Miracle-dz/UniFAR-FTUs huggingface dataset:
Balancing antagonistic time and resource utilization constraints in over-subscribed scheduling problems

Previous research has demonstrated the utility of constraint-based problem structuring and multiperspective scheduling for effective balancing conflicting objects in constraint-relaxable scheduling problems. Work aimed at applying these concepts to over-subscribed scheduling problems is discussed. The focus is on the problem of constructing short-term schedules for the Hubble Space Telescope, where complex state-dependent constraints on resource utilization interact antagonistically with the ability to satisfy absolute time constraints on execution of goal activities. Two time-bounded heuristic scheduling strategies were defined. The performance of each in balancing this tradeoff was studied experimentally. On the basis of results indicating the differential superiority of each strategy, a composite multiperspective strategy based on recognition of characteristics of the current problem-solving state is defined. Its experimental performance indicates the benefits of constraint-based problem structuring in over-subscribed domains. <<ETX>>
Eclipse observations of high-frequency oscillations in active region coronal loops

One of the mechanisms proposed for heating the corona above solar active regions is the damping of magnetohydro- dynamic (MHD) waves. Continuing on previous work, we provide observational evidence for the existence of high-frequency MHD waves in coronal loops observed during the August 1999 total solar eclipse. A wavelet analysis is used to identify twenty 4 × 4 arcsec 2 areas showing intensity oscillations. All detections lie in the frequency range 0.15-0.25 Hz (7-4 s), last for at least 3 periods at a confidence level of more than 99% and arise just outside known coronal loops. This leads us to suggest that they occur in low emission-measure or different temperature loops associated with the active region.
Structural and Thermodynamic Basis for the Binding of TMC114, a Next-Generation Human Immunodeficiency Virus Type 1 Protease Inhibitor

ABSTRACT TMC114, a newly designed human immunodeficiency virus type 1 (HIV-1) protease inhibitor, is extremely potent against both wild-type (wt) and multidrug-resistant (MDR) viruses in vitro as well as in vivo. Although chemically similar to amprenavir (APV), the potency of TMC114 is substantially greater. To examine the basis for this potency, we solved crystal structures of TMC114 complexed with wt HIV-1 protease and TMC114 and APV complexed with an MDR (L63P, V82T, and I84V) protease variant. In addition, we determined the corresponding binding thermodynamics by isothermal titration calorimetry. TMC114 binds approximately 2 orders of magnitude more tightly to the wt enzyme (Kd = 4.5 × 10−12 M) than APV (Kd = 3.9 × 10−10 M). Our X-ray data (resolution ranging from 2.2 to 1.2 Å) reveal strong interactions between the bis-tetrahydrofuranyl urethane moiety of TMC114 and main-chain atoms of D29 and D30. These interactions appear largely responsible for TMC114's very favorable binding enthalpy to the wt protease (−12.1 kcal/mol). However, TMC114 binding to the MDR HIV-1 protease is reduced by a factor of 13.3, whereas the APV binding constant is reduced only by a factor of 5.1. However, even with the reduction in binding affinity to the MDR HIV protease, TMC114 still binds with an affinity that is more than 1.5 orders of magnitude tighter than the first-generation inhibitors. Both APV and TMC114 fit predominantly within the substrate envelope, a property that may be associated with decreased susceptibility to drug-resistant mutations relative to that of first-generation inhibitors. Overall, TMC114's potency against MDR viruses is likely a combination of its extremely high affinity and close fit within the substrate envelope.
Vetting SSL Usage in Applications with SSLINT

Secure Sockets Layer (SSL) and Transport Layer Security (TLS) protocols have become the security backbone of the Web and Internet today. Many systems including mobile and desktop applications are protected by SSL/TLS protocols against network attacks. However, many vulnerabilities caused by incorrect use of SSL/TLS APIs have been uncovered in recent years. Such vulnerabilities, many of which are caused due to poor API design and inexperience of application developers, often lead to confidential data leakage or man-in-the-middle attacks. In this paper, to guarantee code quality and logic correctness of SSL/TLS applications, we design and implement SSLINT, a scalable, automated, static analysis system for detecting incorrect use of SSL/TLS APIs. SSLINT is capable of performing automatic logic verification with high efficiency and good accuracy. To demonstrate it, we apply SSLINT to one of the most popular Linux distributions -- Ubuntu. We find 27 previously unknown SSL/TLS vulnerabilities in Ubuntu applications, most of which are also distributed with other Linux distributions.
Exploiting dataflow to extract Java instruction level parallelism on a tag-based multi-issue semi in-order (TMSI) processor

