gebhart/patrepeval huggingface dataset:
A nonself sugar mimic of the HIV glycan shield shows enhanced antigenicity (2010)

Antibody 2G12 uniquely neutralizes a broad range of HIV-1 isolates by binding the high-mannose glycans on the HIV-1 surface glycoprotein, gp120. Antigens that resemble these natural epitopes of 2G12 would be highly desirable components for an HIV-1 vaccine. However, host-produced (self)-carbohydrate motifs have been unsuccessful so far at eliciting 2G12-like antibodies that cross-react with gp120. Based on the surprising observation that 2G12 binds nonproteinaceous monosaccharide D-fructose with higher affinity than D-mannose, we show here that a designed set of nonself, synthetic monosaccharides are potent antigens. When introduced to the terminus of the D1 arm of protein glycans recognized by 2G12, their antigenicity is significantly enhanced. Logical variation of these unnatural sugars pinpointed key modifications, and the molecular basis of this increased antigenicity was elucidated using high-resolution crystallographic analyses. Virus-like particle protein conjugates containing such nonself glycans are bound more tightly by 2G12. As immunogens they elicit higher titers of antibodies than those immunogenic conjugates containing the self D1 glycan motif. These antibodies generated from nonself immunogens also cross-react with this self motif, which is found in the glycan shield, when it is presented in a range of different conjugates and glycans. However, these antibodies did not bind this glycan motif when present on gp120.
Regulation of MSCF receptors on microglia in the normal and injured mouse central nervous system: A quantitative immunofluorescence study using confocal laser microscopy (1998)

The macrophage colony-stimulating factor (MCSF) is a 40-76-kD glycoprotein that plays an important role in the activation and proliferation of microglia both in vitro and in injured neural tissue. Here, we examined the regulation of MCSF receptor (MCSFR) and MCSF in the normal and injured mouse central nervous system (CNS) by using confocal laser microscopy, quantitative immunofluorescence, and reverse transcriptase-polymerase chain reaction (RT-PCR) techniques. Immunohistochemistry on fixed, floating tissue sections demonstrated low to moderate MCSFR immunoreactivity (MCSFR-IR) on microglia in the gray and white matter throughout the mouse CNS in the forebrain, brainstem, cerebellum, and spinal cord. High levels of MCSFR-IR were restricted to the superficial layer of the spinal cord dorsal horn, substantia nigra, and area postrema, a CNS region that lacks the blood-brain barrier. CNS injury led to a strong and specific increase in MCSFR-IR in the directly injured dorsal forebrain, in the cervical spinal cord (C2) after transection of the sensory, minor occipital nerve, and in the axotomized facial motor nucleus. Further investigation at the mRNA level in the facial nucleus model showed that this increase was accompanied by a rapid induction of the transcript for MCSFR, with a peak 1-2 days after injury, but only a constitutive expression of MCSF-mRNA. In summary, although normal levels of MCSF receptor in most microglia are low, microglial activation is accompanied by a rapid and massive increase. In view of the constitutive expression of MCSF, the early upregulation of the MCSF receptor may play a central role in preparing these macrophage-related cells to take part in the cellular response to CNS injury.
Inheritance of Altered Palmitic Acid Percentage in Two Soybean Mutants (1988)

Journal Article Inheritance of Altered Palmitic Acid Percentage in Two Soybean Mutants Get access E. A. Erickson, E. A. Erickson Dekalb-Pfizer GeneticsDekalb, Illinois Search for other works by this author on: Oxford Academic PubMed Google Scholar J. R. Wilcox, J. R. Wilcox USDA-ARS and Department of Agronomy, Purdue UniversityWest Lafayette, Indiana Address reprint requests to Dr. Wilcox, Department of Agronomy, Purdue University, West Lafayette, IN 47907. Search for other works by this author on: Oxford Academic PubMed Google Scholar J. F. Cavins J. F. Cavins USDA-ARS, Northern Regional Research CenterPeoria, Illinois Search for other works by this author on: Oxford Academic PubMed Google Scholar Journal of Heredity, Volume 79, Issue 6, November 1988, Pages 465–468, https://doi.org/10.1093/oxfordjournals.jhered.a110552 Published: 01 November 1988
Middle East Respiratory Syndrome Coronavirus Quasispecies That Include Homologues of Human Isolates Revealed through Whole-Genome Analysis and Virus Cultured from Dromedary Camels in Saudi Arabia (2014)

