gebhart/patrepeval huggingface dataset:
The Antibody Repertoire of Early Human B Cells I. High Frequency of Autoreactivity and Polyreactivity (1990)

Cord blood and fetal liver B cells were immortalized using Epstein-Barr virus, and IgM antibodies from the resulting lines and clones were examined for their binding to a variety of auto-antigens and micro-organisms by ELISA and fluorescence assays. Auto-antigens tested included Fc of IgG, ssDNA and dsDNA, cardiolipin, histones 1-4, collagens type I and II, thyroglobulin, cytoskeletal components, and a tissue section screen. Of 71 cell lines tested, all but 19 showed some autoreactivity. All 32 fetal liver lines reacted to some self-antigens. In cord blood clones, 16 out of 26 bound to auto-antigens. Many of the clones reacted with more than one auto-antigen and were 'polyreactive'. Some of the cord blood clones bound to extracts of micro-organisms, showing specificity for both endogenous and exogenous antigens. The high frequency of CD5+ B cells in the cord blood (greater than 50%) and fetal liver (greater than 70%) argues for many of these clones being derived from this subset. Therefore, our data support the concept that many 'early' B cells produce polyreactive IgM which can bind to a variety of different auto-antigens and micro-organisms. These IgM antibodies are similar to those described by others as 'natural antibodies'.
Artificial neural networks: a tutorial (1996)

Artificial neural nets (ANNs) are massively parallel systems with large numbers of interconnected simple processors. The article discusses the motivations behind the development of ANNs and describes the basic biological neuron and the artificial computational model. It outlines network architectures and learning processes, and presents some of the most commonly used ANN models. It concludes with character recognition, a successful ANN application.
Autocrine or Paracrine Inflammatory Actions of Corticotropin-Releasing Hormone in Vivo (1991)

Corticotropin-releasing hormone (CRH) functions as a regulator of the hypothalamic-pituitary-adrenal axis and coordinator of the stress response. CRH receptors exist in peripheral sites of the immune system, and CRH promotes several immune functions in vitro. The effect of systemic immunoneutralization of CRH was tested in an experimental model of chemically induced aseptic inflammation in rats. Intraperitoneal administration of rabbit antiserum to CRH caused suppression of both inflammatory exudate volume and cell concentration by approximately 50 to 60 percent. CRH was detected in the inflamed area but not in the systemic circulation. Immunoreactive CRH is therefore produced in peripheral inflammatory sites where, in contrast to its systemic indirect immunosuppressive effects, it acts as an autocrine or paracrine inflammatory cytokine.
Adherence of Candida to Cultured Vascular Endothelial Cells: Mechanisms of Attachment and Endothelial Cell Penetration (1985)

To elucidate the pathogenesis of hematogenous Candida infections, we developed an in vitro model of Candida adherence to and penetration of human endothelial cells. We enhanced or inhibited adherence in order to probe mechanisms of attachment. Adherence of Candida albicans showed a linear relation to Candida inoculum (range, 10(2)-10(5) cfu, r = .99, P less than .01) and exceeded that of less virulent Candida species and that of Saccharomyces cerevisiae (P less than .01). Candida immune serum blocked attachment (greater than 95% inhibition; P less than .001), however, this activity was abolished by immunoprecipitation of immune serum with C. albicans mannan (P less than .001) and was unaffected by immunoprecipitation with S. cerevisiae mannan or by adsorption with particulate chitin. Adherence was diminished by exposing C. albicans to heat (greater than 99% inhibition; P less than .01), UV light (98% inhibition; P less than .01), or sodium periodate (greater than 72% inhibition; P less than .01). An extract from heat-exposed C. albicans blocked adherence (greater than 51% inhibition; P less than .001). Transmission electron microscopy demonstrated that viable or killed Candida organisms were attached to endothelial cells, were enveloped by membrane processes from the endothelial cell surface, and were incorporated into the endothelial cells within phagosomes. Cytochalasin B blocked incorporation without blocking surface attachment.
Grouping of Feline Calicivirus Field Isolates Using Monoclonal Antibodies. (1997)

