gebhart/patrepeval huggingface dataset:
Sampling node pairs over large graphs (2013)

Characterizing user pair relationships is important for applications such as friend recommendation and interest targeting in online social networks (OSNs). Due to the large scale nature of such networks, it is infeasible to enumerate all user pairs and so sampling is used. In this paper, we show that it is a great challenge even for OSN service providers to characterize user pair relationships even when they possess the complete graph topology. The reason is that when sampling techniques (i.e., uniform vertex sampling (UVS) and random walk (RW)) are naively applied, they can introduce large biases, in particular, for estimating similarity distribution of user pairs with constraints such as existence of mutual neighbors, which is important for applications such as identifying network homophily. Estimating statistics of user pairs is more challenging in the absence of the complete topology information, since an unbiased sampling technique such as UVS is usually not allowed, and exploring the OSN graph topology is expensive. To address these challenges, we present asymptotically unbiased sampling methods to characterize user pair properties based on UVS and RW techniques respectively. We carry out an evaluation of our methods to show their accuracy and efficiency. Finally, we apply our methods to two Chinese OSNs, Doudan and Xiami, and discover significant homophily is present in these two networks.
Transcript Profiling Suggests That Differential Metabolic Adaptation of Mice to a High Fat Diet Is Associated with Changes in Liver to Muscle Lipid Fluxes (2004)

Genetically homogenous C57Bl/6 mice display differential metabolic adaptation when fed a high fat diet for 9 months. Most become obese and diabetic, but a significant fraction remains lean and diabetic or lean and non-diabetic. Here, we performed microarray analysis of "metabolic" transcripts expressed in liver and hindlimb muscles to evaluate: (i) whether expressed transcript patterns could indicate changes in metabolic pathways associated with the different phenotypes, (ii) how these changes differed from the early metabolic adaptation to short term high fat feeding, and (iii) whether gene classifiers could be established that were characteristic of each metabolic phenotype. Our data indicate that obesity/diabetes was associated with preserved hepatic lipogenic gene expression and increased plasma levels of very low density lipoprotein and, in muscle, with an increase in lipoprotein lipase gene expression. This suggests increased muscle fatty acid uptake, which may favor insulin resistance. In contrast, the lean mice showed a strong reduction in the expression of hepatic lipogenic genes, in particular of Scd-1, a gene linked to sensitivity to diet-induced obesity; the lean and non-diabetic mice presented an additional increased expression of eNos in liver. After 1 week of high fat feeding the liver gene expression pattern was distinct from that seen at 9 months in any of the three mouse groups, thus indicating progressive establishment of the different phenotypes. Strikingly, development of the obese phenotype involved re-expression of Scd-1 and other lipogenic genes. Finally, gene classifiers could be established that were characteristic of each metabolic phenotype. Together, these data suggest that epigenetic mechanisms influence gene expression patterns and metabolic fates.
Anti-IgM but not anti-IgD antibodies inhibit cell division of normal human mature B cells (1992)

Insolubilized anti-IgD antibody markedly increased DNA synthesis in and cell division of normal peripheral blood B cells (PBL-B) when used in combination with IL-4. Anti-IgM antibodies also induced DNA synthesis of PBL-B, but their ability to induce cell division was less than that of anti-IgD antibodies even when used in combination with IL-4. Moreover, anti-IgM antibodies inhibited cell division of PBL-B stimulated with insolubilized anti-IgD antibody plus IL-4 without affecting DNA synthesis. Anti-IgM antibodies also inhibited Staphylococcus aureus Cowan I-induced cell division of PBL-B without affecting DNA synthesis. These results indicate that cross-linkage of surface IgM (sIgM) in mature B cells generates negative signals to inhibit cell division of mature B cells. Because anti-IgD antibodies did not inhibit cell division at all, the role of sIgD in the regulation of cell division of mature B cells may be quite different from that of sIgM. IFN-alpha/beta promoted cell division of PBL-B stimulated with insolubilized anti-IgD antibody plus IL-4. They also counteracted the inhibitory effect of anti-IgM antibody on cell division of PBL-B.
Source routing with protocol-oblivious forwarding (POF) to enable efficient e-Health data transfers (2016)

