gebhart/patrepeval huggingface dataset:
Strong enhancement of the lanthanide-centred luminescence in complexes with 4-alkylated 2,2′;6′,2″-terpyridines † (2000)

The stability and photophysical properties of trivalent lanthanide complexes with 2,2′;6′,2′′-terpyridines substituted in the 4 position (L1, t-butyl; L2, ethyl) have been compared to those with the unsubstituted ligand terpy. The stability constants log β3 of complexes with L1 and terpy are similar and reflect a preference for the harder heavier members of the series. Cyclic voltammetry of the [Eu(L)3][ClO4]3 complexes show a considerable cathodic shift of the EuIII–EuII reduction potential on going from terpy to L2 and L1. The energy of the LMCT states, indirectly determined from the half peak potentials for ligand oxidation and europium(III) reduction, is too high to allow an effective non-radiative deactivation by this pathway. Complexes of the substituted ligands [Ln(Li)3][ClO4]3 (Ln = Eu or Tb) show a substantial increase in the quantum yields of the metal-centred luminescence in acetonitrile solution compared to the terpy reference systems: QEu = 0.10 (L1), 0.11 (L2) vs. 0.013 (terpy), and QTb = 0.67 (L1), 0.34 (L2) vs. 0.047 (terpy). The main factor responsible for this enhancement arises from a facilitated intersystem crossing in L1, L2 and in their complexes, as demonstrated by the ratio of the fluorescence and phosphorescence intensity of both the “free” ligands and their lanthanum(III) tris complexes. This effect is tentatively assigned to the electron donating substituents in the 4 position affecting the mixing of energetically close singlet and triplet ligand states.
Cross-dataset learning and person-specific normalisation for automatic Action Unit detection (2015)

Automatic detection of Facial Action Units (AUs) is crucial for facial analysis systems. Due to the large individual differences, performance of AU classifiers depends largely on training data and the ability to estimate facial expressions of a neutral face. In this paper, we present a real-time Facial Action Unit intensity estimation and occurrence detection system based on appearance (Histograms of Oriented Gradients) and geometry features (shape parameters and landmark locations). Our experiments show the benefits of using additional labelled data from different datasets, which demonstrates the generalisability of our approach. This holds both when training for a specific dataset or when a generic model is needed. We also demonstrate the benefits of using a simple and efficient median based feature normalisation technique that accounts for person-specific neutral expressions. Finally, we show that our results outperform the FERA 2015 baselines in all three challenge tasks - AU occurrence detection, fully automatic AU intensity and pre-segmented AU intensity estimation.
A Three-Dimensional, Noninterpenetrating Metal−Organic Framework with the Moganite Topology:  A Simple (4<sup>2</sup>.6<sup>2</sup>.8<sup>2</sup>)(4.6<sup>4</sup>.8)<sub>2</sub> Net Containing Two Kinds of Topologically Nonequivalent Points (2004)

Self assembly of Cu(2+) with the multifunctional ligand 2-(4-pyridyl)thiazole-4-carboxylic acid (Pytac) affords the neutral 3D coordination polymer [Cu(3)(Pytac)(6)](H(2)O)(14) (hereafter, SZL-1), which has the rare moganite topology. The mineral moganite has a topology that is closely related to the well-known quartz topology, but the two topologies are differentiated by the number of topologically inequivalent nodes. Whereas only one kind of node is present in quartz, two types of topologically inequivalent nodes are present in moganite. The title compound, which has three vertices in its repeat unit, has two types of topologically inequivalent nodes with the overall vertex symbol (4(2)x6(2)x8(2))(4x6(4)x8)(2) corresponding to the moganite net. Prior to this report, few metal-organic framework materials (MOFs) have been found to contain more than one type of node, and SZL-1 is the first MOF with the moganite topology.
Self organization and energy efficient TDMA MAC protocol by wake up for wireless sensor networks (2005)

This paper proposes novel energy efficient self-organization and medium access control (MAC) protocols for wireless sensor networks. The proposed protocol is based on time division multiple access (TDMA) principle and are referred to as TDMA. In the proposed protocol, a sensor utilizes its assigned slot only when it is sending or receiving information, otherwise its receiver and transmitter are turned off to avoid unnecessary neighbor listening. In order to accelerate the receive response, wake-up packets are used to activate a sleeping node. When compared with the existing energy efficient MAC protocols, such as 10% S-MAC, the performance results show that the proposed TDMA-W protocol consumes only 1.5% to 15% of the S-MAC power, yielding 6 to 67 folds enhancement in battery life.
Evaluation of four serological tests for bovine paratuberculosis (1992)

