gebhart/patrepeval huggingface dataset:
Antibiotic Treatment of Experimental Pneumonic Plague in Mice (1998)

A mouse model was developed to evaluate the efficacy of antibiotic treatment of pneumonic plague; streptomycin was compared to antibiotics with which there is little or no clinical experience. Infection was induced by inhalation of aerosolized Yersinia pestis organisms. Antibiotics were administered by intraperitoneal injection every 6 hours for 5 days, at doses that produced levels of drug in serum comparable to those observed in humans treated for other serious infections. These studies compared in vitro to in vivo activity and evaluated the efficacy of antibiotics started at different times after exposure. Early treatment (started 24 h after challenge, when 0 of 10 mice tested had positive blood cultures) with netilmicin, ciprofloxacin, ofloxacin, ceftriaxone, ceftazidime, aztreonam, ampicillin, and rifampin (but not cefazolin, cefotetan, or ceftizoxime) demonstrated efficacy comparable to streptomycin. Late treatment (started 42 h after exposure, when five of five mice tested had positive blood cultures) with netilmicin, ciprofloxacin, ofloxacin, and a high dose (20 mg/kg of body weight every 6 h) of gentamicin produced survival rates comparable to that with streptomycin, while all of the beta-lactam antibiotics (cefazolin, cefotetan, ceftriaxone, ceftazidime, aztreonam, and ampicillin) and rifampin were significantly inferior to streptomycin. In fact, all groups of mice treated late with beta-lactam antibiotics experienced accelerated mortality rates compared to normal-saline-treated control mice. These studies indicate that netilmicin, gentamicin, ciprofloxacin, and ofloxacin may be alternatives for the treatment of pneumonic plague in humans. However, the beta-lactam antibiotics are not recommended, based upon poor efficacy in this mouse model of pneumonic plague, particularly when pneumonic plague may be associated with bacteremia.
TINNITUS AND SUCIDE (1994)

A retrospective study of tinnitus sufferers who had committed suicide was undertaken. A questionnaire was compiled, and circulated world-wide. Adequate information was obtained on 28 suicides. An association between suicide and left-sided tinnitus reported previously, was not conclusively replicated. In fact, no particular tinnitus parameter, or associated audiological symptom was over-represented in the suicide series. Demographically, tinnitus suicide victims were characterized by being male, elderly, and socially isolated. There was a high prevalence of psychiatric morbidity, in particular depression (70%). A suicide attempt within the year preceding suicide occurred in five individuals.
Activation of gene expression by small molecule transcription factors (2000)

Eukaryotic transcriptional activators are minimally comprised of a DNA binding domain and a separable activation domain; most activator proteins also bear a dimerization module. We have replaced these protein modules with synthetic counterparts to create artificial transcription factors. One of these, at 4.2 kDa, mediates high levels of DNA site-specific transcriptional activation in vitro. This molecule contains a sequence-specific DNA binding polyamide in place of the typical DNA binding region and a nonprotein linker in place of the usual dimerization peptide. Thus our activating region, a designed peptide, functions outside of the archetypal protein context, as long as it is tethered to DNA. Because synthetic polyamides can, in principle, be designed to recognize any specific sequence, these results represent a key step toward the design of small molecules that can up-regulate any specified gene.
C-Terminal Arginine Cluster Is Essential for Receptor Binding of Norovirus Capsid Protein (2006)

Noroviruses are the major viral pathogens of epidemic acute gastroenteritis affecting people worldwide. They have been found to recognize human histo-blood group antigens as receptors. The P domain of norovirus capsid protein was found to be responsible for binding to viral receptors, and the recombinant P protein forms P dimers and P particles in vitro. In this study, we demonstrate that a highly conserved arginine (R) cluster at the C terminus of the P domain is critical for receptor binding and P particle formation of the P proteins. Deletions of the R cluster abolished these functions. Replacement of the R cluster with histidines (another positively charged amino acid) resulted in low efficiency of receptor binding and P particle formation, while replacement with alanines led to loss of both functions completely. The R cluster also contains a highly conserved trypsin digestion site. A treatment of capsid protein or P domain mutants from both genogroup I (Norwalk virus) and genogroup II (VA387) noroviruses with trypsin resulted in a removal of the R cluster and the S domain, leaving a P polypeptide of 31.3 kDa (Norwalk virus) or 34.3 kDa (VA387), similar to the soluble P protein found in vivo. Our findings imply that the proteolytic process could be a necessary step for norovirus replication in the host.
Copper-Catalyzed Amidation of Allylic and Benzylic CH Bonds (2006)

