gebhart/patrepeval huggingface dataset:
A multicast mechanism with ordering on overlapping groups (2002)

The paper proposes a new mechanism for group communication which guarantees the total ordering of message delivery, especially the ordering on the members common to overlapping groups. The mechanism is based on a method which propagates messages to all destinations along trees. The approach has the following advantages over the propagation tree mechanism: (1) greater parallelism (messages can be sent to destinations by using broadcast networks); (2) less latency time (it takes less time to have a message reach all the destinations); and (3) more flexible to dynamic membership changes, (each change of process membership does not involve a restructuring of propagation trees).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A New Synthetic Route to (North)-Methanocarba Nucleosides Designed as A3 Adenosine Receptor Agonists (2004)

Activation of the A3 adenosine receptor (AR) is associated with cerebroprotective, cardioprotective, and anticancer effects. Among potent and selective A3 AR agonists are novel methanocarba adenosine analogues in which the conformation of a pseudo-ribose moiety is locked in the North (N) hemisphere of the pseudorotational cycle. 5'-Uronamide (N)-methanocarba nucleosides, such as MRS1898 and MRS2346, are examples of full agonists of the human A3 AR. An improved convergent approach from easily accessible 2,3-O-isopropylidene-d-erythrose (2b), and the combination of a strategic intramolecular cyclopropanation step plus the acid-catalyzed isomerization of an isopropylidene group, provided a suitable pseudosugar precursor (23) for the synthesis of MRS1898, MRS2346, and related analogues. This new synthetic route uses readily available building blocks and opens the way for the preparation of a variety of targets on a reasonable scale.
Protection by recombinant alpha 1-antitrypsin Ala357 Arg358 against arterial hypotension induced by factor XII fragment. (1987)

The specificity of serpin superfamily protease inhibitors such as alpha 1-antitrypsin or C1 inhibitor is determined by the amino acid residues of the inhibitor reactive center. To obtain an inhibitor that would be specific for the plasma kallikrein-kinin system enzymes, we have constructed an antitrypsin mutant having Arg at the reactive center P1 residue (position 358) and Ala at residue P2 (position 357). These modifications were made because C1 inhibitor, the major natural inhibitor of kallikrein and Factor XIIa, contains Arg at P1 and Ala at P2. In vitro, the novel inhibitor, alpha 1-antitrypsin Ala357 Arg358, was more efficient than C1 inhibitor for inhibiting kallikrein. Furthermore, Wistar rats pretreated with alpha 1-antitrypsin Ala357 Arg358 were partially protected from the circulatory collapse caused by the administration of beta-Factor XIIa.
The GLABRA2 gene encodes a homeo domain protein required for normal trichome development in Arabidopsis. (1994)

The GLABRA2 gene (GL2) is one of several genes known to have a role in trichome development in Arabidopsis. Mutations at this locus result in abnormal trichome expansion. We have identified several gl2 mutants from a T-DNA-mutagenized population of plants. The T-DNA insert in one of the mutant lines cosegregated with the recessive gl2 phenotype and thus served as a molecular tag to isolate genomic DNA at the putative GL2 locus. RFLP analysis of the segregating population and subsequent molecular complementation experiments established that the GL2 gene had been cloned. The predicted polypeptide from one of the ORFs contained on this fragment showed significant identity to the homeo domain sequence. The construction of a full-length cDNA by RT-PCR confirmed the presence of a homeo box in the GL2 gene and showed that it is substantially different from other recently cloned homeo box genes in plants. The expression pattern of GL2, as demonstrated by in situ hybridization, indicated that the gene is expressed in trichome progenitor cells and at stages associated with trichome development. This suggests that GL2 may regulate events required for the directional cell expansion observed during trichome formation.
The TerraMax autonomous vehicle (2006)