To design a Java processor with traditional modern processor architecture, the instruction level parallelism (ILP) is not readily exploitable due to stack operands dependencies. This paper presents a dataflow-based instruction tagging scheme. With instruction tagging, the independent bytecode instruction groups with stack dependences are identified. The different bytecode instruction group can be executed in parallel because there are no stack dependences among them. With the instruction tagging scheme, we propose a tag-based multi-issue semi-in-order (TMSI) Java processor. The processor takes advantage of instruction-tagging and stack-folding to generate the tagged register-based instructions. When the tagged instructions are ready, they are bundled out-of-order depending on data availability to form VLIW-like instruction words and issued in-order. To achieve high performance, a VLIW engine is employed. We have conducted some experiments in our TMSI simulation environment using SPECjvm98 and Linpack workload. The results indicate that the proposed processor has good performance gain
Quantifying the Limitation to World Cereal Production Due To Soil Phosphorus Status

Phosphorus (P) is an essential element for plant growth. Low P availability in soils is likely to limit crop yields in many parts of the world, but this effect has never been quantified at the global scale by process‐based models. Here we attempt to estimate P limitation in three major cereals worldwide for the year 2000 by combining information on soil P distribution in croplands and a generic crop model, while accounting for the nature of soil‐plant P transport. As a global average, the diffusion‐limited soil P supply meets the crop's P demand corresponding to the climatic yield potential, due to the legacy soil P in highly fertilized areas. However, when focusing on the spatial distribution of P supply versus demand, we found strong limitation in regions like North and South America, Africa, and Eastern Europe. Averaged over grid cells where P supply is lower than demand, the global yield gap due to soil P is estimated at 22, 55, and 26% in winter wheat, maize, and rice. Assuming that a fraction (20%) of the annual P applied in fertilizers is directly available to the plant, the global P yield gap lowers by only 5–10%, underlying the importance of the existing soil P supply in sustaining crop yields. The study offers a base for exploring P limitation in crops worldwide but with certain limitations remaining. These could be better accounted for by describing the agricultural P cycle with a fully coupled and mechanistic soil‐crop model.
Empirical Validation of Pooled Whole Genome Population Re-Sequencing in Drosophila melanogaster

The sequencing of pooled non-barcoded individuals is an inexpensive and efficient means of assessing genome-wide population allele frequencies, yet its accuracy has not been thoroughly tested. We assessed the accuracy of this approach on whole, complex eukaryotic genomes by resequencing pools of largely isogenic, individually sequenced Drosophila melanogaster strains. We called SNPs in the pooled data and estimated false positive and false negative rates using the SNPs called in individual strain as a reference. We also estimated allele frequency of the SNPs using “pooled” data and compared them with “true” frequencies taken from the estimates in the individual strains. We demonstrate that pooled sequencing provides a faithful estimate of population allele frequency with the error well approximated by binomial sampling, and is a reliable means of novel SNP discovery with low false positive rates. However, a sufficient number of strains should be used in the pooling because variation in the amount of DNA derived from individual strains is a substantial source of noise when the number of pooled strains is low. Our results and analysis confirm that pooled sequencing is a very powerful and cost-effective technique for assessing of patterns of sequence variation in populations on genome-wide scales, and is applicable to any dataset where sequencing individuals or individual cells is impossible, difficult, time consuming, or expensive.
Modeling and Control System Design of a Grid Connected VSC Considering the Effect of the Interface Transformer Type

