gebhart/patrepeval huggingface dataset:
Ex vivo culture of circulating breast tumor cells for individualized testing of drug susceptibility (2014)

Circulating tumor cells (CTCs) are present at low concentrations in the peripheral blood of patients with solid tumors. It has been proposed that the isolation, ex vivo culture, and characterization of CTCs may provide an opportunity to noninvasively monitor the changing patterns of drug susceptibility in individual patients as their tumors acquire new mutations. In a proof-of-concept study, we established CTC cultures from six patients with estrogen receptor-positive breast cancer. Three of five CTC lines tested were tumorigenic in mice. Genome sequencing of the CTC lines revealed preexisting mutations in the PIK3CA gene and newly acquired mutations in the estrogen receptor gene (ESR1), PIK3CA gene, and fibroblast growth factor receptor gene (FGFR2), among others. Drug sensitivity testing of CTC lines with multiple mutations revealed potential new therapeutic targets. With optimization of CTC culture conditions, this strategy may help identify the best therapies for individual cancer patients over the course of their disease.
Arthritis in rats after systemic injection of streptococcal cells or cell walls. (1977)

Further investigation of the biological properties of streptococcal cells and their components has produced a model of erosive synovitis in rats. A single intraperitoneal injection of an aqueous suspension of whole cell sonicate of group A streptococci into Sprague-Dawley rats induced an acute arthritis which evolved into a prolonged inflammatory process characterized by several complete or partial remissions, joint deformity, and ankylosis. The toxic moiety is a peptidoglycan-polysaccharide fragment of the cell wall which persists in tissue. Histologic features of the arthritis include an acute exudative phase followed by an erosive synovitis that leads to destruction of cartilage and subchondral bone and fibrous ankylosis of the joints. The arthropathic properties of whole cell sonicates of several species of streptococci are compared along with studies of the ability of heat-killed, whole cells of groups A, B, and C streptococci to induce arthritis in rats. Whole cells induce arthritis after a latent period of 57-120 days when group A cells are injected and 7-10 days when group B cells are tested.
A molecular linkage map of tomato displaying chromosomal locations of resistance gene analogs based on a<i>Lycopersicon esculentum</i>×<i>Lycopersicon hirsutum</i>cross (2002)

A molecular linkage map of tomato was constructed based on a BC1 population (N = 145) of a cross between Lycopersicon esculentum Mill. line NC84173 (maternal and recurrent parent) and Lycopersicon hirsutum Humb. and Bonpl. accession PI126445. NC84173 is an advanced breeding line that is resistant to several tomato diseases, not including early blight (EB) and late blight (LB). PI126445 is a self-incompatible accession that is resistant to many tomato diseases, including EB and LB. The map included 142 restriction fragment length polymorphism (RFLP) markers and 29 resistance gene analogs (RGAs). RGA loci were identified by PCR amplification of genomic DNA from the BC1 population, using ten pairs of degenerate oligonucleotide primers designed based on conserved leucine-rich repeat (LRR), nucleotide binding site (NBS), and serine (threonine) protein kinase (PtoKin) domains of known resistance genes (R genes). The PCR-amplified DNAs were separated by denaturing polyacrylamide gel electrophoresis (PAGE), which allowed separation of heterogeneous products and identification and mapping of individual RGA loci. The map spanned 1469 cM of the 12 tomato chromosomes with an average marker distance of 8.6 cM. The RGA loci were mapped to 9 of the 12 tomato chromosomes. Locations of some RGAs coincided with locations of several known tomato R genes or quantitative resistance loci (QRLs), including Cf-1, Cf-4, Cf-9, Cf-ECP2, rx-1, and Cm1.1 (chromosome 1); Tm-1 (chromosome 2); Asc (chrromosme 3); Pto, Fen, and Prf (chromosome 5); 01-1, Mi, Ty-1, Cm6.1, Cf-2, CF-5, Bw-5, and Bw-1 (chromosome 6); I-1, 1-3, and Ph-1 (chromosome 7); Tm-2a and Fr1 (chromosome 9); and Lv (chromosome 12). These co-localizations indicate that the RGA loci were either linked to or part of the known R genes. Furthermore, similar to that for many R gene families, several RGA loci were found in clusters, suggesting their potential evolutionary relationship with R genes. Comparisons of the present map with other molecular linkage maps of tomato, including the high density L. esculentum x Lycopersicon pennellii map, indicated that the lengths of the maps and linear order of RFLP markers were in good agreement, though certain chromosomal regions were less consistent than others in terms of the frequency of recombination. The present map provides a basis for identification and mapping of genes and QTLs for disease resistance and other desirable traits in PI126445 and other L. hirsutum accessions, and will be useful for marker-assisted selection and map-based gene cloning in tomato.
Parametric down-conversion photon-pair source on a nanophotonic chip (2016)

