gebhart/patrepeval huggingface dataset:
Molecular Determinants ofListeria monocytogenesVirulence (2004)

Listeria monocytogenes is the etiological agent of listeriosis, a severe human foodborne infection characterized by gastroenteritis, meningitis, encephalitis, abortions, and perinatal infections. This gram-positive bacterium is a facultative intracellular pathogen that induces its own uptake into nonphagocytic cells and spreads from cell to cell using an actin-based motility process. This review covers both well-established and recent advances in the characterization of L. monocytogenes virulence determinants and their role in the pathophysiology of listeriosis.
An Induced Proximity Model for NF-κB Activation in the Nod1/RICK and RIP Signaling Pathways (2000)

Nod1 is an Apaf-1-like molecule composed of a caspase-recruitment domain (CARD), nucleotide-binding domain, and leucine-rich repeats that associates with the CARD-containing kinase RICK and activates nuclear factor kappaB (NF-kappaB). We show that self-association of Nod1 mediates proximity of RICK and the interaction of RICK with the gamma subunit of the IkappaB kinase (IKKgamma). Similarly, the RICK-related kinase RIP associated via its intermediate region with IKKgamma. A mutant form of IKKgamma deficient in binding to IKKalpha and IKKbeta inhibited NF-kappaB activation induced by RICK or RIP. Enforced oligomerization of RICK or RIP as well as of IKKgamma, IKKalpha, or IKKbeta was sufficient for induction of NF-kappaB activation. Thus, the proximity of RICK, RIP, and IKK complexes may play an important role for NF-kappaB activation during Nod1 oligomerization or trimerization of the tumor necrosis factor alpha receptor.
Immunohistochemical Localization of Netrin-1 in the Embryonic Chick Nervous System (1997)

Netrin-1 has profound in vitro effects on the growth properties of vertebrate embryonic axons. In addition, netrin-1 mRNA is found in the floor plate of the embryonic nervous system, an intermediate target of many axons, including commissural axons that are affected by netrin-1 in vitro. Moreover, genetic studies of netrin-1 homologs in Caenorhabditis elegans and Drosophila implicate these proteins in commissure formation. We raised polyclonal antisera that recognize chick netrin-1 in fixed tissue sections. The antisera were used to immunohistochemically map netrin-1 in the embryonic spinal cord, brain, and retina. The relationship between netrin-1 localization and the growth of pioneering axons suggests roles for netrin-1 in the regulation of circumferential, commissural, and longitudinal axon growth in the spinal cord and brain. The data also suggest that the primary or sole effect of netrin-1 on pioneering spinal cord commissural axons is haptotactic. Furthermore, the pattern of netrin-1 localization raises the possibility that this protein helps mediate neuronal migration in the spinal cord, brain, and retina.
Endothelin-B receptor mutations in patients with isolated Hirschsprung disease from a non-inbred population (1996)

Hirschsprung disease (HSCR), or aganglionic megacolon, is the most common cause of congenital intestinal obstruction. Two different loci have been found to be tightly linked to HSCR on chromosomes 10 and 13, respectively. Recently, mutations in the RET protooncogene on chromosome 10q11.2 were identified in several HSCR patients. In addition, a missense mutation in the endothelin-B receptor (EDNRB) gene on chromosome 13q22 was found in an inbred Mennonite kindred affected by HSCR and associated abnormalities, demonstrating the involvement of EDNRB in HSCR pathogenesis. To test whether mutations in the EDNRB gene could account for Hirschsprung in patients from non-inbred populations, we analysed DNA samples from 17 probands of Italian origin with HSCR. We have identified two novel EDNRB mutations: a missense mutation in a sporadic case, S305N, which leads to a change of a serine to an asparagine, disrupting a putative phosphorylation site; and a single nucleotide deletion in a familial case, N378I, resulting in a truncated protein. Both mutations were found in one of the healthy parents, and neither of these mutations were found in any of the normal individuals tested. These data confirm the involvement of EDNRB in HSCR pathogenesis and demonstrate that EDNRB mutations could contribute to HSCR disease in non-inbred populations.
Effect of low‐level GaAlAs laser irradiation on the proliferation rate of human periodontal ligament fibroblasts: an in vitro study (2003)