ABSTRACT Complete Middle East respiratory syndrome coronavirus (MERS-CoV) genome sequences were obtained from nasal swabs of dromedary camels sampled in the Kingdom of Saudi Arabia through direct analysis of nucleic acid extracts or following virus isolation in cell culture. Consensus dromedary MERS-CoV genome sequences were the same with either template source and identical to published human MERS-CoV sequences. However, in contrast to individual human cases, where only clonal genomic sequences are reported, detailed population analyses revealed the presence of more than one genomic variant in individual dromedaries. If humans are truly infected only with clonal virus populations, we must entertain a model for interspecies transmission of MERS-CoV wherein only specific genotypes are capable of passing bottleneck selection. IMPORTANCE In most cases of Middle East respiratory syndrome (MERS), the route for human infection with the causative agent, MERS coronavirus (MERS-CoV), is unknown. Antibodies to and viral nucleic acids of MERS-CoV have been found in dromedaries, suggesting the possibility that they may serve as a reservoir or vector for human infection. However, neither whole viral genomic sequence nor infectious virus has been isolated from dromedaries or other animals in Saudi Arabia. Here, we report recovery of MERS-CoV from nasal swabs of dromedaries, demonstrate that MERS-CoV whole-genome consensus sequences from dromedaries and humans are indistinguishable, and show that dromedaries can be simultaneously infected with more than one MERS-CoV. Together with data indicating widespread dromedary infection in the Kingdom of Saudi Arabia, these findings support the plausibility of a role for dromedaries in human infection.
Capture, Unfolding, and Detection of Individual tRNA Molecules Using a Nanopore Device (2015)

Transfer RNAs (tRNA) are the most common RNA molecules in cells and have critical roles as both translators of the genetic code and regulators of protein synthesis. As such, numerous methods have focused on studying tRNA abundance and regulation, with the most widely used methods being RNA-seq and microarrays. Though revolutionary to transcriptomics, these assays are limited by an inability to encode tRNA modifications in the requisite cDNA. These modifications are abundant in tRNA and critical to their function. Here, we describe proof-of-concept experiments where individual tRNA molecules are examined as linear strands using a biological nanopore. This method utilizes an enzymatically ligated synthetic DNA adapter to concentrate tRNA at the lipid bilayer of the nanopore device and efficiently denature individual tRNA molecules, as they are pulled through the α-hemolysin (α-HL) nanopore. Additionally, the DNA adapter provides a loading site for ϕ29 DNA polymerase (ϕ29 DNAP), which acts as a brake on the translocating tRNA. This increases the dwell time of adapted tRNA in the nanopore, allowing us to identify the region of the nanopore signal that is produced by the translocating tRNA itself. Using adapter-modified Escherichia coli tRNA(fMet) and tRNA(Lys), we show that the nanopore signal during controlled translocation is dependent on the identity of the tRNA. This confirms that adapter-modified tRNA can translocate end-to-end through nanopores and provide the foundation for future work in direct sequencing of individual transfer RNA with a nanopore-based device.
Vaccination of Healthy Volunteers with Human Papillomavirus Type 16 L2E7E6 Fusion Protein Induces Serum Antibody that Neutralizes across Papillomavirus Species (2006)

Oncogenic human papillomavirus (HPV) infection is a necessary cause of cervical cancer. Therefore, vaccination to prevent or eliminate HPV infection could reduce the incidence of cervical cancer. A fusion protein comprising HPV16 L2, E6, and E7 is a candidate combination preventive and therapeutic HPV vaccine. The L1- and L2-specific and neutralizing serum antibody titers and peripheral blood mononucleocyte antigen-specific proliferative responses generated by vaccination thrice at monthly intervals with HPV16 L2E7E6 were compared in two studies: a phase I randomized double-blind placebo controlled dose escalation trial in 40 healthy volunteers and a phase II trial of HPV16 L2E7E6 at the maximum dose in 29 women with high-grade anogenital intraepithelial neoplasia (AGIN). Vaccination of healthy volunteers induced L2-specific serum antibodies that were detected 1 month after the final vaccination (P(binomial) < 0.001). There was a significant trend to seroconversion for HPV16 and HPV18 neutralizing antibodies with increasing vaccine dose (P = 0.006 and P = 0.03, respectively). Seroconversion for HPV18 neutralizing antibodies showed a significant positive trend with increasing dose (P = 0.03) and was associated with seroconversion for HPV16 neutralizing antibodies (P(exact) = 0.04). The antigen-specific proliferative response of vaccinated healthy volunteers also showed a significant trend with increasing vaccine dose (P = 0.04). However, AGIN patients responded less effectively to vaccination than healthy patients for induction of HPV16 L2-specific antibody (P < 0.001) and proliferative responses (P < 0.001). Vaccination of healthy volunteers thrice with 533-mug HPV16 L2E7E6 at monthly intervals induced L2-specific serum antibodies that neutralized across papillomavirus species. Responses in AGIN patients were infrequent.
Polylactide−Poly(dimethylsiloxane)−Polylactide Triblock Copolymers as Multifunctional Materials for Nanolithographic Applications (2010)

