gebhart/patrepeval huggingface dataset:
Cellular Retinoid-Binding Proteins (1987)

A number of specific carrier proteins for members of the vitamin A family have been discovered. Two of these proteins bind all-trans-retinol and are found within cells important in vitamin A metabolism or function. These two proteins have considerable sequence homology and have been named cellular retinol-binding protein (CRBP) and cellular retinol-binding protein, type II (CRBP [II]). A third intracellular protein, cellular retinoic acid-binding protein (CRABP) also is structurally similar but binds only retinoic acid. Although retinol appears to be bound quite similarly by the two retinol-binding proteins, subtle differences are apparent that appear to be related to the different functions of the two proteins. That, coupled with the specific cellular locations of the two proteins, suggests their roles. Cellular retinol-binding protein appears to have several roles, including (1) delivering retinol to specific binding sites within the nucleus and (2) participating in the transepithelial movement of retinol across certain blood-organ barriers. In contrast, CRBP (II) appears to be involved in the intestinal absorption of vitamin A and, in particular, may direct retinol to a specific esterifying enzyme, resulting in the production of fatty acyl esters of retinol that are incorporated into chylomicrons for release to the lymph. Like CRBP, CRABP can deliver its ligand retinoic acid to specific binding sites within the nucleus, sites different from those for retinol. The nuclear binding of retinol and retinoic acid may be part of the mechanism by which vitamin A directs the state of differentiation of epithelial tissue.
Anthrax vaccination and joint related adverse reactions in light of biological warfare scenarios. (2003)

We believe that civilian doctors need to become familiar with the adverse reactions that can be expected to follow the use of AVA. Both civilian and military doctors need to be vigilant in reporting all such reactions to VAERS, so that more information can be gathered about AVA. We also believe that an anthrax vaccine with an improved safety profile is needed if it is to be used in populations, either military or civilian, that are not under imminent threat of attack by biological warfare agents. It should also be kept in mind that the widespread use of anthrax vaccination may cause potential producers of biological weapons and terrorists to seek to produce anthrax strains that are not neutralized by the current vaccine.
Effective Image Retrieval Based on Hidden Concept Discovery in Image Database (2007)

This paper addresses content-based image retrieval in general, and in particular, focuses on developing a hidden semantic concept discovery methodology to address effective semantics-intensive image retrieval. In our approach, each image in the database is segmented into regions associated with homogenous color, texture, and shape features. By exploiting regional statistical information in each image and employing a vector quantization method, a uniform and sparse region-based representation is achieved. With this representation, a probabilistic model based on statistical-hidden-class assumptions of the image database is obtained, to which the expectation-maximization technique is applied to analyze semantic concepts hidden in the database. An elaborated retrieval algorithm is designed to support the probabilistic model. The semantic similarity is measured through integrating the posterior probabilities of the transformed query image, as well as a constructed negative example, to the discovered semantic concepts. The proposed approach has a solid statistical foundation; the experimental evaluations on a database of 10000 general-purposed images demonstrate its promise and effectiveness.
trans-Acting virulence functions of the octopine Ti plasmid from Agrobacterium tumefaciens (1984)

All Ti plasmid-encoded virulence functions that were studied act in trans. An octopine Ti plasmid-specific vir operon, called vir-O, located on an EcoRI restriction fragment has been characterized. Sequences with promoter activity in Escherichia coli were identified for a second vir operon, called vir-C, which was located close to the position of vir-O.
Critical Role of Molecular Electrostatic Potential on Charge Generation in Organic Solar Cells (2018)

