gebhart/patrepeval huggingface dataset:
Solid-Phase Synthesis of Acyclic and Cyclic Amino Acid Derived Urea Peptidomimetics Using Phoxime Resin (1999)

The use of Phoxime resin 2 (phosgenated p-nitrophenyl(polystyrene)ketoxime) in the synthesis of acyclic and heterocyclic amino acid derived ureas is described. Resin 2 was previously shown to be a useful precursor in the solid-phase preparation of nonsymmetric ureas from thermolysis of corresponding primary amine oxime carbamates and subsequent trapping with an amine in solution. Generation of functionalized polymer-supported primary amine oxime carbamates (3 and 9) for further diversification was accomplished by addition of amino acids or substituted hydrazines to resin 2. The use of these functionalized oxime carbamate resins for the generation of acyclic α-ureidoacetamides 5, 3-aminohydantoins 7, and 1,2,4-triazine-3,6-diones 8 is suitable for combinatorial library generation.
Safe and efficient sharing of persistent objects in Thor (1996)

Thor is an object-oriented database system designed for use in a heterogeneous distributed environment. It provides highly-reliable and highly-available persistent storage for objects, and supports safe sharing of these objects by applications written in different programming languages.Safe heterogeneous sharing of long-lived objects requires encapsulation: the system must guarantee that applications interact with objects only by invoking methods. Although safety concerns are important, most object-oriented databases forgo safety to avoid paying the associated performance costs.This paper gives an overview of Thor's design and implementation. We focus on two areas that set Thor apart from other object-oriented databases. First, we discuss safe sharing and techniques for ensuring it; we also discuss ways of improving application performance without sacrificing safety. Second, we describe our approach to cache management at client machines, including a novel adaptive prefetching strategy.The paper presents performance results for Thor, on several OO7 benchmark traversals. The results show that adaptive prefetching is very effective, improving both the elapsed time of traversals and the amount of space used in the client cache. The results also show that the cost of safe sharing can be negligible; thus it is possible to have both safety and high performance.
Mini‐Tn 7 transposons for site‐specific tagging of bacteria with fluorescent proteins (2004)

The mini-Tn7 transposon system is a convenient tool for site-specific tagging of bacteria in which the tagging DNA is inserted at a unique and neutral chromosomal site. We have expanded the panel of mini-Tn7 delivery plasmids expressing different fluorescent proteins (stable and unstable) from the Escherichia coli lac derived promoter, P(A1/04/03), or from the growth-rate-dependent Escherichia coli promoter PrrnB P1. The mini-Tn7 transposons were inserted and tested in the soil bacterium, Pseudomonas putida KT2440. Successful and site-specific tagging was verified by Southern blots as well as by PCR. Furthermore, the effect of fluorescent protein expression on the cellular growth rate was tested by growth competition assays.
A novel population of Gr-1+-activated macrophages induced during acute toxoplasmosis (2003)

Macrophages are potent mediators of parasite control following in vitro activation, yet the subsets of mononuclear cells that contribute to resistance in vivo remain poorly defined. To identify effector cells that contribute to the control of Toxoplasma gondii during the initial stages of disseminated infection, we developed a low-dose intraperitoneal challenge model. A population of unusual macrophage-like cells was recruited to the peritoneal cavity during the first 4 days postinfection. Surprisingly, these cells expressed the granulocyte marker Gr-1 and the macrophage marker CD68. They also expressed high levels of major histocompatibility complex class II and low levels of F4/80 and CD11b and were negative for the immature myeloid cell marker CD31, the dendritic cell marker CD11c, and the B cell marker B220. Gr-1+ macrophages produced interleukin-12 p40, generated reactive nitrogen intermediates during acute infection, and inhibited virulent type I and nonvirulent type II strains of the parasite in vitro. Gr-1+ macrophages were the primary cell type recruited in response to nonvirulent type II strain parasites, and large numbers of neutrophils (Gr-1+/CD68-) were also recruited to the peritoneum in response to virulent type I strain parasites. Our findings suggest that activated CD68+/Gr-1+ macrophages contribute to parasite control during infection by directly inhibiting parasite replication and through production of T helper cell type I cytokines.
Oligosaccharides Interfere with the Establishment and Progression of Experimental Pneumococcal Pneumonia (1997)