A cellular effect of the soft laser application is clearly discernible. Clinical studies are needed to evaluate whether the application of low-level laser therapy might be beneficial in regenerative periodontal therapy.
A non-local cost aggregation method for stereo matching (2012)

Matching cost aggregation is one of the oldest and still popular methods for stereo correspondence. While effective and efficient, cost aggregation methods typically aggregate the matching cost by summing/averaging over a user-specified, local support region. This is obviously only locally-optimal, and the computational complexity of the full-kernel implementation usually depends on the region size. In this paper, the cost aggregation problem is re-examined and a non-local solution is proposed. The matching cost values are aggregated adaptively based on pixel similarity on a tree structure derived from the stereo image pair to preserve depth edges. The nodes of this tree are all the image pixels, and the edges are all the edges between the nearest neighboring pixels. The similarity between any two pixels is decided by their shortest distance on the tree. The proposed method is non-local as every node receives supports from all other nodes on the tree. As can be expected, the proposed non-local solution outperforms all local cost aggregation methods on the standard (Middlebury) benchmark. Besides, it has great advantage in extremely low computational complexity: only a total of 2 addition/subtraction operations and 3 multiplication operations are required for each pixel at each disparity level. It is very close to the complexity of unnormalized box filtering using integral image which requires 6 addition/subtraction operations. Unnormalized box filter is the fastest local cost aggregation method but blurs across depth edges. The proposed method was tested on a MacBook Air laptop computer with a 1.8 GHz Intel Core i7 CPU and 4 GB memory. The average runtime on the Middlebury data sets is about 90 milliseconds, and is only about 1.25× slower than unnormalized box filter. A non-local disparity refinement method is also proposed based on the non-local cost aggregation method.
Revolutionizing the landscape of colorectal cancer treatment: The potential role of immune checkpoint inhibitors (2020)

Colorectal cancer (CRC) represents the third cause of cancer-related mortalities worldwide. The progression of CRC to the metastatic phase significantly compromises the overall survival rates. Despite the advances in the therapeutic protocols, CRC treatment is still challenging. Cancer immunotherapy joined the ranks of surgery, chemotherapy, radiotherapy and targeted therapy as the fifth pillar in the foundation of cancer therapeutics. Interruption of the immunosuppressive signals within the tumor microenvironment and reactivation of antitumor immunity via targeting the molecular immune checkpoints generated promising therapeutic outcomes in several types of hard-to-treat cancers. The year 2017 witnessed the first US Food and Drug Administration (FDA) approval of immune checkpoint inhibitor (ICI) immunotherapy for the management of CRC. The approval was granted to pembrolizumab (anti-PD-1) for the treatment of patients with advanced/metastatic solid malignancies with mismatch-repair deficiency including CRCs. Such natively immunogenic tumors constitute only a minor percentage of all CRCs. Therefore, it is imperative to utilize novel combinatorial regimens to enhance the response of a wider range of CRC tumors to cancer immunotherapy and help in extending the survival rates in patients with advanced/metastatic disease. This review highlights the novel approaches under clinical development to overcome the resistance of CRCs to immunotherapy and improve the therapeutic outcomes.
Complement C3a, CpG Oligos, and DNA/C3a Complex Stimulate IFN-α Production in a Receptor for Advanced Glycation End Product-Dependent Manner (2010)

The receptor for advanced glycation end products (RAGE) is a multiligand transmembrane receptor implicated in a number of diseases including autoimmune diseases. To further understand the pathogenic mechanism of RAGE in these diseases, we searched for additional ligands. We discovered that C3a bound to RAGE with an EC(50) of 1.9 nM in an ELISA, and the binding was increased both in magnitude (by >2-fold) and in affinity (EC(50) 70 pM) in the presence of human stimulatory unmethylated cytosine-guanine-rich DNA A (hCpGAs). Surface plasmon resonance and fluorescence anisotropy analyses demonstrated that hCpGAs could bind directly to RAGE and C3a and form a ternary complex. In human PBMCs, C3a increased IFN-α production in response to low levels of hCpGAs, and this synergy was blocked by soluble RAGE or by an Ab directed against RAGE. IFN-α production was reduced in response to mouse CpGAs and C3a in RAGE(-/-) mouse bone marrow cells compared wild-type mice. Taken together, these data demonstrate that RAGE is a receptor for C3a and CpGA. Through direct interaction, C3a and CpGA synergize to increase IFN-α production in a RAGE-dependent manner and stimulate an innate immune response. These findings indicate a potential role of RAGE in autoimmune diseases that show accumulation of immunostimulatory DNA and C3a.
Antimicrobial activity and spectrum of LY146032, a lipopeptide antibiotic, including susceptibility testing recommendations (1987)

