gebhart/patrepeval huggingface dataset:
A framework for understanding network intelligence (2002)

The term network intelligence is widely used in the field of communication networks. A number of new and potentially limiting concepts and products based on the concept of network intelligence have been introduced, including smart flows, intelligent routing, and intelligent web switching. Many intelligent systems focus on a specific service, function, or device, and do not provide true end-to-end network intelligence. True network intelligence requires more than a set of disconnected elements; it requires an interconnecting and functionally coupled architecture that enables the various functional levels to interact and communicate with each other. We propose a uniform framework for understanding end-to-end communication network intelligence (CNI), which is defined as the ability of a network to act appropriately in a changing environment. We consider an appropriate action to be one that increases the optimal and efficient use of network resources in delivering services, and we define success as the achievement of behavior subgoals that support the service provider's ultimate goals, which are defined external to the network system. The framework presented incorporates the functional elements of intelligence into computational modules and interconnects the modules into networks and hierarchies that have spatial, logical, and temporal properties. Based on the framework proposed, we describe an end-to-end multiservice network application spanning the network management layer, optical layer, switching/routing layer, services layer, and other layers.
Broad Conservation of Milk Utilization Genes inBifidobacterium longumsubsp.infantisas Revealed by Comparative Genomic Hybridization (2010)

Human milk oligosaccharides (HMOs) are the third-largest solid component of milk. Their structural complexity renders them nondigestible to the host but liable to hydrolytic enzymes of the infant colonic microbiota. Bifidobacteria and, frequently, Bifidobacterium longum strains predominate the colonic microbiota of exclusively breast-fed infants. Among the three recognized subspecies of B. longum, B. longum subsp. infantis achieves high levels of cell growth on HMOs and is associated with early colonization of the infant gut. The B. longum subsp. infantis ATCC 15697 genome features five distinct gene clusters with the predicted capacity to bind, cleave, and import milk oligosaccharides. Comparative genomic hybridizations (CGHs) were used to associate genotypic biomarkers among 15 B. longum strains exhibiting various HMO utilization phenotypes and host associations. Multilocus sequence typing provided taxonomic subspecies designations and grouped the strains between B. longum subsp. infantis and B. longum subsp. longum. CGH analysis determined that HMO utilization gene regions are exclusively conserved across all B. longum subsp. infantis strains capable of growth on HMOs and have diverged in B. longum subsp. longum strains that cannot grow on HMOs. These regions contain fucosidases, sialidases, glycosyl hydrolases, ABC transporters, and family 1 solute binding proteins and are likely needed for efficient metabolism of HMOs. Urea metabolism genes and their activity were exclusively conserved in B. longum subsp. infantis. These results imply that the B. longum has at least two distinct subspecies: B. longum subsp. infantis, specialized to utilize milk carbon, and B. longum subsp. longum, specialized for plant-derived carbon metabolism.
Schedule-dependence of C-CAM1 adenovirus gene therapy in a prostate cancer model. (1999)

Sustained expression of C-CAM1 is required for optimal tumor suppression. The schedule-dependence of C-CAM1's antitumor activity should be taken into account in optimizing gene therapy in clinical settings.
Involvement of the CDw50 molecule in allorecognition (1990)

The CDw50 differentiation antigen is defined by 101-1D2 and 140-11 monoclonal antibodies (mAb), both produced and characterized in our laboratory. This molecule is broadly expressed on hematopoetic cells but not on other cells. In this report we show that these 2 mAb recognize different epitopes of the same molecule, which are resistant to neuraminidase and proteases. We also demonstrate that the CDw50 antigen is expressed on thymocytes and T lymphocytes as an N-glycosylated glycoprotein monomer with a relative molecular weight (Mr) of 130,000 daltons with intrachain disulfide bonds, and that this molecule is resistant to treatment with phosphatidylinositol (PI) phospholipase C and therefore probably not PI-anchored to the membrane. CDw50 is a poorly or non-constitutively phosphorylated molecule that becomes phosphorylated by treatment with phorbol 12-myristate 13-acetate (PMA) of peripheral blood mononuclear cells (PBMC). The addition of affinity-purified CDw50 mAb inhibits primary mixed lymphocyte culture (MLC) but not secondary MLC, cytotoxicity or proliferation induced by mitogens. The inhibition of alloreactivity is mediated at the level of both responding and stimulator cells.
Identification of a Bardet-Biedl syndrome locus on chromosome 3 and evaluation of an efficient approach to homozygosity mapping (1994)