[Structure: see text] A copper-catalyzed amidation of allylic and benzylic C-H bonds with both primary and secondary sulfonamides is described. The reaction is applicable to the coupling of a diverse set of hydrocarbon species with aryl, heteroaryl, and alkyl sulfonamides and is tolerant of a variety of functional groups. Mechanistic insight has been gained through the isolation of a benzylic acetate intermediate, which was demonstrated to undergo facile conversion to the substituted sulfonamide product under copper catalysis.
Dendritic cell‐derived IL‐15 controls the induction of CD8 T cell immune responses (2003)

The development and the differentiation of CD8(+) T cells are dependent on IL-15. Here, we have studied the source and mechanism of how IL-15 modulates CD8(+) T cell-mediated Th1 immune responses by employing two delayed-type hypersensitivity (DTH) models. IL-15-deficient (IL-15(-/-)) mice or mice treated with soluble IL-15Ralpha as an IL-15 antagonist showed significantly reduced CD8(+) T cell-dependent DTH responses, while activation of CD4(+) T cell and B cell functions remained unaffected. Injection of antigen-labeled dendritic cells (DC) from IL-15(+/+), IL-15(-/-) or IL-15Ralpha(-/-) mice revealed that DC-derived IL-15 is an absolute requirement for the initiation of DTH response. The re-establishment of the interaction of IL-15 with the IL-15Ralpha by incubating IL-15(-/-) DC with IL-15 completely restored the capacity to prime T cells for DTH induction in vivo. Moreover, IL-15 also enhanced secretion of pro-inflammatory cytokines by DC and triggered in vitro CD8(+) T cell proliferation and IL-2 release. Taken together, the data suggest that an autocrine IL-15/IL-15Ralpha signaling loop in DC is essential for inducing CD8(+)-dependent Th1 immune responses in mice. Therefore, targeted manipulation of this loop promises to be an effective, novel strategy for therapeutic modulation of clinically relevant DTH reactions.
Activated Human T Lymphocytes Express a Functional C3a Receptor (2000)

The C3a molecule is an anaphylatoxin of the C system with a wide spectrum of proinflammatory effects predominantly on cells of myeloid origin. In this study we investigated the expression of the high affinity receptor for C3a (C3aR) in human T lymphocytes using receptor-specific mAb. C3aR expression was detected in CD4(+) and CD8(+) blood- or skin-derived T cell clones (TCC) from birch pollen-sensitized patients with atopic dermatitis. No significant difference in C3aR expression in CD4(+) or CD8(+) TCCs could be observed. In contrast to C3a(desArg), C3a led to a transient calcium flux in TCCs expressing the C3aR, whereas C3aR-negative TCCs were unreactive. Circulating T cells from patients suffering from severe inflammatory skin diseases expressed the C3aR, whereas no expression of C3aR could be found in unstimulated T lymphocytes from patients with mild inflammatory skin diseases or from healthy individuals. Type I IFNs, which are potent stimulators of cellular immunity, were identified as up-regulators of C3aR expression in vitro in freshly isolated or cloned T lymphocytes. Moreover, C3aR(+) T cells were found at the sites of injection in IFN-beta-treated patients with multiple sclerosis. These data provide direct evidence for the expression of C3aR on activated human T lymphocytes; this may point to a biological function of C3a in T cell-dependent diseases.
Cu(I) Binding and Transfer by the N Terminus of the Wilson Disease Protein (2007)

Wilson and Menkes diseases are genetic disorders of copper metabolism caused by mutations in the Wilson (WND) and Menkes (MNK) copper-transporting P1B-type ATPases. The N termini of these ATPases consist of six metal binding domains (MBDs). The MBDs interact with the copper chaperone Atox1 and are believed to play roles in catalysis and in copper-mediated cellular relocalization of WND and MNK. Although all six MBDs have similar folds and bind one Cu(I) ion via a conserved CXXC motif, biochemical and genetic data suggest that they have distinct functions. Most studies aimed at characterizing the MBDs have employed smaller polypeptides consisting of one or two domains. The role of each MBD is probably defined by its environment within the six-domain N terminus, however. To study the properties of the individual domains within the context of the intact Wilson N terminus (N-WND), a series of variants in which five of the six metal binding CXXC motifs are mutated to SXXS was generated. For each variant, the Cu(I) binding affinity and the ability to exchange Cu(I) with Atox1 were investigated. The results indicate that Atox1 can deliver Cu(I) to and remove Cu(I) from each MBD, that each MBD has stronger Cu(I) retention properties than Atox1, and that all of the MBDs as well as Atox1 have similar K(Cu) values of (2.2-6.3) x 10(10) m(-1). Therefore, the specific role of each MBD is not conferred by its position within the intact N-WND but may be related to interactions with other domains and partner proteins.
cDNA cloning of human plasminogen activator-inhibitor from endothelial cells. (1986)