Highly immiscible block copolymers are attractive materials for applications in nanolithography due to their ability to self-assemble on length scales that are difficult to access by conventional lithography. The incorporation of inorganic domains into such block copolymers provides etch contrast that can potentially reduce processing times and costs in nanolithographic applications. We explored thin films of polylactide-poly(dimethylsiloxane)-polylactide (PLA-PDMS-PLA) triblock copolymers as multifunctional nanolithographic templates. We demonstrate the formation of well-ordered arrays of hexagonally packed PDMS cylinders oriented normal to the substrate, the orthogonal etchability of these cylinders and the PLA matrix, and the formation of etch-resistant domains that can be used as pattern transfer masks.
INTERLEUKIN-13, IN COMBINATION WITH ANTI-INTERLEUKIN-12, INCREASES GRAFT PROLONGATION AFTER PORTAL VENOUS IMMUNIZATION WITH CULTURED ALLOGENEIC BONE MARROW-DERIVED DENDRITIC CELLS1 (1996)

Portal venous (pv) transfusion before transplant with large numbers (100 x 10(6)) of irradiated multiple minor histoincompatible spleen cells (B10.Br) augments allogeneic skin graft survival in C3H mice. We have shown in earlier studies that this is correlated with preferential activation for production of type 2 cytokines (interleukin [IL]-4 and IL-10) and decreased production of type 1 cytokines (IL-2 and interferon [IFN] gamma). We have also shown that recombinant (r)IL-12, in association with anti-IL-10 monoclonal antibody, can reverse in vivo the graft prolongation afforded by pv immunization and the altered cytokine production that follows. Adoptive transfer of inhibition of graft rejection is possible at early times after pv immunization, using plastic adherent cells obtained from the liver of treated mice. We show below that within 4 days of pv immunization, dendritic cells (NLDC-145+) isolated from the thymus, mesenteric lymph node (MLN), and.
Human T cells resistant to complement lysis by bivalent antibody can be efficiently lysed by dimers of monovalent antibody (2002)

We have previously shown that bivalent human gamma1 CD3 monoclonal antibody (mAb) is ineffective at mediating lysis of human T cells with human complement. In this paper we have used genetic engineering and sulfur chemistry to prepare 2 types of human gamma1 CD3 mAb dimer, with the aim of improving complement lysis activity. The IgG molecules forming the dimers were linked together at their C-termini by stable bismaleimide thioether bridges. The first dimer was composed of 2 bivalent mAb molecules. This dimer proved incapable of lysing human T-cell blasts with human, rabbit, or guinea pig complement. The second dimer consisted of 2 molecules of a monovalent derivative (possessing a single Fab domain) of the bivalent mAb. This dimer was highly lytic with human complement, with a lytic titer 64-fold greater than that of the nondimerized monovalent mAb. The maximum level of lysis of human T-cell blasts achieved with this monovalent mAb dimer was equal to that obtained with the therapeutic antilymphocyte mAb alemtuzumab, but its lytic titer was 4-fold greater. The monovalent mAb dimer was also found to be lytic in the presence of rabbit and guinea pig complement. Dimerization of monovalent antibodies may provide a general strategy for improving the cytolytic activity of other mAbs that are normally unable to induce lysis with complement. The monovalent CD3 mAb dimer may have potential for development as an agent for immunotherapy of T-cell leukemia.
Olefin metathesis catalysts bearing a pH-responsive NHC ligand: a feasible approach to catalyst separation from RCM products (2008)

