gebhart/patrepeval huggingface dataset:
Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. (2002)

Two newly isolated strains of obligately anaerobic bacteria from human faeces are shown here to be related to Fusobacterium prausnitzii, which is regarded as one of the most abundant colonizers of the human colon. These strains, along with Fusobacterium prausnitzii ATCC 27768(T) and 27766, are non-motile and produce butyrate, formate and lactate, but not hydrogen as fermentation products. A new finding is that all four strains produce D-lactate, but not L-lactate. The strains have a requirement for acetate in the growth medium and this may account for the previously reported requirement for rumen fluid. The DNA G+C content of the four strains is 47-57 mol%. Together with phylogenetic analysis based on 16S rRNA sequencing, this establishes that Fusobacterium prausnitzii strains are only distantly related to Fusobacterium sensu stricto and are more closely related to members of Clostridium cluster IV (the Clostridium leptum group). It is proposed that a new genus, Faecalibacterium gen. nov. be created; this genus should include Faecalibacterium prausnitzii gen. nov., comb. nov. ATCC 27768(T) (= NCIMB 13872(T)) (formerly Fusobacterium prausnitzii) as the type species together with ATCC 27766 and the newly isolated strains A2-165 and L2-6.
Mucosal and systemic immune responses to a recombinant protein expressed on the surface of the oral commensal bacterium Streptococcus gordonii after oral colonization. (1995)

To circumvent the need to engineer pathogenic microorganisms as live vaccine-delivery vehicles, a system was developed which allowed for the stable expression of a wide range of protein antigens on the surface of Gram-positive commensal bacteria. The human oral commensal Streptococcus gordonii was engineered to surface express a 204-amino acid allergen from hornet venom (Ag5.2) as a fusion with the anchor region of the M6 protein of Streptococcus pyogenes. The immunogenicity of the M6-Ag5.2 fusion protein was assessed in mice inoculated orally and intranasally with a single dose of recombinant bacteria, resulting in the colonization of the oral/pharyngeal mucosa for 10-11 weeks. A significant increase of Ag5.2-specific IgA with relation to the total IgA was detected in saliva and lung lavages when compared with mice colonized with wild-type S. gordonii. A systemic IgG response to Ag5.2 was also induced after oral colonization. Thus, recombinant Gram-positive commensal bacteria may be a safe and effective way of inducing a local and systemic immune response.
Strontium Ranelate: Dose-Dependent Effects in Established Postmenopausal Vertebral Osteoporosis--A 2-Year Randomized Placebo Controlled Trial (2002)

peer reviewed
Using digital libraries as a community hall for worldwide information spiral development (1999)

Our concept of a digital library from a user's viewpoint is explained by using a three-layer model of information distribution: information provider, information broker, and information user. Our worldwide communication-hall prototype consists of the virtual personal library client, called Webshelf, an information publishing server, and a hypermedia archive server, Webarchive. It allows users to virtually personalize information on the Web, organize it, create new information, and publish this new information. Webarchive offers an effective solution to the information volatility problem by storing all of the information obtained by users and managing link consistency. © 1999 Scripta Technica, Syst Comp Jpn, 30(1): 1–12, 1999
A novel fabrication method of macroporous biodegradable polymer scaffolds using gas foaming salt as a porogen additive (2000)

Highly open porous biodegradable poly(L-lactic acid) ¿PLLA scaffolds for tissue regeneration were fabricated by using ammonium bicarbonate as an efficient gas foaming agent as well as a particulate porogen salt. A binary mixture of PLLA-solvent gel containing dispersed ammonium bicarbonate salt particles, which became a paste state, was cast in a mold and subsequently immersed in a hot water solution to permit the evolution of ammonia and carbon dioxide within the solidifying polymer matrix. This resulted in the expansion of pores within the polymer matrix to a great extent, leading to well interconnected macroporous scaffolds having mean pore diameters of around 300-400 microm, ideal for high-density cell seeding. Rat hepatocytes seeded into the scaffolds exhibited about 95% seeding efficiency and up to 40% viability at 1 day after the seeding. The novelty of this new method is that the PLLA paste containing ammonium bicarbonate salt particles can be easily handled and molded into any shape, allowing for fabricating a wide range of temporal tissue scaffolds requiring a specific shape and geometry.
Cell model of inflammation (2008)

