Miracle-dz/UniFAR-FTUs huggingface dataset:
Design , Simulation and Control of Hydraulic System Topographies with Integrated Energy Recovery

1. A full literature review was completed. 2. A dynamic model of the system was completed and simulation results were used to design and construct the test rig. 3. A fully operational test rig (mini backhoe arm) has been installed and instrumented in the ABE Fluid Power laboratory at Purdue University. 4. Data has been collected on the test rig while operating the system in various modes. 5. Results have been published at various conferences (see references section).
Anti-SAT: Mitigating SAT Attack on Logic Locking

Logic locking is a technique that is proposed to protect outsourced IC designs from piracy and counterfeiting by untrusted foundries. A locked IC preserves the correct functionality only when a correct key is provided. Recently, the security of logic locking is threatened by a new attack called SAT attack, which can decipher the correct key of most logic locking techniques within a few hours even for a reasonably large key-size. This attack iteratively solves SAT formulas which progressively eliminate the incorrect keys till the circuit is unlocked. In this paper, we present a circuit block (referred to as Anti-SAT block) to enhance the security of existing logic locking techniques against the SAT attack. We show using a mathematical proof that the number of SAT attack iterations to reveal the correct key in a circuit comprising an Anti-SAT block is an exponential function of the key-size thereby making the SAT attack computationally infeasible. Besides, we address the vulnerability of the Anti-SAT block to various removal attacks and investigate obfuscation techniques to prevent these removal attacks. More importantly, we provide a proof showing that these obfuscation techniques for making Anti-SAT un-removable would not weaken the Anti-SAT block’s resistance to SAT attack. Through our experiments, we illustrate the effectiveness of our approach to securing modern chips fabricated in untrusted foundries.
Influence of the Two-Layer Preservation Method on Human Pancreatic Islet Isolation: A Meta-Analysis

Introduction There has been continuous debate on whether the Two-Layer Method (TLM) is superior to the University of Wisconsin solution (UW) for preserving human pancreas prior to islet isolation. The objective of the current meta-analysis is to assess which method is superior. Methods We searched electronic databases (MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials) for relevant human trials published in the English language from January 2000 to October 2013. Data on donor characteristics and islet isolation outcomes were extracted. Results 14 articles containing 18 human studies were included in this meta-analysis. In comparison to UW alone, TLM alone produced a significantly higher islet yield (weighted mean difference, 776.32; 95% confidence interval; 370.82-1181.82; P = .0002). TLM alone also yielded higher proportion of transplantable preparations (odds ratio, 1.60; 95% confidence interval; 1.15-2.23; P = .005). The following measures did not differ: islet viability (weighted mean difference, 2.10; −2.41-6.60; P = .360), purity (weighted mean difference, −0.92; −3.75-1.91; P = .520) and function assessed by measuring the stimulation index (weighted mean difference, 0.17; −0.21-0.55; P = .380). When comparing TLM following UW storage with UW alone, the results were similar to the previous ones. Conclusions This data indicates that the TLM can improve islet yield and increase the opportunities of human pancreatic islet transplantation. Therefore, the TLM should be recommended for preserving human pancreas prior to islet isolation.
SAMBLASTER: fast duplicate marking and structural variant read extraction

Motivation: Illumina DNA sequencing is now the predominant source of raw genomic data, and data volumes are growing rapidly. Bioinformatic analysis pipelines are having trouble keeping pace. A common bottleneck in such pipelines is the requirement to read, write, sort and compress large BAM files multiple times. Results: We present SAMBLASTER, a tool that reduces the number of times such costly operations are performed. SAMBLASTER is designed to mark duplicates in read-sorted SAM files as a piped post-pass on DNA aligner output before it is compressed to BAM. In addition, it can simultaneously output into separate files the discordant read-pairs and/or split-read mappings used for structural variant calling. As an alignment post-pass, its own runtime overhead is negligible, while dramatically reducing overall pipeline complexity and runtime. As a stand-alone duplicate marking tool, it performs significantly better than PICARD or SAMBAMBA in terms of both speed and memory usage, while achieving nearly identical results. Availability and implementation: SAMBLASTER is open-source C++ code and freely available for download from https://github.com/GregoryFaust/samblaster. Contact: imh4y@virginia.edu
A Systems Approach for Tumor Pharmacokinetics

