gebhart/patrepeval huggingface dataset:
Expression of rib-1, a Caenorhabditis elegans Homolog of the Human Tumor Suppressor EXT Genes, Is Indispensable for Heparan Sulfate Synthesis and Embryonic Morphogenesis (2007)

The proteins encoded by all of the five cloned human EXT family genes (EXT1, EXT2, EXTL1, EXTL2, and EXTL3), members of the hereditary multiple exostoses gene family of tumor suppressors, are glycosyltransferases required for the biosynthesis of heparan sulfate. In the Caenorhabditis elegans genome, only two genes, rib-1 and rib-2, homologous to the mammalian EXT genes have been identified. Although rib-2 encodes an N-acetylglucosaminyltransferase involved in initiating the biosynthesis and elongation of heparan sulfate, the involvement of the protein encoded by rib-1 in the biosynthesis of heparan sulfate remains unclear. Here we report that RIB-1 is indispensable for the biosynthesis and for embryonic morphogenesis. Despite little individual glycosyltransferase activity by RIB-1, the polymerization of heparan sulfate chains was demonstrated when RIB-1 was coexpressed with RIB-2 in vitro. In addition, RIB-1 and RIB-2 were demonstrated to interact by pulldown assays. To investigate the functions of RIB-1 in vivo, we depleted the expression of rib-1 by deletion mutagenesis. The null mutant worms showed reduced synthesis of heparan sulfate and embryonic lethality. Notably, the null mutant embryos showed abnormality at the gastrulation cleft formation stage or later and arrested mainly at the 1-fold stage. Nearly 100% of the embryos died before L1 stage, although the differentiation of some of the neurons and muscle cells proceeded normally. Similar phenotypes have been observed in rib-2 null mutant embryos. Thus, RIB-1 in addition to RIB-2 is indispensable for the biosynthesis of heparan sulfate in C. elegans, and the two cooperate to synthesize heparan sulfate in vivo. These findings also show that heparan sulfate is essential for post-gastrulation morphogenic movement of embryonic cells and is indispensable for ensuring the normal spatial organization of differentiated tissues and organs.
Mechanisms of psoralen photosensitization reactions. (1984)

The basic aspects of cutaneous photosensitization reactions and the mode of therapeutic effectiveness of psoralens used extensively in the photochemotherapy of psoriasis and vitiligo have been reviewed. Psoralen-induced skin photosensitization and the therapeutic action of psoralens involve two distinct types of reactions that occur independently of each other and concurrently when the psoralen-treated skin (oral or topical) is exposed to 320-400 nm UV radiation. The first, type I, occurs in the absence of oxygen (anoxic) reaction and primarily involves photoreactions with DNA; the second, type II, is a sensitized reaction dependent on oxygen and involves the formation of singlet oxygen (1O2), superoxide anion (O-.2), and hydroxy radicals. The photoreactive form of psoralen is its triplet state, and the sites of reaction are 1) the cell membrane of the epidermal, dermal, and endothelial cells; 2) the cytoplasmic constituents, such as enzymes, RNA, lysosomes, etc.; 3) the cell nuclei (DNA and chromatin); and 4) psoralen-sensitized production of 1O2, O-.2, and hydroxy radicals, which we believe are responsible for cell membrane damage and vasodilation. The major damage would be initiated by a type I reaction and would be seen in the form of nuclear damage to DNA resulting from the interaction of psoralen with DNA and to a lesser extent with RNA. The skin photosensitization response (erythema, edema, membrane damage, etc.) would result from a type II reaction involving the generation of 1O2. In vitro and in vivo metabolism of 4,5',8-trimethylpsoralen and 8-methoxypsoralen is briefly outlined.
Hematopoietic progenitor kinase 1 (HPK1) is required for LFA-1–mediated neutrophil recruitment during the acute inflammatory response (2013)

