gebhart/patrepeval huggingface dataset:
A Bacterium Associated with Disease of Pond Cultured Channel Catfish, Ictalurus punctatus (1979)

A new bacterial disease affecting primarily pond reared fingerling channel catfish, Ictalurus punctatus, is described from 17 instances reported from June 1976 through December 1978. Terramycin medicated feed controlled the disease when early diagnosis was possible. Terramycin resistant strains were not detected. The causitive organism was confirmed as a previously unidentified species of Edwardsiella by the Center for Disease Control Atlanta Georgia. The disease is referred to as Enteric Septicemia of Catfish (ESC). Optimum growth temperature is between 25 and 30 °C; this correlated with pond water temperatures during instances of mortality on fish farms. Koch's postulates were fulfilled using channel catfish fingerlings in 40-L aquaria. Key words: Fish disease, bacterial fish pathogen, enteric bacteria, channel catfish diseases
Recording brain activities in unshielded Earth’s field with optically pumped atomic magnetometers (2020)

Understanding the relationship between brain activity and specific mental function is important for medical diagnosis of brain symptoms, such as epilepsy. Magnetoencephalography (MEG), which uses an array of high-sensitivity magnetometers to record magnetic field signals generated from neural currents occurring naturally in the brain, is a noninvasive method for locating the brain activities. The MEG is normally performed in a magnetically shielded room. Here, we introduce an unshielded MEG system based on optically pumped atomic magnetometers. We build an atomic magnetic gradiometer, together with feedback methods, to reduce the environment magnetic field noise. We successfully observe the alpha rhythm signals related to closed eyes and clear auditory evoked field signals in unshielded Earth's field. Combined with improvements in the miniaturization of the atomic magnetometer, our method is promising to realize a practical wearable and movable unshielded MEG system and bring new insights into medical diagnosis of brain symptoms.
Use of Animal Models to Define Complement Functions (2000)

There appears to be little doubt that the complement system and its activation products play important roles in expression of both immune and inflammatory responses. Defining of the role of the complement system, especially in the context of the inflammatory response, has been deduced on the basis of strategies listed in Table 1. The use of laboratory animals with naturally occurring genetic deficiencies of complement components has provided important clues into the biological roles of complement. Guinea pigs with a genetic deficiency of C4 have defective clearance of intravenously infused sheep red blood cells containing IgG antibody directed toward surface epitopes (1,2). This defect can be corrected by restoration of whole hemolytic activity of serum complement (CH50), at which time clearance of sensitized red cells becomes very rapid, presumably through engagement of complement receptors on phagocytic cells of the spleen and liver. Rabbits with genetic deficiency of C6 exhibit acute inflammatory vasculitis in the reversed passive Arthus reaction in skin, the intensity of the reaction being similar to the inflammatory response C6-intact rabbits, but with less hemorrhage in thr skin lesions in the absence of C6 (3).
Cloning of the Glutamine:Fructose-6-phosphate Amidotransferase Gene from Yeast (1989)

The activity of the amino sugar-synthesizing enzyme L-glutamine:D-fructose-6-phosphate aminotransferase (EC 2.6.1.16) in haploid a cells of Saccharomyces cerevisiae increases 1.7-fold after alpha factor addition. The gene (the gene should be called GFA1 for glutamine:fructose-6-phosphate amidotransferase) for the enzyme has been cloned by complementing the gcn1 mutation (Whelan, W. L., and Ballou, C. E. (1975) J. Bacteriol. 125, 1545-1557). Its expression is increased 2-3 times within 15 min when the mating pheromone is added. The gene codes for a protein of 716 amino acids in length. It is highly homologous (64%) to the corresponding gene of Escherichia coli, except for a sequence coding for 83 amino acids (numbers 204-286), which is lacking in E. coli. The amino-terminal region of the coding sequence also shows a high degree of homology to the corresponding sequence of the E. coli and S. cerevisiae L-glutamine:phosphoribosylpyrophosphate amidotransferase. In the promotor region of the S. cerevisiae L-glutamine:D-fructose-6-phosphate amidotransferase gene the heptanucleotide "TGAAACA," shown to be required for pheromone control of transcription (Kronstad, J. W., Holly, J. A., and MacKay, V. L. (1987) Cell 50, 369-377), is present six times.
Frequent c-myc oncogene activation and infrequent presence of Epstein- Barr virus genome in AIDS-associated lymphoma (1988)

