gebhart/patrepeval huggingface dataset:
Distinguishing variables of Boolean function via distinct subBDDs (2002)

Boolean matching, checking whether two completely specified Boolean functions are logically equal, is widely used in logic synthesis. It is well known that BDD is a common tool for Boolean matching. The identifiableness of two BDDs' structures means that two Boolean functions are equal. But BDD varies with different variable order. So, before constructing BDDs and checking equivalence, variables must be recognized. Various signatures have been presented to determine the variable mapping relations between two Boolean functions. In this paper, we propose using special parts of BDD to distinguish variables. On the basis of these distinct subBDDs, we take use of a group of signatures to recognize variables efficiently. Experimental results on MCNC benchmark circuits were shown that our algorithm is indeed effective in solving matching problem and runtime for benchmark cordic is greatly shortened.
Dual-Recognition Förster Resonance Energy Transfer Based Platform for One-Step Sensitive Detection of Pathogenic Bacteria Using Fluorescent Vancomycin–Gold Nanoclusters and Aptamer–Gold Nanoparticles (2017)

The effective monitoring, identification, and quantification of pathogenic bacteria is essential for addressing serious public health issues. In this study, we present a universal and facile one-step strategy for sensitive and selective detection of pathogenic bacteria using a dual-molecular affinity-based Förster (fluorescence) resonance energy transfer (FRET) platform based on the recognition of bacterial cell walls by antibiotic and aptamer molecules, respectively. As a proof of concept, Vancomycin (Van) and a nucleic acid aptamer were employed in a model dual-recognition scheme for detecting Staphylococcus aureus (Staph. aureus). Within 30 min, by using Van-functionalized gold nanoclusters and aptamer-modified gold nanoparticles as the energy donor and acceptor, respectively, the FRET signal shows a linear variation with the concentration of Staph. aureus in the range from 20 to 10<sup>8</sup> cfu/mL with a detection limit of 10 cfu/mL. Other nontarget bacteria showed negative results, demonstrating the good specificity of the approach. When employed to assay Staph. aureus in real samples, the dual-recognition FRET strategy showed recoveries from 99.00% to the 109.75% with relative standard derivations (RSDs) less than 4%. This establishes a universal detection platform for sensitive, specific, and simple pathogenic bacteria detection, which could have great impact in the fields of food/public safety monitoring and infectious disease diagnosis.
Memories that last forever: strategies for optimizing vaccine T-cell memory (2009)

For acute self-limiting infections a vaccine is successful if it elicits memory at least as good as the natural experience; however, for persistent and chronic infections such as HIV, hepatitis C virus (HCV), human papillomavirus (HPV), and human herpes viruses, this paradigm is not applicable. At best, during persistent virus infection the person must be able to maintain the integrity of the immune system in equilibrium with controlling replicating virus. New vaccine strategies are required that elicit both potent high-avidity CD8(+) T-cell effector/memory and central memory responses that can clear the nidus of initial virus-infected cells at mucosal surfaces to prevent mucosal transmission or significantly curtail development of disease. The objective of an HIV-1 T-cell vaccine is to generate functional CD8(+) effector memory cells at mucosal portals of virus entry to prevent viral transmission. In addition, long-lived CD8(+) and CD4(+) central memory cells circulating through secondary lymphoid organs and resident in bone marrow, respectively, are needed to provide a concerted second wave of defense that can contain virus at mucosal surfaces and prevent systemic dissemination. Further understanding of factors which can influence long-lived effector and central memory cell differentiation will significantly contribute to development of effective T-cell vaccines. In this review we will focus on discussing mechanisms involved in T-cell memory and provide promising new approaches toward expanding current vaccine strategies to enhance antiviral memory.
Probing the ATP Site of GRP78 with Nucleotide Triphosphate Analogs (2016)