It has already been confirmed that software-defined networking (SDN) can make the networks more programmable, adaptive and application aware. However, due to the large-scale and geographically-distributed nature of wide-area networks (WAN), the scalability could become a critical issue if we incorporate SDN for WANs (i.e., realizing SD-WANs). In this paper, we design and implement a novel network system that can leverage source routing with the protocol-oblivious forwarding (POF) to facilitate efficient e-Health data transfers with low setup latency. We develop the POF-based source routing protocol to realize a pipeline based packet processing procedure, which can replace the table-lookup based approach in traditional SDN networks and make the forwarding plane more efficient. The proposed scheme is demonstrated experimentally, and the results verify that with it, the flow-tables installed in each core switches in a POF-controlled SD-WAN can be minimized and the path setup latency of traffic flows can be reduced significantly as well.
Extraction and analysis of indole derivatives from fungal biomass (1994)

The occurrence and extraction of indole derivatives in six species from four genera of higher fungi were investigated. By using pure methanol for extraction of the mushrooms analysis revealed the highest concentrations of psilocybin and baeocystin. The psilocin content of the species was higher by using aqueous solutions of alcohols than with methanol alone but was an artificial phenomenon caused by enzymatic destruction of psilocybin. The extraction with dilute acetic acid yielded better results than with the water containing alcohols. The simple one-step procedure with methanol for the quantitative extraction is still the safest method to obtain the genuine alkaloids from fungal biomass.
Bessel beam asymmetry control for glass dicing applications (2018)

Controllable fracture propagation in glass can be obtained by locally weakening the material. The high aspect ratio laser-induced modifications, required for thick glass dicing, can be obtained by use of Bessel-like beams, which have a long non-diffractive length with a small quasi-propagation-invariant central core. We demonstrate the possibility to form elongated modifications in glass with dominant transverse crack propagation direction using axicon-generated asymmetrical Bessel beam. Furthermore, the axicon tilt operation is introduced to add additional astigmatic aberrations for Bessel beam asymmetry control. Dicing results were compared using symmetrical and asymmetrical axicon-generated Bessel beams.
Impaired Ganglioside Metabolism in Huntington's Disease and Neuroprotective Role of GM1 (2010)

Huntington's disease (HD) is a neurodegenerative disorder caused by the expansion of a polyglutamine stretch in the protein huntingtin (Htt). HD neurons are dysfunctional at multiple levels and have increased susceptibility to stress and apoptotic stimuli. We have discovered that synthesis of the ganglioside GM1 is reduced in fibroblasts from HD patients and in cell and animal models of HD, and that decreased GM1 levels contribute to heighten HD cell susceptibility to apoptosis. The apoptotic susceptibility is recapitulated through inhibition of ganglioside synthesis in wild-type striatal cells, suggesting that decreased GM1 levels might be one of the key events leading to HD pathogenesis and progression. Administration of GM1 restores ganglioside levels in HD cells and promotes activation of AKT and phosphorylation of mutant Htt, leading to decreased mutant Htt toxicity and increased survival of HD cells. Our data identify GM1 as a potential treatment for HD.
35-GHz Intrinsic Bandwidth for Direct Modulation in 1.3-&lt;tex&gt;$mu$&lt;/tex&gt;m Semiconductor Lasers Subject to Strong Injection Locking (2004)

Significant enhancement in modulation bandwidth of semiconductor lasers subject to strong optical injection is experimentally and theoretically studied. At least two folds of improvement is achieved under study. By using an optical probing method, a modulation bandwidth of 35 GHz that is free from electrical parasitic effects is observed in the injection-locked laser system. The achieved bandwidth approaches the maximum modulation bandwidth set by the K factor for the free-running laser. Discussions are presented for an even larger modulation bandwidth using the injection-locking technique.
Dihydroorotate Dehydrogenase Is a High Affinity Binding Protein for A77 1726 and Mediator of a Range of Biological Effects of the Immunomodulatory Compound (1995)