Chemical and physical stimuli trigger a cutaneous response by first inducing the main epidermal cells, keratinocytes, to produce specific mediators that are responsible for the initiation of skin inflammation. Activation modulates cell communication, namely leucocyte recruitment and blood-to-skin extravasation through the selective barrier of the vascular ECs (endothelial cells). In the present study, we describe an in vitro model which takes into account the various steps of human skin inflammation, from keratinocyte activation to the adhesion of leucocytes to dermal capillary ECs. Human adult keratinocytes were subjected to stress by exposure to UV irradiation or neuropeptides, then the conditioned culture medium was used to mimic the natural micro-environmental conditions for dermal ECs. A relevant in vitro model must include appropriate cells from the skin. This is shown in the present study by the selective reaction of dermal ECs compared with EC lines from distinct origins, in terms of leucocyte recruitment, sensitivity to stress and nature of the stress-induced secreted mediators. This simplified model is suitable for the screening of anti-inflammatory molecules whose activity requires the presence of various skin cells.
Replication of Infectious Bursal Disease Virus in Continuous Cell Lines (1987)

Three mammalian continuous cell lines--MA-104, Vero, and BGM-70--were tested for their ability to support replication of infectious bursal disease virus (IBDV). Selected tissue-culture-adapted vaccine strains and tissue-culture-adapted field isolates of IBDV replicated in the MA-104, Vero, and BGM-70 cells; cytopathic effects were most pronounced in the BGM-70 cells. The cytopathic effects of the viruses in BGM-70 cells and chicken embryo fibroblast (CEF) cultures were similar. Virus-neutralization titers of selected serum samples determined in BGM-70 cultures compared well with those obtained from CEF cultures.
Superresolution imaging by dynamic single-pixel compressive sensing system (2013)

We present a superresolution imaging method based on the dynamic single-pixel compressive sensing (CS) system. Different from the traditional static CS, this system is slowly moving in parallel with the scene during the compressive sampling, implying that the measurements are possible to contain the information about the scene with the subpixel resolution. Here we first build the dynamic compressive sampling model and give the recovery method via traditional CS scheme, and then we propose the image superresolution recovery method in the CS framework, where a subdivision scheme is used. The proposed method not only has remarkable superresolution performance, but also has low requirements on the imaging system, since it is associated with the single-pixel imager, which is one of the simplest systems in the existing CS imaging architectures. The feasibility of the proposed method is demonstrated by the numerical simulations as well as the optical experiments.
ChemInform Abstract: A METHOD FOR THE OXIDATION OF SEC,TERT‐1,2‐DIOLS TO ALPHA‐HYDROXY KETONES WITHOUT CARBON‐CARBON CLEAVAGE (1974)

Abstract Bei sek.‐tert. Glykolen kann durch Verwendung von Kombinationen aus Methylsulfiden und Chlor oder N‐Chlorsuccinirnid, von Dimethylsulfoxid und Chlor eine ′(Q selektive Oxidation der sek. Carbinolgruppe zur Ketongruppe bewirkt werden.
Detecting malware domains at the upper DNS hierarchy (2011)

In recent years Internet miscreants have been leveraging the DNS to build malicious network infrastructures for malware command and control. In this paper we propose a novel detection system called Kopis for detecting malware-related domain names. Kopis passively monitors DNS traffic at the upper levels of the DNS hierarchy, and is able to accurately detect malware domains by analyzing global DNS query resolution patterns.

