Miracle-dz/UniFAR-FTUs huggingface dataset:
A Survey of Automatic Protocol Reverse Engineering Approaches, Methods, and Tools on the Inputs and Outputs View

A network protocol defines rules that control communications between two or more machines on the Internet, whereas Automatic Protocol Reverse Engineering (APRE) defines the way of extracting the structure of a network protocol without accessing its specifications. Enough knowledge on undocumented protocols is essential for security purposes, network policy implementation, and management of network resources. This paper reviews and analyzes a total of 39 approaches, methods, and tools towards Protocol Reverse Engineering (PRE) and classifies them into four divisions, approaches that reverse engineer protocol finite state machines, protocol formats, and both protocol finite state machines and protocol formats to approaches that focus directly on neither reverse engineering protocol formats nor protocol finite state machines. The efficiency of all approaches’ outputs based on their selected inputs is analyzed in general along with appropriate reverse engineering inputs format. Additionally, we present discussion and extended classification in terms of automated to manual approaches, known and novel categories of reverse engineered protocols, and a literature of reverse engineered protocols in relation to the seven layers’ OSI (Open Systems Interconnection) model.
Micro/nano-scale strategies for engineering in vitro the celular microenvironment using biodegradable biomaterials

Biological tissues result of a specific spatial organization of cells, extracellular matrix (ECM) molecules, and soluble factors. These micro and nanoscaled biological entities organize into regional tissue architectures, creating highly complex and heterogeneous cellular microenvironments. To generate functional tissue equivalents in vitro, engineered biomaterials should mimic the structural, chemical and cellular complexity by recapitulating the unique native microenvironments. Thus, the main goal of this thesis was to engineer biodegradable polymers using various micro and nanofabrication techniques, with specific structural, biochemical and cellular cues for improved performance. The main governing hypotheses of this thesis were: 1) substrates with improved structural properties can be engineered using biodegradable polymers that have previously shown good results in in vivo studies, 2) biochemical cues can be incorporated into biodegradable polymers, yielding biomaterials with integrated chemical cues for improved cellular performance, and 3) these structural and biochemical cues can be incorporated into a single system. To develop biomaterials with structural cues, micromolding of poly(butylene succinate) (PBS) was performed to engineer surfaces with features at a microscale that induced the alignment of human adipose stem cells. Although this polymeric material has been processed at a macroscale into scaffolds, this was the first report on the engineering of this material at a microscale, demonstrated by the development of twenty features with different dimensions. Improved substrates with structural cues were also engineered using the polysaccharide gellan gum (GG), which has been extensively studied at 3B’s Research Group. Microcapsules of GG, aimed at being used as drug or cell carriers and/or delivery agents, were engineered using a two-phase system. The principle of hydrophobic-hydrophilic repulsion forces was combined with a microfabrication process by means of a needle/syringe pump system. Microcapsules with different diameters were produced by varying the system parameters. As an original proof-of-concept, fluorescent beads, cell suspensions and cell aggregates were encapsulated within this microfabrication system. To develop biomaterials with enhanced biochemical cues, GG was chemically modified with ester bonds, yielding novel hydrogels crosslinkable by ultraviolet (UV) light. Methacrylated GG (MeGG) hydrogels were formed using physical and chemical mechanisms resulting in hydrogels with tunable mechanical properties, matching those of natural tissues from soft to hard, as the brain or collagenous bone. In a subsequent step, this material was combined
The influence of handle-avatar mapping uncertainty on torque fidelity of 6-DOF haptic rendering

The handle-avatar mapping from the handle of a desktop haptic device (i.e., the handle) to the virtual tool (i.e., the avatar) is subject to several uncertainties, including uncertain held positions of the human hand, un-modeled hand position on the virtual tool, and difference between the shape of the virtual tool and that of the physical handle. The influence of these uncertainties on the force/torque fidelity of 6-DOF haptic rendering is analyzed in this paper. A model of force/torque error induced by these uncertainties is introduced to measure the influences under different contact scenarios. A method based on adding a handle-hand avatar to the virtual tool is proposed to reduce the uncertainties and thus to improve simulation fidelity. Psychophysical experiments were carried out. Experiment results show that the subjective feeling of the human operator is consistent with the theoretical analysis results. Most subjects can feel the increase on torque fidelity after using the proposed method.
Crowd-Machine Collaboration for Item Screening