Quantum-photonic chips, which integrate quantum light sources alongside active and passive optical elements, as well as single-photon detectors, show great potential for photonic quantum information processing and quantum technology. Mature semiconductor nanofabrication processes allow for scaling such photonic integrated circuits to on-chip networks of increasing complexity. Second-order nonlinear materials are the method of choice for generating photonic quantum states in the overwhelming majority of linear optic experiments using bulk components, but integration with waveguide circuitry on a nanophotonic chip proved to be challenging. Here, we demonstrate such an on-chip parametric down-conversion source of photon pairs based on second-order nonlinearity in an aluminum-nitride microring resonator. We show the potential of our source for quantum information processing by measuring the high visibility anti-bunching of heralded single photons with nearly ideal state purity. Our down-conversion source yields measured coincidence rates of 80 Hz, which implies MHz generation rates of correlated photon pairs. Low noise performance is demonstrated by measuring high coincidence-to-accidental ratios. The generated photon pairs are spectrally far separated from the pump field, providing great potential for realizing sufficient on-chip filtering and monolithic integration of quantum light sources, waveguide circuits and single-photon detectors.
Cyclooxygenase is an immediate-early gene induced by interleukin-1 in human endothelial cells. (1990)

The monokine interleukin-1 (IL-1) inhibits endothelial cell growth and induces prostacyclin production in human endothelial cells. Since cyclooxygenase (Cox) is the rate-limiting enzyme in the synthesis of prostanoids, we evaluated the ability of IL-1 to stimulate Cox expression by human umbilical vein endothelial cells (HUVEC) in vitro. Our data demonstrate that 1) the Cox mRNA is expressed at low levels in untreated cells; 2) IL-1 alpha induces the Cox mRNA within 2 h, and this induction is sustained for more than 24 h; 3) IL-1 alpha induction is dose-dependent; 4) cycloheximide potentiates the induction of the Cox mRNA by IL-1 alpha while actinomycin D prevents the induction, and 5) IL-1 alpha also stimulates Cox production in a time-dependent fashion which correlates with the increase in prostacyclin synthesis. These data suggest that Cox is an immediate-early gene induced by IL-1 in HUVEC and may contribute to the regulation of the endothelial cell differentiation pathway in vitro.
A seamless handover scheme in LISP networks (2013)

The Locator Identifier Separation Protocol (LISP) has been made as an identifier-locator separation scheme. However, the issue of handover for mobile host is still a serious challenge in LISP. The existing LISP-based handover schemes tend to induce large handover delay and packet loss. To overcome such problems, we propose a new handover control scheme, in which the Map Request and Reply messages are exchanged between old access router and new access router after handover. Then, the locator update operation is performed so as to provide the route optimization. From the ns-2 simulation results, it is shown that the proposed scheme can give better performance than the existing LISP-based schemes in terms of handover delay and throughput.
Characterization of the Interaction of Sclerostin with the Low Density Lipoprotein Receptor-related Protein (LRP) Family of Wnt Co-receptors (2012)

LRP5 and LRP6 are proteins predicted to contain four six-bladed β-propeller domains and both bind the bone-specific Wnt signaling antagonist sclerostin. Here, we report the crystal structure of the amino-terminal region of LRP6 and using NMR show that the ability of sclerostin to bind to this molecule is mediated by the central core of sclerostin and does not involve the amino- and carboxyl-terminal flexible arm regions. We show that this structured core region interacts with LRP5 and LRP6 via an NXI motif (found in the sequence PNAIG) within a flexible loop region (loop 2) within the central core region. This sequence is related closely to a previously identified motif in laminin that mediates its interaction with the β-propeller domain of nidogen. However, the NXI motif is not involved in the interaction of sclerostin with LRP4 (another β-propeller containing protein in the LRP family). A peptide derived from the loop 2 region of sclerostin blocked the interaction of sclerostin with LRP5/6 and also inhibited Wnt1 but not Wnt3A or Wnt9B signaling. This suggests that these Wnts interact with LRP6 in different ways.
Selective recognition of cyclic RGD peptides of NMR defined conformation by alpha IIb beta 3, alpha V beta 3, and alpha 5 beta 1 integrins. (1994)