Oligosaccharides that block the adherence of bacteria to epithelial cells in vitro--lacto-N-neotetraose (LNnT) and its alpha2-3- and alpha2-6-sialylated derivatives--were tested for their abilities to attenuate the course of pneumococcal pneumonia and to prevent colonization of the nasopharynx in animal models. Intratracheal administration of these agents concurrently with bacteria dramatically decreased pneumococcal load in the lungs of rabbits and conferred protection from bacteremia. The oligosaccharides ameliorated pneumonia and bacteremia when given therapeutically 24 h after infection was established. When administered intranasally, neoglycoconjugates of the active oligosaccharides prevented colonization of the nasopharynx of infant rats. In addition to in vitro anti-adherence properties, LNnT acted directly on cultured lung epithelial cell lines to induce changes such that pneumococcal adherence was prevented for prolonged periods. These activities encourage continued development of oligosaccharides as a class of potentially preventive and therapeutic agents for infectious diseases.
DNS Encoding of Geographical Location (1994)

This document defines the format of a new Resource Record (RR) for the Domain Naming System (DNS), and reserves a corresponding DNS type mnemonic and numerical code. This definition deals with associating geographical host location mappings to host names within a domain. The data shown in this document is fictitious and does not necessarily reflect the real Internet.
Rationale and development of multispecific antibody drugs (2010)

Bispecific antibodies (bsAbs) have been on the scene for decades and represent the next generation of antibody-based therapeutics. Unlike monospecific, monoclonal antibodies (mAbs), bsAbs can target two or more disease mechanisms as a single agent and can offer certain unique therapeutic strategies that are difficult to acheive with mAbs. The lessons learned during the past 35 years of mAb development and 25 years of bsAbs experience are shaping development of the next generation of bsAbs and multispecific antibody-based drugs. Recent improvements in manufacturability and drug-like properties of certain BsAb formats, and clinical success for a few BsAbs, are reviving this area. In this article, we discuss the potential limitations of the first-generation mAbs and opportunities to improve upon existing mAb drugs, factors driving the multispecific antibody field and the strengths, weaknesses and development status of representative multispecific antibody concepts.
Stemming Algorithms: A Comparative Study and their Analysis (2012)

Stemming is an approach used to reduce a word to its stem or root form and is used widely in information retrieval tasks to increase the recall rate and give us most relevant results. There are number of ways to perform stemming ranging from manual to automatic methods, from language specific to language independent each having its own advantage over the other. This paper represents a comparative study of various available stemming alternatives widely used to enhance the effectiveness and efficiency of information retrieval.
Blood Testosterone Threshold for Androgen Deficiency Symptoms (2004)

There are few systematic studies of the relationship between blood testosterone concentrations and the symptoms of overt androgen deficiency. Because most testosterone preparations are relatively short-term, the rapid changes in blood testosterone concentrations they cause make it difficult to define any testosterone threshold. By contrast, subdermal testosterone implants provide stable blood testosterone concentrations over days to weeks, while gradually declining to baseline over 5-7 months. Hence, this provides an opportunity to define a blood testosterone threshold for androgen deficiency symptoms by observing androgen-deficient men as their familiar androgen deficiency symptoms return as testosterone pellets slowly dissolve. Among 52 androgen-deficient men who underwent 260 implantations over 5 yr, at the time of return of androgen deficiency symptoms the blood total and free testosterone concentrations were highly reproducible within individuals (F = 0.8, P = 0.49 and F = 1.4, 0.24, respectively) but varied markedly between men (F = 167 and F = 138, both P < 0.001), indicating that each person had a consistent testosterone threshold for androgen deficiency symptoms that differed markedly between individuals. The most reported symptoms of androgen deficiency were lack of energy, lack of motivation, and reduced libido. The symptomatic threshold was significantly lower in men with secondary hypogonadism compared with men with primary or mixed hypogonadism (total, 9.7 +/- 0.5 nmol/liter vs. 11.7 +/- 0.4 nmol/liter and 10.2 +/- 0.3 nmol/liter, P = 0.006; free, 146 +/- 10 pmol/liter vs. 165 +/- 6 pmol/liter and 211 +/- 18 pmol/liter, P = 0.002) but was not affected by the underlying cause of hypogonadism or by specific symptoms of any severity. Despite a wide range in individual thresholds for androgen deficiency symptoms, the mean blood testosterone threshold corresponded to the lower end of the eugonadal reference range for young men. The implications of these observations for the development of more specific quality-of-life measures, as well as for other potential androgen deficiency states such as chronic diseases and aging, remain to be determined.
A Clinical Trial of Retroviral-Mediated Transfer of arev-Responsive Element Decoy Gene Into CD34+Cells From the Bone Marrow of Human Immunodeficiency Virus-1–Infected Children (1999)

