gebhart/patrepeval huggingface dataset:
Evaluation in mice of Brucella ovis attenuated mutants for use as live vaccines against B. ovis infection (2014)

Brucella ovis causes ram contagious epididymitis, a disease for which a specific vaccine is lacking. Attenuated Brucella melitensis Rev 1, used as vaccine against ovine and caprine brucellosis caused by B. melitensis, is also considered the best vaccine available for the prophylaxis of B. ovis infection, but its use for this purpose has serious drawbacks. In this work, two previously characterized B. ovis attenuated mutants (Δomp25d and Δomp22) were evaluated in mice, in comparison with B. melitensis Rev 1, as vaccines against B. ovis. Similarities, but also significant differences, were found regarding the immune response induced by the three vaccines. Mice vaccinated with the B. ovis mutants developed anti-B. ovis antibodies in serum of the IgG1, IgG2a and IgG2b subclasses and their levels were higher than those observed in Rev 1-vaccinated mice. After an antigen stimulus with B. ovis cells, splenocytes obtained from all vaccinated mice secreted similar levels of TNF-α and IL12(p40) and remarkably high amounts of IFN-γ, a crucial cytokine in protective immunity against other Brucella species. By contrast, IL-1α -an enhancer of T cell responses to antigen- was present at higher levels in mice vaccinated with the B. ovis mutants, while IL-10, an anti-inflammatory cytokine, was significantly more abundant in Rev 1-vaccinated mice. Additionally, the B. ovis mutants showed appropriate persistence, limited splenomegaly and protective efficacy against B. ovis similar to that observed with B. melitensis Rev 1. These characteristics encourage their evaluation in the natural host as homologous vaccines for the specific prophylaxis of B. ovis infection.
Fast 3-D dark-field reflection-mode photoacoustic microscopy in vivo with a 30-MHz ultrasound linear array (2008)

We present an in vivo dark-field reflection-mode photoacoustic microscopy system that performs cross-sectional (B-scan) imaging at 50 Hz with real-time beamforming and 3-D imaging consisting of 166 B-scan frames at 1 Hz with postbeamforming. To our knowledge, this speed is currently the fastest in photoacoustic imaging. A custom-designed light delivery system is integrated with a 30-MHz ultrasound linear array to realize dark-field reflection-mode imaging. Linear mechanical scanning of the array produces 3-D images. The system has axial, lateral, and elevational resolutions of 25, 70, and 200 microm, respectively, and can image 3 mm deep in scattering biological tissues. Volumetric images of subcutaneous vasculature in rats are demonstrated in vivo. Fast 3-D photoacoustic microscopy is anticipated to facilitate applications of photoacoustic imaging in biomedical studies that involve dynamics and clinical procedures that demand immediate diagnosis.
Poly (propyleneimine) dendrimer based nanocontainers for targeting of efavirenz to human monocytes/macrophagesin vitro (2007)

Cells of the mononuclear phagocytic system, in particular monocytes/macrophages (Mo/Mac) serve as a reservoir for human immunodeficiency virus (HIV) and are believed to be responsible for its dissemination throughout the body and especially into the brain. Treatment of HIV infection, therefore, must reach these cells in addition to the lymphocytes. The purpose of the present study is to develop poly(propyleneimine) (PPI) dendrimer-based nanocontainers for targeting of efavirenz (EFV) to Mo/Mac. Fifth generation PPI dendrimer, t-Boc-glycine conjugated PPI dendrimer (TPPI) and mannose conjugated dendrimers were synthesized and characterized. While the haemolytic activity and cytotoxicity of PPI dendrimer was found to be very high, the toxicity of t-Boc-glycine conjugated dendrimer and mannose conjugated dendrimers were found to be negligible. The entrapment efficiency of mannose conjugated dendrimer was found to be 47.4%, followed by that of PPI dendrimer (32.15%) and t-Boc-glycine conjugated dendrimer (23.1%). The in vitro drug release profile shows that while PPI dendrimer releases the drug by 24 h, the dendrimer-based nanocontainers prolong the release rate up to 144 h (83 +/- 0.4% in case of t-Boc-glycine conjugated dendrimer and 91 +/- 0.3% in mannose conjugated dendrimer). The cellular uptake of EFV was found to be both concentration and time dependent. Significant increase in cellular uptake of EFV by Mo/Mac cells were observed in case of mannose conjugated dendrimer which is 12 times higher than that of free drug and 5.5 times higher than that of t-Boc-glycine conjugated dendrimer. While mannose conjugated dendrimer was taken up by the lectin receptors of the cells, phagocytosis of t-Boc-glycine conjugated dendrimer might be responsible for its enhanced uptake. Results suggest that the proposed carriers hold potential to increase the efficacy and reduce the toxicity of antiretroviral therapy.
IFN-gamma is the inducer of indoleamine 2,3-dioxygenase in allografted tumor cells undergoing rejection. (1990)