The standard complement fixation (CF) test, a commercial agarose gel immunodiffusion (AGID) test (ImmuCell Corporation, Portland, Maine), and two commercial enzyme-linked immunosorbent assays (ELISAs; Allied Laboratories, Glenwood Springs, Colo. [Allied ELISA], and the CSL, Limited, [Parkville, Victoria, Australia] enzyme immunoassay [CSL ELISA]) were evaluated by using sera from the Repository for Paratuberculosis Specimens. The case definition of subclinical bovine paratuberculosis was isolation of Mycobacterium paratuberculosis from fecal samples or internal organs of dairy cattle without diarrhea or weight loss. Animals designated as free of the disease originated exclusively from certified paratuberculosis-free herds in Wisconsin. None of the cattle evaluated had been vaccinated for paratuberculosis. Among 177 M. paratuberculosis-infected cattle, the CF test, the AGID test, the Allied ELISA, and the CSL ELISA had test sensitivities of 38.4, 26.6, 58.8, and 43.4%, respectively, and specificities of 99.0, 100.0, 95.4, and 99.0%, respectively. Only 108 of the infected cattle were confirmed by culture or by a commercial DNA probe (IDEXX Corporation, Portland, Maine) to be shedding the organism in fecal samples at the time of serological testing. Among the 108 M. paratuberculosis fecal shedders, the CF test, the AGID test, the Allied ELISA, and the CSL ELISA were positive for 54.6, 40.7, 65.7, and 56.5% of the cows, respectively; and among the 69 cows that were nonshedders, the tests were positive for 14.5, 4.3, 47.8, and 24.6% of the cows, respectively. There was a significant difference (P < 0.05) in the rate of positive test results for all four tests between these two groups of animals. The CF test performed well when it was compared with the other serological tests if a titer of >/- 1.8 was classified as a positive test result.
In vivo and in vitro effects of doxycycline on leucocyte membrane receptors. (1985)

Tetracyclines, particularly doxycycline, have adverse effects on granulocyte function in vitro. We have examined the effects of doxycycline on membrane receptors for IgG (Fc gamma-R) and C3b (C3b-R) on granulocytes and lymphocytes, as well as on the sheep erythrocyte receptor (E-R) on T lymphocytes. Acne patients given doxycycline orally had a lower percentage of Fc gamma-R positive granulocytes (57%) than before treatment (80%) or compared to healthy controls (81%). Following in vitro doxycycline incubation, normal granulocytes showed decreased levels of Fc gamma-R positive cells. This effect was counteracted by the addition of magnesium during incubation. The deleterious effect of doxycycline on granulocyte functions may be due to decreased levels of Fc gamma-R bearing granulocytes. Doxycycline in vivo or in vitro had no significant effect on the proportion of C3b-R bearing granulocytes or lymphocytes or the T lymphocyte percentage. After in vitro irradiation with light at 340-380 nm, however, both granulocytes and lymphocytes preincubated with doxycycline showed up to 50% decrease in Fc gamma-R bearing cells, while control cells without doxycycline were unaffected.
Thermoacoustic and Photoacoustic Tomography of Thick Biological Tissues toward Breast Imaging (2005)

Microwave-based thermoacoustic tomography (TAT) and laser-based photoacoustic tomography (PAT) in a circular scanning configuration were both developed to image deeply seated lesions and objects in biological tissues. Because malignant breast tissue absorbs microwaves more strongly than benign breast tissue, cancers were imaged with good spatial resolution and contrast by TAT in human breast mastectomy specimens. Based on the intrinsic optical contrast between blood and chicken breast muscle, an embedded blood object that was 5 cm deep in the tissue was also detected using PAT at a wavelength of 1064 nm.
Thermodynamic analysis of the lactose repressor-operator DNA interaction (1986)