Bardet-Biedl syndrome is an autosomal recessive disorder characterized by mental retardation, obesity, retinitis pigmentosa, polydactyly and hypogonadism. Individuals with this disorder also have an increased incidence of hypertension, diabetes mellitus, and renal and cardiac anomalies. We previously identified a locus on chromosome 16 causing this disorder, and provided evidence that Bardet-Biedl syndrome is heterogeneous. In this study, we identify another Bardet-Biedl syndrome locus on chromosome 3 and confirm the non-allelic heterogeneity of this disorder in Bedouin populations. In addition, we demonstrate the feasibility of using pooled DNA samples from members of large kindreds as an efficient approach to homozygosity mapping.
The Three-Dimensional Structure at 6 A Resolution of a Human γG1 Immunoglobulin Molecule (1971)

A three-dimensional electron density map has been calculated at 6 A resolution for a human γG1 immunoglobulin molecule. X-ray diffraction data have been collected for the native protein crystals and for three heavy atom derivatives prepared by soaking crystals in p-chloromercuribenzenesulfonate, Hg(CN)2, and PtCl6=. The electron density map is interpreted in terms of four possible models, of which a T-shaped model is favored. The dimensions of this model are compared with those reported by other physical and chemical techniques for immunoglobulin molecules.
Aberration correction by maximizing generalized sharpness metrics (2003)

The technique of maximizing sharpness metrics has been used to estimate and compensate for aberrations with adaptive optics, to correct phase errors in synthetic-aperture radar, and to restore images. The largest class of sharpness metrics is the sum over a nonlinear point transformation of the image intensity. How the second derivative of the point nonlinearity varies with image intensity determines the effects of various metrics on the imagery. Some metrics emphasize making shadows darker, and other emphasize making bright points brighter. One can determine the image content needed to pick the best metric by computing the statistics of the image autocorrelation or of the Fourier magnitude, either of which is independent of the phase error. Computationally efficient, closed-form expressions for the gradient make possible efficient search algorithms to maximize sharpness.
Transcription and replication of mitochondrial DNA (2000)

The physical isolation of mammalian mitochondrial DNA (mtDNA) over 30 years ago marked the beginning of studies of its structure, replication and the expression of its genetic content. Such analyses have revealed a number of surprises: novel DNA structural features of the circular genome such as the displacement loop (D-loop); multiple sized and deleted forms of the circular genome; a minimal set of mitochondrially encoded rRNAs and tRNAs needed for translation; a bacteriophage-like, nuclear-encoded mitochondrial RNA polymerase for transcription; and a direct linkage between transcription and the commitment to replication of the leading mtDNA strand that centres on the nuclear encoded mitochondrial transcription factor A. One of the more recent revelations is the existence, near the D-loop, of an atypical, stable RNA-DNA hybrid (or R-loop) at the origin of mammalian leading-strand DNA replication, composed of the parent DNA strands and an RNA transcript. In mammalian mitochondrial systems, all of the proteins known to be involved in DNA replication are encoded in the nucleus. Thus alterations and deficiencies in mtDNA replication must arise from mutations in mtDNA regulatory sequences and nuclear gene defects. Further studies of the relationships between nuclear-encoded proteins and their mtDNA target sequences could result in strategies to manipulate genotypes within cellular mtDNA populations.
Substitution of Aspartic Acid for Methionine-306 in Factor VIIa Abolishes the Allosteric Linkage between the Active Site and the Binding Interface with Tissue Factor (2001)