The depletion of an essential amino acid, tryptophan, caused by induction of indoleamine 2,3-dioxygenase (IDO), has been shown to be a mechanism involving self-defense against inhaled microorganisms and tumor growth. We recently reported that the IDO is dramatically (approximately 50-fold) induced in allografted tumor (3-methylcholanthrene-induced ascites type tumor cells) cells undergoing rejection, and that the enzyme is induced by factor(s) released through the interaction of allografted tumor cells with infiltrating leukocytes. The culture supernatant of infiltrating leukocytes, which were harvested on day 7 after tumor transplantation, induced the highest IDO activity in the tumor cells. The inducer activity was completely neutralized by the addition of antibody to IFN-gamma but not by antibody to IFN-alpha/beta. Approximately 6 U/ml of IFN-gamma was detected by an ELISA assay in the 12-h culture supernatant with 2 x 10(6) leukocytes/ml, and rIFN-gamma at 6 U/ml induced IDO in 3-methylcholanthrene-induced ascites type tumor cells to the same extent as IFN-gamma in the culture supernatant. Moreover, i.p. administration of antibody to IFN-gamma almost completely inhibited the induction of IDO in the allografted tumor cells. These observations indicate that the factor responsible for IDO induction in the allografted tumor cells is IFN-gamma.
Escherichia colipromoter sequences predictin vitroRNA polymerase selectivity (1984)

We describe a simple algorithm for computing a homology score for Escherichia coli promoters based on DNA sequence alone. The homology score was related to 31 values, measured in vitro, of RNA polymerase selectivity, which we define as the product KBk2, the apparent second order rate constant for open complex formation. We found that promoter strength could be predicted to within a factor of +/-4.1 in KBk2 over a range of 10(4) in the same parameter. The quantitative evaluation was linked to an automated (Apple II) procedure for searching and evaluating possible promoters in DNA sequence files.
The Structure and Function of Yeast Centromeres (1985)

Orthologs and paralogs are two fundamentally different types of homologous genes that evolved, respectively, by vertical descent from a single ancestral gene and by duplication. Orthology and paralogy are key concepts of evolutionary genomics. A ...Read More
Secretion of lipids induced by inhibition of peptidoglycan synthesis in streptococci (1977)

Inhibition of peptidoglycan synthesis causes an immediate and massive secretion of both newly synthesized and "old" lipids from several species of bacteria, including streptococci, Staphylococcus epidermidis, and Bacillus subtilis. Lipid secretion occurs in the absence of detectable bacterial lysis. This novel phenomenon was examined in more detail in three strains of streptococci: S. sanguis (group H), S. pyogenes (group A), And S. pneumoniae. The secretion of lipids is specifically induced by inhibitors of peptidoglycan synthesis; it is not caused by inhibitors of protein, ribonucleic acid, or deoxyribonucleic acid synthesis. The occurrence appears to be reversible since penicillin-induced secretion comes to a halt upon the timely addition of penicillinase, correlating with resumption of culture growth. All cellular lipids are secreted in essentially the same proportions as those found in the drug treated bacteria. It is suggested that continued peptidoglycan synthesis may be essential for the integration and retention of lipid material in the plasma membrane.
Pulmonary Delivery of Metoprolol Reduces Ventricular Rate During Atrial Fibrillation and Accelerates Conversion to Sinus Rhythm (2019)

