gebhart/patrepeval huggingface dataset:
A generalized method of subcloning DNA fragments by restriction site reconstruction: application to sequencing the amino-terminal coding region of the transforming gene of Gazdar marine sarcoma virus (1982)

The technique of restriction site reconstruction was generalized so as to allow the subcloning of any DNA fragment and its subsequent reexcision with EcoRI, XbaI, XhoI or HindIII. After excision, the 3' terminus of each strand will be derived from the starting nucleic acid, permitting the use of such fragments as primers for nucleotide sequencing by primer extension methods. The technique was used to subclone a 56 base pair BstNI-DdeI fragment of Moloney murine sarcoma virus (Mo-MSV) as a unique HindIII-HindIII fragment. This fragment then served as a primer to sequence a portion of the RNA genome of Gazdar murine sarcoma virus (Gz-MSV). The nucleotide sequence which was obtained indicated that the transforming gene of Gz-MSV arose by at least two recombination events involving murine leukemia virus (MLV) and the cellular homologue c-mos. This analysis suggests that a virus indistinguishable from Mo-MSV was an intermediate in the formation of Gz-MSV.
Isolation of Cultivation-Resistant Oomycetes, First Detected as Amplicon Sequences, from Roots of Herbicide-Terminated Winter Rye (2017)

The dynamics of microbial communities associated with dying cover crops are of interest because of potential impacts on disease in a subsequent crop, and because of the importance of microbial activity on plant residue to soil organic matter dynamics and nutrient cycling. We used high throughput amplicon sequencing to characterize the composition and structure of oomycete and fungal communities associated with a rye cover crop, and to track their community dynamics in the first several weeks after herbicide was applied to terminate the cover crop. The dominant oomycetes associated with cereal rye roots were Pythium volutum, Pythium sp. F86 (an unknown species within clade B), and Lagena radicicola. Because P. volutum is sensitive to common additives in isolation media, and L. radicicola is an obligate intracellular parasite, a unique aspect of this work is to reveal the dominance of oomycete taxa that would have been missed entirely under a traditional cultivation-based approach. Based on first detection in an amplicon sequencing survey, we were able to isolate P. volutum and Pythium sp. F86. We demonstrate that both species are pathogenic on corn, and that corn seedlings grown in the field following a rye cover crop show elevated rates of infection by P. volutum, highlighting a potential disease risk associated with cover cropping. P. volutum and Pythium sp. F86 exhibited contrasting spatial patterns of abundance, with nearly complete turnover of the dominant species across the field site. In contrast to the strong spatial structuring and low diversity of oomycete communities, fungal communities associated with a cereal rye cover crop were more diverse and dynamic, with some displacement of basidiomycetes by ascomycetes over time. Several plant pathogens, as well as putative beneficial organisms, were detected among fungal communities associated with rye roots. This work sheds light on microbial community dynamics on dying host plants, highlights the power of culture-independent microbial community assessment to yield new insights, and suggests the need for informed management to reduce seedling disease risk in corn following rye cover crops.
Plasma amino acid profile associated with fatty liver disease and co-occurrence of metabolic risk factors (2017)

Fatty liver disease (FLD) increases the risk of diabetes, cardiovascular disease, and steatohepatitis, which leads to fibrosis, cirrhosis, and hepatocellular carcinoma. Thus, the early detection of FLD is necessary. We aimed to find a quantitative and feasible model for discriminating the FLD, based on plasma free amino acid (PFAA) profiles. We constructed models of the relationship between PFAA levels in 2,000 generally healthy Japanese subjects and the diagnosis of FLD by abdominal ultrasound scan by multiple logistic regression analysis with variable selection. The performance of these models for FLD discrimination was validated using an independent data set of 2,160 subjects. The generated PFAA-based model was able to identify FLD patients. The area under the receiver operating characteristic curve for the model was 0.83, which was higher than those of other existing liver function-associated markers ranging from 0.53 to 0.80. The value of the linear discriminant in the model yielded the adjusted odds ratio (with 95% confidence intervals) for a 1 standard deviation increase of 2.63 (2.14-3.25) in the multiple logistic regression analysis with known liver function-associated covariates. Interestingly, the linear discriminant values were significantly associated with the progression of FLD, and patients with nonalcoholic steatohepatitis also exhibited higher values.
Size-Dependent Vibration of Circular Cylindrical Polymeric Microshells Reinforced with Graphene Platelets (2019)