The enzyme factor VIIa (FVIIa) triggers the blood coagulation cascade upon association with tissue factor (TF). The TF-induced allosteric enhancement of FVIIa's activity contributes to the procoagulant activity of the complex, and Met-306 in the serine protease domain of FVIIa participates in this event. We have characterized FVIIa variants mutated in position 306 with respect to their ability to be stimulated by TF. The amidolytic activity of FVIIa mutants with Ser, Thr, and Asn in position 306 was stimulated 9-, 12-, and 7-fold, respectively, by soluble TF as compared to 22-fold for wild-type FVIIa. In contrast, the activity of Met306Asp-FVIIa only increased about 2-fold and that of Met306Asp/Asp309Ser-FVIIa increased about 1.5-fold. Modeling suggests that Asp in position 306 prevents the TF-induced stimulation of FVIIa by disrupting essential intermolecular hydrogen bonds. The ability of the FVIIa variants to catalyze factor X activation and the amidolytic activity were enhanced to a similar extent by soluble TF. This indicates that factor X does not promote its own activation through interactions with exosites on FVIIa made accessible upon FVIIa-TF assembly. Met306Asp-FVIIa binds soluble TF with a dissociation constant of 13 nM (about 3-fold higher than that of FVIIa), and, in sharp contrast to FVIIa, its binding kinetics are unaltered after inactivation with D-Phe-Phe-Arg chloromethyl ketone. We conclude that a single specific amino acid replacement, substitution of Asp for Met-306, virtually prevents the TF-induced allosteric changes which normally result in dramatically increased FVIIa activity and eliminates the effect of the active site inhibitor on TF affinity.
SEVEN NEW SPECIES OF THE GENUS OCTONOBA (ARANEAE: ULOBORIDAE) FROM THE RYUKYUS, JAPAN (1981)

Seven new species of the genus Octonoba are described from the Ryukyus. These species inhabit only a few islands in the limited extent, and their distributions are not overlapping one another.
Endothelin-1 stimulates contraction of rat glomerular mesangial cells and potentiates beta-adrenergic-mediated cyclic adenosine monophosphate accumulation. (1990)

The newly isolated peptide, endothelin-1 (ET-1), is a potent pressor agent that reduces GFR and the glomerular ultrafiltration coefficient. Recent evidence demonstrates that ET-1 mobilizes intracellular Ca2+ [( Ca2+]i) in glomerular mesangial cells by activating the phosphoinositide cascade. The present experiments were designed to examine whether ET-1 stimulates mesangial cell contraction and regulates the synthesis of PGE2 and cAMP, which dampen vasoconstrictor-induced mesangial contraction. ET-1 (greater than or equal to 1 nM) reduced the cross-sectional area of rat mesangial cells cultured on three-dimensional gels of collagen type I. ET-1 also caused complex rearrangements of F-actin microfilaments consistent with a motile response. Contraction in response to ET-1 occurred only at concentrations that activate phospholipase C, and contraction was unaffected by blockade of dihydropyridine-sensitive Ca2+ channels. Elevation of [Ca2+]i with ionomycin, to equivalent concentrations of [Ca2+]i achieved with ET-1, also reduced mesangial cell cross-sectional area. ET-1 (0.1 microM) also evoked [3H]arachidonate release and a fivefold increase in PGE2 synthesis as well as increased synthesis of PGF2 alpha and small changes of TXB2. ET-1 caused a minor increase in intracellular cAMP accumulation only in the presence of 3-isobutyl-1-methylxanthine. ET-1 also amplified cAMP production in response to isoproterenol. TPA and ionomycin, alone and in combination, failed to mimic the potentiating effect of ET-1; however, indomethacin blocked ET-1-induced potentiation of isoproterenol-stimulated cAMP, which was restored by addition of exogenous 10 nM PGE2. Thus the present data demonstrate that ET-1 stimulates mesangial cell contraction via pharmacomechanical coupling and activates phospholipase A2 to produce PGE2, PGF2 alpha, and TXB2. ET-1 also amplified beta adrenergic-stimulated cAMP accumulation by a PGE2-dependent mechanism.
Interleukin-12 protects thermally injured mice from herpes simplex virus type 1 infection (1996)