Compared to previous DNS reputation systems such as Notos [3] and Exposure [4], which rely on monitoring traffic from local recursive DNS servers, Kopis offers a new vantage point and introduces new traffic features specifically chosen to leverage the global visibility obtained by monitoring network traffic at the upper DNS hierarchy. Unlike previous work Kopis enables DNS operators to independently (i.e., without the need of data from other networks) detect malware domains within their authority, so that action can be taken to stop the abuse. Moreover, unlike previous work, Kopis can detect malware domains even when no IP reputation information is available.

We developed a proof-of-concept version of Kopis, and experimented with eight months of real-world data. Our experimental results show that Kopis can achieve high detection rates (e.g., 98.4%) and low false positive rates (e.g., 0.3% or 0.5%). In addition Kopis is able to detect new malware domains days or even weeks before they appear in public blacklists and security forums, and allowed us to discover the rise of a previously unknown DDoS botnet based in China.
A modular approach to constructing protocol converters (2002)

A modular approach is proposed for constructing a converter for two protocols that go through different phases, performing separate functions in each phase. The construction of such a converter consists of three steps: (1) the decomposition of protocols into distinct functions; (2) the construction of functional converters for each pair of functions selected by the converter designer; and (3) the merging of local functions with functional converters to construct the final converter. The final converter not only contains a common subset of functions of the two protocols, but also includes functionalities specified to each protocol.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
ChemInform Abstract: Synthesis of BaZrS3 in the Presence of Excess Sulfur. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Polymer Brushes with Liquid Crystalline Side Chains (1999)

We report on the synthesis and the properties of side-chain liquid-crystal polymer (LCP) brushes attached to silicon oxide surfaces. The polymer monolayers have been generated at the surface of the substrate in situ following a “grafting-from” procedure. The mesogenic group of the LC brushes consists of a phenylbenzoate moiety linked to the methacrylate main chain via a flexible spacer. The thickness of the brush and the grafting density of the surface-attached polymer molecules can be controlled by adjusting the monomer concentration during brush growth and the reaction time of the polymerization, respectively. LC brushes with a thickness of up to 200 nm in the dry, solvent-free state have been obtained. The transition temperatures between the nematic and the isotropic state have been studied and compared to those of spin-cast films of the same polymer. The optical textures are investigated as a function of layer thickness, temperature, and sample history. The textures exhibit a strong memory effect in the sense that the exact same texture reappears after isotropization by heating or solvent exposure and returning to the nematic state.
The Effect of γ‐Linolenic Acid on Human Diabetic Peripheral Neuropathy: A Double‐blind Placebo‐controlled Trial (1990)

Twenty-two patients with distal diabetic polyneuropathy confirmed both clinically and by objective nerve function studies, completed a double-blind, placebo-controlled study to assess the effect of dietary supplementation with gamma-linolenic acid on their neuropathy. Patients received either 360 mg gamma-linolenic acid (12 patients) or indistinguishable placebo capsules (10 patients) for 6 months. All patients were assessed at the beginning and end of the study period by neuropathy symptom and sign scoring, motor and sensory nerve conduction studies, and thermal threshold measurements. When compared with the placebo group, patients on gamma-linolenic acid showed statistically significant improvement in neuropathy symptom scores (p less than 0.001), median nerve motor conduction velocity (p less than 0.01) and compound muscle action potential amplitude (p less than 0.01), peroneal nerve motor conduction velocity (p less than 0.05) and compound muscle action potential amplitude (p less than 0.05), median (p less than 0.01) and sural (p less than 0.001) sensory nerve action potential amplitude and ankle heat threshold (p less than 0.001) and cold threshold (p less than 0.01) values. gamma-Linolenic acid therapy might have a useful role in the prevention and treatment of distal diabetic polyneuropathy.
Specific interaction of one subunit of eukaryotic initiation factor eIF-3 with 18S ribosomal RNA within the binary complex, eIF-3.small ribosomal subunit, as shown by cross-linking experiments (1982)