This paper investigates size-dependent vibration of graphene platelet (GPL) reinforced circular cylindrical polymeric microshells. The microshells are composed of multilayers with GPL fillers uniformly dispersed in each individual layer, but GPL weight fraction changes layer-by-layer along the thickness direction. The effective Young’s modulus is predicted by the modified Halpin–Tsai model, while effective Poisson’s ratio and mass density are determined by the rule of mixture. Four different patterns of GPL dispersion are considered to achieve the functionally graded property of the microshells. Based on Love’s thin shell theory and the modified couple stress theory, the governing equations are derived by using Hamilton’s principle. Then, the Navier and Galerkin methods are utilized to solve natural frequencies of GPL reinforced polymeric (GPLRP) microshells. A parametric study is conducted, with a particular focus on the effects of the GPL distribution pattern, the weight fraction, the geometries of the GPL and the microshells, as well as the total number of layers of the microshells.
Arbitrary Dispersion Compensation of Periodic Waveforms using On-chip Discrete Phase Filters (2021)

We propose a discrete phase filter design suitable for arbitrary dispersion compensation of periodic waveforms using waveguide Bragg gratings in silicon. Higher-order dispersion compensation (equivalent to 5,000 km long optical fiber) of a 40-GHz picosecond pulse train is experimentally demonstrated using mm-long phase filters.
Dynamic Programming Strategies for the Traveling Salesman Problem with Time Window and Precedence Constraints (1997)

The Traveling Salesman Problem with Time Window and Precedence Constraints (TSP-TWPC) is to find an Hamiltonian tour of minimum cost in a graph G = (X, A) of n vertices, starting at vertex 1, visiting each vertex i ∈ X during its time window and after having visited every vertex that must precede i, and returning to vertex 1. The TSP-TWPC is known to be NP-hard and has applications in many sequencing and distribution problems. In this paper we describe an exact algorithm to solve the problem that is based on dynamic programming and makes use of bounding functions to reduce the state space graph. These functions are obtained by means of a new technique that is a generalization of the “State Space Relaxation” for dynamic programming introduced by Christofides et al. (Christofides, N., A. Mingozzi, P. Toth. 1981b. State space relaxation for the computation of bounds to routing problems. Networks 11 145–164.). Computational results are given for randomly generated test problems.
Analysis of nanometer vacuum gap formation in thermo-tunneling devices (2008)

Combined thermionic emission and tunneling of hot electrons (thermo-tunneling) has emerged as a potential new solid-state cooling technology. Practical implementation of thermo-tunneling, however, requires the formation of a nanometer-sized gap spanning macroscopically significant surfaces. This paper describes a numerical and experimental investigation into the formation of a nanometer-sized tunneling gap based on the combined action of electrostatic, elastic and Lorentz forces. Experimental data reported here were used to tune the model and extract estimates for the size of the tunneling area and the gap size, respectively. The effect of changing the strength of the magnetic field was also investigated. The presented one-dimensional (1D) analysis of the relative magnitudes of these forces indicates possible stable operation.
CONTACT BY ACTIVATED LYMPHOCYTES PROMOTES ENDOTHELIAL CELL RELEASE OF MATRIX: A MODEL FOR ENDOTHELIALITIS? (1999)