Kinetic and equilibrium constants for lactose repressor-operator DNA interaction have been examined as a function of salt concentration, size and sequence context of the operator DNA, and temperature. Significant salt effects were observed on kinetic and equilibrium parameters for pLA 322-8, an operator-containing derivative of pBR 322, and pIQ, an operator and pseudooperator-containing derivative of pBR 322. The association rate constant and equilibrium constant for the 40 base pair operator fragment were also salt dependent. Data for all the DNAs were consistent with a sliding mechanism for repressor-operator association/dissociation [Berg, O. G., & Blomberg, C. (1978) Biophys. Chem. 8, 271-280]. Calculation of the number of ionic interactions based on salt dependence yielded a value of approximately 8 for repressor binding to pIQ and pLA 322-8 vs. approximately 6 for the repressor-40 base pair fragment. These data and the differences in binding parameters for the plasmids vs. the 40 base pair operator are consistent with the formation of an intramolecular ternary complex in the plasmid DNAs. Unusual biphasic temperature dependence was observed in the equilibrium and dissociation rate constants for pLA 322-8, pIQ, and the 40 base pair fragment. These observations coupled with a discontinuity found in the inducer association rate constant as a function of temperature suggest a structural change in the protein. The large positive entropy contributions associated with repressor binding to all the DNAs examined provide the significant driving force for the reaction and are consistent with involvement of ionic and apolar interactions in complex formation.
Antimicrobial Activity of Novel Dendrimeric Peptides Obtained by Phage Display Selection and Rational Modification (2005)

A large 10-mer phage peptide library was panned against whole Escherichia coli cells, and an antimicrobial peptide (QEKIRVRLSA) was selected. The peptide was synthesized in monomeric and dendrimeric tetrabranched form (multiple antigen peptide [MAP]), which generally allows a dramatic increase of peptide stability to peptidases and proteases. The antibacterial activity of the dendrimeric peptide against E. coli was much higher than that of the monomeric form. Modification of the original sequence, by residue substitution or sequence shortening, produced three different MAPs, M4 (QAKIRVRLSA), M5 (KIRVRLSA), and M6 (QKKIRVRLSA) with enhanced stability to natural degradation and antimicrobial activity against a large panel of gram-negative bacteria. The MICs of the most potent peptide, M6, were as low as 4 to 8 microg/ml against recent clinical isolates of multidrug-resistant Pseudomonas aeruginosa and members of the Enterobacteriaceae. The same dendrimeric peptides showed high stability to blood proteases, low hemolytic activity, and low cytotoxic effects on eukaryotic cells, making them promising candidates for the development of new antibacterial drugs.
Making sense from antisense: A review of experimental data and developing ideas on sense–antisense peptide recognition (1992)

Peptides encoded in the antisense strand of DNA have been predicted and found experimentally to bind to sense peptides and proteins with significant selectivity and affinity. Such sense--antisense peptide recognition has been observed in many systems, most often by detecting binding between immobilized and soluble interaction partners. Data obtained so far on sequence and solvent dependence of interaction support a hydrophobic-hydrophilic (amphipathic) model of peptide recognition. Nonetheless, the mechanistic understanding of this type of molecular recognition remains incomplete. Improving this understanding likely will require expanding the types of characteristics measured for sense--antisense peptide complexes and hence the types of analytical methods applied to such interactions. Understanding the mechanism of sense--antisense peptide recognition also may provide insights into mechanisms of native (sense) peptide and protein interactions and protein folding. Such insight may be helpful to learn how to design macromolecular recognition agents in technology for separation, diagnostics and therapeutics.
Applicatons of Ink-Jet Printing Technology to BioMEMS and Microfluidic Systems (2002)

Applications of microfluidics and MEMS (micro-electromechanical systems) technology are emerging in many areas of biological and life sciences. Non-contact microdispensing systems for accurate, high-throughput deposition of bioactive fluids can be an enabling technology for these applications. In addition to bioactive fluid dispensing, ink-jet based microdispensing allows integration of features (electronic, photonic, sensing, structural, etc.) that are not possible, or very difficult, with traditional photolithographic-based MEMS fabrication methods. Our single fluid and mutlifluid (MatrixJet™) piezoelectric microdispensers have been used for spot synthesis of peptides, production of microspheres to deliver drugs/biological materials, microprinting of biodegradable polymers for cell proliferation in tissue engineering requirements, and spot deposition for DNA, diagnostic immunoassay, antibody and protein arrays. We have created optical elements, sensors, and electrical interconnects by microdeposition of polymers and metal alloys. We have also demonstrated the integration of a reverse phase microcolumn within a piezoelectric dispenser for use in the fractionation of peptides for mass spectrometer analysis.
Nucleotide sequences and operon structure of plasmid-borne genes mediating uptake and utilization of raffinose in Escherichia coli (1989)