The binding of purified fibrinogen receptor alpha IIb beta 3, vitronectin receptor alpha V beta 3, and fibronectin receptor alpha 5 beta 1 to their corresponding ligands in solid-phase binding assays was used to examine the inhibitory activity of various linear and cyclic penta- and hexapeptides of different conformation containing RGD or RAD sequences. Cyclic peptides with different defined backbone conformations were designed by introducing a single D-amino acid or a proline at different positions in the ring. The data were calibrated for alpha IIb beta 3 integrin incorporated into a planar lipid bilayer by a physical method (total internal reflection fluorescence microscopy) which yielded KD = 1.7 microM for a linear RGD peptide and KD = 0.03 microM for fibrinogen. With this integrin, three cyclic hexapeptides ([GRGDFL], [ARGDFV], [GRGDFV]) were 2-4-fold more inhibitory than the linear GRGDS peptide in solid-phase assays and showed similar inhibition as the fibrinogen ligand. Six peptides had the same or a 2-fold lower activity as the linear reference peptide, and three peptides were up to 7-fold less active. Replacement of Arg or Asp by their stereoisomers or Gly by Ala resulted in a 100-1000-fold reduction in activity. With the two other integrins, a single cyclic pentapeptide [RGDFV] was 10-fold more active (alpha V beta 3) or equal in activity (alpha 5 beta 1) to linear GRGDS, while all of the other cyclic peptides were moderately or distinctly less active. Changes in the RGD sequence caused a less dramatic reduction in binding strength for alpha V beta 3 and alpha 5 beta 1 than for alpha II beta 3. Inhibitory activity was compared with the distance between the C beta atoms of Arg and Asp residues as determined by NMR and indicated that the optimum distance is in the range of 0.75-0.85 nm for alpha IIb beta 3 and at or below 0.67 nm for alpha V beta 3 and alpha 5 beta 1. This indicates that alpha IIb beta 3 less sensitive to variations in the RGD backbone structure and can accommodate a larger distance than the integrins alpha V beta 3 and alpha 5 beta 1.
Preparation of  Y 3Al5 O 12 ‐ Based Phosphor Powders (1987)

Phosphor materials are important in cathode ray tube (CRT) and electroluminescence display technologies. Phosphor materials based on garnet are used extensively because of their high optical emission intensity and long life. In this study, we prepared cerium‐doped YAG powders by freeze drying of precursor solutions and by mechanically mixing the constituent oxide powders. The freeze dried powders, due to a homogeneous distribution of cations in their precursor solutions, formed the garnet phase at 1300°C, 300°C lower than that required for the constituent oxide mixtures, and they also had a higher optical emission intensity than those prepared from oxide mixtures. Furthermore, Ce‐doped powder was heat‐treated in molten salt to increase the particle size and to give a more equiaxed particle shape such that their subsequent packing density in CRT faceplate could be increased. However, the molten salt treatment introduced a small amount of the distorted tetragonal phase among the cubic garnet phase and decreased the optical emission intensity.
Understanding Zika Virus Stability and Developing a Chimeric Vaccine through Functional Analysis (2017)

Analysis of a recently observed high-resolution structure of ZIKV led to a hypothesis that its unusual stability may contribute to the associated, unique disease outcomes. Here we performed a functional analysis to demonstrate that viral prM-E genes are the main determinants for the high stability of ZIKV. The extra hydrogen-bond interaction (observed in the high-resolution structure) between ZIKV E proteins did not enhance virion stability, whereas the extended loop of E protein (CD loop in domain III) was essential for ZIKV assembly. More importantly, we found that a chimeric ZIKV with DENV-2 prM-E genes and a chimeric DENV-2 with ZIKV prM-E genes were highly attenuated in A129 mice. Mice immunized with these chimeric viruses generated robust neutralizing antibody responses and were fully protected from DENV-2 and ZIKV challenge, respectively, indicating that these chimeric viruses could be further developed as vaccine candidates.
Retinoblastoma Gene Promoter Directs Transgene Expression Exclusively to the Nervous System (2001)