287 Transient focal loosening of an endothelial cell's (EC) basement membrane attachment may be an important event in endothelial invasion in acute rejection (endothelialitis). We studied the mechanisms of endothelial cell detachment from matrix-coated plastic following contact by lymphocytes as an in vitro model of modulation of EC basement membrane adhesion. 3H-methyl thymidine labeled human umbilical vein endothelial cells were plated on either fibronectin or type I collagen matrices. Human PBL were depleted of monocytes, stimulated with PHA, then added to the EC monolayer. Specifically detached EC were quantitated as the fraction of the total less spontaneously detached EC. Co-culture of lectin-activated, but not resting PBL, with monolayers of EC induced progressive endothelial cell detachment from the underlying matrix. Injury of the EC monolayer required direct cell contact with the activated lymphocytes since no detachment was seen when the PBL were placed above a transwell membrane. Moreover plasma membranes prepared from activated but not resting PBL induced EC detachment. Neither inhibition of perforin function using concanamycin A, nor fas-ligand or TNF/LT signalling using blocking antibodies abrogated EC detachment. Adherent EC stimulated with activated PBL did not show evidence of apoptosis using TUNEL and annexin V staining at timepoints before EC detachment was observed. Neither the matrix metalloproteinase inhibitors o-phenanthroline or BB-94, nor aprotinin blocked EC detachment. EC detachment was largely inhibited when the EC β1 integrin was frozen in the high-affinity conformation using mAb or Mg+2. Activation of endothelial cell β1 integrin inhibited transendothelial migration of lymphocytes in vitro. Thus contact of activated PBL with the endothelial cell induces changes in the EC attachment to the underlying matrix which involves changes in the EC β1 integrin conformation. Decreased endothelial β1 integrin affinity for matrix may be a central event in lymphocyte-mediated vascular injury and leukocyte migration into sites of the mechanisms of inflammation.
The Effects of Montmorency Tart Cherry Concentrate Supplementation on Recovery Following Prolonged, Intermittent Exercise (2016)

This study investigated Montmorency tart cherry concentrate (MC) supplementation on markers of recovery following prolonged, intermittent sprint activity. Sixteen semi-professional, male soccer players, who had dietary restrictions imposed for the duration of the study, were divided into two equal groups and consumed either MC or placebo (PLA) supplementation for eight consecutive days (30 mL twice per day). On day 5, participants completed an adapted version of the Loughborough Intermittent Shuttle Test (LISTADAPT). Maximal voluntary isometric contraction (MVIC), 20 m Sprint, counter movement jump (CMJ), agility and muscle soreness (DOMS) were assessed at baseline, and 24, 48 and 72 h post-exercise. Measures of inflammation (IL-1-β, IL-6, IL-8, TNF-α, hsCRP), muscle damage (CK) and oxidative stress (LOOH) were analysed at baseline and 1, 3, 5, 24, 48 and 72 h post-exercise. Performance indices (MVIC, CMJ and agility) recovered faster and muscle soreness (DOMS) ratings were lower in the MC group (p < 0.05). Additionally, the acute inflammatory response (IL-6) was attenuated in the MC group. There were no effects for LOOH and CK. These findings suggest MC is efficacious in accelerating recovery following prolonged, repeat sprint activity, such as soccer and rugby, and lends further evidence that polyphenol-rich foods like MC are effective in accelerating recovery following various types of strenuous exercise.
Theoretical Study Related to the Carcinogenic Activity of Polycyclic Aromatic Hydrocarbon Derivatives (1999)

Ab initio, density functional, and semiempirical calculations concerning the reactivity of polycyclic aromatic hydrocarbons (PAHs) were performed. The reactions considered were those related to the carcinogenic activity of PAHs. The increased reactivity of the diol epoxide derivatives is explained by the greater propensity of benzene diol epoxide to undergo acid-catalyzed opening of the epoxide ring, as well as its thermodynamic tendency to react with nucleophiles in substitution reactions. However, rearrangement to phenol was the favored path for benzene oxide. Bay-region compounds were found to open spontaneously upon protonation, thus revealing a greater reactivity in the rate-determining step of the mechanism of carcinogenesis. A correlation was observed between the exothermicity of the process and the charge delocalization in the resulting carbocation. The enhanced activity of bay-region methyl-substituted compounds was attributed to the instability of the closed structures due to steric interactions rather than stabilization of the carbocations by hyperconjugation.
Tubular breast cancer. A retrospective study. (2014)