In this paper, modeling and control system design of a three-phase VSC system are investigated. The linear model and the control design are developed in the stationary-frame. The model shows a highly coupled system along and coordinates when using a -Y transformer vs. two completely decoupled subsystems in the case of Y-Y transformer. This issue was often overlooked in literature. The developed model includes the phase shift caused by the -Y transformer to address its effect on the steady-state and the dynamic behaviors under balanced and unbalanced distorted three phase conditions. Linear state-space model of the closed-loop system is developed to study the dynamics and stability of the two configurations. Modal analysis shows that the phase shift introduced by the -Y configuration can reduce the ultimate gain of the open loop system by 62% as compared to the system interfaced using Y-Y configuration. The developed linear model has been simulated in MATLAB/SIMULINK and validated using a detailed switching model in PSCAD/EMTDC under balanced and unbalanced three-phase conditions. The proposed control method can provide fast active and reactive power control with a minimum harmonics distortion in the line current.
An Applied Knowledge Framework to Study Complex Systems

The complexity of knowledge production on complex systems is well-known, but there still lacks knowledge framework that would both account for a certain structure of knowledge production at an epistemological level and be directly applicable to the study and management of complex systems. We set a basis for such a framework, by first analyzing in detail a case study of the construction of a geographical theory of complex territorial systems, through mixed methods, namely qualitative interview analysis and quantitative citation network analysis. We can therethrough inductively build a framework that considers knowledge entreprises as perspectives, with co-evolving components within complementary knowledge domains. We finally discuss potential applications and developments.
Detection and Characterization of Protein Interactions In Vivo by a Simple Live-Cell Imaging Method

Over the last decades there has been an explosion of new methodologies to study protein complexes. However, most of the approaches currently used are based on in vitro assays (e.g. nuclear magnetic resonance, X-ray, electron microscopy, isothermal titration calorimetry etc). The accurate measurement of parameters that define protein complexes in a physiological context has been largely limited due to technical constrains. Here, we present PICT (Protein interactions from Imaging of Complexes after Translocation), a new method that provides a simple fluorescence microscopy readout for the study of protein complexes in living cells. We take advantage of the inducible dimerization of FK506-binding protein (FKBP) and FKBP-rapamycin binding (FRB) domain to translocate protein assemblies to membrane associated anchoring platforms in yeast. In this assay, GFP-tagged prey proteins interacting with the FRB-tagged bait will co-translocate to the FKBP-tagged anchor sites upon addition of rapamycin. The interactions are thus encoded into localization changes and can be detected by fluorescence live-cell imaging under different physiological conditions or upon perturbations. PICT can be automated for high-throughput studies and can be used to quantify dissociation rates of protein complexes in vivo. In this work we have used PICT to analyze protein-protein interactions from three biological pathways in the yeast Saccharomyces cerevisiae: Mitogen-activated protein kinase cascade (Ste5-Ste11-Ste50), exocytosis (exocyst complex) and endocytosis (Ede1-Syp1).
A UNIFIED MODEL FOR PREDICTING HUMAN HEPATIC, METABOLIC CLEARANCE FROM IN VITRO INTRINSIC CLEARANCE DATA IN HEPATOCYTES AND MICROSOMES

The aim of this study was to evaluate a unified method for predicting human in vivo intrinsic clearance (CLint, in vivo) and hepatic clearance (CLh) from in vitro data in hepatocytes and microsomes by applying the unbound fraction in blood (fub) and in vitro incubations (fuinc). Human CLint, in vivo was projected using in vitro data together with biological scaling factors and compared with the unbound intrinsic clearance (CLint, ub, in vivo) estimated from clinical data using liver models with and without the various fu terms. For incubations conducted with fetal calf serum (n = 14), the observed CLint, in vivo was modeled well assuming fuinc and fub were equivalent. CLint, ub, in vivo was predicted best using both fub and fuinc for other hepatocyte data (n = 56; r2 = 0.78, p = 3.3 × 10–19, average fold error = 5.2). A similar model for CLint, ub, in vivo was established for microsomal data (n = 37; r2 = 0.77, p = 1.2 × 10–12, average fold error = 6.1). Using the model for CLint, ub, in vivo (including a further empirical scaling factor), the CLh in humans was also calculated according to the well stirred liver model for the most extensive dataset. CLint, in vivo and CLh were both predicted well using in vitro human data from several laboratories for acidic, basic, and neutral drugs. The direct use of this model using only in vitro human data to predict the metabolic component of CLh is attractive, as it does not require extra information from preclinical studies in animals.
[The effect of two different oral antiseptics on dental plaque formation (de novo biofilm) and on gingival inflammation].

