gebhart/patrepeval huggingface dataset:
Phase Stability Technique for Inverse Scattering in Optical Coherence Tomography (2006)

We present a technique for maintaining phase stability in a three-dimensional optical coherence tomography system. When determining the inverse scattering solution, phase stable measurements are required to ensure proper object reconstruction. The proposed method uses a reference object placed above the specimen to facilitate the retrieval of accurate constant phase surfaces throughout the specimen. Our algorithm locates the reference object, determines the phase and group delay, and corrects the phase disturbance accordingly
Detection of Autoantibodies to Thyroid Peroxidase in Autoimmune Thyroid Diseases by Micro-ELISA and Immunoblotting* (1986)

Serum autoantibodies to thyroid peroxidase (TPO) in patients with thyroid autoimmune diseases were studied by micro-ELISA and immunoblotting. Twenty-four patients, 15 with Graves' disease and 9 with Hashimoto's thyroiditis, whose serum titers were greater than 3200 on the microsomal hemagglutination test (except for 1 patient with a titer of 800) had autoantibodies to TPO. Both immunoglobulin G and M classes of autoantibodies were detected, with the former being more prominent. When TPO and thyroid microsomes were used as a target in a competitive binding inhibition test, the results suggested that TPO was a major thyroid microsomal antigen. On the other hand, immunoblotting analysis showed 3-4 bands in the 45-60K region stained by patients' sera in addition to human TPO with mol wt of 100K and 107K; only the latter 2 bands stained with antiporcine TPO antibody. In the majority of sera, TPO bands were clearer than others, although some sera showed the clearest band with a mol wt of 55K. These results indicate that patients with autoimmune thyroid disease often have autoantibodies to TPO that can be detected by micro-ELISA and immunoblotting, and that TPO is a major component of the thyroid microsomal antigen.
Mutational analysis of the active centre of coronavirus 3C-like proteases (2002)

Formation of the coronavirus replication-transcription complex involves the synthesis of large polyprotein precursors that are extensively processed by virus-encoded cysteine proteases. In this study, the coding sequence of the feline infectious peritonitis virus (FIPV) main protease, 3CL(pro), was determined. Comparative sequence analyses revealed that FIPV 3CL(pro) and other coronavirus main proteases are related most closely to the 3C-like proteases of potyviruses. The predicted active centre of the coronavirus enzymes has accepted unique replacements that were probed by extensive mutational analysis. The wild-type FIPV 3CL(pro) domain and 25 mutants were expressed in Escherichia coli and tested for proteolytic activity in a peptide-based assay. The data strongly suggest that, first, the FIPV 3CL(pro) catalytic system employs His(41) and Cys(144) as the principal catalytic residues. Second, the amino acids Tyr(160) and His(162), which are part of the conserved sequence signature Tyr(160)-Met(161)-His(162) and are believed to be involved in substrate recognition, were found to be indispensable for proteolytic activity. Third, replacements of Gly(83) and Asn(64), which were candidates to occupy the position spatially equivalent to that of the catalytic Asp residue of chymotrypsin-like proteases, resulted in proteolytically active proteins. Surprisingly, some of the Asn(64) mutants even exhibited strongly increased activities. Similar results were obtained for human coronavirus (HCoV) 3CL(pro) mutants in which the equivalent Asn residue (HCoV 3CL(pro) Asn(64)) was substituted. These data lead us to conclude that both the catalytic systems and substrate-binding pockets of coronavirus main proteases differ from those of other RNA virus 3C and 3C-like proteases.
Mutagenesis of the Bacterial RNA Polymerase Alpha Subunit for Improvement of Complex Phenotypes (2009)

Combinatorial or random methods for strain engineering have been extensively used for the improvement of multigenic phenotypes and other traits for which the underlying mechanism is not fully understood. Although the preferred method has traditionally been mutagenesis and selection, our laboratory has successfully used mutant transcription factors, which direct the RNA polymerase (RNAP) during transcription, to engineer complex phenotypes in microbial cells. Here, we show that it is also possible to impart new phenotypes by altering the RNAP core enzyme itself, in particular through mutagenesis of the alpha subunit of the bacterial polymerase. We present the use of this tool for improving tolerance of Escherichia coli to butanol and other solvents and for increasing the titers of two commercially relevant products, L-tyrosine and hyaluronic acid. In addition, we explore the underlying physiological changes that give rise to the solvent-tolerant mutant.
Serologic Evidence of Brucella and Pseudorabies in Mississippi Feral Swine (2012)