Recent advances in genome inspired target discovery, small molecule screens, development of biological and nanotechnology have led to the introduction of a myriad of new differently sized agents into the clinic. The differences in small and large molecule delivery are becoming increasingly important in combination therapies as well as the use of drugs that modify the physiology of tumors such as anti-angiogenic treatment. The complexity of targeting has led to the development of mathematical models to facilitate understanding, but unfortunately, these studies are often only applicable to a particular molecule, making pharmacokinetic comparisons difficult. Here we develop and describe a framework for categorizing primary pharmacokinetics of drugs in tumors. For modeling purposes, we define drugs not by their mechanism of action but rather their rate-limiting step of delivery. Our simulations account for variations in perfusion, vascularization, interstitial transport, and non-linear local binding and metabolism. Based on a comparison of the fundamental rates determining uptake, drugs were classified into four categories depending on whether uptake is limited by blood flow, extravasation, interstitial diffusion, or local binding and metabolism. Simulations comparing small molecule versus macromolecular drugs show a sharp difference in distribution, which has implications for multi-drug therapies. The tissue-level distribution differs widely in tumors for small molecules versus macromolecular biologic drugs, and this should be considered in the design of agents and treatments. An example using antibodies in mouse xenografts illustrates the different in vivo behavior. This type of transport analysis can be used to aid in model development, experimental data analysis, and imaging and therapeutic agent design.
Lazy abstraction

One approach to model checking software is based on the abstract-check-refine paradigm: build an abstract model, then check the desired property, and if the check fails, refine the model and start over. We introduce the concept of lazy abstraction to integrate and optimize the three phases of the abstract-check-refine loop. Lazy abstraction continuously builds and refines a single abstract model on demand, driven by the model checker, so that different parts of the model may exhibit different degrees of precision, namely just enough to verify the desired property. We present an algorithm for model checking safety properties using lazy abstraction and describe an implementation of the algorithm applied to C programs. We also provide sufficient conditions for the termination of the method.
TREC 2010 Web Track Notebook: Term Dependence, Spam Filtering and Quality Bias

Many existing retrieval approaches treat all the documents in the collection equally, and do not take into account the content quality of the retrieved documents. In our submissions for TREC 2010 Web Track, we utilize quality-biased ranking methods that are aimed to promote documents that potentially contain high-quality content, and penalize spam and low-quality documents. Our experiments with the ad hoc web topics from TREC 2010 show that features such as the spamminess of the document (as computed by the Waterloo team [6]) and the readability of the document (modeled by the fraction of stopwords in the document) are very important for improving the precision at the top ranks. Promotion of the high-quality Wikipedia pages leads to further retrieval performance improvements. In addition, we found that using Wikipedia as a high-quality document collection for query expansion can ameliorate some of the negative eﬀects of performing pseudo-relevance feedback from a noisy web collection such as ClueWeb09.
Progressive point set surfaces

Progressive point set surfaces (PPSS) are a multilevel point-based surface representation. They combine the usability of multilevel scalar displacement maps (e.g., compression, filtering, geometric modeling) with the generality of point-based surface representations (i.e., no fixed homology group or continuity class). The multiscale nature of PPSS fosters the idea of point-based modeling. The basic building block for the construction of PPSS is a projection operator, which maps points in the proximity of the shape onto local polynomial surface approximations. The projection operator allows the computing of displacements from smoother to more detailed levels. Based on the properties of the projection operator we derive an algorithm to construct a base point set. Starting from this base point set, a refinement rule using the projection operator constructs a PPSS from any given manifold surface.
Sequential Monte Carlo Methods for Statistical Analysis of Tables

We describe a sequential importance sampling (SIS) procedure for analyzing two-way zero–one or contingency tables with fixed marginal sums. An essential feature of the new method is that it samples the columns of the table progressively according to certain special distributions. Our method produces Monte Carlo samples that are remarkably close to the uniform distribution, enabling one to approximate closely the null distributions of various test statistics about these tables. Our method compares favorably with other existing Monte Carlo-based algorithms, and sometimes is a few orders of magnitude more efficient. In particular, compared with Markov chain Monte Carlo (MCMC)-based approaches, our importance sampling method not only is more efficient in terms of absolute running time and frees one from pondering over the mixing issue, but also provides an easy and accurate estimate of the total number of tables with fixed marginal sums, which is far more difficult for an MCMC method to achieve.
Fabrication and testing of highly efficient resonance domain diffractive optical elements

Structuring of optical surfaces with surface-relief diffractive optical elements is an enabling technology for achieving considerable spatially varying changes in light propagation direction and wavefront curvature. This way, Bragg effects, angular and spectral selectivity and nearly 100% diffraction efficiency usually attributed to volume optical holograms can be achieved by surface relief computer generated holograms and diffractive optical elements. Several methods for fabricating deep "resonance domain" diffraction structures with periods, exceeding the subwavelength limit but near to the wavelength, were compared and optimized. Results of direct e-beam writing RIE etching, SEM and AFM measurements for fused silica gratings with period of 520 nm and groove depth of 1000 nm, designed for nearly 100% diffraction efficiency in the green 532 nm laser light, are presented.
Comparing and Validating Measurements of Dependability Attributes