The plasmid-borne raf operon encodes functions required for inducible uptake and utilization of raffinose by Escherichia coli. Raf functions include active transport (Raf permease), alpha-galactosidase, and sucrose hydrolase, which are negatively controlled by the Raf repressor. We have defined the order and extent of the three structural genes, rafA, rafB, and rafD; these are contained in a 5,284-base-pair nucleotide sequence. By comparisons of derived primary structures with known subunit molecular weights and an N-terminal peptide sequence, rafA was assigned to alpha-galactosidase (708 amino acids), rafB was assigned to Raf permease (425 amino acids), and rafD was assigned to sucrose hydrolase (476 amino acids). Transcription was shown to initiate 13 nucleotides upstream of rafA; a putative promoter, a ribosome-binding site, and a transcription termination signal were identified. Striking similarities between Raf permease and lacY-encoded lactose permease, revealed by high sequence conservation (76%), overlapping substrate specificities, and similar transport kinetics, suggest a common origin of these transport systems. alpha-Galactosidase and sucrose hydrolase are not related to host enzymes but have their counterparts in other species. We propose a modular origin of the raf operon and discuss selective forces that favored the given gene organization also found in the E. coli lac operon.
Revisiting IL-2: Biology and therapeutic prospects (2018)

Interleukin-2 (IL-2), the first cytokine that was molecularly cloned, was shown to be a T cell growth factor essential for the proliferation of T cells and the generation of effector and memory cells. On the basis of this activity, the earliest therapeutic application of IL-2 was to boost immune responses in cancer patients. Therefore, it was a surprise that genetic deletion of the cytokine or its receptor led not only to the expected immune deficiency but also to systemic autoimmunity and lymphoproliferation. Subsequent studies established that IL-2 is essential for the maintenance of Foxp3<sup>+</sup> regulatory T cells (T<sub>reg</sub> cells), and in its absence, there is a profound deficiency of T<sub>reg</sub> cells and resulting autoimmunity. We now know that IL-2 promotes the generation, survival, and functional activity of T<sub>reg</sub> cells and thus has dual and opposing functions: maintaining T<sub>reg</sub> cells to control immune responses and stimulating conventional T cells to promote immune responses. It is well documented that certain IL-2 conformations result in selective targeting of T<sub>reg</sub> cells by increasing reliance on CD25 binding while compromising CD122 binding. Recent therapeutic strategies have emerged to use IL-2, monoclonal antibodies to IL-2, or IL-2 variants to boost T<sub>reg</sub> cell numbers and function to treat autoimmune diseases while dealing with the continuing challenges to minimize the generation of effector and memory cells, natural killer cells, and other innate lymphoid populations.
Data-driven visual similarity for cross-domain image matching (2011)

The goal of this work is to find visually similar images even if they appear quite different at the raw pixel level. This task is particularly important for matching images across visual domains, such as photos taken over different seasons or lighting conditions, paintings, hand-drawn sketches, etc. We propose a surprisingly simple method that estimates the relative importance of different features in a query image based on the notion of "data-driven uniqueness". We employ standard tools from discriminative object detection in a novel way, yielding a generic approach that does not depend on a particular image representation or a specific visual domain. Our approach shows good performance on a number of difficult cross-domain visual tasks e.g., matching paintings or sketches to real photographs. The method also allows us to demonstrate novel applications such as Internet re-photography , and painting2gps. While at present the technique is too computationally intensive to be practical for interactive image retrieval, we hope that some of the ideas will eventually become applicable to that domain as well.
New Clinical Color Threshold Test for Eye Disease (1987)

Selective loss of sensitivity to blue light, when it is detected by the short wavelength-sensitive cones (B cones), is a common early sign of many retinal and visual pathway disorders. A reliable clinical test is needed to allow detection of this defect. We describe a new, simple forced-choice clinical test of B cone function which is brief, reliable, and free of patient criteria for seeing. Test results are relatively unaltered by up to 2 D of uncorrected refractive error and the usual small fixation changes the patient makes during the test. A comparison of three different test results, all obtained within 5 min, allows measurement of R and/or G cone function free of age and individual differences caused by yellowing of the ocular media in the B cone test result. The test has been used to demonstrate B cone sensitivity losses related to the severity of retinopathy in 60 diabetics, as well as selective B cone loss in glaucoma and ocular hypertension.
Optimization of phase change RAM write performance for large memory array (2008)

This paper analyzes the crystallization statistics and optimizes the performance of complex doped GST on 256 kb memory arrays in 180 nm CMOS technology. A novel method of deriving an optimized SET strategy from the RESET current distribution is developed. This significantly improves performance and results in 200 ns SET time. A large Rreset/Rset ratio can be maintained even after 8E6 cycles.
Ultra-thin TEM Sample Preparation with Advanced Backside FIB Milling Method (2010)

