The observed frequency of late and very late stent thrombosis was less in CoCr-EES (4%) versus SES (21%; P=0.029) and PES (26%; P=0.008). Neointimal thickness was comparable among the groups, whereas the percentage of uncovered struts was strikingly lower in CoCr-EES (median=2.6%) versus SES (18.0%; P<0.0005) and PES (18.7%; P<0.0005). CoCr-EES showed a lower inflammation score (with no hypersensitivity) and less fibrin deposition versus SES and PES. The observed frequency of neoatherosclerosis, however, did not differ significantly among the groups (CoCr-EES=29%; SES=35%; PES=19%). CoCr-EES had the least frequency of stent fracture (CoCr-EES=13%; SES=40%; PES=19%; P=0.007 for CoCr-EES versus SES), whereas fracture-related restenosis or thrombosis was comparable among the groups (CoCr-EES=6.5%; SES=5.5%; PES=1.2%). Conclusions— CoCr-EES demonstrated greater strut coverage with less inflammation, less fibrin deposition, and less late and very late stent thrombosis compared with SES and PES in human autopsy analysis. Nevertheless, the observed frequencies of neoatherosclerosis and fracture-related adverse pathological events were comparable in these devices, indicating that careful long-term follow-up remains important even after CoCr-EES placement.
MicroRNA-145 downregulation associates with advanced tumor progression and poor prognosis in patients suffering osteosarcoma

Purpose Microribonucleic acid (miRNA)-145 (miR-145) has been identified as a tumor suppressor in several types of human cancers. Especially, miR-145 expression has been found to be significantly decreased in osteosarcoma tissues, and enforced expression of this miRNA could inhibit invasion and angiopoiesis of osteosarcoma cells. However, its clinical significance in osteosarcoma is still unclear. Therefore, the aim of this study was to analyze the association of miR-145 expression with clinicopathologic features and prognosis in patients suffering osteosarcoma. Methods miR-145 expression was detected by quantitative real-time reverse transcriptase polymerase chain reaction analysis using 166 pairs of osteosarcoma and noncancerous bone tissues. Then, the associations of miR-145 expression with clinicopathological factors or survival of patients suffering osteosarcoma were determined. Results The expression levels of miR-145 in osteosarcoma tissues were significantly lower than those in corresponding noncancerous bone tissues (P < 0.0001). In addition, miR-145 downregulation more frequently occurred in osteosarcoma specimens with advanced clinical stage (P = 0.003) and positive distant metastasis (P = 0.008). Moreover, the univariate analysis demonstrated that osteosarcoma patients with low miR-145 expression had poorer overall (P = 0.003) and disease-free survival (P < 0.001). Furthermore, the multivariate analysis identified low miR-145 expression as an independent prognostic factor for both overall (P = 0.01) and disease-free survival (P = 0.008). Conclusion For the first time, the current data offer convincing evidence that the down-regulation of miR-145 may be associated with tumor aggressiveness and tumor metastasis of osteosarcoma, and that this miRNA may be an independent prognostic marker for osteosarcoma patients.
Effect of Peroxynitrite Scavenging on Endothelial Cells Stimulated by Plasma from Women with Preeclampsia: A Proteomic Approach

Hypothesis: Increased peroxynitrite formation in endothelial cells incubated with plasma from women with preeclampsia alters the expression of specific endothelial proteins. Methods: We used a proteomic approach to examine the effect of a peroxynitrite scavenger (FeTPPS, 5 μmol/L) on the expression of endothelial proteins in response to plasma from women with preeclampsia. After treatment, cells were subjected to two-dimensional gel electrophoresis and proteins were identified using mass spectrometry. Results: Peroxynitrite scavenging decreased the expression of structural proteins, cytokeratin, actin-γ-1, and moesin, and the calcium-binding protein, calumenin. Conclusions: This study has identified novel proteins that are regulated by peroxynitrite in response to plasma from women with preeclampsia.
Association between MTHFR Polymorphisms and Acute Myeloid Leukemia Risk: A Meta-Analysis