Abstract The TerraMax vehicle is based on Oshkosh Truck's Medium Tactical Vehicle Replacement truck platform and was one of the five vehicles able to successfully reach the finish line of the 132 miles DARPA Grand Challenge desert race. Due to its size (30 000 pounds, 27 ′ 0 ″ long, 8 ′ 4 ″ wide, and 8 ′ 2 ″ high) and the narrow passages, TerraMax had to travel slowly, but its capabilities demonstrated the maturity of the overall system. Rockwell Collins developed, integrated, and installed the intelligent Vehicle Management System, which includes vehicle sensor management, navigation, and vehicle control systems. The University of Parma provided the vehicle's vision system, while Oshkosh Truck Corp. provided project management, system integration, low level controls hardware, modeling and simulation support, and the vehicle. © 2006 Wiley Periodicals, Inc.
Effects of T-helper 2-type cytokines, interleukin-3 (IL-3), IL-4, IL-5, and IL-6 on the survival of cultured human mast cells (1995)

Although stem cell factor (SCF) has been identified as a critical cytokine for the development of human mast cells from their progenitors, the effects of other cytokines on human mast cells are less well understood. We examined the effects of several cytokines on the survival of human mast cells of 100% purity generated in suspension cultures of umbilical cord blood mononuclear cells in the presence of 100 ng/mL recombinant human (rh) SCF and interleukin-6 (IL-6). Mast cells suspended in conventional serum-containing medium died over a period of 2 to 6 days after the withdrawal of SCF and IL-6. The cells became pyknotic and underwent DNA fragmentation characteristic of apoptosis. The addition of SCF, IL-3, IL-4, IL-5, or IL-6 to the cultures in both serum-containing and serum-free medium prolonged their survival in a dose-dependent manner. Some other cytokines, such as IL-2, IL-9, IL-10, IL-11, tumor necrosis factor-alpha, transforming growth factor-beta 1, and nerve growth factor, had no survival-promoting effect at 100 ng/mL. Preincubation of mast cells with SCF, IL-4, IL-5, or IL-6 for 24 hours during sensitization with IgE enhanced IgE/anti-IgE antibody-induced histamine release from mast cells, whereas IL-3 showed a negligible effect. Polymerase chain reaction amplification of alpha-chains of IL-3 receptor (R), IL-4 R, IL-5 R, and IL-6 R yielded products of the correct size predicted from the sequence of each receptor. The binding assay using 125I-labeled IL-3 indicated that these mast cells bear receptors for IL-3. These findings suggest that IL-3, Il-4, IL-5, and IL-6, which are mainly produced by T-helper 2 lymphocytes, might regulate the functions of human mast cells in vivo via specific receptors in allergic reactions.
Identification of a Domain which Affects Kinetics and Antagonistic Potency of Clozapine at 5-HT3 Receptors (2009)

The widely used atypical antipsychotic clozapine is a potent competitive antagonist at 5-HT(3) receptors which may contribute to its unique psychopharmacological profile. Clozapine binds to 5-HT(3) receptors of various species. However, the structural requirements of the respective binding site for clozapine remain to be determined. Differences in the primary sequences within the 5-HT(3A) receptor gene in schizophrenic patients may result in an alteration of the antipsychotic potency and/or the side effect profile of clozapine. To determine these structural requirements we constructed chimeras with different 5-HT(3A) receptor sequences of murine and human origin and expressed these mutants in human embryonic kidney (HEK) 293 cells. Clozapine antagonises recombinant mouse 5-HT(3A) receptors with higher potency compared to recombinant human 5-HT(3A) receptors. 5-HT activation curves and clozapine inhibition curves yielded the parameters EC(50) and IC(50) for all receptors tested in the range of 0.6 - 2.7 microM and 1.5 - 83.3 nM, respectively. The use of the Cheng-Prusoff equation to calculate the dissociation constant K(b) values for clozapine revealed that an extracellular sequence (length 86 aa) close to the transmembrane domain M1 strongly determines the binding affinity of clozapine. K(b) values of clozapine were significantly lower (0.3-1.1 nM) for receptors containing the murine sequence and higher when compared with receptors containing the respective human sequence (5.8-13.4 nM). Thus, individual differences in the primary sequence of 5-HT(3) receptors may be crucial for the antipsychotic potency and/or the side effect profile of clozapine.
Sighted automation and fine resolution imaging (2004)