Full-length cDNA for plasminogen activator inhibitor (PAI-1) was isolated from a human umbilical vein endothelial cell (HUVEC) lambda gt11 cDNA library. Three overlapping clones were identified by immunologic screening of 10(6) recombinant phage using a rabbit anti-human fibrosarcoma PAI-1 antiserum. The fusion proteins encoded by these three clones also react strongly with a monoclonal mouse anti-human fibrosarcoma PAI-1 antibody. By nucleotide sequence analysis, PAI-1 cDNA encodes a protein containing 402 amino acids with a predicted, nonglycosylated molecular mass of 45 kD. Identity of this material as authentic PAI-1 was confirmed by the presence of high level homology with the primary amino acid sequence of an internal peptide prepared from purified rat hepatoma PAI-1. The predicted amino acid sequence also reveals extensive homology with other members of the serine protease inhibitor gene family. Cultured HUVECs contain two PAI-1 mRNA species, both encoded by a single gene, differing by 1 kb in the 3' untranslated region. The PAI-1 gene is located on human chromosome 7.
A fully programmable memory management system optimizing queue handling at multi gigabit rates (2004)

Two of the main bottlenecks when designing a network embedded system are very often the memory bandwidth and its capacity. This is mainly due to the extremely high speed of the state-of-the-art network links and to the fact that in order to support advanced quality of service (QoS), per-flow queueing is desirable. In this paper we describe the architecture of a memory manager that can provide up to 10Gbs of aggregate throughput while handling 512K queues. The presented system supports a complete instruction set and thus we believe it can be used as a hardware component in any suitable embedded system, particularly network SoCs that implement per flow queuing. When designing this scheme several optimisation techniques have been evaluated and the most cost and performance effective ones used. These techniques minimize both the memory bandwidth and the memory capacity needed, which is considered a main advantage of the proposed scheme. The proposed architecture uses a simple DRAM for data storage and a typical SRAM for keeping data structures-pointers, therefore minimising the system's cost. The device has been fabricated within a novel programmable network processor designed for efficient protocol processing in high speed networking applications. It consists of 155K Gates and occupies 5.23 mm in UMC 0.18υ CMOS.
A model for the description and prediction of the response of laying hens to amino acid intake (1973)

Synopsis A model which describes the response of groups of laying hens to different levels of amino acid intake is presented. The model is based on the assumption of simple linear relationships between amino acid intake and the output characteristics, egg production and maintenance, for individual birds. The response for a group of birds is then derived as the average of the individual responses. The shape of this flock—response curve depends on seven parameters, namely the mean maximum egg output (Ē max), variation in E max, mean body weight (W), variation in W, the correlation between egg output and body weight, and two constants (a and b) representing respectively the quantities of amino acid required for unit egg output and for maintenance of unit body weight. Three methods of manipulating the model are described. These use (i) a computer simulation procedure; (ii) the exact solution for the model and (iii) some reasonable approximations for practical application. The use of the model for describing experimental data and for predicting amino acid requirements is discussed, and the main limiting assumptions and some possible extensions of the principles involved are pointed out.
Metabolism and Excretion of [14C] Febuxostat, a Novel Nonpurine Selective Inhibitor of Xanthine Oxidase, in Healthy Male Subjects (2010)