Two novel ruthenium-based olefin metathesis catalysts, H(2)ITap(PCy(3))Cl(2)Ru[double bond, length as m-dash]CH-Ph and H(2)ITapCl(2)Ru[double bond, length as m-dash]CH-(C(6)H(4)-O-iPr) (H(2)ITap = 1,3-bis(2',6'-dimethyl-4'-dimethylaminophenyl)-4,5-dihydroimidazol-2-ylidene), were synthesized bearing a pH-responsive NHC ligand with two aromatic NMe(2) groups. The crystal structures of complexes and were determined via X-ray crystallography. Both catalysts perform ring opening metathesis polymerization (ROMP) of cyclooctene (COE) at faster rates than their commercially available counterparts H(2)IMes(PCy(3))Cl(2)Ru[double bond, length as m-dash]CH-Ph and H(2)IMesCl(2)Ru[double bond, length as m-dash]CH-(C(6)H(4)-O-iPr) (H(2)IMes = 1,3-bis(2',4',6'-trimethylphenyl)-4,5-dihydroimidazol-2-ylidene) and perform at similar rates during ring closing metathesis (RCM) of diethyldiallylmalonate (DEDAM). Upon addition of 2 equiv. of HCl, catalyst is converted into a mixture of several mono and diprotonated Ru-carbene species 12' which are soluble in methanol but degrade within a few hours at room temperature. Catalyst can be protonated with 2 equiv. of HCl and the resulting complex is moderately water-soluble. The complex is stable in aqueous solution in air for >4 h, but over prolonged periods of time shows degradation in acidic media due to hydrolysis of the NHC-Ru bond. Catalysts and perform RCM of diallylmalonic acid in acidic protic media with only moderate activity at 50 degrees C and do not produce polymer in the ROMP of cationic 7-oxanorbornene derivative under the same conditions. Catalyst was used for Ru-seperation studies when RCM of DEDAM or 3,3-diallypentadione (DAP) was conducted in low-polar organic solution and the Ru-species was subsequently precipitated by addition of strong acid. The Ru-species were removed by (1) filtration and (2) filtration and subsequent extraction with water. The residual Ru-levels could be reduced to as far as 11 ppm (method 2) and 24 ppm (method 1) without the use of chromatography or other scavenging methods.
Hypoxic-Ischemic Injury Induces Macrophage Inflammatory Protein-1α Expression in Immature Rat Brain (2002)

These data implicate MIP-1alpha as a mediator of the complex and sustained inflammatory response initiated by perinatal HI braininjury.
Chemoprevention of Colon Cancer by Organoselenium Compounds and Impact of High- or Low-Fat Diets (1997)

In this model system, p-methoxy-BSC and p-XSC are effective agents for the chemoprevention of colon cancer. The effects of p-XSC were enhanced in animals fed a low-fat diet.
High Capacity Li-Rich Positive Electrode Materials with Reduced First-Cycle Irreversible Capacity Loss (2015)

The first charge–discharge cycling behaviors of two sets of Li–Ni–Mn–Co type positive electrode materials were compared. The samples in each set have similar Ni–Mn–Co ratios but different Li-to-total metal ratio (Li/M). The samples that were Li-rich with a Li[LixM(1–x)]O2 structure showed a typical 4.5 V "oxygen loss" plateau and a typical irreversible capacity loss near 25%. Surprisingly, other samples with lower Li/M ratios that still exhibited a 4.5 V "oxygen loss" plateau exhibited an irreversible capacity loss as low as 4.0% of their first charge capacity. XRD analysis revealed that all samples were single-phase layered oxides. A separate and a detailed XRD analysis combined with dQ/dV analysis showed that the reduced irreversible capacity loss was not caused by the admixture of a spinel phase. ICP-OES results and the oxidation state versus atomic occupancy rules suggested the presence of metal site vacancies in the pristine materials with low IRC, which were confirmed by densities measured with a helium pycnometer. The results presented here show that the small irreversible capacity is a consequence of (a) metal site vacancies, leading to Li[□qM(1–q)]O2 structures, where □ is a metal site vacancy, which leads to (b) no Li atoms in the transition metal layer. These materials still have Li/M > 1, so they are "Li-rich", but they are "traditional layered materials" with no Li in the transition metal layer. This study identifies a new route for fabricating high capacity Li-rich positive electrode materials with small irreversible capacity loss.
Voltage-Tunable Far-Infrared Emission from Si Inversion Layers (1976)

We have observed voltage-tunable far-infrared emission from inversion layers of $n$-channel metal-oxide-simiconductor field-effect transistors fabricated on $p$-type (100) Si. The radiation is emitted by the electronic transition from the two-dimensional excited-state ${E}_{1}$ sub-band of the inversion layer to its ground-state ${E}_{0}$ sub-band. Population of the excited-state sub-band is realized by heating up the electron distribution with an electric field applied along the channel.
Effect of protein coating of flocked swabs on the collection and release of clinically important bacteria (2014)