A protein with high affinity (Kd 12 nM) for the immunomodulatory compound A77 1726 has been isolated from mouse spleen and identified as the mitochondrial enzyme dihydroorotate dehydrogenase (EC 1.3.3.1). The purified protein had a pI 9.6-9.8 and a subunit Mr of 43,000. Peptides derived from the mouse protein displayed high microsequence similarity to human and rat dihydroorotate dehydrogenase with, respectively, 35 and 39 out of 43 identified amino acids identical. Dihydroorotate dehydrogenase catalyzes the fourth step in de novo pyrimidine biosynthesis. The in vitro antiproliferative effects of A77 1726 are mediated by enzyme inhibition and can be overcome by addition of exogenous uridine. The rank order of potency of A77 1726 and its analogues in binding or enzyme inhibition was similar to that for inhibition of the mouse delayed type hypersensitivity response. It is proposed that inhibition of dihydroorotate dehydrogenase is an in vivo mechanism of action of the A77 1726 class of compounds. This was confirmed using uridine to counteract inhibition of the murine acute graft versus host response.
Molecular and cellular characterization of the 29-kilodalton peripheral membrane protein of Entamoeba histolytica: differentiation between pathogenic and nonpathogenic isolates (1992)

To further characterize the 29-kDa surface antigen of Entamoeba histolytica, we analyzed the complete nucleotide sequence and compared the immunoreactivity of this antigen in pathogenic and nonpathogenic strains. Five cDNA clones (one 1.0-kb full-length clone, designated p13, and four partial-length clones) encoding the antigen were analyzed for allelic variation. Comparison of the nucleotide sequences revealed several single-nucleotide substitutions in all five cDNAs, two of which resulted in amino acid differences. Localization of the antigen to the amebic surface in a previous report (B. E. Torian, B. M. Flores, V. L. Stroeher, F. S. Hagen, and W. E. Stamm, Proc. Natl. Acad. Sci. USA 87:6358-6362, 1990) was corroborated by transmission electron microscopy showing colloidal gold particles on the surface of the trophozoites. Computer analysis of the deduced amino acid sequence predicted that the protein encoded by p13 was a hydrophilic peripheral membrane protein, and these data were confirmed by a Triton X-114 membrane extraction showing the presence of the 29-kDa antigen primarily in the aqueous phase of the detergent partition. Monoclonal antibodies to a fusion peptide differentiated between pathogenic and nonpathogenic clinical strains of E. histolytica in immunoblots. Although no immunoreactive epitopes were detected on nonpathogenic strains, Northern (RNA) analysis and DNA-DNA hybridization with a 700-bp cDNA probe demonstrated that mRNA and the gene encoding the 29-kDa surface antigen were present in both pathogenic and nonpathogenic clinical isolates.
A water-soluble carbon monoxide-releasing molecule (CORM-3) lowers intraocular pressure in rabbits (2008)

Treatment with CORM-3 is associated with a reduction in IOP in two different rabbit models of ocular hypertension. These results support previous findings on the effect of haem oxygenase-derived CO on IOP and suggest a direct involvement of CO system in the regulation of ocular pressure probably through the modulation of aqueous humour dynamics.
Image coding based on a fractal theory of iterated contractive image transformations (1992)

The author proposes an independent and novel approach to image coding, based on a fractal theory of iterated transformations. The main characteristics of this approach are that (i) it relies on the assumption that image redundancy can be efficiently exploited through self-transformability on a block-wise basis, and (ii) it approximates an original image by a fractal image. The author refers to the approach as fractal block coding. The coding-decoding system is based on the construction, for an original image to encode, of a specific image transformation-a fractal code-which, when iterated on any initial image, produces a sequence of images that converges to a fractal approximation of the original. It is shown how to design such a system for the coding of monochrome digital images at rates in the range of 0.5-1.0 b/pixel. The fractal block coder has performance comparable to state-of-the-art vector quantizers.
Porcine peripheral blood dendritic cells and natural interferon‐producing cells (2003)