GRP78, a member of the ER stress protein family, can relocate to the surface of cancer cells, playing key roles in promoting cell proliferation and metastasis. GRP78 consists of two major functional domains: the ATPase and protein/peptide-binding domains. The protein/peptide-binding domain of cell-surface GRP78 has served as a novel functional receptor for delivering cytotoxic agents (e.g., a apoptosis-inducing peptide or taxol) across the cell membrane. Here, we report our study on the ATPase domain of GRP78 (GRP78ATPase), whose potential as a transmembrane delivery system of cytotoxic agents (e.g., ATP-based nucleotide triphosphate analogs) remains unexploited. As the binding of ligands (ATP analogs) to a receptor (GRP78ATPase) is a pre-requisite for internalization, we determined the binding affinities and modes of GRP78ATPase for ADP, ATP and several ATP analogs using surface plasmon resonance and x-ray crystallography. The tested ATP analogs contain one of the following modifications: the nitrogen at the adenine ring 7-position to a carbon atom (7-deazaATP), the oxygen at the β-γ bridge position to a carbon atom (AMPPCP), or the removal of the 2'-OH group (2'-deoxyATP). We found that 7-deazaATP displays an affinity and a binding mode that resemble those of ATP regardless of magnesium ion (Mg++) concentration, suggesting that GRP78 is tolerant to modifications at the 7-position. By comparison, AMPPCP's binding affinity was lower than ATP and Mg++-dependent, as the removal of Mg++ nearly abolished binding to GRP78ATPase. The AMPPCP-Mg++ structure showed evidence for the critical role of Mg++ in AMPPCP binding affinity, suggesting that while GRP78 is sensitive to modifications at the β-γ bridge position, these can be tolerated in the presence of Mg++. Furthermore, 2'-deoxyATP's binding affinity was significantly lower than those for all other nucleotides tested, even in the presence of Mg++. The 2'-deoxyATP structure showed the conformation of the bound nucleotide flipped out of the active site, explaining the low affinity binding to GRP78 and suggesting that the 2'-OH group is essential for the high affinity binding to GRP78. Together, our results demonstrate that GRP78ATPase possesses nucleotide specificity more relaxed than previously anticipated and can tolerate certain modifications to the nucleobase 7-position and, to a lesser extent, the β-γ bridging atom, thereby providing a possible atomic mechanism underlying the transmembrane transport of the ATP analogs.
Dos, a Heme-Binding PAS Protein from <i>Escherichia coli</i>, Is a Direct Oxygen Sensor (2000)

A direct sensor of O(2), the Dos protein, has been found in Escherichia coli. Previously, the only biological sensors known to respond to O(2) by direct and reversible binding were the FixL proteins of Rhizobia. A heme-binding region in Dos is 60% homologous to the O(2)-sensing PAS domain of the FixL protein, but the remainder of Dos does not resemble FixL. Specifically, the C-terminal domain of Dos, presumed to be a regulatory partner that couples to its heme-binding domain, is not a histidine kinase but more closely resembles a phosphodiesterase. The absorption spectra of Dos indicate that both axial positions of the heme iron are coordinated to side chains of the protein. Nevertheless, O(2) and CO bind to Dos with K(d) values of 13 and 10 microM, respectively, indicating a strong discrimination against CO binding. Association rate constants for binding of O(2) (3 mM(-)(1) s(-)(1)), CO (1 mM(-)(1) s(-)(1)) and even NO (2 mM(-)(1) s(-)(1)) are extraordinarily low and very similar. Displacement of an endogenous ligand, probably Met 95, from the heme iron in Dos triggers a conformational change that alters the activity of the enzymatic domain. This sensing mechanism differs from that of FixL but resembles that of the CO sensor CooA of Rhodospirillum rubrum. Overall the results provide evidence for a heme-binding subgroup of PAS-domain proteins whose working range, signaling mechanisms, and regulatory partners can vary considerably.
Evacuation models and disaster psychology (2010)

In evacuation models of buildings, neighborhoods, areas, cities and countries important psychological parameters are not frequently used. In this paper the relevance of some important variables from disaster psychology will be discussed. Modeling psychological variables will enhance prediction of human behavior during evacuations. John Leach’s Dynamic Disaster Model describes three phases and five stages: A Pre-impact phase (Threat Stage and Warning Stage), an Impact phase, and a Post-impact phase (Recoil Stage, Rescue Stage and Post-traumatic Stage). In each phase and stage specific human behavior has been supposed to be a psychological response to a disaster. These responses are remarkably consistent and transferable across kinds of disasters. Evacuation happens during Pre-impact phase, Impact phase and Post-impact phase (Recoil Stage and, or Rescue Stage). People’s cognitive and emotional states and overt behavior will be very different across the phases. During the Pre-impact phase risk estimation is very low, so evacuation is not seen as an inevitable action. Heavy stress and denial of life-threatening events during the Impact phase will hinder effective evacuation. Inactivity, apathy and childlike dependency on other people during the Recoil Stage will restrain survivors from active evacuation. Evacuation models will be more effective if phases and accompanying human behavior are taken into account.
Electronic and crystallographic structure of apatites (2003)