Feral swine (Sus scrofa) are an ever-increasing problem across the United States. Besides physical environmental damage that they cause, they may harbor and transmit a number of pathogens to humans, livestock, and other domestic animals. We sampled feral swine across the state of Mississippi for titers to several diseases. Antibodies against Brucella were found in 16 of 499 (3.2%) feral swine, and antibodies against pseudorabies (porcine herpes virus, type 1; Herpesveridae sp.) virus were identified in 37 of 499 (7.4%) feral swine from across the state of Mississippi. Evidence of classical swine fever, African swine fever, swine influenza, and foot-and-mouth disease were not identified in any of the feral swine examined.
Membrane potential measurements in renal afferent and efferent arterioles: actions of angiotensin II (1997)

An adaptation of the in vitro perfused hydronephrotic rat kidney model allowing in situ measurement of arteriolar membrane potentials is described. At a renal perfusion pressure of 80 mmHg, resting membrane potentials of interlobular arteries (22 +/- 2 microns) and afferent (14 +/- 1 microns) and efferent arterioles (12 +/- 1 microns) were -40 +/- 2 (n = 8), -40 +/- 1 (n = 45), and -38 +/- 2 mV (n = 22), respectively (P = 0.75). Using a dual-pipette system to stabilize the impalement site, we measured afferent and efferent arteriolar membrane potentials during angiotensin II (ANG II)-induced vasoconstriction. ANG II (0.1 nM) reduced afferent arteriolar diameters from 13 +/- 1 to 8 +/- 1 microns (n = 8, P = 0.005) and membrane potentials from -40 +/- 2 to -29 +/- mV (P = 0.012). ANG II elicited a similar vasoconstriction in efferent arterioles, decreasing diameters from 13 +/- 1 to 8 +/- 1 microns (n = 8, P = 0.004), but failed to elicit a significant depolarization (-39 +/- 2 for control; -36 +/- 3 mV for ANG II; P = 0.27). Our findings thus indicate that resting membrane potentials of pre- and postglomerular arterioles are similar and lie near the threshold activation potential for L-type Ca channels. ANG II-induced vasoconstriction appears to be closely coupled to membrane depolarization in the afferent arteriole, whereas mechanical and electrical responses appear to be dissociated in the efferent arteriole.
Lack of Replicative Senescence in Cultured Rat Oligodendrocyte Precursor Cells (2001)

Most mammalian somatic cells are thought to have a limited proliferative capacity because they permanently stop dividing after a finite number of divisions in culture, a state termed replicative cell senescence. Here we show that most oligodendrocyte precursor cells purified from postnatal rat optic nerve can proliferate indefinitely in serum-free culture if prevented from differentiating; various cell cycle-inhibitory proteins increase, but the cells do not stop dividing. The cells maintain high telomerase activity and p53- and Rb-dependent cell cycle checkpoint responses, and serum or genotoxic drugs induce them to acquire a senescence-like phenotype. Our findings suggest that some normal rodent precursor cells have an unlimited proliferative capacity if cultured in conditions that avoid both differentiation and the activation of checkpoint responses that arrest the cell cycle.
Adenosine inhibits platelet-activating factor, but not tumour necrosis factor-alpha-induced priming of human neutrophils. (1993)