Absorption, metabolism, and excretion of one 80 mg oral dose of [(14)C] febuxostat ([thiazole-4-(14)C] 2-[3-cyano-4-isobutoxyphenyl]-4-methyl-5-thiazolecarboxylic acid) were studied in 6 healthy subjects. Mean cumulative recovery in excreta was 94% (49% urine and 45% feces) of the dose over 9 days; 87% of the dose was profiled. Seventeen radioactive peaks were observed in urine and fecal chromatograms. Unchanged febuxostat contributed to a combined total in excreta of 10% to 18% of the dose, indicating that it was extensively metabolized and well absorbed. Metabolites were 67M-1 (10%) and 67M-2 (11%) hydroxylated febuxostat, febuxostat acyl-glucuronide (30%), 67M-4 di-carboxylic acid (14%), 67M-1 sulfate conjugate (3%), and dehydrated 67M-1/67M-2 acyl-glucuronide (0.5%). Febuxostat and these metabolites accounted for 82% of profiled dose; unidentified peaks individually contributed <1.3% of the dose. Febuxostat and total radioactivity plasma C(max) values were observed at 0.5 hour postdose, suggesting that febuxostat was quickly absorbed. At 4 hours postdose, plasma chromatographic profiles contained 6 peaks: febuxostat (85%), 67M-1 (4%), 67M-2 (5%), febuxostat acyl-glucuronide (4%), 67M-4 (1%), and 67M-1 sulfate (0.5%). Compared to total radioactivity, febuxostat accounted for 94% at C(max) and 83% of the area under the concentration-time curve (AUC) values. Based on the whole blood to plasma total radioactivity, little radioactivity was associated with red blood cells.
Conformal dielectric-filled edge-slot antennas with inductive-post tuning (1979)

A class of circumferential-slot antennas, called edge-slot antennas, that are ideally suited for conformal mounting on conducting bodies of revolution has been developed. The simplest form of the antenna is a disk of dielectric substrate that is copper-plated on both sides and mounted between two parts of the conducting body so that the aperture coincides with the surface. The antenna is excited by a single coaxial stub at the center and is tuned for proper operating frequency by inductive posts that connect the two copper-plated sides of the disk. By varying the number and location of the inductive posts the operating frequency of a disk can be tuned over a 6:1 range. Instantaneous bandwidths of three percent are typical. In practice, plated-through holes are used as inductive posts to provide mounting and access holes. The single coaxial feed excites azimuthally symmetric fields that are not significantly distorted by the symmetrically placed inductive posts. Therefore, radiation patterns of edge-slot excited bodies display a high degree of azimuthal symmetry. The small size, light weight, and inexpensive fabrication procedure make the edge-slot antenna attractive for many applications.
Kinetic and Inhibition Studies of Dihydroxybenzoate-AMP Ligase from Escherichia coli (2010)

Inhibition of siderophore biosynthetic pathways in pathogenic bacteria represents a promising strategy for antibacterial drug development. Escherichia coli synthesize and secrete the small molecule iron chelator siderophore, enterobactin, in response to intracellular iron depletion. Here we describe a detailed kinetic analysis of EntE, one of six enzymes in the enterobactin synthetase gene cluster. EntE catalyzes the ATP-dependent condensation of 2,3-dihydroxybenzoic acid (DHB) and phosphopantetheinylated EntB (holo-EntB) to form covalently arylated EntB, a product that is vital for the final assembly of enterobactin. Initial velocity studies show that EntE proceeds via a bi-uni-uni-bi ping-pong kinetic mechanism with a k(cat) equal to 2.8 s(-1) and K(m) values of 2.5, 430, and 2.9 microM for DHB, ATP, and holo-EntB-ArCP, respectively. Inhibition and direct binding experiments suggest that, during the first half-reaction (adenylation), DHB binds first to the free enzyme, followed by ATP and the release of pyrophosphate to form the adenylate intermediate. During the second half-reaction (ligation), phosphopantetheinylated EntB binds to the enzyme followed by the release of products, AMP and arylated EntB. Two hydrolytically stable adenylate analogues, 5'-O-[N-(salicyl)sulfamoyl]adenosine (Sal-AMS) and 5'-O-[N-(2,3-dihydroxybenzoyl)sulfamoyl]adenosine (DHB-AMS), are shown to act as slow-onset tight-binding inhibitors of the enzyme with (app)K(i) values of 0.9 and 3.8 nM, respectively. Direct binding experiments, via isothermal titration calorimetry, reveal low picomolar dissociation constants for both analogues with respect to EntE. The tight binding of Sal-AMS and DHB-AMS to EntE suggests that these compounds may be developed further as effective antibiotics targeted to this enzyme.
In vitro evaluation of 1-(2-chloroethyl)-1-nitroso-3-(2-hydroxyethyl)urea linked to 4-acetoxy-bisdesmethyltamoxifen, estradiol and dihydrotestosterone. (1990)