Recruitment of polymorphonuclear neutrophils (PMNs) to sites of acute inflammation critically depends on β2 integrins (CD11/CD18). Recently, the mammalian actin-binding protein 1 (mAbp1) was identified as an important adaptor protein regulating PMN trafficking downstream of β2 integrins. Here, we show that mAbp1 constitutively co-immunoprecipitated with hematopoietic progenitor kinase 1 (HPK1) in neutrophil-like differentiated HL-60 (dHL-60) cells. HPK1 was enriched at the lamellipodium of polarized dHL-60 cells, where it colocalized with mAbp1 and actin. Functional analysis of PMNs from HPK1-deficient mice showed that HPK1 was critical for CXCL1-induced lymphocyte function-associated antigen 1 (LFA-1)-mediated PMN adhesion to ICAM-1 under flow conditions. Accordingly, CXCL1-mediated induction of high-affinity LFA-1 required HPK1, but macrophage antigen 1 (Mac-1) affinity regulation was independent of HPK1. Intravital microscopy of the mouse cremaster muscle confirmed the defect of CXCL1-induced leukocyte adhesion in HPK1-deficient mice. Furthermore, β2 integrin-mediated post-adhesion processes-adhesion strengthening, spreading, and directed mechanotactic crawling of PMNs under flow conditions-involved HPK1 in vitro and in vivo. Upon intrascrotal administration of tumor necrosis factor α (TNF-α), PMN adhesion and extravasation were severely compromised in HPK1-deficient mice. In summary, our results indicate that HPK1 is critically involved in LFA-1-mediated PMN trafficking during acute inflammation.
Antibodies from patients with heparin-induced thrombocytopenia/thrombosis are specific for platelet factor 4 complexed with heparin or bound to endothelial cells. (1994)

Heparin-induced thrombocytopenia/thrombosis (HITP) is thought to be mediated by immunoglobulins that activate plate- lets in the presence of pharmacologic concentrations of hepa- rin, but the molecular basis for this relatively common and of- ten serious complication of heparin therapy has not been estab- lished. We found that plasma from each of 12 patients with HITP contained high titer (. 1:200) antibodies that reacted with immobilized complexes of heparin and platelet factor 4 (PF4), a heparin-binding protein contained in platelet alpha- granules. Recombinant human PF4 behaved similarly to PF4 isolated from platelets in this assay system. Complexes formed at an apparent heparin/PF4 molecular ratio of -1:2 (fresh heparin) and -1:12 (outdated heparin) were most effective in binding antibody. Immune complexes consisting of PF4, hepa- rin, and antibody reacted with resting platelets; this interaction was inhibited by a monoclonal antibody specific for the FcyRII receptor and by excess heparin. Human umbilical vein endothe- lial cells, known to express heparin-like glycosaminoglycan molecules on their surface, were recognized by antibody in the presence of PF4 alone; this reaction was inhibited by excess heparin, but not by anti-Fc'yRII. Antibodies reactive with hepa- rin/PF4 were not found in normal plasma, but IgG and 1gM antibodies were detected at dilutions of 1:10 (IgG) and 1:50 (IgM) in 3 of 50 patients (6%) with other types of immune thrombocytopenia. These findings indicate that antibodies as- sociated with HITP react with PF4 complexed with heparin in solution or with glycosaminoglycan molecules on the surface of endothelial cells and provide the basis for a new hypothesis to explain the development of thrombocytopenia with thrombosis or disseminated intravascular coagulation in patients sensitive to heparin. ( J. Clin. Invest.
Bacterial Homologue of Human Blood Group A Transferase (2008)

A bacterial version of human blood group A transferase was identified and found to be able to accept five naturally existing H-antigen core structures as good substrates, demonstrating its versatility for synthesis of blood group A antigens. Furthermore, this enzyme was applied in the engineering of bacterial cell surface polysaccharides by remodeling blood group B mimicry into blood group A mimicry.
Patterns of Burn Adjustment (1992)

For many years, burn professionals have attempted to assess the outcomes of different types of burn injury and the factors that are related to good patterns of coping with the aftermath of thermal injury. Most writers have attempted to use objective criteria such as return to work or preexisting psychologic problems (e.g., alcoholism) in determining the success of rehabilitation, but much controversy over the forms of assessment persists. It is agreed that antisocial personality, organic brain syndromes, and lack of social support all undermine good recovery for patients with burns. The authors have attempted to look at the subjective side of the patient's adjustment by providing representative examples of several types of burn adjustment in terms of personality features, all of which would tend to complement other approaches. The use of denial, the ways in which hostility is managed by the patient, and how he or she uses key persons in the environment are examined. The cognitive, emotional (affective), and behavioral styles of patients are examined as part of this pilot study of cluster patterns or types of adjustment.
Modulation of in vitro anaphylaxis of guinea‐pig isolated tracheal segments by azelastine, inhibitors of arachidonic acid metabolism and selected antiallergic drugs (1986)