Immuno-serological characterizations of feline calicivirus (FCV) field isolates and vaccine strains were examined using neutralizing monoclonal antibodies (MAbs) raised against the F4 strain of FCV and polyclonal antisera. Neutralizing test (NT) with present MAbs showed that 29 isolates and 2 vaccine strains of FCV were divided into 4 groups, but 8 isolates could not be classified into any groups. The results of NT using polyclonal antisera were varied and indicated that the neutralizing activities of these sera were not related to the expression of neutralizing epitopes detected by MAbs used in the present study. These results demonstrated a heterogeneity among FCV isolates circulating concurrently in Japan and the possibility of grouping of calicivirus field isolates using MAbs.
Activin receptor–like kinase 1 is implicated in the maturation phase of angiogenesis (2002)

Activin receptor-like kinase 1 (ALK-1) is an orphan type I receptor of the transforming growth factor beta (TGF-beta) receptor family. In vivo studies have demonstrated that this endothelial-specific receptor is implicated in angiogenesis. In this study, we addressed the cellular function of ALK-1 in cultured human microvascular endothelial cells from the dermis (HMVEC-d's) using adenoviral expression of a constitutively active form of ALK-1 (ALK-1QD). We observed that ALK-1QD expression inhibits cell proliferation through an arrest in the G1 phase in the cell cycle. ALK-1QD expression also inhibited migration. This inhibition was also observed in other endothelial cells (human microvascular endothelial cells [HMEC-1's], HMVECs from the lung, and human umbilical vein endothelial cells [HUVECs]). Finally, ALK-1QD expression decreased re-adhesion and spreading to different matrices. This led us to examine the dynamic formation of adhesion complexes. We demonstrated that while beta-gal-infected cells reorganized actin stress fibers and focal adhesion complexes at the edge of a wound, ALK-1QD-infected cells did not. To identify downstream genes implicated in ALK-1 cellular responses, we next performed a cDNA array analysis of the expressed genes. There were 13 genes found to be significantly induced or suppressed by ALK-1QD. Among them, 2 genes encoded cell cycle-related proteins (c-myc and p21/waf1), 3 encoded components of the cytoskeleton-focal adhesion complex (beta-actin, paxillin, and zyxin), and 2 encoded members of the TGF-beta family (BMPRII and GDF-15). Taken together, our results suggest that ALK-1 is implicated in the maturation phase of angiogenesis. Disruption of this latter phase of angiogenesis may be an important step in the development of hereditary hemorrhagic telangiectasia.
The Chemistry of Tea (2000)

Tea is one of the most popular beverages consumed worldwide. It is the brew prepared from the leaves of the plant Camellia sinensis. Freshly harvested tea leaves require processsing to convert them into green, oolong and black teas. An estimated 2.5 million metric tons of dried tea are manufactured annually. The distinctive flavor and color of various teas are due to the chemical changes that occur during processing. The two major groups of compounds in tea leaves are catechins and methylxanthins.
A 1 GBIT/second GaAs DES chip (1992)

A data encryption chip implementing the DES algorithm has been developed. The implementation is based on a Vitesse FURY 15K gate array. Custom-designed precharged logic is used to achieve an encryption rate of 1 GBit/s, using a 250 MHz clock.
Vacuum vapor deposited thin films of a perylene dicarboximide derivative: Microstructure versus deposition parameters (1988)

The microscopic physical structure in thin films of vapor deposited, large heterocyclic organic molecules is strongly dependent on the deposition parameters. The scale of the microstructure can vary enormously compared to inorganic systems, strongly affecting the macroscopic properties. Multiple polymorphs frequently characterize these systems. We have extended our previous work with the perylene dicarboximides to include a phenethyl derivative. Films in the 300–1000 Å thickness range, deposited on metal and transparent substrates at varying rates and substrate temperatures from −165 to 155 °C, with and without vacuum annealing, have been characterized by scanning electron microscopy, ultraviolet/visible, and infrared (IR) spectroscopies, and polarization modulation reflectivity changes. Evidence is presented for a critical substrate temperature between −22 and −32 °C. Also a polymorphic phase sensitivity to deposition substrate temperature and rate is demonstrated, consistent with an exothermic peak observed by differential scanning calorimetry of the vapor deposited material, and an annealing induced molecular reorientation observed by reflection absorption IR.
A multimodal perceptual user interface for video-surveillance environments (2005)