Abstract Sixteen cases of histologic intermediate-grade and high-grade AIDS- associated non-Hodgkin's lymphoma (NHL) were studied for the presence and patterns of c-myc gene and bcl-2 locus rearrangements. The presence of Epstein-Barr virus (EBV) sequences and proteins and HTLV-I sequences were also investigated. c-myc gene rearrangements analogous to those observed in sporadic Burkitt lymphomas were detected in 12 of 16 cases. Six of 16 cases had detectable EBV sequences and proteins. None of the cases displayed bcl-2 rearrangements or contained HTLV-I sequences. These data suggest a frequent role for c-myc activation in the pathogenesis of AIDS-associated NHL, independent of histologic type. Conversely, EBV does not appear to be directly involved in lymphomagenesis in the majority of AIDS-associated NHLs.
Large margin classification using the perceptron algorithm (1998)

We introduce and analyze a new algorithm for linear classification which combines Rosenblatt‘s perceptron algorithm with Helmbold and Warmuth‘s leave-one-out method. Like Vapnik‘s maximal-margin classifier, our algorithm takes advantage of data that are linearly separable with large margins. Compared to Vapnik‘s algorithm, however, ours is much simpler to implement, and much more efficient in terms of computation time. We also show that our algorithm can be efficiently used in very high dimensional spaces using kernel functions. We performed some experiments using our algorithm, and some variants of it, for classifying images of handwritten digits. The performance of our algorithm is close to, but not as good as, the performance of maximal-margin classifiers on the same problem, while saving significantly on computation time and programming effort.
603 Covalent attachment of a TLR7/8 agonist to tumor-targeting antibodies drives potent anti-tumor efficacy by synergistically activating FcgR- and TLR- signaling and enables safe systemic administration (2020)

<h3>Background</h3> Immune stimulating antibody conjugates (ISACs) covalently attach TLR7/8 immune stimulants to tumor-targeting antibodies. ISACs can be delivered systemically and act locally in the tumor microenvironment by requiring the following biological steps to elicit immune activation: 1) tumor antigen recognition, 2) Fc receptor mediated phagocytosis by myeloid antigen presenting cells (APCs), and 3) activation of endosomal TLR7 and TLR8. Here, we demonstrate that covalent attachment of our TLR7/8 agonist to tumor-targeting antibodies not only enables the resulting ISACs to be safely administered systemically in preclinical models, but also unexpectedly promotes synergy between the FcgR and TLR pathways that results in amplified anti-tumor immunity in mice and robust immune activation in human leukocytes as compared to the co-administration of the components. <h3>Methods</h3> ISAC activity and mechanistic studies were analyzed via flow cytometry, ELISA and CyTOF following in vitro coculture of human leukocytes with tumor cell lines. In vivo efficacy of HER2-targeting ISACs following systemic administration was assessed in a trastuzumab-resistant HER2+ human tumor xenograft model. Safety and tolerability were assessed in tumor-bearing mice and healthy non-human primates (NHP). <h3>Results</h3> While co-administration of intratumoral TLR7/8 agonist and intraperitoneal trastuzumab failed to control tumor growth, systemic administration of the same TLR7/8 agonist and trastuzumab in our ISAC format was efficacious and induced complete tumor regression in an Fc- and TLR-dependent manner. Analysis of primary human leukocytes stimulated with ISACs in tumor co-culture assays indicated that ISACs elicit amplified and sustained phosphorylation of Fc and TLR signaling pathways, such as pERK1/2 and pIRF-7, as compared to the unconjugated mixture of the same TLR7/8 agonist and tumor targeted antibody. ISAC stimulation was largely restricted to antigen presenting cells such as dendritic cells and plasmacytoid dendritic cells that express the relevant Fc receptors and TLR7 and/or TLR8. Modifications to the ISAC that reduce FcgR engagement (N297A/Q) or render the agonist inactive halted ISAC-mediated activation and in vivo anti-tumor efficacy. Lastly, our HER2-targeting ISACs were well-tolerated when delivered systemically in mice and NHPs. <h3>Conclusions</h3> Our ISACs enable potent TLR agonists to be safely administered systemically in preclinical models. ISACs provide distinct and unexpected advantages over unconjugated TLR agonists, notably by driving synergy between FcgR and TLR pathways, leading to robust myeloid activation and anti-tumor efficacy. These data support the evaluation of BDC-1001, a HER2-targeted ISAC in the ongoing Phase 1/2 trial (NCT04278144).
Fully Human Therapeutic Monoclonal Antibodies (2005)