In this paper we describe how crowd and machine classifier can be efficiently combined to screen items that satisfy a set of predicates. We show that this is a recurring problem in many domains, present machine-human (hybrid) algorithms that screen items efficiently and estimate the gain over human-only or machine-only screening in terms of performance and cost.
Inhibition of GLO1 in Glioblastoma Multiforme Increases DNA-AGEs, Stimulates RAGE Expression, and Inhibits Brain Tumor Growth in Orthotopic Mouse Models

Cancers that exhibit the Warburg effect may elevate expression of glyoxylase 1 (GLO1) to detoxify the toxic glycolytic byproduct methylglyoxal (MG) and inhibit the formation of pro-apoptotic advanced glycation endproducts (AGEs). Inhibition of GLO1 in cancers that up-regulate glycolysis has been proposed as a therapeutic targeting strategy, but this approach has not been evaluated for glioblastoma multiforme (GBM), the most aggressive and difficult to treat malignancy of the brain. Elevated GLO1 expression in GBM was established in patient tumors and cell lines using bioinformatics tools and biochemical approaches. GLO1 inhibition in GBM cell lines and in an orthotopic xenograft GBM mouse model was examined using both small molecule and short hairpin RNA (shRNA) approaches. Inhibition of GLO1 with S-(p-bromobenzyl) glutathione dicyclopentyl ester (p-BrBzGSH(Cp)2) increased levels of the DNA-AGE N2-1-(carboxyethyl)-2′-deoxyguanosine (CEdG), a surrogate biomarker for nuclear MG exposure; substantially elevated expression of the immunoglobulin-like receptor for AGEs (RAGE); and induced apoptosis in GBM cell lines. Targeting GLO1 with shRNA similarly increased CEdG levels and RAGE expression, and was cytotoxic to glioma cells. Mice bearing orthotopic GBM xenografts treated systemically with p-BrBzGSH(Cp)2 exhibited tumor regression without significant off-target effects suggesting that GLO1 inhibition may have value in the therapeutic management of these drug-resistant tumors.
Site-specific Relaxase Activity of a VirD2-like Protein Encoded within the tfs4 Genomic Island of Helicobacter pylori

Background: The complement of factors involved in mobilization of the Helicobacter pylori disease-associated tfs4 genomic island are presently unknown. Results: tfs4 encodes a VirD2-like relaxase with distinctive DNA binding and nicking activity. Conclusion: Tfs4 VirD2 probably initiates mobilization of tfs4 by specific interaction at a chromosomal transfer origin sequence. Significance: Tfs4 VirD2-mediated mobilization of tfs4 may increase pathogenic potential of H. pylori strains. Four different type IV secretion systems are variously represented in the genomes of different Helicobacter pylori strains. Two of these, encoded by tfs3 and tfs4 gene clusters are contained within self-transmissible genomic islands. Although chromosomal excision of tfs4 circular intermediates is reported to be dependent upon the function of a tfs4-encoded XerD tyrosine-like recombinase, other factors required for transfer to a recipient cell have not been demonstrated. Here, we characterize the functional activity of a putative tfs4-encoded VirD2-like relaxase protein. Tfs4 VirD2 was purified as a fusion to maltose-binding protein and demonstrated to bind and nick both supercoiled duplex DNA and oligonucleotides in vitro in a manner dependent upon the presence of Mg2+ but independently of any auxiliary proteins. Unusually, concentration-dependent nicking of duplex DNA appeared to require only transient protein-DNA interaction. Although phylogenetically distinct from established relaxase families, site-specific cleavage of oligonucleotides by Tfs4 VirD2 required the nick region sequence 5′-ATCCTG-3′ common to transfer origins (oriT) recognized by MOBP conjugative relaxases. Cleavage resulted in covalent attachment of MBP-VirD2 to the 5′-cleaved end, consistent with conventional relaxase activity. Identification of an oriT-like sequence upstream of tfs4 virD2 and demonstration of VirD2 protein-protein interaction with a putative VirC1 relaxosome component indicate that transfer initiation of the tfs4 genomic island is analogous to mechanisms underlying mobilization of other integrated mobile elements, such as integrating conjugative elements, requiring site-specific targeting of relaxase activity to a cognate oriT sequence.
Investigating the impact of biomass quality on near-infrared models for switchgrass feedstocks