An ab initio study of four different stoichiometric apatites (oxyapatite, hydroxyapatite, fluorapatite, and chlorapatite) is presented. The calculations were performed using density-functional theory with the local-density approximation for exchange and correlation, and a full relaxation of the electronic structure, the atomic arrangement, and the unit cell. Hexagonal unit cells were obtained for all four apatites, and the calculated atomic arrangements are in close agreement with observation in those cases for which the structure is firmly established. A zero-temperature structure is predicted for oxyapatite, and two possible configurations were found for the ${\mathrm{Cl}}^{\ensuremath{-}}$ ions in chlorapatite. The possibility of the monoclinic structure in hydroxyapatite and chlorapatite was also studied but no indication of greater stability with respect to the hexagonal structure was found. A relationship between the structure of the apatites and that of pure calcium is discussed.
Hierarchical interconnect modeling (2002)

Interconnect parasitics are competing with devices for impact on performance and therefore accurate interconnect modeling is called for. However, fully accurate 3D modeling is not always necessary nor feasible and a hierarchical modeling approach is advocated. Electromagnetic models, transmission lines, and lumped elements can be incorporated as linear circuit elements, reduced, and simulated with device-level models.
The Body-Mass Index, Airflow Obstruction, Dyspnea, and Exercise Capacity Index in Chronic Obstructive Pulmonary Disease (2004)

The BODE index, a simple multidimensional grading system, is better than the FEV1 at predicting the risk of death from any cause and from respiratory causes among patients with COPD.
Polymerisation von äthylen und propylen zu amorphen copolymerisaten mit katalysatoren aus vanadiumoxychlorid und aluminiumhalogenalkylen (1962)

Abstract Die Herstellung hochmolekularer amorpher Äthylen/Propylen‐Copolymerisate (Äthylen/Propylen‐Kautschuk = APK) mit Z IEGLER mischkatalysatoren aus Vanadiumoxychlorid und Äthylaluminiumdichlorid bzw. Äthylaluminiumsesquichlorid wird beschrieben. Ein frisch hergestellter Mischkatalysator hat eine sehr hohe Aktivität, die beim Lagern („Altern”︁) stark abfällt. Die Alterung ist mit einer Reduktion des Vanadiums in Richtung zur zweiwertigen Stufe verknüpft. Man erhält die größten Polymerisatmengen — auf den Mischkatalysator bezogen —, wenn man den Katalysator in Gegenwart der Monomeren bildet. Der starke Abfall der Aktivität mit der Zeit führt dazu, daß bei einer kontinuierlichen Polymerisation im Rührkessel die Verweilzeit im Bereich von 4 bis 120 Min. einen relativ geringen Einfluß auf die pro Katalysatoreinheit erzeugte Polymerisatmenge hat. Die Copolymerisate zeigen eine hohe chemische Einheitlichkeit. Die kontinuierliche Polymerisation im Rohr führt zu Copolymerisaten, deren Makromoleküle während des Wachstums von einem sich kontinuierlich ändernden Monomerengemisch umgeben sind, da während der Polymerisation eine stärkere Verarmung an Äthylen als an Propylen eintritt. Die Makromoleküle ändern daher ihre Zusammensetzung vom Anfang bis zum Ende der Ketten; es entstehen „unsymmetrische Copolymerisate”︁ oder „Diagonalcopolymerisate”︁. Die so erhaltenen Copolymerisate sind chemisch uneinheitlich, dagegen bezüglich ihrer Molekulargewichtsverteilung ziemlich einheitlich. Sowohl die kontinuierlich erzeugten Rührkessel‐ wie die Rohrpolymerisate liefern nach der Vulkanisation Produkte mit guten gummielastischen Eigenschaften. Die Lösungsgeschwindigkeit der Monomeren im Dispergiermittel hat einen großen Einfluß auf den Ablauf der Polymerisation, da sie viel geringer ist als die Polymerisationsgeschwindigkeit.
A novel catalytic sensor for monitoring the concentration of mixed combustible gases (1991)