LY146032, a new lipopeptide, was found to have a spectrum of gram-positive antimicrobial activity that includes activity against staphylococci (methicillin susceptible and resistant), beta-hemolytic Streptococcus spp., pneumococci, viridans group Streptococcus spp., anaerobic gram-positive cocci, Clostridium spp., and enterococci. The new lipopeptide was generally bactericidal and showed more rapid killing of Listeria spp. (MIC, 1 to 2 micrograms/ml) and staphylococci than either vancomycin or teicoplanin. The 30-micrograms disk was preferred to the 15-micrograms disk on the basis of the preliminary interpretive criteria for susceptibility which indicated zone diameters of greater than or equal to 16 mm for susceptible strains (MIC, less than or equal to 2.0 micrograms/ml) and greater than or equal to 12 mm for resistant strains (MIC, greater than or equal to 8.0 micrograms/ml). These criteria are valid pending the testing of additional gram-positive strains which have LY146032 MICs of greater than or equal to 8 micrograms/ml.
Energy Transfer-Based Multiplexed Assay of Proteases by Using Gold Nanoparticle and Quantum Dot Conjugates on a Surface (2008)

Rapid and sensitive assay of proteases and their inhibition in a high-throughput manner is of great significance in the diagnostic and pharmaceutical fields. We developed a multiplexed assay system of proteases and their inhibition by measuring the energy transfer between quantum dots (QDs) and gold nanoparticles (AuNPs) on a glass slide. In this system, while the photoluminescence (PL) of donor QDs immobilized on a surface was quenched due to the presence of AuNPs (energy acceptor) in close proximity, the protease activity caused modulation in the efficiency of the energy transfer between the acceptor and donor, thus enabling the protease assay. In comparison to the QD-dye system, the conjugate of the QD-AuNP gave rise to higher energy transfer efficiency, resulting in quantitative assay of proteases with more sensitivity. When matrix metalloproteinase, caspase, and thrombin were tested, a multiplexed assay was successfully achieved since the AuNP could be used as a common energy acceptor in conjunction with QDs having different colors. Our system is anticipated to find applications in the diagnosis of protease-related diseases and screening of potential drugs with high sensitivity in a high-throughput way.
Impaired Production of Lymphokines and Immune (Gamma) Interferon in the Acquired Immunodeficiency Syndrome (1984)

To examine the cellular immune defect that predisposes patients with the acquired immunodeficiency syndrome (AIDS) to opportunistic infections, we tested T lymphocytes from 16 patients for the capacity to secrete macrophage-activating products (lymphokines) including gamma interferon. Mononuclear cells from 10 of 11 patients did not generate an effective lymphokine in response to mitogen, and 11 of 16 produced subnormal levels of gamma interferon (less than 300 U per milliliter). In addition, upon stimulation with specific microbial antigen, cells from none of 14 patients generated active lymphokines, and cells from 13 to 14 completely failed to secrete gamma interferon. However, the antimicrobial function of monocytes from the patients was intact, and once stimulated with normal lymphokines or gamma interferon alone, macrophages derived from patients' monocytes responded with enhanced and effective intracellular antimicrobial activity. These results suggest that impaired lymphokine production may predispose patients with AIDS to opportunistic infections, and they provide a rationale for using gamma interferon as immunotherapy.
Asymmetric Faradaic systems for selective electrochemical separations (2017)

Asymmetric Faradaic system based on organometallic electrodes shows suppression of parasitic water reactions and remarkable selectivity in redox-mediated electrosorption of micropollutants.
Human Antibody Response Following Multiple Injections of Bovine Collagen (1991)