The aim of this study was to determine the impact of incorporating switchgrass samples that have been in long term storage on the development of near-infrared (NIR) multivariate calibration models and their predictive capabilities. Stored material contains more variation in their respective spectral signatures due to chemical changes in the bales with storage time. Partial least squares (PLS) regression models constructed using NIR spectra of stored switchgrass possessed an instability that interfered with the correlation between the spectral data and measured chemical composition. The models were improved using calibration sample sets of equal parts stored and fresh switchgrass to more accurately predict the chemical composition of stored switchgrass. Acceptable correlation values (r calibration ) were obtained using a calibration sample set composed of 25 stored samples and 25 samples of fresh switchgrass for cellulose (0.91), hemicellulose (0.74), total carbohydrates (0.76), lignin (0.98), extractives (0.92), and ash (0.87). Increasing the calibration sample set to 100 samples of equal parts stored to senesced material resulted in statistically increased ( p = 0.05) correlations for total carbohydrates (0.89) and ash (0.96). When these models were applied to a separate validation set (equal to 10% of the calibration sample set), high correlation coefficients (r) for predicted versus measured constituent content were observed for cellulose (0.94), total carbohydrates (0.98), lignin (0.91), extractives (0.97), and ash (0.90). For optimization of processing economics, the impact of feedstock storage must be investigated for implementation in conversion processes. While NIR is a well-known high-throughput technique for characterization of senesced switchgrass, the selection of appropriate calibration samples and consequent multivariate models must be taken into careful consideration for NIR application in a biomass storage facility for rapid chemical compositional determination.
Managing the future internet through intelligent in-network substrates

The current Internet has been founded on the architectural premise of a simple network service used to interconnect relatively intelligent end systems. While this simplicity allowed it to reach an impressive scale, the predictive manner in which ISP networks are currently planned and configured through external management systems and the uniform treatment of all traffic are hampering its use as a unifying multi-service network. The future Internet will need to be more intelligent and adaptive, optimizing continuously the use of its resources and recovering from transient problems, faults and attacks without any impact on the demanding services and applications running over it. This article describes an architecture that allows intelligence to be introduced within the network to support sophisticated self-management functionality in a coordinated and controllable manner. The presented approach, based on intelligent substrates, can potentially make the Internet more adaptable, agile, sustainable, and dependable given the requirements of emerging services with highly demanding traffic and rapidly changing locations. We discuss how the proposed framework can be applied to three representative emerging scenarios: dynamic traffic engineering (load balancing across multiple paths); energy efficiency in ISP network infrastructures; and cache management in content-centric networks.
Long-Term Functional Dynamics of an Aphidophagous Coccinellid Community Remain Unchanged despite Repeated Invasions

Aphidophagous coccinellids (ladybeetles) are important providers of herbivore suppression ecosystem services. In the last 30 years, the invasion of exotic coccinellid species, coupled with observed declines in native species, has led to considerable interest in the community dynamics and ecosystem function of this guild. Here we examined a 24-year dataset of coccinellid communities in nine habitats in southwestern Michigan for changes in community function in response to invasion. Specifically we analyzed their temporal population dynamics and species diversity, and we modeled the community’s potential to suppress pests. Abundance of coccinellids varied widely between 1989 and 2012 and became increasingly exotic-dominated. More than 71% of 57,813 adult coccinellids captured over the 24-year study were exotic species. Shannon diversity increased slightly over time, but herbivore suppression potential of the community remained roughly constant over the course of the study. However, both Shannon diversity and herbivore suppression potential due to native species declined over time in all habitats. The relationship between Shannon diversity and herbivore suppression potential varied with habitat type: a positive relationship in forest and perennial habitats, but was uncorrelated in annual habitats. This trend may have been because annual habitats were dominated by a few, highly voracious exotic species. Our results indicated that although the composition of the coccinellid community in southwestern Michigan has changed dramatically in the past several decades, its function has remained relatively unchanged in both agricultural and natural habitats. While this is encouraging from the perspective of pest management, it should be noted that losses of one of the dominant exotic coccinellids could result in a rapid decline in pest suppression services if the remaining community is unable to respond.
The detection and PCR-based characterization of the parasites causing trypanosomiasis in water-buffalo herds in Venezuela