The ability of azelastine to influence antigen-induced contractile responses (Schultz-Dale phenomenon) in isolated tracheal segments of the guinea-pig was investigated and compared with selected antiallergic drugs and inhibitors of arachidonic acid metabolism. Indomethacin produced a significant leftward shift of the antigen concentration-effect curve. The inhibitory activity of azelastine on anaphylactic responses in guinea-pig trachea was dependent on the duration of exposure (preincubation period). The relative order of potency (antianaphylactic activity) at calculated IC50 level was as follows: FPL 55712 (a leukotriene receptor antagonist) greater than nordihydroguaiaretic acid (a lipoxygenase inhibitor) greater than p-bromophenacyl bromide (a phospholipase A2 inhibitor) greater than BW 755c (a dual inhibitor of lipoxygenase and cyclo-oxygenase) greater than theophylline (a phosphodiesterase inhibitor) greater than azelastine greater than diphenhydramine (H1 histamine-receptor antagonist) greater than ketotifen greater than disodium cromoglycate. FPL 55712 (added 5 min before antigen challenge) was about 12 times as potent as azelastine (added 2 h before antigen challenge). The incubation of tracheal segments with azelastine and BW 755c for a period of 30 min was found to inhibit indomethacin-augmented anaphylactic responses. These observations seem to suggest that azelastine and BW 755c interfere with the synthesis/release of the products of lipoxygenase/leukotriene synthetase pathway (e.g., leukotrienes) in the mediation of allergic responses in airway smooth muscles.
Process-Induced Morphological Defects in Epitaxial CVD Silicon Carbide (1997)

Silicon carbide (SiC) semiconductor technology has been advancing rapidly, but there are numerous crystal growth problems that need to be solved before SiC can reach its full potential. Among these problems is a need for an improvement in the surface morphology of epitaxial films that are grown to produce device structures. Various processes before and during epilayer growth lead to the formation of morphological defects observed in SiC epilayers grown on SiC substrates. In studies of both 6H and 4H-SiC epilayers, atomic force microscopy (AFM) and other techniques have been used to characterize SiC epilayer surface morphology. In addition to the well-known micropipe defect, SiC epilayers contain growth pits, triangular features (primarily) in 4H-SiC, and macro step due to step bunching. In work at NASA Lewis, it has been found that factors contributing to the formation of some morphological defects include: defects in the substrate bulk, defects in the substrate surface caused by cutting and polishing the wafer, the tilt angle of the wafer surface relative to the basal plane, and growth conditions. Some of these findings confirm results of other research groups. This paper presents a review of published and unpublished investigations into processes that are relevant to epitaxial film morphology.
Role of renal nerves in sodium retention of cirrhosis and congestive heart failure (1991)

To define the role of renal nerves in renal Na retention of cirrhosis and congestive heart failure (CHF), experiments were done in rats with cirrhosis due to common bile duct ligation (CBDL) and CHF due to myocardial infarction from left coronary artery ligation. Two weeks after induction of CBDL or CHF, diseased and sham diseased (Sham) rats were subjected to bilateral renal denervation (DNX) or sham renal denervation (innervated, INN). Five days after DNX or INN, 26-day metabolic balance studies were carried out in all rats. Daily dietary Na intake averaged 2.0-3.0 meq/day on days 1-6 and 22-26 and averaged 0.120 meq/day on days 7-21. Cumulative Na balance was greater in CBDL and CHF rats, INN or DNX, than in Sham/CBDL or CHF rats throughout the study. On day 6 at the end of the normal dietary Na intake period (days 0-6), cumulative Na balance was not affected by renal denervation in Sham/CBDL or CHF rats (INN, 2.02 +/- 0.19 meq, n = 10; DNX, 2.04 +/- 0.17 meq, n = 11), CBDL rats (INN, 4.21 +/- 0.39 meq, n = 10; DNX, 3.78 +/- 0.37 meq, n = 10), or CHF rats (INN, 3.74 +/- 0.72 meq, n = 9; DNX, 3.22 +/- 0.55 meq, n = 10).(ABSTRACT TRUNCATED AT 250 WORDS)
Wireless multimedia sensor networks: A survey (2007)