Severe burn injury is associated with increased susceptibility to severe herpesvirus infections. Type 2 cytokines [interleukin (IL)-4 and IL-10] released from burn-associated CD8+ type 2 T cells (BA-type 2 T cells) have been shown to play a role in the increased susceptibility of thermally injured mice (TI-mice) to herpes simplex virus type 1 (HSV-1) infection. Because IL-12 has been shown to inhibit the generation of type 2 T cells, murine rIL-12 was injected into TI-mice exposed to HSV-1 to determine whether IL-12 could influence HSV-1 infections in individuals bearing type 2 T cells. rIL-12 improved the resistance of TI-mice or mice inoculated with T6S cells (a BA-type 2 T cell clone) against HSV-1 infection. Type 2 cytokines were detected in sera of TI-mice or mice inoculated with T6S cells (T6S-mice). However, treatment of TI-mice or T6S-mice with rIL-12 inhibited type 2 cytokine production in the sera of these mice. All TI-mice exposed to a lethal dose of HSV-1 survived when they were treated with a mixture of monoclonal antibodies (mAbs) against type 2 cytokines. Staphylococcal enterotoxin A [an interferon-gamma (IFN-gamma) inducer] stimulated serum IFN-gamma production in TI-mice and T6S-mice treated with rIL-12, whereas no IFN-gamma was produced in mice treated with saline. These results suggest that IL-12 has the potential to protect TI-mice infected with a lethal dose of HSV-1 via a shift to type 1 T cell responses from type 2 T cell responses.
NK Cells—From Bench to Clinic (2012)

After decades of mouse and human research, we now know that natural killer (NK) cells have unique properties including memory. Although initially described as major histocompatibility complex (MHC) unrestricted killers, NK cells have several families of receptors that directly recognize MHC including Ly49 receptors in the mouse and killer immunoglobulin-like receptors (KIR) in humans. The strength of this signal is determined by polymorphisms in NK cell inhibitory receptor genes and their MHC ligands inherited on different chromosomes. Inhibitory receptors protect "self"-expressing normal tissue from being killed by NK cells and protecting against autoimmunity. Therefore, for NK cells to kill and produce cytokines, they must encounter activating receptor ligands in the context of "missing self" that occurs with some viral infections and malignant transformation. The second property of inhibitory receptors is to educate or license NK cells to acquire function. This is best demonstrated in the mouse and in humans by enhanced function on self-inhibitory receptor-expressing NK cells when in a host expressing cognate ligate. In contrast, NK cells without inhibitory receptors or with nonself-inhibitory receptors are relatively hyporesponsive. The basic biology of NK cells in response to cytokines, education, and viruses will translate into strategies to manipulate NK cells for therapeutic purposes.
Palladium-Catalyzed Cross-Coupling Reaction of Aryltriethoxysilanes with Aryl Bromides under Basic Aqueous Conditions (2001)

Aryltriethoxysilanes were cross-coupled with aryl bromides in high yield in the presence of a palladium catalyst and aqueous sodium hydroxide.
New technology, same old problem (2005)

HIV replication follows a well-defined pattern during the acute phase of the infection in humans. After reaching a peak during the first few weeks after infection, viral replication resolves to a set-point thereafter. There are still uncertainties regarding the contribution of CD8(+) T cells in establishing this set-point. An alternative explanation, supported by in silico modeling, would imply that viral replication is limited by the number of available targets for infection, i.e. CD4(+)CCR5(+) T cells. Here, we used NOD.SCID.gc(-/-) mice bearing human CD4(+)CCR5(+) and CD8(+) T cells derived from CD34(+) progenitors to investigate the relative contribution of both in viral control after the peak. Using low dose of a CCR5-tropic HIV virus, we observed an increase in viral replication followed by "spontaneous" resolution of the peak, similar to humans. To rule out any possible role for CD8(+) T cells in viral control, we infected mice in which CD8(+) T cells had been removed by a depleting antibody. Globally, viral replication was not affected by the absence of CD8(+) T cells. Strikingly, resolution of the viral peak was equally observed in mice with or without CD8(+) T cells, showing that CD8(+) T cells were not involved in viral control in the early phase of the infection. In contrast, a marked and specific loss of CCR5-expressing CD4(+) T cells was observed in the spleen and in the bone marrow, but not in the blood, of infected animals. Our results strongly suggest that viral replication during the acute phase of the infection in humanized mice is mainly constrained by the number of available targets in lymphoid tissues rather than by CD8(+) T cells.
Convenient Synthetic Method for 5-Trifluoromethyloxazoles and 5-Trifluoromethylthiazoles (1994)

5-(Trifluoromethyl)oxazoles (3) and 5-(trifluoromethyl)thiazoles (4) were conveniently as well as effectively synthesized from 3-(N-tert-butyl-N-methylhydrazono)-1,1,1-trifluoroalkan-2-ones (1) via 5-(trifluoromethyl)-3-oxazoline (2). One-pot conversion of 1 to 4 also proceeded successfully
Polyvinyl alcohol cryogel: An ideal phantom material for MR studies of arterial flow and elasticity (1997)