This paper discusses aspects of fine resolution imaging and associated data processing systems. The work of the authors was driven mostly by the military problem of automatic target acquisition and recognition, and this paper places some emphasis on the authors' contributions to synthetic aperture radar (SAR) developments from the 1950s through the 1970s. In addition to a discussion of the Story, the paper provides a perspective on the general role of fine resolution imaging in sighted automation. The following three important technical breakthroughs are included: (1) coherent optical data processing for SAR and more generally for holography; (2) coherent processing of pulse-Doppler radar data during motion through resolution cells (decades in advance of related techniques for medical imaging); and (3) morphological image processing for automatic pattern recognition and for matched filtering of signal or, rather than plus, noise/clutter.
T cell-mediated immune responses in human newborns: ready to learn? (2005)

Infections with intracellular pathogens are often more severe or more prolonged in young infants suggesting that T cell-mediated immune responses are different in early life. Whereas neonatal immune responses have been quite extensively studied in murine models, studies of T cell-mediated immunity in human newborns and infants are scarce. Qualitative and quantitative differences when compared with adult immune responses have been observed but on the other hand mature responses to certain vaccines and infectious pathogens were demonstrated during the postnatal period and even during foetal life. Herein, we review the evidence suggesting that under appropriate conditions of stimulation, protective T cell-mediated immune responses could be induced by vaccines in early life.
In Vivo Gene Delivery to the Pulmonary Circulation in Rats: Transgene Distribution and Vascular Inflammatory Response (1997)

Although gene delivery to the pulmonary circulation has both experimental and therapeutic potential, the delivery methods, distribution of transgene, and subsequent inflammatory response have been poorly characterized to date. To address these issues, we utilized a 0.76-mm OD (outside diameter) end hole catheter inserted into the internal jugular vein of adult Sprague-Dawley rats, directing the tip into a pulmonary capillary wedge position. We then compared infusion of polycationic lipid:DNA complexes to replication-defective adenovirus with respect to magnitude and distribution of transgene expression using either chloramphenicol acetyltransferase (CAT) or human placental alkaline phosphatase (hpAP) reporter genes. Both lipid:DNA and adenovirus resulted in detectable transgene expression, though maximum lung CAT activity using lipid (gamma AP-DLRIE/DOPE) was approximately 2% of maximum activity using adenovirus (Ad-CAT). Further characterization of expression after transfection with 10(8) pfu (plaque forming units) of Ad-CAT demonstrated persistence of transgene for at least 14 days (lung CAT activity 27% of maximum). Alkaline phosphatase staining demonstrated that both large and small pulmonary arteries as well as the alveolar wall expressed transgene. Although little inflammatory response was detected in conduit arteries, a predominantly mononuclear cell infiltrate surrounded small pulmonary arteries as well as the alveolar spaces in transfected areas of lung. We conclude that percutaneous catheter-mediated gene delivery to the pulmonary circulation in rats using non-viral and viral vectors is feasible. Although an inflammatory response to first generation replication-defective adenovirus was detected, it appeared to be largely restricted to the distal pulmonary circulation and airspace. This technique should prove useful for investigations requiring overexpression of novel genes in the pulmonary artery wall, and could ultimately be used to develop gene-based therapies for pulmonary vascular diseases.
The control of rostrocaudal pattern in the developing spinal cord: specification of motor neuron subtype identity is initiated by signals from paraxial mesoderm (1998)

The generation of distinct classes of motor neurons is an early step in the control of vertebrate motor behavior. To study the interactions that control the generation of motor neuron subclasses in the developing avian spinal cord we performed in vivo grafting studies in which either the neural tube or flanking mesoderm were displaced between thoracic and brachial levels. The positional identity of neural tube cells and motor neuron subtype identity was assessed by Hox and LIM homeodomain protein expression. Our results show that the rostrocaudal identity of neural cells is plastic at the time of neural tube closure and is sensitive to positionally restricted signals from the paraxial mesoderm. Such paraxial mesodermal signals appear to control the rostrocaudal identity of neural tube cells and the columnar subtype identity of motor neurons. These results suggest that the generation of motor neuron subtypes in the developing spinal cord involves the integration of distinct rostrocaudal and dorsoventral patterning signals that derive, respectively, from paraxial and axial mesodermal cell groups.
Incomplete Information in Relational Databases (1984)