Previous observational studies investigating the association between methylenetetrahydrofolate reductase (MTHFR) polymorphisms and acute myeloid leukemia risk (AML) have yielded inconsistent results. The aim of this study is to derive a more precise estimation of the association between MTHFR (C677T and A1298C) polymorphisms and acute myeloid leukemia risk. PubMed and Embase databases were systematically searched to identify relevant studies from their inception to August 2013. Odds ratios (ORs) with 95% confidence intervals (CIs) were the metric of choice. Thirteen studies were selected for C677T polymorphism (1838 cases and 5318 controls) and 9 studies (1335 patients and 4295 controls) for A1298C polymorphism. Overall, pooled results showed that C677T polymorphism was not significant associated with AML risk(OR, 0.98–1.04; 95% CI, 0.86–0.92 to 1.09–1.25). Similar results were observed for the A1298C polymorphism and in subgroup analysis. All comparisons revealed no substantial heterogeneity nor did we detect evidence of publication bias. In summary, this meta-analysis provides evidence that MTHFR polymorphisms were not associated with AML risk. Further investigations are needed to offer better insight into the role of these polymorphisms in AML carcinogenesis.
The C-Type Lectin SIGNR1 Binds Schistosoma mansoni Antigens In Vitro, but SIGNR1-Deficient Mice Have Normal Responses during Schistosome Infection

ABSTRACT The de novo immune response to infectious organisms arises from the innate recognition of pathogen-associated molecular patterns (PAMPs) by the host's pattern recognition receptors (PRRs). As the generation of type 2 cytokine responses by the human trematode parasite Schistosoma mansoni is glycan mediated, there is a particular potential role for a C-type lectin receptor (CLR) to mediate the innate recognition of schistosome PAMPs. One such CLR, dendritic cell-specific intracellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN; CD209), has been shown to recognize glycans expressed by S. mansoni eggs. We show that SIGNR1 (SIGN-related 1; CD209b), a murine homologue of DC-SIGN that is expressed on macrophages, also binds both schistosome-soluble egg antigens and worm antigens in vitro. The generation of schistosome egg-induced pulmonary egg granulomas was not altered in SIGNR1-deficient mice. Following S. mansoni infection, the SIGNR1-deficient mice had an unaltered phenotype with an intact immunological response and no difference in pathology. In this study we demonstrate that although SIGNR1 recognizes S. mansoni antigens in vitro, this CLR is redundant during infection. This study highlights the finding that although there was binding of SIGNR1 to immunogenic factors produced in the S. mansoni life cycle, this recognition does not translate to a functional in vivo role for the PRR during infection.
Unilateral absence of vas deferens: prevalence among 23,013 men seeking vasectomy

ABSTRACT Purpose: To determine the prevalence of unilateral absence of vas deferens (UAVD) in men with both testes seeking vasectomy. Materials and Methods: Computerized charts of 23,013 patients encountered between January 1994 and December 2013 in one university hospital and two community clinics of Quebec City, Canada, were searched. Pre-vasectomy consultation, operative reports and semen analysis results were reviewed to identify cases of UAVD. Cases were categorized as confirmed (unilateral vasectomy and success confirmed by semen analysis) or possible congenital UAVD further sub-categorized according to whether or not a scrotal anomaly was present. Results: Among 159 men identified as potentially having UAVD, chart review revealed that 47 had only one testicle, 26 had bilateral vasa, and four were misdiagnosed (post-vasectomy semen analysis [PVSA] showing motile sperm after unilateral vasectomy) leaving 82 men deemed cases of UAVD (0.36%, 95% confidence interval 0.28% to 0.43%). These were classified as confirmed (n=48, 0.21%) and possible (n=34, 0.15%; 22 without and 12 with scrotal anomalies) congenital UAVD. The misdiagnosis ratio of UAVD was low when scrotal content was otherwise normal (1:48), but higher if anomalies were present (3:12). Conclusions: Most surgeons who perform vasectomy will encounter cases of UAVD. In most suspected cases, it is safe and effective to proceed with unilateral vasectomy under local anesthesia while stressing the need for PVSA. Further studies or scrotal exploration may be considered in patient with prior scrotal surgery.
The Utilization of Bark to Make Rigid Polyurethane Foams