This paper investigates sources of uncertainty in measurement results obtained using three different fault injection techniques. Two software-implemented and one test port-based technique are characterized and compared. The three techniques can be used to inject the same faults, which are defined in a shared database. Due to the uncertainties associated with the techniques, which we identify and discuss, the results of injecting a given fault may differ to some extent. The paper analyzes the results of using the three techniques to inject faults into two experimental targets: a brake-by-wire controller and a partitioning operating system. The objective of the experiments is to determine whether the results of the different techniques are metrologically compatible and, consequently, meaningful when disseminated and compared. Our observations indicate that, even though the outcome of many individual experiments is affected by uncertainties, the three techniques produce similar average results over a large number of experiments.
Understanding the monetary transmission mechanism in the United Kingdom: The role of nominal and real rigidities

This paper aims to contribute to our understanding of the monetary transmission mechanism in the United Kingdom by estimating two Dynamic Stochastic General Equilibrium models and assessing the role of nominal and real rigidities within them. We rst obtain an empirical representation of the monetary transmission mechanism in the United Kingdom and then estimate the models by minimising the di¤erence between this representation and its model equivalents. We nd that both models can explain the data reasonably well without relying on undue amounts of price and wage stickiness. The views expressed are those of the authors and do not necessarily reect those of the Bank of England. The authors would like to thank Emilio Fernandez-Corugedo, Simon Price and seminar participants at the Bank of England and Université Paris 1 Panthéon Sorbonne for useful comments. The usual disclaimer applies. Part of this research was conducted while the rst author was visiting the Bank of England, for whose hospitality he is thankful. yPSE, Université Paris 1 Panthéon-Sorbonne and EPEE, Université dEvry Val dEssonne, E-mail: kamber@univ-paris1.fr zBank of England, Threadneedle Street, London EC2R 8AH. E-mail: Stephen.Millard@bankofengland.co.uk
Deficient Production of Hexadecenoic Acid in the Skin Is Associated in Part with the Vulnerability of Atopic Dermatitis Patients to Colonization by Staphylococcus aureus

Background and Objectives: As one of the major skin fatty acids, cis-6-hexadecenoic acid (C16:1Δ6) exhibits a specific antibacterial activity and might play a specific role in the defense mechanism against Staphylococcus aureus, in healthy subjects whereas S. aureus frequently colonizes the skin of patients with atopic dermatitis (AD). Methods: Fatty acid composition of sebum at the recovery level was analyzed by gas chromatography and S. aureus colonizing the skin was assessed by the ‘cup-scrub’ method (9 patients and 10 healthy controls). To evaluate in vivo effect of C16:1Δ6 on colonization, C16:1Δ6 was applied for 2 weeks on the upper arm skin of another group of AD patients (11 patients). Results: Analysis of sebum lipids revealed that there is a significant lower free C16:1Δ6 content in nonlesional skin from AD patients compared with healthy controls. This lower content is also accompanied by a significantly lower level of C16:1Δ6 in the total fatty acid composition of sebum (analyzed following hydrolysis). The lower level of free C16:1Δ6 correlated significantly (R2 = 0.41, p < 0.01) with the numbers of S. aureus colonizing nonlesional skin. Topical application of free C16:1Δ6 on the skin of AD patients for 2 weeks abolished the markedly increased bacterial count in 6 out of the 8 AD patients tested. Conclusions: Free C16:1Δ6 may be involved in the defense mechanism against S. aureus in healthy skin and this deficit triggers the susceptibility of the skin to colonization by S. aureus in AD.
Penetration of Moxifloxacin into Peripheral Compartments in Humans

ABSTRACT To characterize the penetration of moxifloxacin (BAY 12-8039) into peripheral target sites, the present study aimed at measuring unbound moxifloxacin concentrations in the interstitial space fluid by means of microdialysis, an innovative clinical sampling technique. In addition, moxifloxacin concentrations were measured in cantharides-induced skin blisters, saliva, and capillary plasma and compared to total- and free-drug concentrations in venous plasma. For this purpose, 12 healthy volunteers received moxifloxacin in an open randomized crossover fashion either as a single oral dose of 400 mg or as a single intravenous infusion of 400 mg over 60 min. An almost-complete equilibration of the free unbound plasma fraction of moxifloxacin with the interstitial space fluid was observed, with mean area under the concentration-time curve (AUC)interstitial fluid/AUCtotal-plasma ratios ranging from 0.38 to 0.55 and mean AUCinterstitial fluid/AUCfree-plasma ratios ranging from 0.81 to 0.86. The skin blister concentration/plasma concentration ratio reached values above 1.5 after 24 h, indicating a preferential penetration of moxifloxacin into inflamed lesions. The moxifloxacin concentrations in saliva and capillary blood were similar to the corresponding levels in plasma. Our data show that moxifloxacin concentrations attained in the interstitial space fluid in humans and in skin blister fluid following single doses of 400 mg exceed the values for the MIC at which 90% of isolates are inhibited for most clinically relevant bacterial strains, notably including penicillin-resistant Streptococcus pneumoniae. These findings support the use of moxifloxacin for the treatment of soft tissue and respiratory tract infections in humans.
An Investigation of the Genetic Variation between Blissus occiduus Barber and Blissus leucopterus leucopterus (Say)