Our retrospective analysis showed no treatment benefit for either anti-hormonal or chemotherapeutical regimens. Post-operative radiotherapy, however, improved the survival rate of patients with tubular carcinoma (log-rank=5, p=0.025). Our data suggest that post-operative radiotherapy is an important treatment to prolong survival for patients suffering from tubular breast cancer.
FlashLinQ: A synchronous distributed scheduler for peer-to-peer ad hoc networks (2010)

This paper proposes FlashLinQ - a synchronous peer-to-peer wireless PHY/MAC network architecture for distributed channel allocation. By leveraging the fine-grained parallel channel access of OFDM, FlashLinQ develops an analog energy-level based signaling scheme that enables SIR (Signal to Interference Ratio) based distributed scheduling. This new signaling mechanism and the corresponding allocation algorithms permit efficient channel-aware spatial resource allocation, leading to significant gains over a CSMA/CA system with RTS/CTS. FlashLinQ is a complete system architecture including (i) timing and frequency synchronization derived from cellular spectrum, (ii) peer discovery, (iii) link management, and (iv) channel-aware distributed power, data-rate and link scheduling. We implement FlashLinQ over licensed spectrum on a DSP/FPGA platform. In this paper, we present performance results for FlashLinQ using both implementation and simulations.
Improving Security and Efficiency in Attribute-Based Data Sharing (2011)

With the recent adoption and diffusion of the data sharing paradigm in distributed systems such as online social networks or cloud computing, there have been increasing demands and concerns for distributed data security. One of the most challenging issues in data sharing systems is the enforcement of access policies and the support of policies updates. Ciphertext policy attribute-based encryption (CP-ABE) is becoming a promising cryptographic solution to this issue. It enables data owners to define their own access policies over user attributes and enforce the policies on the data to be distributed. However, the advantage comes with a major drawback which is known as a key escrow problem. The key generation center could decrypt any messages addressed to specific users by generating their private keys. This is not suitable for data sharing scenarios where the data owner would like to make their private data only accessible to designated users. In addition, applying CP-ABE in the data sharing system introduces another challenge with regard to the user revocation since the access policies are defined only over the attribute universe. Therefore, in this study, we propose a novel CP-ABE scheme for a data sharing system by exploiting the characteristic of the system architecture. The proposed scheme features the following achievements: 1) the key escrow problem could be solved by escrow-free key issuing protocol, which is constructed using the secure two-party computation between the key generation center and the data-storing center, and 2) fine-grained user revocation per each attribute could be done by proxy encryption which takes advantage of the selective attribute group key distribution on top of the ABE. The performance and security analyses indicate that the proposed scheme is efficient to securely manage the data distributed in the data sharing system.
Development of Chelating Agent-Based Polymeric Gel System for Hydraulic Fracturing (2018)

Hydraulic Fracturing is considered to be one of the most important stimulation methods. Hydraulic Fracturing is carried out by inducing fractures in the formation to create conductive pathways for the flow of hydrocarbon. The pathways are kept open either by using proppant or by etching the fracture surface using acids. A typical fracturing fluid usually consists of a gelling agent (polymers), cross-linkers, buffers, clay stabilizers, gel stabilizers, biocide, surfactants, and breakers mixed with fresh water. The numerous additives are used to prevent damage resulting from such operations, or better yet, enhancing it beyond just the aim of a fracturing operation. This study introduces a new smart fracturing fluid system that can be either used for proppant fracturing (high pH) or acid fracturing (low pH) operations in sandstone formations. The fluid system consists of glutamic acid diacetic acid (GLDA) that can replace several additives, such as cross-linker, breaker, biocide, and clay stabilizer. GLDA is also a surface-active fluid that will reduce the interfacial tension eliminating the water-blockage effect. GLDA is compatible and stable with sea water, which is advantageous over the typical fracturing fluid. It is also stable in high temperature reservoirs (up to 300 °F) and it is also environmentally friendly and readily biodegradable. The new fracturing fluid formulation can withstand up to 300 °F of formation temperature and is stable for about 6 h under high shearing rates (511 s−1). The new fracturing fluid formulation breaks on its own and the delay time or the breaking time can be controlled with the concentrations of the constituents of the fluid (GLDA or polymer). Coreflooding experiments were conducted using Scioto and Berea sandstone cores to evaluate the effectiveness of the developed fluid. The flooding experiments were in reasonable conformance with the rheological properties of the developed fluid regarding the thickening and breaking time, as well as yielding high return permeability.
The Origins of Noncovalent Catalysis of Intermolecular Diels−Alder Reactions by Cyclodextrins, Self-Assembling Capsules, Antibodies, and RNAses (2002)