In human, germ line mutations in the tumor suppressor retinoblastoma (Rb) predispose individuals to retinoblastoma, whereas somatic inactivation of Rb contributes to the progression of a large spectrum of cancers. In mice, Rb is highly expressed in restricted cell lineages including the neurogenic, myogenic, and hematopoietic systems, and disruption of the gene leads to specific embryonic defects in these tissues. The symmetry between Rb expression and the defects in mutant mice suggest that transcriptional control of Rb during embryogenesis is pivotal for normal development. We have initiated studies to dissect the mechanisms of transcriptional regulation of Rb during development by promoter lacZ transgenic analysis. DNA sequences up to 6 kilobase pairs upstream of the mouse Rb promoter, isolated from two different genomic libraries, directed transgene expression exclusively to the developing nervous system, excluding skeletal muscles and liver. Expression of the transgene in the central and peripheral nervous systems, including the retina, recapitulated the expression of endogenous Rb during embryogenesis. A promoter region spanning approximately 250 base pairs upstream of the transcriptional starting site was sufficient to confer expression in the central and peripheral nervous systems. To determine whether this expression pattern was conserved, we isolated the human Rb 5' genomic region and generated transgenic mice expressing lacZ under control of a 1.6-kilobase pair human Rb promoter. The human Rb promoter lacZ mice also expressed the transgene primarily in the nervous system in several independent lines. Thus, transgene expression directed by both the human and mouse Rb promoters is restricted to a subset of tissues in which Rb is normally expressed during embryogenesis. Our findings demonstrate that regulatory elements directing Rb expression to the nervous system are delineated within a well defined core promoter and are regionally separated from elements, yet to be identified, that are required for expression of Rb in the developing hematopoietic and skeletal muscle systems.
Liver Fibrosis: Possible Involvement of EMT (2007)

Hepatic fibrosis is a wound-healing process in the liver with acute and chronic injury and is characterized by an excess production and deposition of extracellular matrix components. Hepatic stellate cells as well as portal fibroblasts play a pivotal role in the liver fibrogenesis. Regarding the origin of these mesenchymal cells, two hypotheses emerge. One hypothesis argues in favor of BM-derived progenitor cells and a second hypothesis favors epithelial-mesenchymal transition (EMT) in the local formation of these mesenchymal cells from hepatic epithelium. In this short review, we describe (1) the principle mechanisms of hepatic fibrosis, (2) the cells which play a crucial role in hepatic fibrosis, and (3) the possible involvement of EMT in the process of hepatic fibrosis and carcinogenesis.
Nonthermal Effects of Nd:YAG Laser on Biological Functions of Human Skin Fibroblasts in Culture (1984)

Previous studies have indicated that laser can selectively affect the biological functions of cells. In the present study, the role of a thermal component in laser-induced alterations in the biology of human skin fibroblasts was examined. Cells were cultured on 96-well tissue culture plates, subjected to treatment with the Nd:YAG laser (wavelength 1,064 nm), and the temperature of the medium was monitored by a microprobe connected to a telethermometer . For comparison, parallel cultures were heated to the same temperatures by tungsten-halogen lamp. The cell cultures were analyzed for collagen synthesis by incubating the cultures with [3H]proline, and the collagen production was assayed by the synthesis of nondialyzable [3H]hydroxyproline. The rate of DNA replication was also determined by measuring the uptake of [3H]thymidine. A marked decrease of collagen production and thymidine incorporation was noted in the cultures subjected to Nd:YAG laser. No such decreases were noted in cultures heated to the corresponding temperatures by tungsten-halogen lamp. The results thus indicate that the biochemical alteration caused by the Nd:YAG laser in human fibroblast functions cannot be explained on the basis of thermal effects.
Properties of drug-containing spherical pellets produced by a hot-melt extrusion and spheronization process (2003)