Abstract Revealing the charge generation is a crucial step to understand the organic photovoltaics. Recent development in non‐fullerene organic solar cells (OSCs) indicates efficient charge separation even with negligible energetic offset between the donor and acceptor materials. These new findings trigger a critical question concerning the charge separation mechanism in OSCs, traditionally believed to result from sufficient energetic offset between the polymer donor and fullerene acceptor. We propose a new mechanism, which involves the molecular electrostatic potential, to explain efficient charge separation in non‐fullerene OSCs. Together with the new mechanism, we demonstrate a record efficiency of ~12% for systems with negligible energetic offset between donor and acceptor materials. Our analysis also rationalizes different requirement of the energetic offset between fullerene‐based and non‐fullerene OSCs, and paves the way for further design of OSC materials with both high photocurrent and high photovoltage at the same time.
A fully integrated dual-mode CMOS power amplifier for WCDMA applications (2012)

Integrating a CMOS RF power amplifier (PA) into a single-chip transceiver is one of the most challenging works in implementing radio front-ends, which presents many advantages in handheld applications. Especially, low-power efficiency enhancement (LPEE) techniques, considering the probability distribution function of the practical wireless communication environments, extend the battery lifetime in handheld devices. Therefore, there are many studies for the LPEE in handheld CMOS PAs using transmission-line transformers (TLTs) with parallel amplifiers. Designing a series/parallel-combining transformer (SCT/PCT) is one of the key factors in the implementation of a dual-mode CMOS PA. However, the dual-mode performances of the PA must be optimized by using one output TLT structure. It is expected that there are difficulties in designing a highly efficient dual-mode PA. Therefore, this paper introduces a fully integrated dual-mode CMOS PA with a proposed output TLT with 2 control switches, which allows an LPEE with a back-off region of 10dB or more with a very low quiescent current.
Amorphous Si∕Au wafer bonding (2007)

The authors report a rapid reaction between Au and amorphous Si (a-Si), which occurred at a much faster rate compared to the case of crystal Si∕Au reaction. With an amorphous Si coating layer on crystal Si (c-Si) wafer, air voids and craters were prevented from forming at the Si∕Au bonding interface, but were usually found at the crystal Si∕Au bonding interface. The uniform liquid eutectic Au–Si alloy quickly formed at the Au/amorphous Si bonding interface is the key for the prevention of air voids and craters. This amorphous Si∕Au bonding process enables the feasibility of eutectic Au∕Si bonding for wafer bonding applications.
Host-targeting protein 1 (SpHtp1) from the oomycete <i>Saprolegnia parasitica</i> translocates specifically into fish cells in a tyrosine-O-sulphate–dependent manner (2012)

The eukaryotic oomycetes, or water molds, contain several species that are devastating pathogens of plants and animals. During infection, oomycetes translocate effector proteins into host cells, where they interfere with host-defense responses. For several oomycete effectors (i.e., the RxLR-effectors) it has been shown that their N-terminal polypeptides are important for the delivery into the host. Here we demonstrate that the putative RxLR-like effector, host-targeting protein 1 (SpHtp1), from the fish pathogen Saprolegnia parasitica translocates specifically inside host cells. We further demonstrate that cell-surface binding and uptake of this effector protein is mediated by an interaction with tyrosine-O-sulfate-modified cell-surface molecules and not via phospholipids, as has been reported for RxLR-effectors from plant pathogenic oomycetes. These results reveal an effector translocation route based on tyrosine-O-sulfate binding, which could be highly relevant for a wide range of host-microbe interactions.
Modeling and simulation of individual user behavior for building performance predictions (2007)

User behavior is a key to the correct prediction of building performance. Performance is meant here not only in relation to energy consumption, but more importantly to user satisfaction and, in commercial buildings, job performance. The contributions of this paper are static and dynamic models of individual users and user activities in an office environment in relation to building control systems. The models are based on a well structured general model of five different domains of building entities, including user activities. Models for specific simulation projects are refinements of this general model. It is shown how multi-agent based simulations can be automatically derived from such models. A case study of an university office with irregular occupancy is introduced as an example.
Seamless Lesion Insertion for Data Augmentation in CAD Training (2016)