This paper concerns the semantics of Codd's relational model of data. Formulated are precise conditions that should be satisfied m a semantically meaningful extension of the usual relational operators, such as projection, selection, union, and join, from operators on relations to operators on tables with "null values" of various kinds allowed. These conditions require that the system be safe in the sense that no incorrect conclusion is derivable by usmg a specified subset [l of the relational operators; and that it be complete in the sense that all valid conclusions expressible by relational expressions using operators in fl are in fact derivable in this system. Two such systems of practical interest are shown. The first, based on the usual Codd's null values, supports projection and selection. The second, based on many different ("marked") null values or variables allowed to appear in a table, ~s shown to correctly support projection, posmve selection (with no negation occurring in the selection condition), union, and renaming of attributes, which allows for processing arbitrary conjunctive queries. A very desirable property enjoyed by this system is that all relational t~perators on tables are performed in exactly the same way as in the case of the usual relations. A third system, mainly of theoretical interest, supporting projection, selection, union, join, and renaming, is also discussed. Under a so-called closed world assumption, it can also handle the operator of difference. It is based on a device called a condiUonal table and is crucial to the proof of the correctness of the second system. All systems considered allow for relational expressions contaming arbitrardy many different relation symbols, and no form of the universal relation assumption is required.
GPI-anchored receptor clusters transiently recruit Lyn and Gα for temporary cluster immobilization and Lyn activation: single-molecule tracking study 1 (2007)

The signaling mechanisms for glycosylphosphatidylinositol-anchored receptors (GPI-ARs) have been investigated by tracking single molecules in living cells. Upon the engagement or colloidal gold-induced cross-linking of CD59 (and other GPI-ARs) at physiological levels, CD59 clusters containing three to nine CD59 molecules were formed, and single molecules of Galphai2 or Lyn (GFP conjugates) exhibited the frequent but transient (133 and 200 ms, respectively) recruitment to CD59 clusters, via both protein-protein and lipid-lipid (raft) interactions. Each CD59 cluster undergoes alternating periods of actin-dependent temporary immobilization (0.57-s lifetime; stimulation-induced temporary arrest of lateral diffusion [STALL], inducing IP(3) production) and slow diffusion (1.2 s). STALL of a CD59 cluster was induced right after the recruitment of Galphai2. Because both Galphai2 and Lyn are required for the STALL, and because Lyn is constitutively recruited to CD59 clusters, the STALL of CD59 clusters is likely induced by the Galphai2 binding to, and its subsequent activation of, Lyn within the same CD59 cluster.
Renal Masses: Quantitative Assessment of Enhancement with Dynamic MR Imaging (2002)

The optimal percentage of enhancement threshold for distinguishing cysts from malignancies with the imaging technique prescribed was 15%, and the optimal timing for measurement was 2-4 minutes after administration of contrast material.
In-the-wire authentication: Protecting client-side critical data fields in secure network transactions (2009)

Secure Internet services like online banking require a "trusted terminal" on the client-side. However, even where strong client-side security is employed, the client PC is often used for input and output of sensitive information like PINs/passwords, amounts, account numbers, etc. These transactions are therefore vulnerable to manipulation by malware. A method is presented here allowing web users to share small amounts of secret information including passwords and account numbers with a large number of existing Internet services by creating a cryptographically secure trusted path between the web user and the service. The trusted path is created with the support of a hand-held user terminal device "in-the-wire" between the user's PC and the service thus preventing malware on the user's PC from manipulating login and other sensitive data. A key feature is that the trusted terminal device can be retrofitted on the client-side and require no changes to the server-side. This creates a new class of client-centric communications security hardware allowing web users to protect their transactions using strong hardware security without relying on service providers. It offers the industry an alternative to the current service-centric approach which is often hamstrung by a chicken-and-egg problem of critical mass adoption.
Synthetic biology approaches to engineering the nitrogen symbiosis in cereals (2014)