INTRODUCTION Since the discovery that periodontal diseases are caused by microbial plaque the interest of many scientists has been focused on oral antiseptics. There are very few mouthrinses with oral antiseptic effect originally designed in our country. One of these is Ozosept solution. OBJECTIVE This study evaluated the effect of Ozosept solution (phenol compound) on the oral hygiene and gingival inflammation, in comparison with Hibidex DAP solution (chlorhexidine digluconate). METHODS Two groups, each of 21 persons, which did not significantly differ concerning Silness-Löe plaque index (PI) and Löe-Sillnes gingival index (GI), used one of the studied oral antiseptic for a 15-day period. Oral hygiene was maintained by subjects' habitual home methods, and no technique of professionally advised brushing was performed during the experimental period. RESULTS At the end of the study, PI and GI scores were lowered to a statistically high significance in both groups of participants in comparison to the indexes at the beginning of the study. At the end of the study, PI and GI scores did not significantly differ between the two analyzed groups. No side effects, which were recorded in the Hibidex DAP group (tooth and filling staining 9.5% and 4.74% respectively, transitory tongue numbness 28.6% and reduced taste sensation 14.3%), were registered in the group of subjects using Ozosept solution. CONCLUSION It is concluded that Ozosept solution is effective in the control of dental plaque--biofilm accumulation and gingival inflammation, and produces no side effects related to chlorhexidine digluconate usage.
A new CMOS wideband RF front-end for multistandard low-IF wireless receivers

A wideband radio-frequency (RF) receiver front-end is designed in 0.18 /spl mu/m CMOS technology with a new linearization technique that makes the circuit suitable for operating at low supply voltage. The proposed front-end circuit includes an input low noise wideband amplifying stage (LNA) of new configuration with output linearized transconductance stage, and a switching stage. Dual-loop resistive feedback applied around the LNA allows one to achieve input wideband matching. Linearity is enhanced by attenuating the effective transconductance of the transconductance stage. With an RF input signal of 1.9 GHz, the proposed front-end circuit exhibits 15.5 dB conversion gain, 7.2 dB SSB noise figure, -11.2 dBm 1-dB compression point, and -1.5 dBm third-order input intercept-point (IIP3) in simulations. The input wideband matching to 50 /spl Omega/ is achieved with -3 dB bandwidth of around 3 GHz. The input return loss (S11) varies from -26 dB to -10.5 dB in the frequency range of DC to 3.5 GHz. The proposed front-end consumes 22.3 mA DC current from 1.8 V supply voltage and occupies an area of 0.9/spl times/0.85 mm/sup 2/.
Analysis of the Oxidative Damage Repair Genes NUDT1, OGG1, and MUTYH in Patients from Mismatch Repair Proficient HNPCC Families (MSS-HNPCC)