Monoclonal antibody (mAb) therapy has been facilitated by a number of technologic advances over the past 30 years. Whereas hybridoma development of murine mAbs was requisite for the development of mAbs as drugs, the inherent immunogenicity of rodent sequences in humans has presented obstacles to the clinical application of mAbs. Sensitization to mAb therapeutics poses significant risk to the patient and may blunt the efficacy of these therapies. The advent of chimeric antibodies lessened but did not eliminate the rodent content of mAbs; thus, immunogenicity remained a concern. Further elimination of rodent sequences enabled the production of humanized mAbs, followed by current technology using phage display and, finally, transgenic mice technology, which allows for the generation of fully human therapeutic mAbs. The reduced immunogenicity of this new generation of mAbs is expected to enhance efficacy, safety, and ease of use. In addition to providing replacements for existing mAb drugs, new technologies have greatly facilitated the optimization and modification of mAbs, opening numerous therapeutic avenues.
Tracking menus (2003)

We describe a new type of graphical user interface widget, known as a "tracking menu." A tracking menu consists of a cluster of graphical buttons, and as with traditional menus, the cursor can be moved within the menu to select and interact with items. However, unlike traditional menus, when the cursor hits the edge of the menu, the menu moves to continue tracking the cursor. Thus, the menu always stays under the cursor and close at hand.In this paper we define the behavior of tracking menus, show unique affordances of the widget, present a variety of examples, and discuss design characteristics. We examine one tracking menu design in detail, reporting on usability studies and our experience integrating the technique into a commercial application for the Tablet PC. While user interface issues on the Tablet PC, such as preventing round trips to tool palettes with the pen, inspired tracking menus, the design also works well with a standard mouse and keyboard configuration.
The Monte Carlo Simulation of the Biological Effect of the 10 B(n,α) 7 Li Reaction in Cells and Tissue and Its Implication for Boron Neutron Capture Therapy (1987)

The energy deposition in the nucleus of cells exposed to the 10B(n, alpha)7Li neutron capture reaction has been calculated and compared to the measured biological effect of this reaction. It was found that a considerable distribution of hit sizes to the nucleus occurs. The comparison of hit size frequency with the observed survival indicates that not every hit, independent of its size, can lead to cell death. This implies the existence of a hit size effectiveness function. The analysis shows that the location of boron relative to the radiation-sensitive volume of the cell is of great importance and that average dose values alone are of limited use for predicting the biological effect of this reaction. Boron accumulating in the cell nucleus is much more efficient in cell killing than the same amount of boron uniformly distributed; its presence in one cell, however, has little effect on its neighboring cells in a tissue. When boron is present on the cell surface of a tissue (as presumably delivered by antibodies), its cell-killing effect is greatly reduced compared to that in uniform distribution. However, in this case much of the dose to one cell comes from neutron capture reactions occurring on the surface of its neighbor cells. These data have implications for the choice of boron carries in neutron capture therapy. The mathematical analysis carried out here is similar to that proposed recently for low-level exposure effects of radiation, taking mutation and/or carcinogenesis as biological effects. The results here show that high-level exposure to high-LET particles (resulting in cell killing) should be treated in an analogous manner.
Drug effects on the ischemia- and reperfusion-induced arrhythmias in the conscious rats. (1992)