In Nebraska, there are two chinch bug species that are of major economic importance: the common chinch bug, Blissus leucopterus leucopterus (Say) and the western chinch bug, B. occiduus Barber. The lack of key morphological characters to accurately differentiate between these two species in the immature stage and their extensive overlap of plant hosts and geographic distribution underscore the need to identify molecular markers to distinguish between these two chinch bugs. The objective of this research was to investigate the genetic diversity between B. l. leucopterus and B. occiduus using Amplified Fragment Length Polymorphism (AFLP). Five primer combinations were selected from 20 primer combinations to be used for testing 15 samples of each chinch bug species. The five primer combinations included a total of 151 AFLP markers. Of these, 148 AFLP markers (or 98.01%) were polymorphic between populations. Within B. occiduus, 133 AFLP markers (or 88.08%) were polymorphic and within B. l. leucopterus, 132 AFLP markers (or 87.42%) were polymorphic. Approximately 63% of the variation in the data set could be attributed to genetic variation within the populations according to the AMOVA analysis. Conversely, approximately 37% of the genetic variation occurred between populations. Several distinct molecular markers were identified that can be employed to distinguish between the two species when morphological characteristics show minimal, if any differences, during the immature stages. This research provides a genetic marker that can be used to differentiate between these two economically important chinch bug species. This new diagnostics tool will allow species-specific management options to be employed. In addition, this baseline data can advance future research on chinch bug genetics, including comparisons of additional species.
An Energy-Efficient Target-Tracking Strategy for Mobile Sensor Networks

In this paper, an energy-efficient strategy is proposed for tracking a moving target in an environment with obstacles, using a network of mobile sensors. Typically, the most dominant sources of energy consumption in a mobile sensor network are sensing, communication, and movement. The proposed algorithm first divides the field into a grid of sufficiently small cells. The grid is then represented by a graph whose edges are properly weighted to reflect the energy consumption of sensors. The proposed technique searches for near-optimal locations for the sensors in different time instants to route information from the target to destination, using a shortest path algorithm. Simulations confirm the efficacy of the proposed algorithm.
Named Entity Recognition in 140 Characters or Less

In this paper, we explore the problem of recognizing named entities in microposts, a genre with notoriously little context surrounding each named entity and inconsistent use of grammar, punctuation, capitalization, and spelling conventions by authors. In spite of the challenges associated with information extraction from microposts, it remains an increasingly important genre. This paper presents the MIT Information Extraction Toolkit (MITIE) and explores its adaptability to the micropost genre.
Gating charge interactions with the S1 segment during activation of a Na+ channel voltage sensor

Voltage-gated Na+ channels initiate action potentials during electrical signaling in excitable cells. Opening and closing of the pore of voltage-gated ion channels are mechanically linked to voltage-driven outward movement of the positively charged S4 transmembrane segment in their voltage sensors. Disulfide locking of cysteine residues substituted for the outermost T0 and R1 gating-charge positions and a conserved negative charge (E43) at the extracellular end of the S1 segment of the bacterial Na+ channel NaChBac detects molecular interactions that stabilize the resting state of the voltage sensor and define its conformation. Upon depolarization, the more inward gating charges R2 and R3 engage in these molecular interactions as the S4 segment moves outward to its intermediate and activated states. The R4 gating charge does not disulfide-lock with E43, suggesting an outer limit to its transmembrane movement. These molecular interactions reveal how the S4 gating charges are stabilized in the resting state and how their outward movement is catalyzed by interaction with negatively charged residues to effect pore opening and initiate electrical signaling.
Consistency of Spectral Partitioning of Uniform Hypergraphs under Planted Partition Model

Spectral graph partitioning methods have received significant attention from both practitioners and theorists in computer science. Some notable studies have been carried out regarding the behavior of these methods for infinitely large sample size (von Luxburg et al., 2008; Rohe et al., 2011), which provide sufficient confidence to practitioners about the effectiveness of these methods. On the other hand, recent developments in computer vision have led to a plethora of applications, where the model deals with multi-way affinity relations and can be posed as uniform hypergraphs. In this paper, we view these models as random m-uniform hypergraphs and establish the consistency of spectral algorithm in this general setting. We develop a planted partition model or stochastic blockmodel for such problems using higher order tensors, present a spectral technique suited for the purpose and study its large sample behavior. The analysis reveals that the algorithm is consistent for m-uniform hypergraphs for larger values of m, and also the rate of convergence improves for increasing m. Our result provides the first theoretical evidence that establishes the importance of m-way affinities.