Intratracheal delivery of metoprolol effectively reduces ventricular rate during AF and accelerates conversion to normal sinus rhythm in a pig model of acetylcholine-induced AF.
Efforts toward Expansion of the Genetic Alphabet:  Structure and Replication of Unnatural Base Pairs (2007)

Expansion of the genetic alphabet has been a long-time goal of chemical biology. A third DNA base pair that is stable and replicable would have a great number of practical applications and would also lay the foundation for a semisynthetic organism. We have reported that DNA base pairs formed between deoxyribonucleotides with large aromatic, predominantly hydrophobic nucleobase analogues, such as propynylisocarbostyril (dPICS), are stable and efficiently synthesized by DNA polymerases. However, once incorporated into the primer, these analogues inhibit continued primer elongation. More recently, we have found that DNA base pairs formed between nucleobase analogues that have minimal aromatic surface area in addition to little or no hydrogen-bonding potential, such as 3-fluorobenzene (d3FB), are synthesized and extended by DNA polymerases with greatly increased efficiency. Here we show that the rate of synthesis and extension of the self-pair formed between two d3FB analogues is sufficient for in vitro DNA replication. To better understand the origins of efficient replication, we examined the structure of DNA duplexes containing either the d3FB or dPICS self-pairs. We find that the large aromatic rings of dPICS pair in an intercalative manner within duplex DNA, while the d3FB nucleobases interact in an edge-on manner, much closer in structure to natural base pairs. We also synthesized duplexes containing the 5-methyl-substituted derivatives of d3FB (d5Me3FB) paired opposite d3FB or the unsubstituted analogue (dBEN). In all, the data suggest that the structure, electrostatics, and dynamics can all contribute to the extension of unnatural primer termini. The results also help explain the replication properties of many previously examined unnatural base pairs and should help design unnatural base pairs that are better replicated.
Vagal input to the enteric nervous system (2000)

The enteric nervous system (ENS) of the gastrointestinal tract has traditionally been viewed as a system of ganglia that operates largely independently of the brain and spinal cord. Because of this postulated autonomy, the ENS has even been characterised as the “little brain” or the “second brain.” Recent neural tracing studies, however, challenge this canon of ENS autonomy.

The view that the ENS is independent can be traced to several types of observation. Early research on the relationship of the ENS to the central nervous system (CNS) noted that the ENS could support motor activity and a number of local reflexes when the viscera were decentralised or isolated. Langley (1922),1 in his seminal analyses, reinforced the idea of a largely autonomous ENS by noting that the preganglionic axons projecting to the ENS were far outnumbered by the multitude of enteric neurones in the viscera. In the case of the vagus nerve in particular, Langley envisioned a few specialised “mother cells” or “vagal cells” in the ENS that were contacted by preganglionic inputs and that then distributed the relatively small number of inputs to a bigger group of effector neurones within the enteric plexuses. In a related but more modern view, Wood (1987)2 suggested that autonomic preganglionics might project to “command neurones” within the ENS.3 On the sensory side, early observations also noted that individuals with intact peripheral nerves connecting the ENS and CNS had little awareness of visceral afferent feedback.

Although the view of an all-but-autonomous ENS still tends to dominate thinking and teaching about the innervation of the gastrointestinal tract, it should be stressed that the …
Outer membrane protein G: Engineering a quiet pore for biosensing (2008)