In recent years, the growing interest in the wireless sensor network (WSN) has resulted in thousands of peer-reviewed publications. Most of this research is concerned with scalar sensor networks that measure physical phenomena, such as temperature, pressure, humidity, or location of objects that can be conveyed through low-bandwidth and delay-tolerant data streams. Recently, the focus is shifting toward research aimed at revisiting the sensor network paradigm to enable delivery of multimedia content, such as audio and video streams and still images, as well as scalar data. This effort will result in distributed, networked systems, referred to in this paper as wireless multimedia sensor networks (WMSNs). This article discusses the state of the art and the major research challenges in architectures, algorithms, and protocols for wireless multimedia sensor networks. Existing solutions at the physical, link, network, transport, and application layers of the communication protocol stack are investigated. Finally, fundamental open research issues are discussed, and future research trends in this area are outlined.
Lymphoid tumors displaying rearrangements of both immunoglobulin and T cell receptor genes. (1985)

Ig and T beta gene rearrangements can be used as genetic markers of lineage and clonality in the study of B and T cell populations. We have addressed the issue of the respective B and T lineage specificity of these rearrangements by analyzing a panel of 63 lymphoid tumors representative of the various clinicopathologic categories of both B and T neoplasias. We report that approximately 10% of the cases tested displayed rearrangements of both Ig and T beta genes. Despite their dual genotypic pattern, these tumors retain a pure immunophenotype, i.e. they display either B or T cell lineage-restricted cell surface antigens. The implications of these findings for both normal and neoplastic lymphoid differentiation are discussed.
Dynamic Monitoring of Cytotoxicity on Microelectronic Sensors (2005)

A real-time cell electronic sensing (RT-CES) system was used for label-free, dynamic measurement of cell responses to cytotoxicants. Cells were grown onto the surfaces of microelectronic sensors, which are comprised of circle-on-line electrode arrays and are integrated into the bottom surfaces of the microtiter plate. Changes in cell status such as cell number, viability, morphology, and adherence were monitored and quantified by detecting sensor electrical impedance. For cell quantification and viability measurement, the data generated on the RT-CES system correlated well with those from the colorimetric (MTT) assay. For cytotoxicity assessment, cells growing on microelectronic sensors were treated with different cytotoxicants, such as arsenic, mercury, and sodium dichromate. The dynamic responses of the cells to the toxicants were continuously monitored by the RT-CES system. On the basis of the IC50 values, the RT-CES system displays an equal sensitivity to the neutral red uptake assay at specific time points. Furthermore, because the RT-CES system provides real-time information regarding the state of cell morphology and adhesion in addition to cell number, we were able to discern a previously unreported effect of arsenic on NIH 3T3 cells prior to cell death. Also, using the RT-CES system, we were able to monitor cytotoxicity effects that occur within a minute of compound addition. Taken together, the RT-CES system allows for real-time, continuous monitoring and quantitative recording of the whole assay process and provides new insight into the cell-toxicant interaction.
User's hand effects on EMC internal GSM/DCS mobile phone antenna (2006)

The user's hand effects on the EMC GSM/DCS antenna embedded in the mobile phone have been presented. Although the EMC antenna is easy to be integrated into a mobile phone with nearby electronic components or conducting elements, the performance of the antenna is still greatly affected when a user's hand holds the mobile phone. Even when the phone was hand-held at the bottom, large efficiency drops have been observed, especially for the GSM operation.
Localization of the binding site for the monocyte immunoglobulin (Ig) A-Fc receptor (CD89) to the domain boundary between Calpha2 and Calpha3 in human IgA1. (1996)

Immunoglobulin (Ig) A serves as the first line of humoral defense at all mucosal surfaces and is present in large quantities of blood. In playing its role in humoral immunity, IgA interacts with a variety of effector molecules present both in serum and on the surfaces of immune and inflammatory cells. To study these interactions, we previously established expression of human IgA1 in insect cells using recombinant baculoviruses and showed that the expressed antibody is a structurally and functionally intact polypeptide useful for examining the molecular properties of IgA. Indeed, since the C alpha 2 N-linked glycosylation site lies near the Fab-distal pole of C alpha 2, the inability of a mutant IgA1 lacking C alpha 2 N-glycosylation to bind its cognate receptor suggested that the monocyte Fc alpha receptor (mFcalphaR) recognizes IgA at a hinge-distal site encompassing the boundary between the C alpha 2 and C alpha 3 domains. In this report, we utilize both domain-swapped IgA/IgG and point-mutated IgA chimeras to verify the above hypothesis. Using an antigen-specific rosetting assay and a mFc alpha R-expressing cell line, we show that (a) C alpha 2 and C alpha 3 together are necessary and sufficient for binding; (b) neither the IgA hinge nor the tailpiece is necessary for binding; (c) mutations away from the interdomain boundary do not affect binding; and (d) mutations located near the three-dimensional boundary between C alpha 2 and C alpha 3 completely disrupt binding. Taken together, these results localize the mFc alpha R recognition site on IgA to the boundary region between the second and third constant domains--a site analogous to that recognized by Staphylococcus aureus protein A on IgG. The use of this hinge-distal site is, to date, unique among Fc receptors of the Ig superfamily.
Development of Recombinant Vesicular Stomatitis Viruses That Exploit Defects in Host Defense To Augment Specific Oncolytic Activity (2003)