This paper studies gas detectors, especially, gas sensors in which a thermochemical reac-tion takes place on a catalytic element. The novel catalytic sensor is fabricated using micro-electronic thick-film techniques, and it is used to monitor the concentration of combustiblegases and their mixture in a flow reactor. This sensor has two identical platinum films whichare used as the heater, resistance thermometer and the surface of reaction. Catalyst of palla-dium is deposited on one of the platinum film by chemical method, while the other platinumfilm serves as a compensating element. The difference in the minimum reaction temperaturefor the catalytic oxidation of the combustible gas components of mixture by palladium sug-gests that it is possible to analyse such a gas mixture. The purpose of the study is to demon-strate that the sensor fabricated by this process has good sensing characteristics for hydrogenor carbon monoxide gas in the mixture of methane and ethane.
The dual role of complement in cancer and its implication in anti-tumor therapy (2016)

Chronic inflammation has been linked to the initiation of carcinogenesis, as well as the advancement of established tumors. The polarization of the tumor inflammatory microenvironment can contribute to either the control, or the progression of the disease. The emerging participation of members of the complement cascade in several hallmarks of cancer, renders it a potential target for anti-tumor treatment. Moreover, the presence of complement regulatory proteins (CRPs) in most types of tumor cells is known to impede anti-tumor therapies. This review focuses on our current knowledge of complement's potential involvement in shaping the inflammatory tumor microenvironment and its role on the regulation of angiogenesis and hypoxia. Furthermore, we discuss approaches using complement-based therapies as an adjuvant in tumor immunotherapy.
Active dynamic thermography in mammography (2004)

Abstract: We discuss limitations of the known methods of IR imaging in diagnostics of breast cancer. In conclusion we show that the known methods, based on simple observation of external temperature distribution, are not fully effective. Even advanced pattern recognition could not help in analysis of static images. May active dynamic thermography, known in non-destructive testing of materials, be of any help in breast cancer diagnostics? Analysis of thermal transients forced by external thermal excitation shows, even on simple models, that one may expect a visible improvement in resolution after such excitation. Applied models allow analysis of both static and active thermograms. Basing on the models one may recognise elements of the internal structure of a breast not visible in static pictures. This method, new in clinical practice, seems to be promising, but requires further studies.
Phase Field Study for Self-Assemble of the Second Phase Particles in Coherent Phase Transition (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
On the Distribution of <i>K</i> -tuple Matches for Sequence Homology: A Constant Time Exact Calculation of the Variance (1998)

We study the distribution of a statistic useful in calculating the significance of the number of k-tuple matches detected in biological sequence homology algorithms. The statistic is Rn,k, the total number of heads in head runs of length k or more in a sequence of iid Bernoulli trials of length n. Calculation of the mean is straightforward. Poisson approximation formulas have been used for the variance because they are simple and powerful. Unfortunately, when p = P(Head) is large, the Poisson approximation no longer works well. In our application, p is large, say .75, and we have turned instead to direct calculation of the variance. Surprisingly, we are able to show that the variance, which is based on the interactions of O(n2) random variables, can be computed in constant time, independent of the length of the sequence and probability p. This result can be used to calculate the mean and variance of a number of other head run statistics in constant time. Additionally, we show how to extend the result to sequences generated by a stationary Markov process where the variance can be calculated in O(n) time.
Joint mode selection and resource allocation for D2D communications under queueing constraints (2016)