Regulation of the respiratory burst and its priming by recombinant human tumour necrosis factor-alpha (rhTNF-alpha) and platelet-activating factor (PAF) were investigated in human polymorphonuclear leucocytes (PMN). Adenosine (0.1-10 microM) pretreatment of PMN concentration-dependently inhibited the superoxide anion generation (O2-) in response to formyl-methionyl-leucyl-phenylalanine (FMLP). The priming by PAF (1 microM) for an increased O2- generation by FMLP-stimulated PMN was completely blocked by adenosine pretreatment. In contrast, rhTNF-alpha-induced priming was unaffected by adenosine. In addition, the direct stimulation of PMN O2- by rhTNF-alpha was also unaffected by adenosine as was rhTNF-alpha-induced PAF synthesis. FMLP-induced PAF synthesis was reduced by adenosine to a similar extent as the inhibition of the respiratory burst. Adenosine also inhibited PAF-, but not FMLP-induced increases in intracellular calcium in PMN. These findings indicate that short-term, direct stimulants (FMLP) or priming agents (PAF) are subject to modulation by the endothelial product adenosine, whereas the priming and direct stimulation of the respiratory burst by the longer-acting agent, rhTNF-alpha is unaffected. Moreover, differential inhibition of PMN activation by adenosine reveals important functional differences in the signalling mechanisms initiated by PAF, FMLP and rhTNF-alpha.
Functional Polymeric Microparticles Engineered from Controllable Microfluidic Emulsions (2013)

Functional polymeric microparticles with typical sizes of 1-1000 μm have received considerable attention for many applications. Especially in biomedical fields, polymeric microparticles with advanced functions such as targeted delivery, controlled encapsulation, or "capture and release" show great importance as delivery systems for active molecules and drugs, as imaging agents for analytics and diagnostics, as microreactors for confined bioreactions, and more. Generally, the functions of these microparticles rely on both their structures and the properties of their component materials. Thus, creating unique structures from functional materials provides an important strategy for developing advanced functional polymeric microparticles. Several methods, such as dispersion polymerization, precipitation polymerization, copolymer self-assembly, and phase-separated polymer precipitation can be used to make functional microparticles, but each has limitations, for example, their limited control over the particle size and structure. Using emulsions as templates, however, allows precise control over the size, shape, composition, and structure of the resulting microparticles by tuning those of the emulsions via specific emulsification techniques. Microfluidic methods offer excellent control of emulsion droplets, thereby providing a powerful platform for continuous, reproducible, scalable production of polymeric microparticles with unprecedented control over their monodispersity, structures, and compositions. This approach provides broad opportunities for producing polymeric microparticles with novel structure-property combinations and elaborately designed functions. In this Account, we highlight recent efforts in microfluidic fabrication of advanced polymeric microparticles with well-designed functions for potential biomedical applications, and we describe the development of microfluidic techniques for producing monodisperse and versatile emulsion templates. We begin by describing microparticles made from single emulsions and then describe those from complex multiple emulsions, showing how the resulting microparticles combine novel structures and material properties to achieve their advanced functions. Monodisperse emulsions enable production of highly uniform microparticles of desired sizes to achieve programmed release rates and passive targeting for drug delivery and diagnostic imaging. Phase-separated multiple emulsions allow combination of a variety of functional materials to generate compartmental microparticles including hollow, core-shell, multicore-shell, and hole-shell structures for controlled encapsulation and release, selective capture, and confined bioreaction. We envision that the versatility of microfluidics for microparticle synthesis could open new frontiers and provide promising and exciting opportunities for fabricating new functional microparticles with broad implications for myriad fields.
Complex regulation of csgD promoter activity by global regulatory proteins (2003)

The starvation-induced csgD gene of Salmonella typhimurium encodes for the positive transcriptional regulator of extracellular matrix components curli fimbriae and cellulose. To analyse regulatory elements of csgD promoter (PcsgD) response genetic studies combined with in vitro experiments were performed. Six binding sites (D1 to D6) for OmpR, a transcriptional regulator, were identified by gel shifts and DNase I footprints. While ompR is required for PcsgD expression, binding of OmpR-P to D2 centred immediately upstream of D1 at position -70.5 is proposed to repress PcsgD activity. The elevated expression of regulated and semiconstitutive PcsgD in response to microaerophilic conditions required integration host factor (IHF). Subsequently, two IHF-binding sites were identified up- and downstream of PcsgD. IHF competes with OmpR-P for binding at its upstream site IHF1, which overlaps with D3-D6 and thereby modulates the response to microaerophilic conditions. A complex regulatory network involving IHF, H-NS and OmpR is proposed whereby the nucleo-complex composition in the csgD-csgBA intergenic region is altered in response to oxygen tension.
The alpha v beta 1 integrin functions as a fibronectin receptor but does not support fibronectin matrix assembly and cell migration on fibronectin (1993)