The performance of a classifier is largely dependent on the size and representativeness of data used for its training. In circumstances where accumulation and/or labeling of training samples is difficult or expensive, such as medical applications, data augmentation can potentially be used to alleviate the limitations of small datasets. We have previously developed an image blending tool that allows users to modify or supplement an existing CT or mammography dataset by seamlessly inserting a lesion extracted from a source image into a target image. This tool also provides the option to apply various types of transformations to different properties of the lesion prior to its insertion into a new location. In this study, we used this tool to create synthetic samples that appear realistic in chest CT. We then augmented different size training sets with these artificial samples, and investigated the effect of the augmentation on training various classifiers for the detection of lung nodules. Our results indicate that the proposed lesion insertion method can improve classifier performance for small training datasets, and thereby help reduce the need to acquire and label actual patient data.
Identification of Allelochemicals in <i>Eucalyptus citriodora</i> and <i>Polygonum sachalinense</i> (1994)

The relationship between the allelochemicals, p-menthane-3,8-diols (cis and trans)and the ontogenetic age in Eucalyptus citriodora was elucidated. The diols in the soil from a Eucalyptus grove were analysed by chromatography. On the other hand, the root exudates from Polygonum sachalinense in a recirculating system significantly inhibited lettuce seedling growth. Bioassay of the neutral-acidic fraction on the TLC agar plate showed the inhibitory activity corresponded to the two yellow pigments. Two compounds were isolated and identified as anthraquinone compounds; emodin and physcion. The results indicate that these anthraquinones are responsible for the observed interference in nature and are potent allelochemicals.
Optical Feshbach resonances: Field-dressed theory and comparison with experiments (2015)

Optical Feshbach resonances (OFRs) have generated significant experimental interest in recent years. These resonances are promising for many-body physics experiments, yet the practical application of OFRs has been limited. The theory of OFRs has been based on an approximate model that fails in important detuning regimes, and the incomplete theoretical understanding of this effect has hindered OFR experiments. We present the most complete theoretical treatment of OFRs to date, demonstrating important characteristics that must be considered in OFR experiments and comparing OFRs to the well-studied case of magnetic Feshbach resonances. We also present a comprehensive treatment of the approximate OFR model, including a study of the range of validity for this model. Finally, we derive experimentally useful expressions that can be applied to real experimental data to extract important information about the resonance structure of colliding atoms.
Barium Hydride-Mediated Nitrogen Transfer and Hydrogenation for Ammonia Synthesis: A Case Study of Cobalt (2017)

Industrial ammonia synthesis catalyzed by Fe- and Ru-based catalysts is an energy-consuming process. The development of low-temperature active catalyst has been pursued for a century. Herein, we report that barium hydride (BaH2) can synergize with Co, leading to a much better low-temperature activity, i.e., the BaH2-Co/carbon nanotube (CNT) catalyst exhibits ammonia synthesis activity right above 150 °C; at 300 °C, it is 2 orders of magnitude higher than that of the BaO-Co/CNTs and more than 2.5-times higher than Cs-promoted Ru/MgO. Kinetic analyses reveal that the dissociative adsorption of N2 on the Co-BaH2 catalyst may not be the rate-determining step, as evidenced by the much smaller reaction order of N2 (0.43) and the lower apparent activation energy (58 kJ mol–1) compared with those of the unpromoted and BaO-promoted Co-based catalysts. BaH2, with a negative hydride ion, may act as a strong reducing agent, removing activated N from the Co surface and forming a BaNH species. The hydrogenation of the BaNH species to NH3 and BaH2 can be facilely carried out at 150 °C. The relayed catalysis by Co and BaH2 sites creates an energy-favored pathway that allows ammonia synthesis under milder conditions.
Neutralization of RANTES and Eotaxin Prevents the Loss of Dopaminergic Neurons in a Mouse Model of Parkinson Disease (2016)