A simple model of coronary occlusion and reperfusion in conscious rat was used to test the effects of various drugs on the arrhythmias. Blood pressure and ECG were monitored on a Grass polygraph. Intravenous infusion of test agents started before coronary occlusion and continued through the periods of occlusion and reperfusion. The free radical scavengers (allopurinol 12.3 mg/kg, mannitol 33.0 mg/kg, N-2-mercapto-propionyl glycine 8.6 mg/kg and adenosine 10.0 mg/kg), class 1-4 antiarrhythmic drugs (lidocaine 10.2 mg/kg, quinidine 12.3 mg/kg, propranolol 4.9 mg/kg, amiodarone 5.6 mg/kg and verapamil 1.1 mg/kg), aspirin 24.5 mg/kg and benadryl 3.7 mg/kg reduced the incidence of ventricular fibrillation and shortened the duration of arrhythmias during occlusion and reperfusion. Cimetidine 6.9 mg/kg was ineffective to exert the antiarrhythmic action. These results implicate that multiple factors, such as ionic channels (Na, K and Ca), free radicals, arachidonate metabolites and histamine release may play significant roles in genesis of arrhythmias during myocardial ischemia and reperfusion.
The classroom of the 21 st century (2000)

The Interactive Learning Wall is a Windows/PC-based virtual blackboard system that can be controlled remotely by a classroom instructor and/or students. A laser pointer used by the instructor emulates mouse actions on a computer projection screen. An inexpensive video camera sends each projected frame to a video capture card in the computer; our software detects the bright laser spot, moves a screen cursor, and performs other mouse operations according to user actions. The system frees the instructor to move about the classroom as he/she controls the presentation. Other software allows students, from their laptop computers, to request control of the main computer's mouse and keyboard over a local network. This facilitates student interaction with the main computer's screen to perform tasks like: go to specific parts of the presentation; enter text; annotate diagrams; run programs. Both systems can help increase interactivity between instructor and students in a large classroom environment. Technical details are given in this paper.
Bax Deletion Further Orders the Cell Death Pathway in Cerebellar Granule Cells and Suggests a Caspase-independent Pathway to Cell Death (1997)

Dissociated cerebellar granule cells maintained in medium containing 25 mM potassium undergo an apoptotic death when switched to medium with 5 mM potassium. Granule cells from mice in which Bax, a proapoptotic Bcl-2 family member, had been deleted, did not undergo apoptosis in 5 mM potassium, yet did undergo an excitotoxic cell death in response to stimulation with 30 or 100 microM NMDA. Within 2 h after switching to 5 mM K+, both wild-type and Bax-deficient granule cells decreased glucose uptake to <20% of control. Protein synthesis also decreased rapidly in both wild-type and Bax-deficient granule cells to 50% of control within 12 h after switching to 5 mM potassium. Both wild-type and Bax -/- neurons increased mRNA levels of c-jun, and caspase 3 (CPP32) and increased phosphorylation of the transactivation domain of c-Jun after K+ deprivation. Wild-type granule cells in 5 mM K+ increased cleavage of DEVD-aminomethylcoumarin (DEVD-AMC), a fluorogenic substrate for caspases 2, 3, and 7; in contrast, Bax-deficient granule cells did not cleave DEVD-AMC. These results place BAX downstream of metabolic changes, changes in mRNA levels, and increased phosphorylation of c-Jun, yet upstream of the activation of caspases and indicate that BAX is required for apoptotic, but not excitotoxic, cell death. In wild-type cells, Boc-Asp-FMK and ZVAD-FMK, general inhibitors of caspases, blocked cleavage of DEVD-AMC and blocked the increase in TdT-mediated dUTP nick end labeling (TUNEL) positivity. However, these inhibitors had only a marginal effect on preventing cell death, suggesting a caspase-independent death pathway downstream of BAX in cerebellar granule cells.
Self-Assembled Hydrophobin Protein Films at the Air−Water Interface:  Structural Analysis and Molecular Engineering (2007)

Hydrophobins are amphiphilic proteins produced by filamentous fungi. They function in a variety of roles that involve interfacial interactions, as in growth through the air-water interface, adhesion to surfaces, and formation of coatings on various fungal structures. In this work, we have studied the formation of films of the class II hydrophobin HFBI from Trichoderma reesei at the air-water interface. Analysis of hydrophobin aqueous solution drops showed that a protein film is formed at the air-water interface. This elastic film was clearly visible, and it appeared to cause the drops to take unusual shapes. Because adhesion and formation of coatings are important biological functions for hydrophobins, a closer structural analysis of the film was made. The method involved picking up the surface film onto a solid substrate and imaging the surface by atomic force microscopy. High-resolution images were obtained showing both the hydrophilic and hydrophobic sides of the film at nanometer resolution. It was found that the hydrophobin film had a highly ordered structure. To study the orientation of molecules and to obtain further insight in film formation, we made variants of HFBI that could be site specifically conjugated. We then used the avidin-biotin interaction as a probe. On the basis of this work, we suggest that the unusual interfacial properties of this type of hydrophobins are due to specific molecular interactions which lead to an ordered network of proteins in the surface films that have a thickness of only one molecule. The interactions between the proteins in the network are likely to be responsible for the unusual surface elasticity of the hydrophobin film.
An adaptive multiple echo canceller for slowly time-varying echo paths (1990)