The fibronectin receptor, alpha 5 beta 1, has been shown to be required for fibronectin matrix assembly and plays an important role in cell migration on fibronectin. However, it is not clear whether other fibronectin binding integrins can take the place of alpha 5 beta 1 during matrix assembly and cell migration. To test this, we expressed the human alpha v subunit in the CHO cell line CHO-B2 that lacks the alpha 5 subunit. We found that the human alpha v combined with CHO cell beta 1 to form the integrin alpha v beta 1. Cells that expressed alpha v beta 1 attached to and spread well on fibronectin-coated dishes, but did so less well on vitronectin-coated dishes. This, along with other data, indicated that alpha v beta 1 functions as a fibronectin receptor in CHO-B2 cells. The alpha v beta 1-expressing cells failed to produce a fibronectin matrix or to migrate on fibronectin, although the same cells transfected with alpha 5 do produce a matrix and migrate on fibronectin. The affinity of the alpha v beta 1-expressing cells for fibronectin was fourfold lower than that of the alpha 5 beta 1-expressing cells. In addition, alpha v beta 1 was distributed diffusely throughout the cell surface, whereas alpha 5 beta 1 was localized to focal adhesions when cells were seeded onto fibronectin-coated surfaces. Thus, of the two fibronectin receptors, alpha v beta 1 and alpha 5 beta 1, only alpha 5 beta 1 supports fibronectin matrix assembly and promotes cell migration on fibronectin in the CHO-B2 cells. Possible reasons for this difference in the activities of alpha v beta 1 and alpha 5 beta 1 include the lower affinity of alpha v beta 1 for fibronectin and the failure of this integrin to localize in adhesion plaques on a fibronectin substrate. These results show that two integrins with similar ligand specificities and cell attachment functions may be quite different in their ability to support fibronectin matrix assembly and cell motility on fibronectin.
Gram-scale synthesis and crystal structures of [8]- and [10]CPP, and the solid-state structure of C60@[10]CPP (2012)

A cost-effective gram-scale synthesis of [8]- and [10]cycloparaphenylenes (CPPs) has been developed for the first time. Both [8]- and [10]cycloparaphenylene organized into herringbone geometries in the crystalline state with well-defined cylindrical cavities of 1.1 and 1.4 nm, respectively. With large amounts of material available, the highly efficient convex–concave π–π interactions between [10]CPP and C60 in the solid-state was validated by X-ray diffraction analysis.
Highly Specific Electrochemical Analysis of Cancer Cells using Multi‐Nanoparticle Labeling (2014)

Circulating tumor cells (CTCs) can be collected noninvasively and provide a wealth of information about tumor phenotype. For this reason, their specific and sensitive detection is of intense interest. Herein, we report a new, chip-based strategy for the automated analysis of cancer cells. The nanoparticle-based, multi-marker approach exploits the direct electrochemical oxidation of metal nanoparticles (MNPs) to report on the presence of specific surface markers. The electrochemical assay allows simultaneous detection of multiple different biomarkers on the surfaces of cancer cells, enabling discrimination between cancer cells and normal blood cells. Through multiplexing, it further enables differentiation among distinct cancer cell types. We showcase the technology by demonstrating the detection of cancer cells spiked into blood samples.
Large vocabulary recognition of on-line handwritten cursive words (1996)

This paper presents a writer independent system for large vocabulary recognition of on-line handwritten cursive words. The system first uses a filtering module, based on simple letter features, to quickly reduce a large reference dictionary (lexicon) to a more manageable size; the reduced lexicon is subsequently fed to a recognition module. The recognition module uses a temporal representation of the input, instead of a static two-dimensional image, thereby preserving the sequential nature of the data and enabling the use of a Time-Delay Neural Network (TDNN); such networks have been previously successful in the continuous speech recognition domain. Explicit segmentation of the input words into characters is avoided by sequentially presenting the input word representation to the neural network-based recognizer. The outputs of the recognition module are collected and converted into a string of characters that is matched against the reduced lexicon using an extended Damerau-Levenshtein function. Trained on 2,443 unconstrained word images (11 k characters) from 55 writers and using a 21 k lexicon we reached a 97.9% and 82.4% top-5 word recognition rate on a writer-dependent and writer-independent test, respectively.
Plasmon-resonant gold nanorods as low backscattering albedo contrast agents for optical coherence tomography (2006)