Parkinson disease (PD) is second only to Alzheimer disease as the most common human neurodegenerative disorder. Despite intense investigation, no interdictive therapy is available for PD. Recent studies indicate that both innate and adaptive immune processes are active in PD. Accordingly, we found a rapid increase in RANTES (regulated on activation normal T cell expressed and secreted) and eotaxin, chemokines that are involved in T cell trafficking, in vivo in the substantia nigra pars compacta and the serum of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-intoxicated mice. RANTES and eotaxin were also up-regulated in the substantia nigra pars compacta of post-mortem PD brains as compared with age-matched controls. Therefore, we investigated whether neutralization of RANTES and eotaxin could protect against nigrostriatal degeneration in MPTP-intoxicated mice. Interestingly, after peripheral administration, functional blocking antibodies against RANTES and eotaxin reduced the infiltration of CD4(+) and CD8(+) T cells into the nigra, attenuated nigral expression of proinflammatory molecules, and suppressed nigral activation of glial cells. These findings paralleled dopaminergic neuronal protection, normalized striatal neurotransmitters, and improved motor functions in MPTP-intoxicated mice. Therefore, we conclude that attenuation of the chemokine-dependent adaptive immune response may be of therapeutic benefit for PD patients.
Role of adenosine in asthma (1996)

Several lines of evidence support the hypothesis that adenosine contributes to asthma. Inhaled adenosine provokes bronchoconstriction in asthmatics, but not in nonasthmatics. This process appears to be mediated by mast cell activation, because it can be blocked by antihistamines and inhibitors of mast cell activation. Inhaled adenosine evokes release of mast cell mediators in bronchoalveolar lavage fluid, including histamine, prostaglandin D2, and tryptase, a specific mast cell marker. Also, adenosine potentiates the immunological activation of mast cells in vitro, including rat peritoneal mast cells, mouse bone marrow-derived mast cells, human lung mast cells, and the human mast cell line HMC-1. The receptor subtype that mediates this activation differs between mast cell type, but preliminary evidence suggests that human lung mast cells express A2B receptors. An argument against the contribution of adenosine in asthma has been the "enprofylline paradox." This xanthine (3-(n-propylyl)xanthine) is as effective an antiasthmatic as theophylline (1,3-dimethyl xanthine) but was initially thought not to be an adenosine receptor antagonist. More recent evidence has confirmed that enprofylline blocks A2B receptors with a Ki (7 microM) similar to that of theophylline (13 microM) and well within its therapeutic plasma levels (5-25 microM). This finding, we believe, resolves the enprofylline paradox and supports the hypothesis that adenosine, through A2B receptor activation, contributes to asthma. Preliminary evidence suggests that A2B receptors are indeed present in human lung mast cells. A2B receptors, therefore, may be a potential target for the development of antiasthmatic drugs.
Image based typographic analysis of documents (2002)

An approach to image based typographic analysis of documents is provided. The problem requires a spatial understanding of the document layout as well as knowledge of the proper syntax. The system performs a page synthesis from the stream of formatting commands defined in a DVI file. Since the two-dimensional relationships between document components are not explicit in the page language, the authors develop a representation which preserves the two-dimensional layout, the read-order and the attributes of document components. From this hierarchical representation of the page layout we extract and analyze relevant typographic features such as margins, line and character spacing, and figure placement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Multi‐Component Pharmaceutical Crystalline Phases: Engineering for Performance (2010)

10.1002/9780470681794.ch3.abs This chapter contains sections titled: Introduction Exploring Crystal Form Diversity High-throughput Experimentation Examples of ‘Form and Formulation’ AMG517 and Celecoxib – ‘Spring and Parachute’ Approach Carbamazepine – Stabilization Against a Hydrate Theophylline:Phenobarbital – Two is Better Than One Delaviridine Mesylate – Material Misbehaviour Summary and Outlook References
DNA sequence of the murE-murD region of Bacillus subtilis 168 (1993)