The catalysis of Diels-Alder reactions by noncovalent binding by synthetic, protein, and nucleic acid hosts has been surveyed and compared. These catalysts consist of binding cavities that form complexes containing both the diene and the dienophile; the cycloaddition reaction occurs in the cavity. The binding requires no formation of covalent bonds and is driven principally by the hydrophobic (or solvophobic) effect. A molecular mechanics and dynamics study of the cyclodextrin catalysis of a Diels-Alder reaction is used to exemplify and probe this form of catalysis. Detailed kinetic data is available for catalysis by antibodies, RNA, cyclodextrins, and Rebek's tennis ball capsules. Some of these catalysts stabilize the reactants more than the transition state and consequently will only have catalytic effect under conditions of low substrate-to-catalyst ratios. None of the hosts achieve significant specific binding of transition states that is the hallmark of enzyme catalysis.
Individual Anatomy Demands Various Techniques in Correction of an Anomalous Origin of the Left Coronary Artery in the Pulmonary Artery (1995)

Anomalous origin of the left coronary artery (ALCA) from the pulmonary artery is a rare cardiac anomaly. It can result in decreased myocardial perfusion and impaired left-ventricular function, which can lead to congestive heart failure or even myocardial infarction. Reconstructive surgery of the left coronary artery is the desirable measure in the management of this anomaly. Since July 1992, five patients with ALCA from the pulmonary artery were treated surgically. Age at operation ranged from 3 months to 11 years. Three patients had congestive heart failure and one was in cardiogenic shock. Operative techniques included "tunnel type" surgery in three cases and aortic reimplantation in two. Two operative variations performed successfully in this series are described. There were no postoperative deaths. At the latest follow-up (mean 14 months), all anastomoses were patent and showed antegrade flow. For those patients with ALCA from the pulmonary artery, direct reimplantation of the ALCA to the aorta is the most physiologically appropriate reconstructive solution, and offers good early and late results. Intrapulmonary tunnel from aortopulmonary window to coronary artery is recommended for children in whom aortic reimplantation is not anatomically feasible.
Optical Diagnostics for Thermal Barrier Coatings (2004)

The translucent nature of ceramic oxide thermal barrier coatings (TBCs) provides an opportunity to employ optical probes to monitor temperature gradients and buried damage propagation within the coating. An important advantage of noncontact optical diagnostics is that they are amendable to health monitoring of TBCs in service. In this paper, two optical diagnostic approaches, operating in different wavelength regimes, are discussed. The first approach is the use of mid-infrared reflectance (MIR) to monitor the progression of TBC delamination produced by thermal cycling. This approach takes advantage of the maximum transparency of the TBCs at mid-infrared wavelengths, in particular, between 3 and 5 microns. Recent progress in extending the MIR method to a more practical visual inspection tool will be presented. A second approach, using visible wavelengths, is the embedding of thermographic phosphors within the TBC to add sensing functions to the coating that can provide depth-selective information about temperature gradients and TBC integrity. Emphasis will be given to the use of fluorescence decay time measurements to provide temperature readings from a thermographic phosphor layer residing beneath the TBC.