Abstract The usefulness of PCR-based assays for detecting trypanosomiasis in water buffaloes and other livestock was explored, under field conditions, in Venezuela. The sensitivity and specificity of the assays, which were based on established primer pairs (21-mer/22-mer and ILO1264/ILO1265), were evaluated, partly by comparison with the results of parasitological tests (stained bloodsmears and microhaematocrit centrifugation) and immunological assays (IFAT) run in parallel. The optimised PCR-based assays showed a sensitivity of 10 pg DNA. The use of the 21-mer/22-mer primer pair gave a test that was specific for species in the subgenus Trypanozoon (including Trypanosoma evansi), whereas use of ILO1264/ILO1265 produced a test that was specific for T. vivax. The results of a hybridization assay using T. evansi-DNA and T. vivax-DNA probes indicated no cross-hybridization between the T. evansi and T. vivax PCR products. The results of the bloodsmear examinations, microhaematocrit centrifugations (MHC) and IFAT indicated that 23 (6.7%), 39 (11.4%) and 135 (39.5%) of the 342 blood samples investigated (including 316 from water buffaloes) contained trypanosomes, respectively. The results of the PCR-based assays indicated that 68 (19.9%) of the same blood samples contained T. vivax (or at least T. vivax DNA), and that none contained T. evansi or any other member of the subgenus Trypanozoon. For the detection of trypanosomes, the assay therefore appeared almost twice as sensitive as the MHC. These results are the first on the molecular characterization of the trypanosomes infecting water buffaloes in Venezuela. When the results of the MHC (which is the most practical, and frequently used, alternative detection method) were used as the gold standard, the PCR-based assay for T. vivax was found to have 100% sensitivity, 90.4% specificity, a positive predictive value of 0.57, a positive likelihood ratio of 10.45, and a negative likelihood ratio of 0.00. The assay therefore appears a reasonable choice for detecting T. vivax in the mammalian livestock of Venezuela and elsewhere.
Functional grouping analysis of varying reactor types in the Spiky-RBN AChem

We explore the effects that different reactor types have on Spiky-RBN AChem systems, looking at mass conserving and flow reactors. To assist in analysing the behaviour we introduce an activity measure based on possible system state changes as a result of changes in particle properties. This leads to a discussion on approaches to engineering complex systems towards specific goals.
Optimized on-demand data streaming from sensor nodes

Real-time sensor data enables diverse applications such as smart metering, traffic monitoring, and sport analysis. In the Internet of Things, billions of sensor nodes form a sensor cloud and offer data streams to analysis systems. However, it is impossible to transfer all available data with maximal frequencies to all applications. Therefore, we need to tailor data streams to the demand of applications. We contribute a technique that optimizes communication costs while maintaining the desired accuracy. Our technique schedules reads across huge amounts of sensors based on the data-demands of a huge amount of concurrent queries. We introduce user-defined sampling functions that define the data-demand of queries and facilitate various adaptive sampling techniques, which decrease the amount of transferred data. Moreover, we share sensor reads and data transfers among queries. Our experiments with real-world data show that our approach saves up to 87% in data transmissions.
String model for the dynamics of glass-forming liquids.