Genetic modification of hematopoietic stem cells with genes that inhibit replication of human immunodeficiency virus-1 (HIV-1) could lead to development of T lymphocytes and monocytic cells resistant to HIV-1 infection after transplantation. We performed a clinical trial to evaluate the safety and feasibility of this procedure, using bone marrow from four HIV-1-infected pediatric subjects (ages 8 to 17 years). We obtained bone marrow, isolated CD34(+) cells, performed in vitro transduction with a retroviral vector carrying a rev-responsive element (RRE) decoy gene, and reinfused the cells into these subjects with no evidence of adverse effects. The levels of gene-containing leukocytes in peripheral blood samples in the 1 year after gene transfer/cell infusion have been extremely low. These observations support the potential of performing gene therapy for HIV-1 using hematopoietic cells, but emphasize the need for improved gene transfer techniques.
Design and Synthesis of Antimicrobial Peptides (2007)

The cecropins are a group of potent antimicrobial peptides, initially discovered in insects but later found in other animals including mammals. Synthetic peptide chemistry has played an important role in establishing their primary sequences, as well as the steps in the processing of the biosynthetic preprocecropins. Solid-phase peptide synthesis has been the method of choice. Synthetic chimeric peptides have led to more active products and a better understanding of their mode of action. The structural requirements for high activity include a basic amphipathic N-terminus, a short central flexible sequence and a hydrophobic helical C-terminus. Cecropin-melittin hybrids as small as 15 residues are highly active. In planar lipid bilayers the cecropins form pores which pass ions and carry a current under a voltage gradient. Synthetic D-enantiomers of several antibacterial peptides carry the same current as the natural all-L-peptides and are equally active against several test bacteria. Therefore, the activity is not dependent on chiral interactions between the peptides and the lipid bilayers or the bacterial membranes. Recent examination of retro and retroenantio peptides has further defined the limits of the structural requirements of these peptides. Some of the hybrid peptides are active against Plasmodium falciparum and Mycobacterium smegmatis.
Brain Computer Interfaces, a Review (2012)

A brain-computer interface (BCI) is a hardware and software communications system that permits cerebral activity alone to control computers or external devices. The immediate goal of BCI research is to provide communications capabilities to severely disabled people who are totally paralyzed or 'locked in' by neurological neuromuscular disorders, such as amyotrophic lateral sclerosis, brain stem stroke, or spinal cord injury. Here, we review the state-of-the-art of BCIs, looking at the different steps that form a standard BCI: signal acquisition, preprocessing or signal enhancement, feature extraction, classification and the control interface. We discuss their advantages, drawbacks, and latest advances, and we survey the numerous technologies reported in the scientific literature to design each step of a BCI. First, the review examines the neuroimaging modalities used in the signal acquisition step, each of which monitors a different functional brain activity such as electrical, magnetic or metabolic activity. Second, the review discusses different electrophysiological control signals that determine user intentions, which can be detected in brain activity. Third, the review includes some techniques used in the signal enhancement step to deal with the artifacts in the control signals and improve the performance. Fourth, the review studies some mathematic algorithms used in the feature extraction and classification steps which translate the information in the control signals into commands that operate a computer or other device. Finally, the review provides an overview of various BCI applications that control a range of devices.
A polymorphism (G–>A transition) in the -78 position of the apolipoprotein A-I promoter increases transcription efficiency (1994)