The anticancer efficacies of three 1-(2-chloroethyl)-1-nitroso-3-(2- hydroxyethyl)urea (HECNU) derivatives--4-acetoxybisdesmethyltamoxifen-1,4-hemisuccinate-H ECNU (4-OAc-BDMT-hs-HECNU), 17-beta-estradiol-1,4-hemisuccinate-HECNU (E2-hs-HECNU) and 17-dihydrotestosterone-1,4-hemisuccinate-HECNU (DHT-hs-HECNU)--are compared with their unlinked equimolar mixtures using the estrogen and androgen receptor positive cell line MCF-7. Following 72 h incubation at a concentration of 100 mumol/l, 4-OAc-BDMT-hs-HECNU and DHT-hs-HECNU have a growth inhibitory effect of 76% and 73%, respectively, whereas E2-hs-HECNU causes an inhibition of 55%. Within this time period, DHT-hs-HECNU (100 mumol/l) is more effective as compared to the unlinked equimolar combination of HECNU plus dihydrotestosterone; E2-hs-HECNU (100 mumol/l) is slightly more and 4-OAc-BDMT-hs-HECNU (100 mumol/l) is even less effective than the respective unlinked equimolar mixtures. At this concentration (100 mumol/l) the growth inhibitory effect of 4-OAc-BDMT-hs-HECNU is not antagonized by coincubation with estradiol.
The UL13 virion protein of herpes simplex virus type 1 is phosphorylated by a novel virus-induced protein kinase (1992)

Herpes simplex virus type 1 (HSV-1) induces a protein kinase (PK) activity in infected cell nuclei. In vitro, the enzyme is able to phosphorylate exogenous casein (albeit inefficiently) but not protamine, can use ATP or GTP as a phosphate donor, is stimulated by high salt concentrations and is insensitive to inhibition by heparin. On the basis of these properties, the PK appears to be distinct from previously described cellular enzymes and from the cytoplasmic PK encoded by the viral US3 gene. A major substrate of the enzyme in vitro is a virus-induced protein with an Mr of 57000 (Vmw57). The gene encoding Vmw57 was mapped using recombinants between HSV-1 and HSV-2 to a region of the virus genome containing genes UL9 to UL15. Use of a monospecific rabbit antiserum showed that Vmw57 is a virion structural protein encoded by gene UL13. These results, in conjunction with previous reports that the UL13 protein contains PK sequence motifs, support the notions that the nuclear PK and Vmw57 are identical, and that the observed reactivity is due to autophosphorylation.
Lamin A/C speckles mediate spatial organization of splicing factor compartments and RNA polymerase II transcription (2002)

The A-type lamins have been observed to colocalize with RNA splicing factors in speckles within the nucleus, in addition to their typical distribution at the nuclear periphery. To understand the functions of lamin speckles, the effects of transcriptional inhibitors known to modify RNA splicing factor compartments (SFCs) were examined. Treatment of HeLa cells with alpha-amanitin or 5,6-dichlorobenzimidazole riboside (DRB) inhibited RNA polymerase II (pol II) transcription and led to the enlargement of lamin speckles as well as SFCs. Removal of the reversible inhibitor DRB resulted in the reactivation of transcription and a rapid, synchronous redistribution of lamins and splicing factors to normal-sized speckles, indicating a close association between lamin speckles and SFCs. Conversely, the expression of NH2-terminally modified lamin A or C in HeLa cells brought about a loss of lamin speckles, depletion of SFCs, and down-regulation of pol II transcription without affecting the peripheral lamina. Our results suggest a unique role for lamin speckles in the spatial organization of RNA splicing factors and pol II transcription in the nucleus.
FTICR-mass spectrometry for high-resolution analysis in combinatorial chemistry (2000)

The diversity of compound collections required for finding lead structures in pharmaceutical research can be provided by means of combinatorial organic chemistry. The resultant enormous number of single compounds but also of compound mixtures represents a challenge for the analyst. With the introduction of Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS or FT-MS), a new and, as yet, not widespread mass spectrometric technique (a means of analysis of such compound libraries with a very high mass resolution) high mass accuracy and high sensitivity has become available. Moreover, in combination with electrospray ionization (ESI), not only high-throughput measurements via flow-injection analysis (FIA) but also coupling with separation techniques such as high-performance liquid chromatography (HPLC) or capillary electrophoresis (CE) is possible. Structural verification by way of decomposing ions (MS(n); n > or = 2) using a variety of different dissociation techniques can be performed by FTICR-MS. This is the first review specifically covering applications of FTICR-MS in the field of combinatorial chemistry.