Nitrogen is abundant in the earth's atmosphere but, unlike carbon, cannot be directly assimilated by plants. The limitation this places on plant productivity has been circumvented in contemporary agriculture through the production and application of chemical fertilizers. The chemical reduction of nitrogen for this purpose consumes large amounts of energy and the reactive nitrogen released into the environment as a result of fertilizer application leads to greenhouse gas emissions, as well as widespread eutrophication of aquatic ecosystems. The environmental impacts are intensified by injudicious use of fertilizers in many parts of the world. Simultaneously, limitations in the production and supply of chemical fertilizers in other regions are leading to low agricultural productivity and malnutrition. Nitrogen can be directly fixed from the atmosphere by some bacteria and Archaea, which possess the enzyme nitrogenase. Some plant species, most notably legumes, have evolved close symbiotic associations with nitrogen-fixing bacteria. Engineering cereal crops with the capability to fix their own nitrogen could one day address the problems created by the over- and under-use of nitrogen fertilizers in agriculture. This could be achieved either by expression of a functional nitrogenase enzyme in the cells of the cereal crop or through transferring the capability to form a symbiotic association with nitrogen-fixing bacteria. While potentially transformative, these biotechnological approaches are challenging; however, with recent advances in synthetic biology they are viable long-term goals. This review discusses the possibility of these biotechnological solutions to the nitrogen problem, focusing on engineering the nitrogen symbiosis in cereals.
NTIMIT: a phonetically balanced, continuous speech, telephone bandwidth speech database (2002)

The creation of the network TIMIT (NTIMIT) database, which is the result of transmitting the TIMIT database over the telephone network, is described. A brief description of the TIMIT database is given, including characteristics useful for speech analysis and recognition. The hardware and software required for the transmission of the database is described. The geographic distribution of the TIMIT utterances is described, followed by information regarding calibration signals used to readily determine the effect of the transmission setup and the distortions introduced by the telephone network.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Key Metabolic Enzymes Involved in Remdesivir Activation in Human Lung Cells (2021)

Remdesivir (RDV; GS-5734, Veklury), the first FDA-approved antiviral to treat COVID-19, is a single-diastereomer monophosphoramidate prodrug of an adenosine analogue. RDV is taken up in the target cells and metabolized in multiple steps to form the active nucleoside triphosphate (TP) (GS-443902), which, in turn, acts as a potent and selective inhibitor of multiple viral RNA polymerases. In this report, we profiled the key enzymes involved in the RDV metabolic pathway with multiple parallel approaches: (i) bioinformatic analysis of nucleoside/nucleotide metabolic enzyme mRNA expression using public human tissue and lung single-cell bulk mRNA sequence (RNA-seq) data sets, (ii) protein and mRNA quantification of enzymes in human lung tissue and primary lung cells, (iii) biochemical studies on the catalytic rate of key enzymes, (iv) effects of specific enzyme inhibitors on the GS-443902 formation, and (v) the effects of these inhibitors on RDV antiviral activity against SARS-CoV-2 in cell culture. Our data collectively demonstrated that carboxylesterase 1 (CES1) and cathepsin A (CatA) are enzymes involved in hydrolyzing RDV to its alanine intermediate MetX, which is further hydrolyzed to the monophosphate form by histidine triad nucleotide-binding protein 1 (HINT1). The monophosphate is then consecutively phosphorylated to diphosphate and triphosphate by cellular phosphotransferases. Our data support the hypothesis that the unique properties of RDV prodrug not only allow lung-specific accumulation critical for the treatment of respiratory viral infection such as COVID-19 but also enable efficient intracellular metabolism of RDV and its MetX to monophosphate and successive phosphorylation to form the active TP in disease-relevant cells.