AG-->A transition at -78 base pairs from the transcription start site of the apolipoprotein A-I (apoA-I) gene has been associated with increased apoA-I serum levels in humans. We report here that this mutation (G-->A) increases significantly (5-7-fold) the expression of a reporter gene fused to the apoA-I promoter in human liver and intestine cells. In addition, the presence of A at -78 base pairs from the transcription start site of the gene significantly decreases the binding affinity of a nuclear factor present in liver and intestine cells. We suggest that the reduced affinity of this factor increases the transcription efficiency of the promoter and explains why individuals carrying the A allele have high serum apoA-I levels.
Biophysical and biological properties of quadruplex oligodeoxyribonucleotides (2003)

Single-stranded guanosine-rich oligodeoxyribonucleotides (GROs) have a propensity to form quadruplex structures that are stabilized by G-quartets. In addition to intense speculation about the role of G-quartet formation in vivo, there is considerable interest in the therapeutic potential of quadruplex oligonucleotides as aptamers or non-antisense antiproliferative agents. We previously have described several GROs that inhibit proliferation and induce apoptosis in cancer cell lines. The activity of these GROs was related to their ability to bind to a specific cellular protein (GRO-binding protein, which has been tentatively identified as nucleolin). In this report, we describe the physical properties and biological activity of a group of 12 quadruplex oligonucleotides whose structures have been characterized previously. This group includes the thrombin-binding aptamer, an anti-HIV oligonucleotide, and several quadruplexes derived from telomere sequences. Thermal denaturation and circular dichroism (CD) spectropolarimetry were utilized to investigate the stability, reversibility and ion dependence of G-quartet formation. The ability of each oligonucleotide to inhibit the proliferation of cancer cells and to compete for binding to the GRO-binding protein was also examined. Our results confirm that G-quartet formation is essential for biological activity of GROs and show that, in some cases, quadruplex structures formed in the presence of potassium ions are significantly more active than those formed in the presence of sodium ions. However, not all quadruplex structures exhibit antiproliferative effects, and the most accurate factor in predicting biological activity was the ability to bind to the GRO-binding protein. Our data also indicate that the CD spectra of quadruplex oligonucleotides may be more complex than previously thought.
Merging Biological Self‐Assembly with Synthetic Chemical Tailoring: The Potential for 3‐D Genetically Engineered Micro/Nano‐Devices (3‐D GEMS) (2005)

Appreciable global efforts are underway to develop processes for fabricating three‐dimensional (3‐D) nanostructured assemblies for advanced devices. Widespread commercialization of such devices will require: (i) precise 3‐D fabrication of chemically tailored structures on a fine scale and (ii) mass production of such structures on a large scale. These often‐conflicting demands can be addressed with a revolutionary new paradigm that couples biological self‐assembly with synthetic chemistry: B ioclastic a nd S hape‐preserving I norganic C onversion (BaSIC). Nature provides numerous examples of microorganisms that assemble biominerals into intricate 3‐D structures. Among the most spectacular of these microorganisms are diatoms (unicellular algae). Each of the tens of thousands of diatom species assembles silica nanoparticles into a microshell with a distinct 3‐D shape and pattern of fine (nanoscale) features. The repeated doubling associated with biological reproduction enables enormous numbers of such 3‐D microshells to be generated (e.g., only 40 reproduction cycles can yield &gt;1 trillion 3‐D replicas!). Such genetic precision and massive parallelism are highly attractive for device manufacturing. However, the natural chemistries assembled by diatoms (and other microorganisms) are rather limited. With BaSIC processes, biogenic assemblies can be converted into a wide variety of new functional chemistries, while preserving the 3‐D morphologies. Ongoing advances in genetic engineering promise to yield microorganisms tailored to assemble nanoparticle structures with device‐specific shapes. Large‐scale culturing of such genetically tailored microorganisms, coupled with shape‐preserving chemical conversion (via BaSIC processes), would then provide low‐cost 3‐D G enetically E ngineered M icro/nano‐devices (3‐D GEMs).
Lysophosphatidic acid possesses dual action in cellproliferation. (1994)