Purpose: Several studies have described molecular differences between microsatellite stable hereditary nonpolyposis colorectal cancer (MSS-HNPCC) and microsatellite unstable Lynch syndrome tumors (MSI-HNPCC). These differences highlight the possibility that other instability forms could explain cancer susceptibility in this group of families. The base excision repair (BER) pathway is the major DNA repair pathway for oxidative DNA damage. A defect in this pathway can result in DNA transversion mutations and a subsequent increased cancer risk. Mutations in MUTYH have been associated with increased colorectal cancer (CRC) risk while no association has been described for OGG1 or NUDT1. Experimental Design: We performed mutational screening of the three genes involved in defense against oxidative DNA damage in a set of 42 MSS-HNPCC families. Results: Eight rare variants and 5 frequent variants were found in MSS-HNPCC patients. All variants were previously described by other authors except variant c.285C>T in OGG1. Segregation studies were done and in silico programs were used to estimate the level of amino acid conservation, protein damage prediction, and possible splicing alterations. Variants OGG1 c.137G>A; MUTYH c.1187G>A were detected in Amsterdam I families and cosegregate with cancer. Analysis of OGG1 c.137G>A transcripts showed an inactivation of the splicing donor of exon 1. Conclusions: Two rare variants (OGG1 c.137G>A; MUTYH c.1187G>A) and one common polymorphism (NUDT1 c.426C>T) were associated with CRC risk. We show that the BER pathway can play a significant role in a number of MSS-HNPCC colorectal cancers. More studies could be of interest in order to gain further understanding of yet unexplained CRC susceptibility cases. Clin Cancer Res; 17(7); 1701–12. ©2011 AACR.
Mouse epiblasts change responsiveness to BMP4 signal required for PGC formation through functions of extraembryonic ectoderm

Mouse primordial germ cells (PGCs) are initially identified as a cluster of alkaline phosphatase (AP)‐positive cells within the extraembryonic mesoderm near the posterior part of the primitive streak at embryonic day (E) 7.25. Clonal analysis of epiblast cells has revealed that the putative precursors of PGCs are localized in the proximal epiblast, and we demonstrated that the conditions required for PGC formation are induced in the proximal region of epiblasts by extraembryonic ectoderm. Bone morphogenetic protein (BMP) 4 and BMP8b, which belong to the transforming growth factor‐β (TGF‐β) superfamily, might generate induction signals from extraembryonic ectoderm. Smad1 and Smad5, which are intracellular signaling molecules for BMP4, might also play a critical role in stimulating epiblasts to form PGC. However, how pluripotential epiblasts temporally and spatially respond to BMP signals to form PGCs remains unclear. The present study examines changes of responsiveness to BMP4 for PGC formation in epiblasts and their molecular mechanisms. We initially examined the effect of recombinant human (rh) BMP4 upon cultured epiblasts at different developmental stages, and found that they acquire the ability to respond to BMP4 signals for PGC formation between E5.25 and E5.5. In addition, such competence was conferred upon epiblasts by the extraembryonic ectoderm. We also showed that the increased expression of Smad1 and the onset of Smad5 expression induced by extraembryonic ectoderm might be responsible for quick acquisition of this competence. Furthermore, we show that only proximal epiblast cells maintain responsiveness to BMP4 for PGC formation at E6.0, and that this is associated with the proximal epiblast‐specific expression of Smad5. These results explain why only the proximal region of epiblasts can sustain the ability to form PGCs. Mol. Reprod. Dev. 70: 20–29, 2004. © 2004 Wiley‐Liss, Inc.
Deterministic sorting and randomized median finding on the BSP model

We present new BSP algorithms for deterministic sorting and rmdomized median finding. We sort n general keys by using a partitioning scheme that achieves the requirements of efficiency (one-optimality) and insensitivity against data skew (the accuracy of the splitting keys depends solely on the step distance, which can be adapted to meet the worstcase requirements of our application). Although we employ sampling in order to realize efficiency, we can give a precise worst-case estimation of the maximum imbalance which might occur. We also investigate optimal randomized BSP algorithms for the problem of finding the median of n elements that require, with high-probability, 3rz/(2p) + o(n/p) number of comparisons, for a wide range of values of n and p. Experimental results for the two algorithms are also presented
Paying More Attention to Attention: Improving the Performance of Convolutional Neural Networks via Attention Transfer

Attention plays a critical role in human visual experience. Furthermore, it has recently been demonstrated that attention can also play an important role in the context of applying artificial neural networks to a variety of tasks from fields such as computer vision and NLP. In this work we show that, by properly defining attention for convolutional neural networks, we can actually use this type of information in order to significantly improve the performance of a student CNN network by forcing it to mimic the attention maps of a powerful teacher network. To that end, we propose several novel methods of transferring attention, showing consistent improvement across a variety of datasets and convolutional neural network architectures. Code and models for our experiments are available at this https URL