The Utilization of Bark to Make Rigid Polyurethane Foams Jason D’Souza Doctor of Philosophy Graduate Department of Faculty of Forestry University of Toronto 2016 This work focused on the characterization of polyols derived from the liquefaction or alkoxylation of bark. Regarding liquefaction, it was found that both temperature and solvent structure played a significant role in polyol properties. High temperature liquefaction resulted in the degradation of sugars, while liquefaction at mild temperatures preserved sugar structures as shown by P-NMR. It was also shown that liquefaction at 130 ◦C was ideal in terms of producing a polyol with a relatively flat, broad, plateau of molecular weight distribution, whereas liquefaction at 90 and 160 ◦C produced polyols with a large amount of low molecular weight compounds. Regarding solvent structure, it was found that polyhydric alcohols with short chain primary hydroxyls resulted in less sugar degradation products and less formation of condensation side-products. It is proposed that the highly polar environment promoted grafting and prevented condensation onto other biopolymers. Using organic solvents it was found that ketonic solvents like acetyl acetone and cyclohexanone, through their highly polar carbonyl group could engage in hydrogen bonding through electron donation/proton accepting interactions. These enabled the solvent to reduce the amount of condensation reactions and improve liquefaction yield. The liquefied bark-based polyols were then used to make polyurethane foams. It was found that when a diversity of hydroxyl groups were present the foaming rate was reduced and this may reflect a slower rate of curing and explain why the bark foams had a greater amount of cells that underwent coalescence. It was also observed that the bark foams had a low amount of closed-cell content. Since closed-cell content plays a role in dictating elastic compression, this may explain why the bark foams exhibited a lower elastic modulus. Finally, as a contrast to liquefaction, bark was alkoxylated. It was observed that the conversion yield was higher than liquefaction. The polyols had a high average molecular weight with a broad distribution and far greater solubility. It is proposed that alkoxylation is far less degradative than liquefaction. This may explain why the foams showed improved compressive behaviour compared to the foams made from liquefied bark-based polyols. Through greater characterization of the structure of polyols produced via liquefaction and alkoxylation the relationships between reaction parameters, polyol structure, and foam properties can be better understood. This is an important step towards the utilization of bark to make polyurethane foams.
Selective interaction of peripheral and central nervous system cells with two distinct cell-binding domains of fibronectin

Mechanisms of cell interaction with fibronectin have been studied with proteolytic fibronectin fragments that have well-defined ligand binding properties. Results of a previous study (Rogers, S. L., J. B. McCarthy, S. L. Palm, L. T. Furcht, and P. C. Letourneau, 1985, J. Neurosci., 5:369-378) demonstrated that (a) central (CNS) and peripheral (PNS) nervous system neurons adhere to, and extend neurites on a 33-kD carboxyl terminal fibronectin fragment that also binds heparin, and (b) neurons from the PNS, but not the CNS, have stable interactions with a 75-kD cell-binding fragment and with intact fibronectin. In the present study domain-specific reagents were used in inhibition assays to further differentiate cell surface interactions with the two fibronectin domains, and to define the significance of these domains to cell interactions with the intact fibronectin molecule. These reagents are (a) a soluble synthetic tetrapeptide Arg-Gly-Asp-Ser (RGDS; Pierschbacher, M. D., and E. Ruoslahti, 1984, Nature (Lond.), 309:30- 33) representing a cell-binding determinant in the 75-kD fragment, and (b) an antibody raised against the 33-kD fragment that binds specifically to that fragment. Initial cell attachment to, and neurite extension upon, fibronectin and the two different fragments was evaluated in the presence and absence of the two reagents. Attachment of both PNS and CNS cells to intact fibronectin was reduced in the presence of RGDS, the former more so than the latter. In contrast, the antibody to the 33-kD fragment did not affect attachment of PNS cells to fibronectin, but significantly decreased attachment of CNS cells to the molecule. RGDS inhibited attachment of CNS cells to the molecule. RGDS inhibited attachment of both cell types to the 75-kD fragment to a greater degree than it did attachment to the intact molecule. Cell interaction with the 33-kD fragment was not affected by RGDS. Reduction of neurite lengths (determined after 24 h of culture) by the domain- specific reagents paralleled the reduction in initial adhesion to each substratum. Therefore, it appears that (a) both PNS and CNS cells have receptors for each cell-binding domain of fibronectin, (b) the receptor(s) for the two domains are distinct, with attachment to the 33- kD fragment being independent of RGDS, and (c) the relative importance of each domain to cell interaction with intact fibronectin is different for CNS and PNS cells.
Breaking the DDoS Attack Chain