Peripheral blood contains two major particular infrequent dendritic cells (DC) subsets linking the innate and specific immune system, the myeloid DC and plasmacytoid DC equivalent to the natural interferon-producing cells (NIPC). The functional characterization of these cells demands large volumes of blood, making a large animal model more appropriate and beneficial for certain studies. Here, two subsets of porcine blood mononuclear cells expressing swine workshop cluster 3 (SWC3, a SIRP family member), are described and compared to monocytes. The blood DC specialized in T-cell stimulation were major histocompatibility complex (MHC) class II+, CD80/86+, CD1+/-, CD4-, and in contrast to monocytes CD14-. A CD16- and a CD16+ subset could be discriminated. Granulocyte-macrophage colony-stimulating factor and interleukin-3 were survival factors for this DC subset, and culture induced an up-regulation of MHC class II and CD80/86. The second subset described, are porcine NIPC, typically CD4++, MHC class IIlow, CD80/86low, CD1-, CD8-/low, CD16-/low and CD45RA-/low. Porcine NIPC had high interleukin-3 binding capacity, and survived in response to this cytokine. Their unique function was strong interferon type I secretion after virus stimulation. Both subsets were endocytically active when freshly isolated, and down-regulated this activity after in vitro maturation. Taken together, the present report has delineated porcine blood DC and NIPC, permitting a more detailed understanding of innate immune defences, particularly in response to infections.
The Crystal Structure and Mechanism of 1-l-myo-Inositol- 1-phosphate Synthase (2002)

1-l-myo-Inositol-1-phosphate synthase catalyzes the conversion of d-glucose 6-phosphate to 1-l-myo-inositol-1-phosphate (MIP), the first and rate-limiting step in the biosynthesis of all inositol-containing compounds. It involves an oxidation, intramolecular aldol cyclization, and reduction. We have determined the first crystal structure of MIP synthase. We present structures of both the NAD-bound enzyme and the enzyme bound to an inhibitor, 2-deoxy-glucitol-6-phosphate. While 58 amino acids are disordered in the unbound form of the enzyme in the vicinity of the active site, the inhibitor nucleates the folding of this domain in a striking example of induced fit, serving to completely encapsulate it within the enzyme. Three helices and a long beta-strand are formed in this process. We postulate a mechanism for the conversion based on the structure of the inhibitor-bound complex.
Chemical and Physical Characterization of a TiO2-Coated Fiber Optic Cable Reactor (1996)

Practical application of metal oxide photocatalysts for the remediation of contaminated wastestreams often requires immobilization of the photocatalyst in a fixed-bed reactor configuration that allows the continu ous use of the photocatalyst by eliminating the need for post-process filtration. A novel optical fiber cable reactor (OFR) is used to transmit UV light to solid-supported TiO2 in order to investigate the photocatalytic degradation of pentachlorophenol (PCP), 4-chlorophenol (4-CP), dichloroacetate (DCA), and oxalate (OX). The distribution of light as a function of fiber diameter and the quantum efficiencies as a function of incident light intensity are investigated. Light propagation down individual fibers is found to increase with increasing fiber diameter. An increased linear transmission of light results in increased quantum efficiencies, while a 2-order of magnitude reduction in incident light intensity results in a 4-fold increase (φ = 0.010−0.042) in quantum efficiency for the degradation of 4-chlorophenol. The rates of degradation of dichloroacetate and oxalate have strong pH de pendencies. Relatively high apparent quantum efficien cies of φ = 0.010, 0.015, 0.08, and 0.17 for PCP, 4-CP, DCA, and OX, respectively, and complete mineralization to CO2, H2O, and HCl are observed in the OFR system.
Characterization of malate dehydrogenase from deep-sea psychrophilicVibriosp. strain no. 5710 and cloning of its gene (1996)

A metabolic key enzyme malate dehydrogenase (MDH) was purified from a deep-sea psychrophilic bacterium, Vibrio sp. strain no. 5710. The enzyme displayed an optimal activity shifted toward lower temperature and a pronounced heat lability. A gene encoding this enzyme was isolated and cloned. Recombinant Escherichia coli cells harboring the isolated clone expressed MDH activity with temperature stability identical to that of the parental psychrophile. Nucleotide sequencing of the gene revealed that its primary sequence was similar to that of a mesophile E. coli MDH (78% amino acid identity), for which the three-dimensional structure is known. The enzyme is thus suitable for the analysis of molecular adaptations to low temperatures.
An internet survey of 2,596 people with fibromyalgia (2007)

This survey provides a snap-shot of FM at the end of 2005, as reported by a self-selected population of people. This descriptive data has a heuristic function, in that it identifies several issues for further research, such as the prescribing habits of FM health care providers, the role of emotional precipitants, the impact of obesity, the significance of low back pain and the nature of FM related stiffness.
Treatment of experimental autoimmune encephalomyelitis by feeding myelin basic protein conjugated to cholera toxin B subunit. (1996)