An adaptive structure that cancels multiple echos with slowly time-varying echo path characteristics is presented. The structure consists of two echo path models. One is a primary long-length transversal filter initially used to estimate the echo path in the startup period. The other is a reduced-size filter consisting of several short-length filters used to inherit the significant coefficients of the primary filter after the predetermined conditions are simultaneously satisfied and to function as the echo canceller thereafter. In addition, a monitor/control circuit is used to estimate the time locations of individual dispersive regions from the primary filter and to monitor the short filters to make sure that each one can cover its own dispersive region. With the delays determined, the short filter structure can update the echo path accurately since the number of tap coefficients has been dramatically reduced, increasing the convergence speed. The results of computer simulations utilizing white noise input and speech input are presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
RNA Editing by Adenosine Deaminases That Act on RNA (2002)

ADARs are RNA editing enzymes that target double-stranded regions of nuclear-encoded RNA and viral RNA. These enzymes are particularly abundant in the nervous system, where they diversify the information encoded in the genome, for example, by altering codons in mRNAs. The functions of ADARs in known substrates suggest that the enzymes serve to fine-tune and optimize many biological pathways, in ways that we are only starting to imagine. ADARs are also interesting in regard to the remarkable double-stranded structures of their substrates and how enzyme specificity is achieved with little regard to sequence. This review summarizes ongoing investigations of the enzyme family and their substrates, focusing on biological function as well as biochemical mechanism.
Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana (1993)

Recombinant inbred (RI) lines of Arabidopsis thaliana (Arabidopsis) have been generated from a cross between the ecotypes Landsberg erecta and Columbia. Progeny of 300 individual F 2 seedlings were taken by single seed descent to the F 8 generation. Sixty‐seven loci, scored using 64 RFLP probes and one phenotypic marker, chosen at approximately 20 cM intervals from the two previously published RFLP maps, were mapped using 100 of these RI lines. More than 500 other new loci are currently being mapped using these RI lines by several other groups. These 100 RI lines thus provide the material to map new probes or phenotypic traits polymorphic between Landsberg erecta and Columbia, relative to an increasing number of molecular markers. Higher resolution mapping of distinct chromosomal regions can be achieved by analysing the segregation of particular markers on the additional 200 RI lines.
Nucleotide sequence of the yeast regulatory gene STE7 predicts a protein homologous to protein kinases. (1986)

The nucleotide sequence of the STE7 gene from Saccharomyces cerevisiae has been determined. It is one of several regulatory genes implicated in the control of cell-type-specific gene expression in yeast. The predicted amino acid sequence shows homology to several members of the protein kinase family. These results suggest protein phosphorylation may play a key role in regulation leading to cell-type specialization in yeast.
Significance of Antioxidative Functions of Eicosapentaenoic and Docosahexaenoic Acids in Marine Microorganisms (2007)

Various marine organisms, from animals to bacteria, have n -3 long-chain polyunsaturated fatty acids ( n -3 LC-PUFAs) with 20 or 22 carbon atoms such as docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) ([7][1]). In mammals and fish, DHA accumulates as the most abundant fatty acid among
Anticellular Effects of 9-(2-Hydroxyethoxymethyl) Guanine Against Herpes Simplex Virus-transformed Cells (1979)

SUMMARY The guanine derivative 9-(2-hydroxyethoxymethyl) guanine (acycloguanosine), a potent inhibitor of herpes simplex virus (HSV) multiplication, was found to have marked anticellular activity against HSV-transformed thymidine kinase-positive cells. HSV type 1-transformed cells were more sensitive to the drug than HSV type 2-transformed cells.