The enzyme-linked immunosorbent assay (ELISA) was selected to further characterize the human antibody response to Zyderm (ZCI). Our studies have involved both patients and volunteers. Five patients with delayed cutaneous hypersensitivity reactions to Zyderm were positive for anti-Zyderm antibody. Six of nine patients treated with Zyderm who never displayed cutaneous reactions did develop significant levels of anti-Zyderm serum antibody. Some of these patients progressively increased their antibody levels. None of the volunteers who received multiple skin-test doses (0.1 cc) of Zyderm developed significant levels of anti-Zyderm antibody. Polyvalent anti-Zyderm antibody titers among patients with positive ELISA absorbance ranged from 1:16 to greater than 1:128. All were positive for antibodies of the IgG subtype; half were positive for the IgA subtype. None was positive for IgM or IgE subtype. We did not observe cross-reactivity between patient anti-bovine collagen sera and commercially prepared antibodies to human anti-collagen types I, II, and III. Given the frequency of current Zyderm use, it seems evident that for most patients, biologic exposure to collagen does not pose a health hazard. Nevertheless, because of the scarcity of data pertaining to the long-term significance of humoral anti-Zyderm antibodies, physicians and patients should be aware that unanswered questions remain whenever clinical use of injectable collagen is recommended.
Protein Kinase Cγ Regulates Myosin IIB Phosphorylation, Cellular Localization, and Filament Assembly (2006)

Nonmuscle myosin II is an important component of the cytoskeleton, playing a major role in cell motility and chemotaxis. We have previously demonstrated that, on stimulation with epidermal growth factor (EGF), nonmuscle myosin heavy chain II-B (NMHC-IIB) undergoes a transient phosphorylation correlating with its cellular localization. We also showed that members of the PKC family are involved in this phosphorylation. Here we demonstrate that of the two conventional PKC isoforms expressed by prostate cancer cells, PKCbetaII and PKCgamma, PKCgamma directly phosphorylates NMHC-IIB. Overexpression of wild-type and kinase dead dominant negative PKCgamma result in both altered NMHC-IIB phosphorylation and subcellular localization. We have also mapped the phosphorylation sites of PKCgamma on NMHC-IIB. Conversion of the PKCgamma phosphorylation sites to alanine residues, reduces the EGF-dependent NMHC-IIB phosphorylation. Aspartate substitution of these sites reduces NMHC-IIB localization into cytoskeleton. These results indicate that PKCgamma regulates NMHC-IIB phosphorylation and cellular localization in response to EGF stimulation.
Rare SNP rs12731181 in the miR-590-3p Target Site of the Prostaglandin F 2α Receptor Gene Confers Risk for Essential Hypertension in the Han Chinese Population (2015)

rs12731181 in the seed region of the miR-590-3p target site is associated with increased risk of essential hypertension and represents a new paradigm for FP involvement in blood pressure regulation.
Functional genomics of Phytophthora infestans effectors and Solanum resistance genes (2010)

Potato (Solanum tuberosum L.) is nowadays the most important non-cereal food crop in the world. It is prone to huge annual losses due to late blight, the disease caused by the oomycete pathogen Phytophthora infestans. Modern management of late blight necessitates the use of multiple resistance (R) genes, which requires efficient pipelines for identification, isolation and characterization of R genes. This thesis employs effectoromics, i.e. the use of effectors (pathogenic secreted protein) to probe corresponding R gene(s) in a host plant and sort out their functional redundancy and specificity. Using cytoplasmic RXLR effectors of P. infestans to probe resistant Solanum germplasm for late blight R genes, we were able to: (i) assess the biodiversity of Avr-blb1, characterize the genomic structure of virulent P. infestans isolates on Rpi-blb1 plants and thus provide a technical solution for long-term disease management; (ii) identify the centre of origin of R3a, characterize R3a gene homologues and a functional R gene (Rpi-sto2), and (iii) uncover the potential co-evolution at both R and Avr side for the R2/PiAvr2-PexRD11 interactions, providing more diversity and specificity of R2 homologues, which may be valuable for potato breeding
Low‐dose vasopressin infusion therapy for refractory hypotension in ELBW infants (2009)

Low-dose AVP therapy should be considered as rescue therapy when high-dose catecholamine therapy and/or steroid administration do not produce sufficient increase in the blood pressure. Further investigations are required to prove the efficacy and safety of AVP infusion therapy in preterm infants.
Wnt5a induces homodimerization and activation of Ror2 receptor tyrosine kinase (2008)