Oral administration of autoantigens can prevent and partially suppress autoimmune diseases in a number of experimental models, Depending on the dose of antigen fed, this approach appears to involve distinct yet reversible and short-lasting mechanisms (anergy/deletion and suppression) and usually requires repeated feeding of large (suppression) to massive (anergy/deletion) amounts of autoantigens to be effective. Most importantly, this approach is relatively less effective in animals already systemically sensitized to the fed antigen, such as in animals already harboring autoreactive T cells and, thus, presumably also in humans suffering from an autoimmune disorder. We have previously shown that feeding a single dose of minute amounts of antigens conjugated to cholera toxin B subunit (CTB) can effectively suppress delayed-type hypersensitivity reactions in systemically immune animals. We now report that feeding small amounts of myelin basic protein (MBP) conjugated to CTB either before or after disease induction protected rats from experimental autoimmune encephalomyelitis. Such treatment was as effective in suppressing interleukin 2 production and proliferative responses of lymph node cells to MBP as treatment involving repeated feeding with much larger (50- to 100-fold) doses of free MBP. Different from the latter treatment, which led to decreased production of interferon-gamma in lymph nodes, low-dose oral CTB-MBP treatment was associated with increased interferon-gamma production. Most importantly, low-dose oral CTB-MBP treatment greatly reduced the level of leukocyte infiltration into spinal cord tissue compared with treatment with repeated feeding of large doses of MBP. These results suggest that the protection from experimental autoimmune encephalomyelitis achieved by feeding CTB-conjugated myelin autoantigen involves immunomodulating mechanisms that are distinct from those implicated by conventional protocols of oral tolerance induction.
Novel and potent inhibitors targeting DHODH, a rate-limiting enzyme in de novo pyrimidine biosynthesis, are broad-spectrum antiviral against RNA viruses including newly emerged coronavirus SARS-CoV-2 (2020)

Abstract Emerging and re-emerging RNA viruses occasionally cause epidemics and pandemics worldwide, such as the on-going outbreak of coronavirus SARS-CoV-2. Existing direct-acting antiviral (DAA) drugs cannot be applied immediately to new viruses because of virus-specificity, and the development of new DAA drugs from the beginning is not timely for outbreaks. Thus, host-targeting antiviral (HTA) drugs have many advantages to fight against a broad spectrum of viruses, by blocking the viral replication and overcoming the potential viral mutagenesis simultaneously. Herein, we identified two potent inhibitors of DHODH, S312 and S416, with favorable drug-like and pharmacokinetic profiles, which all showed broad-spectrum antiviral effects against various RNA viruses, including influenza A virus (H1N1, H3N2, H9N2), Zika virus, Ebola virus, and particularly against the recent novel coronavirus SARS-CoV-2. Our results are the first to validate that DHODH is an attractive host target through high antiviral efficacy in vivo and low virus replication in DHODH knocking-out cells. We also proposed the drug combination of DAA and HTA was a promising strategy for anti-virus treatment and proved that S312 showed more advantageous than Oseltamivir to treat advanced influenza diseases in severely infected animals. Notably, S416 is reported to be the most potent inhibitor with an EC50 of 17nM and SI value &gt;5882 in SARS-CoV-2-infected cells so far. This work demonstrates that both our self-designed candidates and old drugs (Leflunomide/Teriflunomide) with dual actions of antiviral and immuno-repression may have clinical potentials not only to influenza but also to COVID-19 circulating worldwide, no matter such viruses mutate or not.
Transformation of “living” carbocationic and other polymerizations to controlled/“living” radical polymerization (1998)

Abstract Transformation of “living” carbocationic polymerization of styrene and isobutene to controlled atom transfer radical polymerization (ATRP) is described and formation of the corresponding AB and ABA block copolymers with styrene (St), methyl methacrylate (MMA, methyl acrylate (MA) and isobornyl acrylate (IBA) was demonstrated. A similar approach was applied to the cationic ring opening polymerization of tetrahydrofuran leading to the AB and ABA block copolymers with St, MMA and MA using ATRP. Site transformation approach was also used for the ring opening metathesis polymerization of norbornene and polycondensation systems using polysulfone as an example. In both cases, AB and ABA block copolymers were efficiently formed with styrene and acrylates.