In this paper a perceptual user interface (PUI) for video-surveillance environments is introduced. This system provides a tool for a video-surveillance control-room, and exploits a novel multimodal user interaction paradigm based on hand gesture and perceptual user interfaces. The proposed system, being simple and intuitive, is expected to be useful in the control of large and dynamic environments. To illustrate our work, we introduce a proof-of concept multimodal, bare-hand gesture-based application and discuss its implementation and the obtained experimental results.
Hepatitis C virus protease NS3/4A cleaves mitochondrial antiviral signaling protein off the mitochondria to evade innate immunity (2005)

Hepatitis C virus (HCV) is a global epidemic manifested mainly by chronic infection. One strategy that HCV employs to establish chronic infection is to use the viral Ser protease NS3/4A to cleave some unknown cellular targets involved in innate immunity. Here we show that the target of NS3/4A is the mitochondrial antiviral signaling protein, MAVS, that activates NF-kappaB and IFN regulatory factor 3 to induce type-I interferons. NS3/4A cleaves MAVS at Cys-508, resulting in the dislocation of the N-terminal fragment of MAVS from the mitochondria. Remarkably, a point mutation of MAVS at Cys-508 renders MAVS resistant to cleavage by NS3/4A, thus maintaining the ability of MAVS to induce interferons in HCV replicon cells. NS3/4A binds to and colocalizes with MAVS in the mitochondrial membrane, and it can cleave MAVS directly in vitro. These results provide an example of host-pathogen interaction in which the virus evades innate immunity by dislodging a pivotal antiviral protein from the mitochondria and suggest that blocking the cleavage of MAVS by NS3/4A may be applied to the prevention and treatment of HCV.
Lymphocytic Proliferative Response to Outer‐Membrane Proteins Isolated from Salmonella (1993)

Porins isolated from Salmonella typhi have been demonstrated to protect against the challenge with this bacteria in mice. The mechanism has not been clarified, but could be associated with activation of both humoral and cellular immunity. In order to evaluate the induction of specific T cell responses, the lymphocytic proliferation to porins isolated from Salmonella typhimurium, Salmonella typhi and Escherichia coli was examined by 3H-thymidine incorporation assay in mice immunized with three different antigens: acetone-killed S. typhimurium, its porins, or outer-membrane proteins (OMPs) isolated from S. typhi. Higher proliferative responses were observed in mice immunized with porins and OMPs compared with those which received the acetone-killed bacteria. Although cross-reactivity was observed between porins, they were not mitogenic. Moreover, porins were able to activate T lymphocytes isolated from mice immunized with S. typhi OMPs. These results suggest that T cell activation, through the release of lymphokines, may play a role in the induction of protective immunity with porins.
Radioimmunoimaging with Longer-Lived Positron-Emitting Radionuclides: Potentials and Challenges (2009)

Radioimmunoimaging and therapy has been an area of interest for several decades. Steady progress has been made toward clinical translation of radiolabeled monoclonal antibodies for diagnosis and treatment of diseases. Tremendous advances have been made in imaging technologies such as positron emission tomography (PET). However, these advances have so far eluded routine translation into clinical radioimmunoimaging applications due to the mismatch between the short half-lives of routinely used positron-emitting radionuclides such as (18)F versus the pharmacokinetics of most intact monoclonal antibodies of interest. The lack of suitable positron-emitting radionuclides that match the pharmacokinetics of intact antibodies has generated interest in exploring the use of longer-lived positron emitters that are more suitable for radioimmunoimaging and dosimetry applications with intact monoclonal antibodies. In this review, we examine the opportunities and challenges of radioimmunoimaging with select longer-lived positron-emitting radionuclides such as (124)I, (89)Zr, and (86)Y with respect to radionuclide production, ease of radiolabeling intact antibodies, imaging characteristics, radiation dosimetry, and clinical translation potential.
Strained silicon thin-film transistors fabricated on glass (2005)

Strained-Si thin-film transistors were fabricated on glass substrate by direct transfer of a 35nm strained Si film onto glass. The strained Si films were originally grown on a relaxed SiGe layer on Si substrate. The tensile strain for the strained Si on glass (SSOG) was found to be 0.80%±0.02%. The effective electron mobility of the fabricated NMOS TFTs is 820cm2∕Vs. These devices show low interface charge densities at the bonding interface and at the gate oxide interface, as confirmed by the low subthreshold swing of 77mV∕dec for the 0.5μm SSOG device.
B cell antigen receptor cross-linking induces phosphorylation of the p21 ras oncoprotein activators SHC and mSOS1 as well as assembly of complexes containing SHC, GRB-2, mSOS1, and a 145-kDa tyrosine-phosphorylated protein. (1994)