Device-to-device (D2D) communication underlaid with cellular networks is a new paradigm, proposed to enhance the performance of cellular networks. By allowing a pair of D2D users to communicate directly and share the same spectral resources with the cellular users, D2D communication can achieve higher spectral efficiency, improve the energy efficiency, and lower the traffic delay. In this paper, we propose a novel channel matching algorithm for joint mode selection and channel allocation with the goal of maximizing the system throughput under statistical queueing constraints. Seven possible modes are considered, namely the D2D cellular mode, D2D dedicated mode, uplink dedicated mode, downlink dedicated mode, uplink reuse mode, downlink reuse mode, and D2D reuse mode. Using tools from stochastic network calculus, the throughput is characterized by determining the effective capacity. We formulate the channel allocation problem as a maximum-weight matching problem, which can be solved by employing the Hungarian algorithm. Via simulation results, we verify the performance improvements achieved by our proposed matching algorithm.
Effect of chondroitin sulphate on material properties and bone remodelling around hydroxyapatite/collagen composites (2007)

Chondroitin sulphate (CS) has an anti-inflammatory effect and increases the regeneration ability of injured bone. The goal of this study was to characterize the material properties and osteoconductive potency of calcium phosphate bone cements modified with CS. The early interface reaction of cancellous bone to a nanokristalline hydroxyapatite cement containing type I collagen (HA/Coll) without and with CS (HA/Coll/CS) in a rat tibia model was evaluated. Cylindrical implants were inserted press-fit into defect of the tibial head. Six specimens per group were analyzed at 2, 4, 7, 14, and 28 days. HA/Coll/CS composite cylinders showed a 15% increase in compressive strength and by investigations with powder X-ray diffraction more nontransformed cement precursor was found. The microstructures of both types of implants were similar. A significantly higher average number of TRAP positive osteoclasts and ED1 positive mononuclear cells were observed in the interface around HA/Coll/CS implants on day 4 and 7 (p < 0.05). At 28 days the direct bone contact and the percentage of newly formed bone were significantly higher around HA/Coll/CS implants (p < 0.05). The addition of CS appears to enhance bone remodelling and new bone formation around HA/Coll composites in the early stages of bone healing. Possible mechanisms are discussed.
Ceftriaxone pretreatment protects rats against cerebral ischemic injury by attenuating microglial activation-induced IL-1β expression (2014)

These findings demonstrate that CTX pretreatment may provide a neuroprotective effect against transient cerebral ischemic injury, partially inhibit in microglial activation and reduce the expression of IL-1β.
Stress Corrosion Cracking of Alloys 600 and 690 and Nos. 82 and 182 Weld Metals in High Temperature Water (1983)

The relative susceptibilities of Alloy 600 and 690 base metals and I-82 and I-182 weld metals to intergranular stress corrosion cracking (IGSCC) in pure water at 288 C were evaluated. A combination of creviced and noncreviced slow strain rate, smooth sustained load, and precracked fracture mechanics tests were employed in the evaluation. Susceptibility was determined as a function of dissolved oxygen content, degree of sensitization, and crevice condition. The results indicated that Alloy 600, and I-182 and I-82 weld metals were susceptible to various degrees of IGSCC in oxygen containing pure water when creviced, and immune to IGSCC when uncreviced. Alloy 690 was immune to IGSCC under all conditions examined. In Alloy 600, no correlation was found between the location of IGSCC and the location of maximum sensitization as determined by a boiling 25% nitric acid test and an electrolytic 8:1 phosphoric acid etch.
How much data is needed to train a medical image deep learning system to achieve necessary high accuracy? (2015)

The use of Convolutional Neural Networks (CNN) in natural image classification systems has produced very impressive results. Combined with the inherent nature of medical images that make them ideal for deep-learning, further application of such systems to medical image classification holds much promise. However, the usefulness and potential impact of such a system can be completely negated if it does not reach a target accuracy. In this paper, we present a study on determining the optimum size of the training data set necessary to achieve high classification accuracy with low variance in medical image classification systems. The CNN was applied to classify axial Computed Tomography (CT) images into six anatomical classes. We trained the CNN using six different sizes of training data set (5, 10, 20, 50, 100, and 200) and then tested the resulting system with a total of 6000 CT images. All images were acquired from the Massachusetts General Hospital (MGH) Picture Archiving and Communication System (PACS). Using this data, we employ the learning curve approach to predict classification accuracy at a given training sample size. Our research will present a general methodology for determining the training data set size necessary to achieve a certain target classification accuracy that can be easily applied to other problems within such systems.