Bacterial outer membrane porins have a robust beta-barrel structure and therefore show potential for use as stochastic sensors based on single-molecule detection. The monomeric porin OmpG is especially attractive compared with multisubunit proteins because appropriate modifications of the pore can be easily achieved by mutagenesis. However, the gating of OmpG causes transient current blockades in single-channel recordings that would interfere with analyte detection. To eliminate this spontaneous gating activity, we used molecular dynamics simulations to identify regions of OmpG implicated in the gating. Based on our findings, two approaches were used to enhance the stability of the open conformation by site-directed mutagenesis. First, the mobility of loop 6 was reduced by introducing a disulfide bond between the extracellular ends of strands beta12 and beta13. Second, the interstrand hydrogen bonding between strands beta11 and beta12 was optimized by deletion of residue D215. The OmpG porin with both stabilizing mutations exhibited a 95% reduction in gating activity. We used this mutant for the detection of adenosine diphosphate at the single-molecule level, after equipping the porin with a cyclodextrin molecular adapter, thereby demonstrating its potential for use in stochastic sensing applications.
Identification of two biologically distinct strains of transmissible mink encephalopathy in hamsters (1992)

Experimental transmission of the Stetsonville, Wisconsin, U.S.A. source of transmissible mink encephalopathy (TME) to outbred Syrian golden hamsters resulted in two distinct syndromes, termed hyper (HY) and drowsy (DY), that diverge by the third hamster passage. The syndromes differed with respect to clinical signs, incubation period, brain titre, brain lesion profile and pathogenicity in mink. HY hamster TME had an incubation period of 65 +/- 1 days and was characterized by clinical signs of hyperaesthesia and cerebellar ataxia. Lethargy and the absence of hyperexcitability or cerebellar ataxia were representative of DY hamster TME which had an incubation period of 168 +/- 2 days. At endstage, HY and DY infected animals had brain titres of 10(9.5) LD50/g and 10(7.4) LD50/g of tissue, respectively, indicating that the replication kinetics of these two strains is different. Hamster TME passaged back into mink revealed that only DY retained mink pathogenicity. This suggests that the DY agent is the major mink pathogen in the Stetsonville TME source that is also pathogenic in hamsters after a long incubation period. The HY agent is likely to be a minor component of the original TME mink brain that replicates more rapidly than DY agent in hamsters, but alone is non-pathogenic in mink. The presence of the HY and DY strains of agent that retain their biological characteristics on repeated hamster passage in the Stetsonville TME source requires that the informational molecule encoding these transmissible agents has the capacity to account for this biological diversity.
Inactivatedpep27mutant as an effective mucosal vaccine against a secondary lethal pneumococcal challenge in mice (2013)

Intranasal immunization with the inactivated pep27 mutant may be able to provide mucosal immunity, and could represent an efficient mucosal vaccine.
Viterbi Detection of Class IV Partial Response on a Magnetic Recording Channel (1986)

The application of Viterbi detection to Class IV partial response on a magnetic recording channel is discussed. The theoretical performance is analyzed in the presence of noise correlation and quantizing errors. A simplified algorithm is described which was implemented on a transverse-scan magnetic tape recorder operating at a linear density of 1800 bits/mm and a transfer rate of 120 Mbits/s. Following an initial 5 bit analog-to-digital conversion of the ternary waveform, the Viterbi detector is implemented entirely in high-speed digital emitter-coupled logic. An advantage of approximately 1.5 dB in effective signal-to-noise ratio is gained over a simple level detector, a result which agrees well with the theoretical development.
Surface-downhole electrical resistivity tomography applied to monitoring of CO2 storage at Ketzin, Germany (2012)

ABSTRACT Surface-downhole electrical resistivity tomography (SD-ERT) surveys were repeatedly carried out to image CO2 injected at the pilot storage Ketzin, Germany. The experimental setup combines surface with downhole measurements by using a permanent electrode array that has been deployed in three wells. Two baseline experiments were performed during the site startup and three repeat experiments were performed during the first year of CO2 injection. By the time of the third repeat, approximately 13,500 tons of CO2 had been injected into the reservoir sandstones at about 650 m depth. Field data and inverted resistivity models showed a resistivity increase over time at the CO2 injector. The lateral extent of the related resistivity signature indicated a preferential CO2 migration toward the northwest. Using an experimental resistivity-saturation relationship, we mapped CO2 saturations by means of the resistivity index method. For the latest repeat, CO2 saturations show values of up to 70% near the injection well, which matches well with CO2 saturations determined from pulsed neutron-gamma logging. The presence of environmental noise, reservoir heterogeneities, and irregularities in the well completions are the main sources of uncertainty for the interpretations. The degradation of the permanently installed downhole components is monitored by means of frequently performed resistance checks. In consistency with the SD-ERT data, these resistance checks indicate a long-term resistivity increase near the CO2 injector. In conclusion, the investigations demonstrate the capability of surface-downhole electrical resistivity tomography to image geologically stored CO2 at the Ketzin site.
Dual band dual polarized basestation antenna FDTD design study (2007)