Ligation of the B cell AgR activates p21ras (Ras). We have investigated the effects of AgR ligation on three proteins that have been implicated as regulators of Ras: SHC, GRB-2, and mSOS1. We show that AgR cross-linking in B cells stimulated tyrosine and serine phosphorylation of SHC. This correlated with the formation of complexes containing SHC, GRB-2, mSOS1, and an unidentified 145-kDa tyrosine-phosphorylated protein. These complexes were present in the cytosol, as well as in the membrane fraction of the cells, where Ras is located. By using a GRB-2 fusion protein to probe blots, we showed that SHC was the major protein that GRB-2 bound to in anti-Ig-stimulated B cells. This argues that SHC couples GRB-2/mSOS1 to the 145-kDa protein and that SHC is likely to be essential for mSOS1 function in B cells. Finally, we found that AgR cross-linking stimulated phosphorylation of mSOS1 and that this could be blocked by an inhibitor of protein kinase C. Thus, signaling by the B cell AgR stimulates phosphorylation of SHC and mSOS1 and induces the formation of membrane-associated complexes containing SHC, GRB-2, mSOS1, and a 145-kDa protein. These events may be important for activation of Ras by the AgR.
Growth Factors in the Treatment of Degenerative Retinal Disorders (2007)

There are currently a number of degenerative conditions, both inherited and acquired, that affect the retina and lead to blindness. Retinal photoreceptors degenerate from inherited conditions, such as retinitis pigmentosa or as a result of light damage or normal ageing; retinal ganglion cells degenerate from optic nerve injury or glaucoma. Current research in this field includes the use of growth factors to: (1) inhibit the degenerative processes; (2) promote regeneration of the retina from the pigmented epithelium; and (3) improve the conditions for transplantation of new cells to the retina by expanding the photoreceptor cell populations in vitro. The results to date have shown that a number of different growth factors promote survival of retinal cells in vitro and in vivo. In addition, some of the same factors can stimulate regeneration in the developing retina and act as mitogens for the retinal progenitor cells. It is likely that a combination of these approaches will ultimately be important for the treatment of the various retinal degenerations.
Synthesis and incorporation of myelin polypeptides into CNS myelin. (1982)

The distribution of newly synthesized proteolipid protein (PLP, 23 kdaltons) and myelin basic proteins (MBPs, 14-21.5 kdaltons) was determined in microsomal and myelin fractions prepared from the brainstems o1 10-30 d-old rats sacrificed at different times after an intracranial injection of 35S-methionine. Labeled MBPs were found in the myelin fraction 2 min after the injection, whereas PLP appeared first in the rough microsomal fraction and only after a lag of 30 min in the myelin fraction. Cell-free translation experiments using purified mRNAs demonstrated that PLP and MBPs are synthesized in bound and free polysomes, respectively. A mechanism involving the cotranslational insertion into the ER membrane and subsequent passage of the polypeptides through the Golgi apparatus is consistent with the lag observed in the appearance of the in vivo-labeled PLP in the myelin membrane. Newly synthesized PLP and MBPs are not proteolytically processed, because the primary translation products synthesized in vitro had the same electrophoretic mobility and N-terminal amino acid sequence as the mature PLP and MBP polypeptides. It was found that crude myelin fractions are highly enriched in mRNAs coding for the MBPs but not in mRNA coding for PLP. This suggests that whereas the bound polysomes synthesizing PLP are largely confined to the cell body, free polysomes synthesizing MBPs are concentrated in oligodendrocyte processes involved in myelination, which explains the immediate incorporation of MBPs into the developing myelin sheath.
Enrichment methods to detect bone marrow micrometastases in breast carcinoma patients: clinical relevance (2004)

These improved methods for the detection of micrometastatic cells in patient BM should help clinicians to predict the clinical status of breast cancer patients at the time of surgery or treatment.
A miniature biofuel cell operating at 0.78 V (2003)