Lysophosphatidic acid (LPA) induces mitogenic responses in cultured fibroblasts through a pertussis toxin-sensitive signaling pathway. In contrast, we have shown that LPA inhibits the proliferation of Sp2/0-Ag14 myeloma cells. To resolve this apparent controversy, LPA-elicited responses in cell proliferation and the underlying second messenger mechanisms were compared in Sp2/0-Ag14 myeloma and NIH 3T3 fibroblast cells. The antimitogenic response was not elicited by micromolar concentrations of phosphatidic acid, phosphatidylglycerol, or diacylglycerol. In NIH 3T3 and Sp2 cells, LPA elicited an increase in inositol trisphosphate and a subsequent transient increase in free cytoplasmic Ca2+. Unlike the mitogenic response in NIH 3T3 cells, the antimitogenic effect was not affected by pertussis toxin; on the contrary, it was accompanied by an increase in cAMP. In Sp2 cells, cAMP analogs, forskolin, and isobutylmethylxanthine inhibited cell proliferation and enhanced LPA action in an additive manner, suggesting that an LPA-elicited increase in cAMP-mediated signaling was responsible for the antimitogenic response. In addition to the mitogenic response in fibroblasts and the antimitogenic response in tumor cell lines, there are some cell types (Jurkat T-cell lymphoma and primary astrocytes) in which LPA is ineffective in altering cell proliferation. The cell-type-specific dual action of LPA suggests that this endogenous lipid mediator when released from activated cells might play an important role as a regulator, rather than a ubiquitous inducer, of cell proliferation.
JNK2 and JNK3 combined are essential for apoptosis in dopamine neurons of the substantia nigra, but are not required for axon degeneration (2008)

Activation of c-jun N-terminal kinase (JNK) by the mitogen-activated protein kinase cascade has been shown to play an important role in the death of dopamine neurons of the substantia nigra, one of the principal neuronal populations affected in Parkinson's disease. However, it has remained unknown whether the JNK2 and JNK3 isoforms, either singly or in combination, are essential for apoptotic death, and, if so, the mechanisms involved. In addition, it has been unclear whether they play a role in axonal degeneration of these neurons in disease models. To address these issues we have examined the effect of single and double jnk2 and jnk3 null mutations on apoptosis in a highly destructive neurotoxin model, that induced by intrastriatal 6-hydroxydopamine. We find that homozygous jnk2/3 double null mutations result in a complete abrogation of apoptosis and a prolonged survival of the entire population of dopamine neurons. In spite of this complete protection at the cell soma level, there was no protection of axons. These studies provide a striking demonstration of the distinctiveness of the mechanisms that mediate cell soma and axon degeneration, and they illustrate the need to identify and target pathways of axon degeneration in the development of neuroprotective therapeutics.
A simulated actuator driven by motor cortical signals (1996)

One problem in motor control concerns the mechanism whereby the central nervous system translates the motor cortical command encoded in cell activity into a coordinated contraction of limb muscles to generate a desired motor output. This problem is closely related to the design of adaptive systems that transform neuronal signals chronically recorded from the motor cortex into the physiologically appropriate motor output of multijoint prosthetic limbs. In this study we demonstrated how this transformation can be carried out by an artificial neural network using as command signals the actual impulse activity obtained from recordings in the motor cortex of monkeys during the performance of a task that required the exertion of force in different directions. The network receives experimentally measured brain signals and recodes them into motor actions of a simulated actuator that mimics the primate arm. The actuator responds to the motor cortical commands with surprising fidelity, generating forces in close quantitative agreement with those exerted by trained monkeys, in both the temporal and spatial domains. Moreover, we show that the time-varying motor output may be controlled by the impulse activity of as few as 15 motor cortical cells. These results outline a potentially implementable computation scheme that utilizes raw neuronal signals to drive artificial mechanical systems.