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.
“没有乐队，但我们却听到了一文乐队”——《马尔霍兰车道》中戴维·林奇对连贯性的逆转 (2005)

(2001)这部从首映之日起就令观众困惑不已的影片中,戴维·林奇成功地将连贯性逆转,通过服从于非逻辑的时空、心理和语言条件的意义(直觉的和情感的感知)营造出影片人物和超现实主义世界的传统意义(逻辑).尽管批评家就能否从中推导出逻辑的意义这一问题存有分歧,但意见对立的双方,在认真研究和反复观看影片时,不是无意忽略就是有意掩饰了林奇对未知领域以及对于语言结构的不信任所表现出的美学兴趣.这方面的缺失,使林奇及其影片损失巨大,事实是否如此尚可争辩.在观看时,考虑到林奇对于意义话语的美学原则是很重要的,这会为他如何将传统逻辑话语服从于非逻辑话语的过程提供一个缜密的解读.本文要仔细研究的是丽塔(劳拉·埃琳娜·哈林饰)这个人物以及作为延迟范例的寂静俱乐部场景.这些范例能使我们看到,只要领会了林奇的美学标准,就可以更充分地评价和理解中的超现实世界,在那个世界中,关于真实,是通过未知的一切--直觉和情感话语的流动和有节奏的推进--被感知(感觉和知道)的.这些可以被理解为矛盾或无意义,理解为象征语言的缺席--概念界线的模糊.
Regulation of Vascular Endothelial Growth Factor in Cardiac Myocytes (1995)

Collateral blood vessels supplement normal coronary blood flow and coronary blood flow compromised by coronary artery disease, thereby protecting the myocardium from ischemia. Collateral vessel formation is the result of angiogenesis. Vascular endothelial growth factor (VEGF), also known as vascular permeability factor (VPF), is a secreted mitogen specific for endothelial cells and an extremely potent angiogenic factor. In the present study, VPF/VEGF mRNA and protein were demonstrated to be markedly stimulated in primary rat cardiac myocytes in vitro in response to reduction of the oxygen tension to 1% or inhibition of the electron transport chain. Four isoforms of VPF/VEGF were coordinately regulated by hypoxia, including a novel isoform not previously described. Phorbol ester and the depolarizing agent veratridine, stimulators of protein kinase C and calcium influx, respectively, were found to markedly increase VPF/VEGF mRNA expression in cardiac myocytes. Forskolin, a potent stimulator of adenylate cyclase, produced a small but significant increase in VPF/VEGF mRNA expression in the cardiac myocytes. However, only H7, an inhibitor of protein kinase C, inhibited the hypoxic induction of VPF/VEGF mRNA; inhibitors of calcium influx and the calcium-calmodulin-dependent protein kinase II as well as inhibition of protein kinase A did not block the hypoxic induction of VPF/VEGF mRNA. This suggests that more than one signal transduction pathway is involved in regulating VPF/VEGF expression. The sensor that regulates the expression of hypoxia-responsive genes has been proposed to be a heme protein. Consistent with this model, transition metals initiate a genetic program similar to hypoxia.(ABSTRACT TRUNCATED AT 250 WORDS)
Elements of the smooth muscle alpha-actin promoter required in cis for transcriptional activation in smooth muscle. Evidence for cell type-specific regulation. (1992)

To assess the role of cis-acting elements within the smooth muscle alpha-actin gene in smooth muscle cells (SMC), we transfected chicken smooth muscle alpha-actin promoter-chloramphenicol acetyltransferase gene fusion plasmids into SMC derived from rat and chicken aortas. In marked contrast to effects in chicken skeletal myoblasts and fibroblasts, p122CAT (positions -122 to +19), containing two conserved CArG elements, elicited a modest increase in chloramphenicol acetyltransferase reporter activity in chicken SMC. Addition of upstream sequences between -122 and -151 (p151CAT) increased activity in adult chicken SMC. Addition of sequence between positions -151 and -257 (p257CAT) resulted in a 7-fold increase in chloramphenicol acetyltransferase activity over that of p151CAT in rat SMC, but not in chicken SMC. A genomic clone encoding the rat smooth muscle alpha-actin gene was isolated, and the 5'-flanking region was partially characterized. Comparison of primary sequence between rat and chicken promoters showed a conserved E box motif at position -214 in the chicken gene and at position -213 in the rat gene. Results of these studies demonstrate that regions upstream of the conserved CArG elements exert potent regulatory effects on transcription and that SMC require different cis-acting elements than other cell types to transcriptionally regulate this gene.