The sequence of a 4.4 kbp region of DNA from Bacillus subtilis 168, lying between sporulation genes spoVD and spoVE, has been determined as part of the B. subtilis genomic sequencing programme. The region contains three genes with high sequence similarity to the murE, mraY and murD genes of Escherichia coli. The products of these genes are likely to catalyse various steps in the formation of the precursors for peptidoglycan synthesis in B. subtilis. The regions at 133 degrees on the standard genetic map of the B. subtilis chromosome, and in the 2 min region of the E. coli genetic map, are now shown to contain a large cluster of functionally related genes. Although the linear order of the genes in the cluster is conserved, three genes that are present in the E. coli chromosome, and which are likely to be essential for peptidoglycan synthesis in both organisms, are absent from this region of the B. subtilis chromosome. In general, the B. subtilis cluster differs from that of E. coli in having more extensive intergenic regions, with less potential for translational coupling.
TCP Dynamic Acknowledgment Delay: Theory and Practice (1998)

We study an on-line problem that is motivated by the networking problem of dynamically adjusting delays of acknowledgments in the Transmission Control Protocol (TCP). The theoretical problem we study is the following. There is a sequence of n packet arrival times A = and a look-ahead coefficient L. The goal is to partition A into k subsequences sigma1, sigma2, ...,sigmak (where a subsequence end is defined by an acknowledgment) that minimizes a linear combination of the cost for the number of acknowledgments sent and the cost for the additional latency introduced by delaying acknowledgments. At each arrival, an oracle provides the algorithm with the times of the next L arrivals. For all the results of our paper, we describe how to incorporate other contraints to better match the true acknowledgment delay problem. We first define two different objective functions for measuring the cost of a solution, each with its own measure of latency cost. For each objective function we first given an O (nsquared)-time dynamic programming algorithm for optimally solbing the off-line problem. Then we describe an on-line algorithm that greedily acknowledges exactly when the cost for an acknowledgment is less than the latency cost incurred by not acknowledging. We show that for this algorithm there is a sequence of n packet arrivals for which it is Omega (squareroot(n))-competitive for the first objective function, 2-competitive for the second function for L = 0, and 1-competitive for the second function for L = 1. Next we present a second on-line algorithm which is a slight modification of the first that we prove is 2-competitive for both objective funcitons. Then for each objective function we give lower bounds on the competitive ration for any deterministic on-line algorithm. These results show that for each objective function, at least one of our algorithms is optimal. Finally, we give some initial empirical results using arrival sequences from real network traffic where we compare the two methods used in TCP for acknowledgment delay with our two on-line algorithms. In all cases we examine perforance with L = 0 and L = 1.
Biology and biogenesis of shed microvesicles (2016)

The ability of cells to transmit bioactive molecules to recipient cells and the extracellular environment is a fundamental requirement for both normal physiology and disease pathogenesis. It has traditionally been thought that soluble factors released from cells were responsible for this cellular signaling but recent research has revealed a fundamental role for microvesicles in this process. Microvesicles are heterogeneous membrane-bound sacs that are shed from the surface of cells into the extracellular environment in a highly regulated process. They are shed following the selective incorporation of a host of molecular cargo including multiple types of proteins and nucleic acids. In addition to providing new insight into the etiology of complex human diseases, microvesicles also show great promise as a tool for advanced diagnosis and therapy as we move forward into a new age of personalized medicine. Here we review current status of the rapidly evolving field of microvesicle biology, highlighting critical regulatory roles for several small GTPases in the biology and biogenesis of shed microvesicles.
Detection of DNA probes using Diels Alder cycloaddition and SERRS (2003)

A number of methods for detecting specific DNA sequences have been used to provide data for use in diagnosis of disease states and examination of gene expression. This study shows how the use of labelled oligonucleotides created by Diels Alder cycloaddition can be used as surface enhanced resonance Raman scattering (SERRS) active probes that provide easily identifiable signals at low concentrations in a mixture. The probes were produced by first tagging the oligonucleotides with a furan residue at the 5'-terminus to act as the diene. Three specifically designed benzotriazole azo maleimide dyes were then used as dienophiles to undergo cycloaddition with the furan modified oligonucleotide to generate SERRS active probes. These probes gave excellent SERRS signals from a silver-PVA film. Surface mapping of the silver PVA film indicated that the distribution of the dyes was uniform and that the number of moles of probe detected at any one time was approximately in the attomole region.