We report the highest voltage miniature biofuel cell to date, a membrane-less cell operating at 37 degrees C in pH 5 buffer at 0.78 V.
Multimodality Imaging In Vivo for Preclinical Assessment of Tumor-Targeted Doxorubicin Nanoparticles (2012)

This study presents a new multimodal imaging approach that includes high-frequency ultrasound, fluorescence intensity, confocal, and spectral imaging to improve the preclinical evaluation of new therapeutics in vivo. Here we use this approach to assess in vivo the therapeutic efficacy of the novel chemotherapy construct, HerDox during and after treatment. HerDox is comprised of doxorubicin non-covalently assembled in a viral-like particle targeted to HER2+ tumor cells, causing tumor cell death at over 10-fold lower dose compared to the untargeted drug, while sparing the heart. Whereas our initial proof-of-principle studies on HerDox used tumor growth/shrinkage rates as a measure of therapeutic efficacy, here we show that multimodal imaging deployed during and after treatment can supplement traditional modes of tumor monitoring to further characterize the particle in tissues of treated mice. Specifically, we show here that tumor cell apoptosis elicited by HerDox can be monitored in vivo during treatment using high frequency ultrasound imaging, while in situ confocal imaging of excised tumors shows that HerDox indeed penetrated tumor tissue and can be detected at the subcellular level, including in the nucleus, via Dox fluorescence. In addition, ratiometric spectral imaging of the same tumor tissue enables quantitative discrimination of HerDox fluorescence from autofluorescence in situ. In contrast to standard approaches of preclinical assessment, this new method provides multiple/complementary information that may shorten the time required for initial evaluation of in vivo efficacy, thus potentially reducing the time and cost for translating new drug molecules into the clinic.
Heterologous production in Wolinella succinogenes and characterization of the quinol:fumarate reductase enzymes from Helicobacter pylori and Campylobacter jejuni (2006)

The epsilon-proteobacteria Helicobacter pylori and Campylobacter jejuni are both human pathogens. They colonize mucosal surfaces causing severe diseases. The membrane protein complex QFR (quinol:fumarate reductase) from H. pylori has previously been established as a potential drug target, and the same is likely for the QFR from C. jejuni. In the present paper, we describe the cloning of the QFR operons from the two pathogenic bacteria H. pylori and C. jejuni and their expression in Wolinella succinogenes, a non-pathogenic -proteobacterium. To our knowledge, this is the first documentation of heterologous membrane protein production in W. succinogenes. We demonstrate that the replacement of the homologous enzyme from W. succinogenes with the heterologous enzymes yields mutants where fumarate respiration is fully functional. We have isolated and characterized the heterologous QFR enzymes. The high quality of the enzyme preparation enabled us to determine unequivocally by analytical ultracentrifugation the homodimeric state of the three detergent-solubilized heterotrimeric QFR enzymes, to accurately determine the different oxidation-reduction ('redox') midpoint potentials of the six prosthetic groups, the Michaelis constants for the quinol substrate, maximal enzymatic activities and the characterization of three different anti-helminths previously suggested to be inhibitors of the QFR enzymes from H. pylori and C. jejuni. This characterization allows, for the first time, a detailed comparison of the QFR enzymes from C. jejuni and H. pylori with that of W. succinogenes.
Chemistry of olefin polymerization reactions with chromium‐based catalysts (2008)

Abstract Detailed GC analysis of oligomers formed in ethylene homopolymerization reactions, ethylene/1‐hexene copolymerization reactions, and homo‐oligomerization reactions of 1‐hexene and 1‐octene in the presence of a chromium oxide and an organochromium catalyst is carried out. A combination of these data with the analysis of 13 C NMR and IR spectra of the respective high molecular weight polymerization products indicates that the standard olefin polymerization mechanism, according to which the starting chain end of each polymer molecule is saturated and the terminal chain end is a CC bond (in the absence of hydrogen in the polymerization reactions), is also applicable to olefin polymerization reactions with both types of chromium‐based catalysts. The mechanism of active center formation and polymerization is proposed for the reactions. Two additional features of the polymerization reactions, co‐trimerization of olefins over chromium oxide catalysts and formation of methyl branches in polyethylene chains in the presence of organochromium catalysts, also find confirmation in the GC analysis. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5330–5347, 2008