Department of Defense (DoD) communications and data networks continue to be targets for adversaries to deny operational use of those networks. Distributed Denial of Service (DDoS) is one such attack strategy that has proven to be an effective method of denying service to military, political, infrastructure, and economic targets. The introduction of botnets as zombies, or computers under control of another entity unbeknownst to the owner, which can be controlled with minimal effort by an obfuscated attacker to degrade or deny usage of networks through overloading capacity, has proven successful time and again. As some network security firms have reported, the United States is a prime target for adversaries, and it is far from impervious to cyber attacks. In their 2011 paper, Hutchins, Cloppert, and Amin discuss the concept of an attacker kill chain for phases of intrusions into networks but do not address other asymmetric cyber threats such as DDoS. In order to fill this gap, this paper provides a survey of the DDoS landscape and examines the application of “kill chain” concepts to the DDoS threat. Leveraging the concepts of detect, deny, disrupt, degrade, deceive, and destroy, the paper explores ways that this chain may be disrupted. Lastly, an overview of the critical and emerging DDoS threats is provided, and considerations are offered for additional technology and research that have potential to significantly reduce the current DDoS threat.
Analysis of mode quality factors and mode reflectivities for nanowire cavity by FDTD technique

The mode frequency and the quality factor of nanowire cavities are calculated from the intensity spectrum obtained by the finite-difference time-domain (FDTD) technique and the Pade/spl acute/ approximation. In a free-standing nanowire cavity with dielectric constant /spl epsiv/=6.0 and a length of 5 /spl mu/m, quality factors of 130, 159, and 151 are obtained for the HE/sub 11/ modes with a wavelength around 375 nm, at cavity radius of 60, 75, and 90 nm, respectively. The corresponding quality factors reduce to 78, 94, and 86 for a nanowire cavity standing on a sapphire substrate with a refractive index of 1.8. The mode quality factors are also calculated for the TE/sub 01/ and TM/sub 01/ modes, and the mode reflectivities are calculated from the mode quality factors.
Induction of the Antimicrobial Peptide CRAMP in the Blood-Brain Barrier and Meninges after Meningococcal Infection

ABSTRACT Antimicrobial peptides are present in most living species and constitute important effector molecules of innate immunity. Recently, we and others have detected antimicrobial peptides in the brain. This is an organ that is rarely infected, which has mainly been ascribed to the protective functions of the blood-brain barrier (BBB) and meninges. Since the bactericidal properties of the BBB and meninges are not known, we hypothesized that antimicrobial peptides could play a role in these barriers. We addressed this hypothesis by infecting mice with the neuropathogenic bacterium Neisseria meningitidis. Brains were analyzed for expression of the antimicrobial peptide CRAMP by immunohistochemistry in combination with confocal microscopy. After infection, we observed induction of CRAMP in endothelial cells of the BBB and in cells of the meninges. To explore the functional role of CRAMP in meningococcal disease, we infected mice deficient of the CRAMP gene. Even though CRAMP did not appear to protect the brain from invasion of meningococci, CRAMP knockout mice were more susceptible to meningococcal infection than wild-type mice and exhibited increased meningococcal growth in blood, liver, and spleen. Moreover, we could demonstrate that carbonate, a compound that accumulates in the circulation during metabolic acidosis, makes meningococci more susceptible to CRAMP.
Dynamic Filter Networks

In a traditional convolutional layer, the learned filters stay fixed after training. In contrast, we introduce a new framework, the Dynamic Filter Network, where filters are generated dynamically conditioned on an input. We show that this architecture is a powerful one, with increased flexibility thanks to its adaptive nature, yet without an excessive increase in the number of model parameters. A wide variety of filtering operation can be learned this way, including local spatial transformations, but also others like selective (de)blurring or adaptive feature extraction. Moreover, multiple such layers can be combined, e.g. in a recurrent architecture. We demonstrate the effectiveness of the dynamic filter network on the tasks of video and stereo prediction, and reach state-of-the-art performance on the moving MNIST dataset with a much smaller model. By visualizing the learned filters, we illustrate that the network has picked up flow information by only looking at unlabelled training data. This suggests that the network can be used to pretrain networks for various supervised tasks in an unsupervised way, like optical flow and depth estimation.