Clinical swab heads are often coated with biopolymers to improve the recovery and survival of organisms. To assess the effect of swab head material coating, water absorption capacity and capture and release characteristics of four pathogenic bacteria from protein coated and uncoated flocked swabs were determined. Demonstration of no uniformly higher recovery of all test bacteria from coated swabs over their corresponding uncoated swabs suggest importance of physicochemical properties of swab tip material compared with biopolymer coating, for swab selection for clinical applications.
STILBAMIDINE AND PENTAMIDINE IN MULTIPLE MYELOMA (1947)

Antimony compounds cure kala-azar, a disease which is accompanied with an increase in the globulin content of the serum.<sup>1</sup>Because of this association, antimony compounds have been tried in other diseases in which hyperglobulinemia occasionally occurs. These preparations have been given in Hodgkin's disease, leukemia and multiple myeloma, but until now favorable reports have not appeared in the literature. Since 1939 diamidine compounds not containing antimony have been successfully employed in the treatment of kala-azar.<sup>2</sup>This report deals with the influence of two diamidine compounds, Stilbamidine (4,4-diamidinostilbene) and Pentamidine (4,4'-[pentamethylenedioxy]dibenzamidine),<sup>3</sup>on multiple myeloma, a disease in which increase of the globulin content of the serum is of frequent occurrence.<sup>4</sup> For 13 patients with multiple myeloma the administration of Stilbamidine, combined with a diet low in animal protein, has had a favorable influence on the pain which is characteristic of this disease. For 2 patients with myeloma
Intranodal Administration of Peptide-Pulsed Mature Dendritic Cell Vaccines Results in Superior CD8+T-Cell Function in Melanoma Patients (2003)

Administration of this peptide-pulsed mature DC vaccine by IN, IV, or ID routes is feasible and safe. IN administration seems to result in superior T-cell sensitization as measured by de novo target-cell recognition and DTH priming, indicating that IN may be the preferred ROA for mature DC vaccines.
The Omega Navigation System (1965)

omega is a very long-range VLF navigation system generating hyperbolic lines-of-position by phase difference measurements of 10.2 kc/s time-shared transmissions. A new multi-frequency signal format is described which will increase the system utility. The background, theory, and results of a six-year developmental effort on the omega navigation system are presented. A worldwide system employing eight stations is feasible. Such a system would be straightforward in use and have an accuracy of one-half to one mile. Operational results of twenty-five shipboard installations are presented.
Conjugated Polymer Actuators for Biomedical Applications (2003)

Abstract Conjugated polymers are electroactive and have found applications as artificial muscles. Actuators that have been developed over the last decade have now reached the early stages of commercialization, particularly for use in biomedical devices. This article reviews the motivation for using this class of actuator, the types of devices that have been fabricated, and some of the biomedical applications that are being developed. Recommendations are presented for future work on understanding the actuation mechanisms, on actuator design, and on the measurement of metrics.
Protein Kinase N (PKN) and PKN-Related Protein Rhophilin as Targets of Small GTPase Rho (1996)

The Rho guanosine 5'-triphosphatase (GTPase) cycles between the active guanosine triphosphate (GTP)-bound form and the inactive guanosine diphosphate-bound form and regulates cell adhesion and cytokinesis, but how it exerts these actions is unknown. The yeast two-hybrid system was used to clone a complementary DNA for a protein (designated Rhophilin) that specifically bound to GTP-Rho. The Rho-binding domain of this protein has 40 percent identity with a putative regulatory domain of a protein kinase, PKN. PKN itself bound to GTP-Rho and was activated by this binding both in vitro and in vivo. This study indicates that a serine-threonine protein kinase is a Rho effector and presents an amino acid sequence motif for binding to GTP-Rho that may be shared by a family of Rho target proteins.
Levels of interleukin-18 and its binding inhibitors in the blood circulation of patients with adult-onset Still's disease (2001)

These data indicate that systemic overproduction of IL-18 may be closely related to the pathogenesis of ASD, despite the restriction on its inflammatory activity by IL-18 binding inhibitors such as IL-18BP. The disease activity appears to be determined on the basis of the relative levels of IL-18 and its specific inhibitors.
Oligobodies: bench made synthetic antibodies. (1999)

Using synthetic peptides and a combinatorial library of 56 mer random oligonucleotides, we have developed reagents that behave as "synthetic antibodies". The results obtained with the protein phosphatase 2A as a model system are shown here. The specificity of these reagents, named "oligobodies", has been demonstrated by Western blot analysis and immunohistochemistry. The oligobodies have enormous advantages compared to antibodies: their production is independent of the immune system, they can be prepared in a few days and there is no need for a purified target protein. These reagents can be produced even if the corresponding protein was never isolated or purified, since only a partial DNA sequence from a database provides enough information to make them.