Vesicular stomatitis virus (VSV) is a negative-stranded RNA virus normally sensitive to the antiviral actions of alpha/beta interferon (IFN-alpha/beta). Recently, we reported that VSV replicates to high levels in many transformed cells due, in part, to susceptible cells harboring defects in the IFN system. These observations were exploited to demonstrate that VSV can be used as a viral oncolytic agent to eradicate malignant cells in vivo while leaving normal tissue relatively unaffected. To attempt to improve the specificity and efficacy of this system as a potential tool in gene therapy and against malignant disease, we have genetically engineered VSV that expresses the murine IFN-beta gene. The resultant virus (VSV-IFNbeta) was successfully propagated in cells not receptive to murine IFN-alpha/beta and expressed high levels of functional heterologous IFN-beta. In normal murine embryonic fibroblasts (MEFs), the growth of VSV-IFNbeta was greatly reduced and diminished cytopathic effect was observed due to the production of recombinant IFN-beta, which by functioning in a manner involving autocrine and paracrine mechanisms induced an antiviral effect, preventing virus growth. However, VSV-IFNbeta grew to high levels and induced the rapid apoptosis of transformed cells due to defective IFN pathways being prevalent and thus unable to initiate proficient IFN-mediated host defense. Importantly, VSV expressing the human IFN-beta gene (VSV-hIFNbeta) behaved comparably and, while nonlytic to normal human cells, readily killed their malignant counterparts. Similar to our in vitro observations, following intravenous and intranasal inoculation in mice, recombinant VSV (rVSV)-IFNbeta was also significantly attenuated compared to wild-type VSV or rVSV expressing green fluorescent protein. However, VSV-IFNbeta retained propitious oncolytic activity against metastatic lung disease in immunocompetent animals and was able to generate robust antitumor T-cell responses. Our data indicate that rVSV designed to exploit defects in mechanisms of host defense can provide the basis for new generations of effective, specific, and safer viral vectors for the treatment of malignant and other disease.
Role of IL-2 in cancer immunotherapy (2016)

Interleukin-2 (IL-2) is one of the key cytokines with pleiotropic effects on immune system. It has been approved for the treatment of metastatic renal cell carcinoma and metastatic melanoma. Recent progress has been made in our understanding of IL-2 in regulating lymphocytes that has led to exciting new directions for cancer immunotherapy. While improved IL-2 formulations might be used as monotherapies, their combination with other anticancer immunotherapies, such as adoptive cell transfer regimens, antigen-specific vaccination, and blockade of immune checkpoint inhibitory molecules, for example cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) and programmed death 1 (PD-1) mono-antibodies, would held the promise of treating metastatic cancer. Despite the comprehensive studies of IL-2 on immune system have established the application of IL-2 for cancer immunotherapy, a number of poignant obstacles remain for future research. In the present review, we will focus on the key biological features of IL-2, current applications, limitations, and future directions of IL-2 in cancer immunotherapy.
Patterning of Metal Films on Arbitrary Substrates by Using Polydopamine as a UV-Sensitive Catalytic Layer for Electroless Deposition (2016)

Patterning metal films on various substrates is essentially important and yet challenging for developing a wide variety of innovative devices. We herein report a versatile approach to pattern metal (gold, silver, or copper) films on arbitrary substrates by using the bio-inspired polydopamine (PDA) thin film as a UV-sensitive adhesive layer for electroless deposition. The PDA film is able to be formed on virtually any solid surfaces under mild condition, and its rich catechol groups allow for electroless deposition of metal films with high adhesion stability. Upon UV irradiation, spatially selective oxidation of PDA film occurs and the local metal deposition is inhibited, thus facilitating successful patterning of metal films. Considering its versatility and simplicity, this strategy may demonstrate great applications in manufacturing various innovative devices.