The authors present a unique application of polyvinyl alcohol (PVA) cryogel as an anthropomorphic, elastic, vascular phantom material that can be used in MR imaging. The composition consists of two nontoxic ingredients: water and PVA. The biomechanical and MR properties can be adjusted to be similar to those of excised porcine aortas by varying the number of freeze-thaw cycles to which the PVA solution is exposed. The authors present the T1, T2, shrinkage, and tensile properties of PVA cryogel tubes as a function of freeze-thaw cycles. MR images of a dual elastic aortic phantom undergoing pulsatile motion are shown.
[Fulminant acne: therapy with 13-cis-retinoic acid and indomethacin]. (1986)

Young men with mild acne vulgaris may rarely experience a very acute exacerbation with ulceration and necrosis of the lesions accompanied by fever, malaise, loss of weight, often by polyarthritis, and occasionally by erythema nodosum. Elevated sedimentation rate and marked leucocytosis are characteristic; microhematuria is often observed. This condition has been called acne fulminans. We report on a young male patient suffering from severe acne fulminans. Systemic 13-cis retinoic acid (Roaccutan, Accutane) and indomethacine (Amuno) treatment rapidly improved the skin and joint lesions. Intracutaneous tests with viral, bacterial, and fungal antigens before and during treatment suggest a temporary cellular immune defect.
High-frequency nonlinearity analysis of common-emitter and differential-pair transconductance stages (1998)

Equations describing the high-frequency nonlinear behavior of common-emitter and differential-pair transconductance stages are derived. The equations show that transconductance stages using inductive degeneration are more linear than those using capacitive or resistive degeneration, and that the common-emitter transconductance stages are more linear than the differential-pair transconductance stages with the same bias current and transconductance. The nonlinearity equations can also be used to explain the class AB behavior of the common-emitter transconductance stage with inductive degeneration.
The family of wood composite materials. (1996)

The development of wood composite materials constitutes a revolution in the forest products industry over the past several decades. This month's feature by Tom Maloney gives us a snapshot of this industry and seeks to clarify some terminology.
Synaptic Desensitization of NMDA Receptors by Calcineurin (1995)

Desensitization is a phenomenon that is common to many ligand-gated ion channels but has been demonstrated only rarely with physiological stimulation. Numerous studies describe desensitization of the N-methyl-D-aspartate (NMDA) subtype of glutamate receptor by exogenous agonists, but whether synaptic stimulation causes desensitization has been unknown. Synaptic stimulation of NMDA receptors on rat hippocampal neurons resulted in desensitization that was prevented by intracellular 1,2-bis(o-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid (BAPTA), adenosine-5'-O-(3-thiotriphosphate) (ATP-gamma-S), or inhibitors of phosphatase 2B (calcineurin), but not by inhibitors of phosphatases 1 and 2A or of tyrosine phosphatases. Synaptic NMDA receptors may fluctuate between phosphorylated and dephosphorylated forms, depending on the rate of synaptic stimulation and the magnitude of the associated influx of calcium through NMDA receptors.
Black-pigmented Gram-negative anaerobes in endodontic infections (1993)

Necrotic dental root canal infections are polymicrobial infections dominated by anaerobic bacteria. The number of different species in one canal is usually low, approx. 4–7 species. The species isolated most frequently belong to the genera Prevotella, Porphyromonas, Fusobacterium, Peptostreptococcus, Eubacterium and Streptococcus. The frequency of isolation of black-pigmented Gram-negative anaerobes in endodontic infections varies from 25% to <50%. Pr. intermedia is the most commonly found pigmented species, followed by Pr. denticola and two Porphyromonas species, P. gingivalis and P. endodontalis. Several studies have shown that P. gingivalis and P. endodontalis are closely related to the presence of acute symptoms in endodontic infections, whereas other black-pigmented Gram-negative anaerobes are not. However, several other species may also be involved in acute infections. Moreover, Porphyromonas species have occasionally been isolated from cases with no symptoms. Although Porphyromonas spp. are clearly related to symptoms at the beginning of therapy, they are not important for the prognosis of the treatment.