Plasmon-resonant gold nanorods are demonstrated as low backscattering albedo contrast agents for optical coherence tomography (OCT). We define the backscattering albedo, a', as the ratio of the backscattering to extinction coefficient. Contrast agents which modify a' within the host tissue phantoms are detected with greater sensitivity by the differential OCT measurement of both a' and extinction. Optimum sensitivity is achieved by maximizing the difference between contrast agents and tissue, |a'(ca) - a'(tiss)|. Low backscattering albedo gold nanorods (14x 44 nm; lambda(max) = 780 nm) within a high backscattering albedo tissue phantom with an uncertainty in concentration of 20% (randomized 2+/-0.4% intralipid) were readily detected at 82 ppm (by weight) in a regime where extinction alone could not discriminate nanorods. The estimated threshold of detection was 30 ppm.
Intrinsic Features in MicroRNA Transcriptomes Link Porcine Visceral Rather than Subcutaneous Adipose Tissues to Metabolic Risk (2013)

MicroRNAs (miRNAs) are non-coding small RNA ∼22 nucleotides in length that can regulate the expression of a wide range of coding genes at the post-transcriptional level. Visceral adipose tissues (VATs) and subcutaneous adipose tissues (SATs), the two main fat compartments in mammals, are anatomically, physiologically, metabolically, and clinically distinct. Various studies of adipose tissues have focused mainly on DNA methylation, and mRNA and protein expression, nonetheless little research sheds directly light on the miRNA transcriptome differences between these two distinct adipose tissue types. Here, we present a comprehensive investigation of miRNA transcriptomes across six variant porcine adipose tissues by small RNA-sequencing. We identified 219 known porcine miRNAs, 97 novel miRNA*s, and 124 miRNAs that are conserved to other mammals. A set of universally abundant miRNAs (i.e., miR-148a-3p, miR-143-3p, miR-27b-3p, miR-let-7a-1-5p, and miR-let-7f-5p) across the distinct adipose tissues was found. This set of miRNAs may play important housekeeping roles that are involved in adipogenesis. Clustering analysis indicated significant variations in miRNA expression between the VATs and SATs, and highlighted the role of the greater omentum in responding to potential metabolic risk because of the observed enrichment in this tissue of the immune- and inflammation-related miRNAs, such as the members of miR-17-92 cluster and miR-181 family. Differential expression of the miRNAs between the VATs and SATs, and miRNA target prediction analysis revealed that the VATs-specific enriched miRNAs were associated mainly with immune and inflammation responses. In summary, the differences of miRNA expression between the VATs and SATs revealed some of their intrinsic differences and indicated that the VATs might be closely associated with increased risk of metabolic disorders.
cDNA Cloning and Characterization of the Human Interleukin 13 Receptor α Chain (1996)

We have cloned cDNAs corresponding to the human interleukin 13 receptor alpha chain (IL-13Ralpha). The protein has 76% homology to murine IL-13Ralpha, with 95% amino acid identity in the cytoplasmic domain. Only weak IL-13 binding activity was found in cells transfected with only IL-13Ralpha; however, the combination of both IL-13Ralpha and IL-4Ralpha resulted in substantial binding activity, with a Kd of approximately 400 pM, indicating that both chains are essential components of the IL-13 receptor. Whereas IL-13Ralpha serves as an alternative accessory protein to the common cytokine receptor gamma chain (gammac) for IL-4 signaling, it could not replace the function of gammac in allowing enhanced IL-2 binding activity. Nevertheless, the overall size and length of the cytoplasmic domain of IL-13Ralpha and gammac are similar, and like gammac, IL-13Ralpha is located on chromosome X.
The Incidence of Transfusion-Associated Hepatitis G Virus Infection and Its Relation to Liver Disease (1997)

HGV was common in a group of volunteer blood donors, and it can be transmitted by transfusion. Most HGV infections were not associated with hepatitis. HGV did not worsen the course of concurrent HCV infection. No causal relation between HGV and hepatitis has been established.
An XML framework for agent-based E-commerce (1999)

ommerceNet's eCo System initiative, launched in 1996, aims to transform the World-Wide Web into an agent-based infrastructure for Internet commerce.