The objectives of this study were to investigate the particle size distribution, morphology and dissolution properties of spherical pellets produced by hot-melt extrusion and spheronization and to compare the properties of hot-melt extruded pellets with beads manufactured by a traditional wet-mass extrusion and spheronization method. Spherical pellets were produced by hot-melt extrusion without the use of water or other solvents. A powder blend of theophylline, Eudragit® Preparation 4135 F, microcrystalline cellulose and polyethylene glycol 8000 was hot melt-extruded and the resulting composite rod was cut into cylindrical pellets. The pellets were then spheronized in a traditional spheronizer at an elevated temperature. The same powder blend was processed using conventional wet-mass techniques. Unlike wet-mass extruded pellets, pellets prepared from hot-melt extrusion displayed both a narrow particle size distribution and controlled drug release in dissolution media less than pH 7.4. Scanning electron microscopy, X-ray diffraction and porosity measurements were employed to explain the differences in drug release rates of theophylline from pellets produced by the two processing techniques. Theophylline release from the hot-melt extruded pellets was described using the Higuchi diffusion model, and drug release rates from wet-granulated and melt-extruded pellets did not change after post-processing thermal treatment.
Unsupervised Cross-Dataset Transfer Learning for Person Re-identification (2016)

Most existing person re-identification (Re-ID) approaches follow a supervised learning framework, in which a large number of labelled matching pairs are required for training. This severely limits their scalability in realworld applications. To overcome this limitation, we develop a novel cross-dataset transfer learning approach to learn a discriminative representation. It is unsupervised in the sense that the target dataset is completely unlabelled. Specifically, we present an multi-task dictionary learning method which is able to learn a dataset-shared but target-data-biased representation. Experimental results on five benchmark datasets demonstrate that the method significantly outperforms the state-of-the-art.
Whispering-gallery mode based opto-electronic oscillators (2010)

We present our recent results related to the development of ultra-compact opto-electronic oscillators based on high-Q whispering gallery mode (WGM) resonators. These oscillators operate in X-, Ku-, and Ka-bands and are able to generate spectrally pure RF signals characterized with less than -120 dBc/Hz phase noise at 100 kHz. The floor of the phase noise (<; -140 dBc/Hz) is limited by the shot noise of the signal received at the photodiode. Both tunable and fixed frequency oscillators are demonstrated.
Video Skimming for Quick Browsing based on Audio and Image Characterization (1995)

Digital video is rapidly becoming an important source for information, entertainment and a host of multimedia applications. With the size of these collections growing to thousands of hours, technology is needed to effectively browse segments in a short time without losing the content of the video. We propose a method to extract the significant audio and video information and create a &amp;quot;skim&amp;quot; video which represents a short synopsis of the original. The extraction of significant information, such as specific objects, audio keywords and relevant video structure, is made possible through the integration of techniques in image and language understanding. The resulting skim is much smaller, and retains the essential content of the original segment. This research is sponsored by the National Science Foundation under grant no. IRI9411299, the National Space and Aeronautics Administration, and the Advanced Research Projects Agency. The views and conclusions contained in this document are those o...
The Hemopexin and O-Glycosylated Domains Tune Gelatinase B/MMP-9 Bioavailability via Inhibition and Binding to Cargo Receptors (2006)

Gelatinase B/matrix metalloproteinase-9 (MMP-9), a key regulator and effector of immunity, contains a C-terminal hemopexin domain preceded by a unique linker sequence of approximately 64 amino acid residues. This linker sequence is demonstrated to be an extensively O-glycosylated (OG) domain with a compact three-dimensional structure. The OG and hemopexin domains have no influence on the cleavage efficiency of MMP-9 substrates. In contrast, the hemopexin domain contains a binding site for the cargo receptor low density lipoprotein receptor-related protein-1 (LRP-1). Furthermore, megalin/LRP-2 is identified as a new functional receptor for the hemopexin domain of MMP-9, able to mediate the endocytosis and catabolism of the enzyme. The OG domain is required to correctly orient the hemopexin domain for inhibition by TIMP-1 and internalization by LRP-1 and megalin. Therefore, the OG and hemopexin domains down-regulate the bioavailability of active MMP-9 and the interactions with the cargo receptors are proposed to be the original function of hemopexin domains in MMPs.