Wnts are secreted glycoproteins that control vital biological processes, including embryogenesis, organogenesis and tumorigenesis. Wnts are classified into several subfamilies depending on the signaling pathways they activate, with the canonical subfamily activating the Wnt/beta-catenin pathway and the non-canonical subfamily activating a variety of other pathways, including the Wnt/calcium signaling and the small GTPase/c-Jun NH2-terminal kinase pathway. Wnts bind to a membrane receptor Frizzled and a co-receptor, the low-density lipoprotein receptor related protein. More recently, both canonical and non-canonical Wnts were shown to bind the Ror2 receptor tyrosine kinase. Ror2 is an orphan receptor that plays crucial roles in skeletal morphogenesis and promotes osteoblast differentiation and bone formation. Here we examine the effects of a canonical Wnt3a and a non-canonical Wnt5a on the signaling of the Ror2 receptor. We demonstrate that even though both Wnt5a and Wnt3a bound Ror2, only Wnt5a induced Ror2 homo-dimerization and tyrosine phosphorylation in U2OS human osteoblastic cells. Furthermore, Wnt5a treatment also resulted in increased phosphorylation of the Ror2 substrate, 14-3-3beta scaffold protein, indicating that Wnt5a binding causes activation of the Ror2 signaling cascade. Functionally, Wnt5a recapitulated the Ror2 activation phenotype, enhancing bone formation in the mouse calvarial bone explant cultures and potentiating osteoblastic differentiation of human mesenchymal stem cells. The effect of Wnt5a on osteoblastic differentiation was largely abolished upon Ror2 down-regulation. Thus we show that Wnt5a activates the classical receptor tyrosine kinase signaling cascade through the Ror2 receptor in cells of osteoblastic origin.
Multiplexed Lipid Dip‐Pen Nanolithography on Subcellular Scales for the Templating of Functional Proteins and Cell Culture (2008)

Molecular patterning processes taking place in biological systems are challenging to study in vivo because of their dynamic behavior, subcellular size, and high degree of complexity. In vitro patterning of biomolecules using nanolithography allows simplification of the processes and detailed study of the dynamic interactions. Parallel dip-pen nanolithography (DPN) is uniquely capable of integrating functional biomolecules on subcellular length scales due to its constructive nature, high resolution, and high throughput. Phospholipids are particularly well suited as inks for DPN since a variety of different functional lipids can be readily patterned in parallel. Here DPN is used to spatially pattern multicomponent micro- and nanostructured supported lipid membranes and multilayers that are fluid and contain various amounts of biotin and/or nitrilotriacetic acid functional groups. The patterns are characterized by fluorescence microscopy and photoemission electron microscopy. Selective adsorption of functionalized or recombinant proteins based on streptavidin or histidine-tag coupling enables the semisynthetic fabrication of model peripheral membrane bound proteins. The biomimetic membrane patterns formed in this way are then used as substrates for cell culture, as demonstrated by the selective adhesion and activation of T-cells.
Secretory carcinoma of the breast containing the ETV6-NTRK3 fusion gene in a male: case report and review of the literature (2005)

SC is a rare slow-growing tumor best treated surgically. There are insufficient data to support the use of adjuvant radiation or chemotherapy. Its association with the ETV6-NTRK3 fusion gene gives some clues for the better understanding of this neoplasm and eventually, the development of specific therapies.
A Novel Human Her-2/neu Chimeric Molecule Expressed by Listeria monocytogenes Can Elicit Potent HLA-A2 Restricted CD8-positive T cell Responses and Impact the Growth and Spread of Her-2/neu-positive Breast Tumors (2009)

This novel L. monocytogenes-hHer-2/neu chimera vaccine proves to be just as effective as the individual vaccines but combines the strength of all three in a single vaccination. These encouraging results support future clinical trials using this chimera vaccine and may be applicable to other cancer types expressing the Her-2/neu molecule such as colorectal and pancreatic cancer.
Neural cell adhesion molecule expression on renal interstitial cells (2007)

These data indicate that a rare subpopulation of NCAM+ interstitial cells could represent renal progenitors, and that NCAM+ interstitial cells can participate in the initial phase of interstitial fibrosis.