We test the applicability of a living polymerization theory to describe cooperative string-like particle rearrangement clusters (strings) observed in simulations of a coarse-grained polymer melt. The theory quantitatively describes the interrelation between the average string length L, configurational entropy Sconf, and the order parameter for string assembly Φ without free parameters. Combining this theory with the Adam-Gibbs model allows us to predict the relaxation time τ in a lower temperature T range than accessible by current simulations. In particular, the combined theories suggest a return to Arrhenius behavior near Tg and a low T residual entropy, thus avoiding a Kauzmann "entropy crisis. "
Transparent Electrodes

Transparent conducting electrodes (TCE) are extensively applied in a great range of optoelectronic and photovoltaic equipment (e.g., solar cells, touch panels, and flexible devices). Carbon-based nanomaterials are considered as suitable replacements to substitute traditional materials to manufacture TCE due to their remarkable characteristics, for example, high optical transmittance and outstanding electrical properties. In comparison with traditional indium tin oxide electrodes, carbon-based electrodes show good mechanical properties, chemical stability, and low cost. Nevertheless, major issues related to the development of good quality manufacture methods to produce carbon-based nanomaterials have to be overcome to meet massive market requirements. Hence, the development of alternative TCE materials as well as appropriate large production techniques that meet the requirements of a proper sheet resistance along with a high optical transparency is a priority. Therefore, in this work, we summarize and discuss novel production and synthesis methods, chemical treatments, and hybrid materials developed to satisfy the worldwide request for carbon-based nanomaterials.
Is the Serum Vitamin D Level at the Time of Hospital-Acquired Acute Kidney Injury Diagnosis Associated with Prognosis?

Background Low circulating vitamin D levels have been suggested to potentially contribute to acute complications in critically ill patients. However, in patients with acute kidney injury (AKI), whether vitamin D deficiency occurs and is a potential contributor to worse early outcomes at the time of AKI diagnosis remains unclear. Methodology/Principal Findings Two hundred patients with AKI were enrolled in our study. Healthy subjects and critically ill patients without AKI served as controls. Serum vitamin D concentrations were measured in the three groups. The patients with AKI were followed up for 90 days and grouped according to median serum vitamin D concentrations. In addition, vitamin D receptor polymorphisms (BsmI and FokI) were measured in these patients; they were also followed up for 90 days and grouped according to vitamin D receptor gene mutations. Low serum 1,25-dihydroxyvitamin D levels (59.56±53.00 pmol/L) were detected in patients with AKI and decreased with increasing severity of AKI. There were no significant findings with respect to 25-hydroxyvitamin D. The 90-day survival curves of individuals with high vitamin D concentrations showed no significant differences compared with the curves of individuals with low concentrations. The survival curves of patients with BB/Bb or FF/Ff genotypes also showed no significant differences compared with patients with bb or ff genotypes. In Cox regression analysis, the vitamin D status in patients with AKI was not an independent prognostic factor as adjusted by age, sex, Sequential Organ Failure Assessment score, or vitamin D receptor polymorphisms. Conclusions/Significance Patients with AKI manifested a marked decrease in the 1,25-dihydroxyvitamin D level at the time of AKI diagnosis, and the degree of 1,25-dihydroxyvitamin D deficiency increased with the severity of AKI. No association between the serum vitamin D level at the time of AKI diagnosis and 90-day all-cause mortality was found in patients with AKI.
OF REMOVAL OF COAL MOISTURE IN THERMAL POWER GENERATION WITH WASTE HEAT RECOVERY

The techno-economic aspects of coal drying with cost effective waste heat recovery mechanism is one of the challenging issues faced while using lignite or high ash brown coal for direct combustion in coal fired thermal power plant. Coal being hygroscopic in nature, re-adsorbs considerable moisture even after conventional drying post wet coal washing condition affecting boiler performance. Particularly moisture in coal affects the pulverization where pulverized coal (PC) firing is adopted. In this paper the impact of coal moisture on useful heat value for PC fired steam generation is evaluated for some typical steam coals so that related change in direct firing coal throughput can be estimated for application of suitable online coal drying mechanism. This assessment can be further used to determine usefulness of pre-combustion coal drying methods like integrated drying and partial coal gasification method, particularly for coal processed through dry or wet coal washing to improve the heat value with the exhaust flue gas immediate upstream of stack.