A wide-band, dual-polarized antenna was designed. The calculation utilizes a small cubic pixel size and long simulation time in order to achieve accuracy in simulations for dual-resonant circuits. The design was measured with no tuning of dimensions after building. The measured bandwidth is 9% narrower than simulated. Also the effect of the feed capacitor volume on the polarization purity was checked.
Design and Implementation of 3D Auditory Scene Visualizer towards Auditory Awareness with Face Tracking (2008)

If machine audition can recognize an auditory scene containing simultaneous and moving talkers, what kinds of awareness will people gain from an auditory scene visualizer? This paper presents the design and implementation of 3D Auditory Scene Visualizer based on the visual information seeking mantra, i.e., ldquooverview first, zoom and filter, then details on demandrdquo. The machine audition system called HARK captures 3D sounds with a microphone array, localizes and separates sounds, and recognizes separated sounds by automatic speech recognition (ASR). The 3D visualizer implemented in Java 3D displays each sound stream as a beam originating from the center of the microphones (overview mode), shows temporal snapshots with/without specifying focusing areas (zoom and filter mode), and shows detailed information about a particular sound stream (details on demand). In the details-ondemand mode, ASR results are displayed in a ldquokaraokerdquo manner, i.e., character-by-character. This three-mode visualization will give the user auditory awareness enhanced by HARK. In addition, a face-tracking system automatically changes the focus of attention by tracking the userpsilas face. The resulting system is portable and can be deployed in any place, so it is expected to give more vivid awareness than expensive high-fidelity auditory scene reproduction systems.
All-dielectric high-efficiency reflection gratings made with multilayer thin-film coatings (1995)

We made a high-efficiency ref lection grating by coating a nine-layer quarter-wave system of ZnS/Na(3)AlF(6) directly onto a surface-relief grating in photoresist. Eff iciencies of 70% and 84% were measured at the firstorder Littrow mount with the laser beam incident from the air side and from the substrate side, respectively. The experimental results are in qualitative agreement with theoretical predictions. The key to further improvement in the diffraction eff iciency is to improve the contour conformation of the coated dielectric layers.
Intra- and Extracellular Immunization Against HIV-1 Infection with Lymphocytes Transduced with an AAV Vector Expressing a Human Anti-gp120 Antibody (1996)

Recently, we developed a novel anti-HIV-1 approach by transducing an anti-gp120 antibody gene into lymphocytes, resulting in the resistance to HIV-1 infection by the combined intra- and extracellular binding activities of the neutralizing antibody. To extend this study, we improved the co-expression of the heavy and light chains of the Fab105 fragment of the anti-gp120 antibody F105 by using an internal ribosome entry site (IRES) sequence. The Fab105 expression cassette was then cloned into an adeno-associated virus (AAV) shuttle vector, and encapsidated recombinant AAV-Fab105 vectors were produced. The Fab105 antibody gene was shown to be transduced into human lymphocytes by using the recombinant AAV viruses. The transduced lymphocytes were able to produce and secrete the Fab105 fragments, while maintaining their normal morphology, growth rates, and responsiveness to mitogen stimulation. The infection of several primary HIV-1 patient isolates was effectively blocked in the transduced lymphocytes. This study indicates that the combined intra- and extracellular immunization approach may be useful for the treatment of HIV-1-infected patients.
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools (2008)

This study illustrates the power of extensive mining of public data repositories using bioinformatics methods to provide answers for a specific biological question. It furthermore demonstrates how the usage of such a combinatorial approach is advantageous for the biologist in terms of experimentation time and costs.