Initiation factor eIF-3 from rat liver forms a binary complex with the small ribosomal subunit. Within this complex, 18S ribosomal RNA can be cross-linked to the 66 000 dalton subunit of eIF-3 by treating the complex with a short bifunctional reagent, diepoxybutane, with a distance of 4A between the reactive groups. In binary complexes containing eIF-3 premodified with the heterobifunctional reagent, methyl-p-azido-benzoylaminoacetimidate (10A), the 66 000 dalton subunit of eIF-3 became covalently bound to 18S rRNA after irradiation of the complex with ultraviolet light. The involvement of only one of the eight eIF-3 subunits in the formation of the covalent RNA-protein complexes indicates a highly specific interaction between 18S rRNA and eIF-3 at the attachment site of the factor on the 40S subunit.
Basal plane misfit dislocations and stress relaxation in III-nitride semipolar heteroepitaxy (2011)

This article presents a theoretical analysis of dislocation behavior and stress relaxation in semipolar III-nitride heteroepitaxy, e.g., for AlxGa1−xN and InyGa1−yN layers grown on {hh2−h−m}- or {h0h−m}-type semipolar planes of GaN substrates. We demonstrate that the shear stresses on the unique inclined basal (0001) plane do not vanish for such growth geometries. This leads to the onset of relaxation processes in semipolar III-nitride heterostructures via dislocation glide in the basal slip systems 〈1−1−20〉(0001) and to the formation of misfit dislocations (MDs) with Burgers vectors of (a/3)〈1−1−20〉-type at the semipolar heterointerface. Next we calculate the Matthews-Blakeslee critical thickness for MD formation in semipolar III-nitride layers together with the MD equilibrium spacings for complete misfit relaxation. The component of the MD Burgers vector normal to the film/substrate interface will cause a crystal lattice tilt in the epilayer with respect to the GaN substrate. The calculated magnitudes of the tilt angles are 0.62° and 0.67° for AlxGa1−xN and InyGa1−yN alloys with compositions of x = 0.20 and y = 0.07, respectively, grown in the (112−2) semipolar orientation. The modeling results are discussed in light of recent experimental observations [A. Tyagi et al., Appl Phys. Lett. 95, 251905 (2009); E. Young et al., Appl. Phys. Express 3, 011004 (2010); and F. Wu et al., J. Appl. Phys. 109, 033505 (2011)] of MDs and crystal lattice tilt in semipolar III-nitride heteroepitaxial layers.
Quantitation of Intact Proteins in Human Plasma Using Top-Down Parallel Reaction Monitoring-MS (2018)

Direct quantitation of proteins in complex biological matrices by mass spectrometry remains a challenge. Here, we describe a novel top-down parallel reaction monitoring-mass spectrometry (PRM-MS) assay, enabled by microflow LC-nanospray MS using a silicon microfluidic LC-MS chip. We demonstrated direct analysis of intact proteins such as somatropin in human plasma, achieving sensitivity (0.1-1.0 fmole) and speed (1-5 min) on par with enzyme-linked immunosorbent assay (ELISA).
Graphical Histories for Visualization: Supporting Analysis, Communication, and Evaluation (2008)

Interactive history tools, ranging from basic undo and redo to branching timelines of user actions, facilitate iterative forms of interaction. In this paper, we investigate the design of history mechanisms for information visualization. We present a design space analysis of both architectural and interface issues, identifying design decisions and associated trade-offs. Based on this analysis, we contribute a design study of graphical history tools for Tableau, a database visualization system. These tools record and visualize interaction histories, support data analysis and communication of findings, and contribute novel mechanisms for presenting, managing, and exporting histories. Furthermore, we have analyzed aggregated collections of history sessions to evaluate Tableau usage. We describe additional tools for analyzing users' history logs and how they have been applied to study usage patterns in Tableau.
Fetal DNA in maternal plasma is elevated in pregnancies with aneuploid fetuses (2000)

Current non-invasive screening methods for the prenatal diagnosis of fetal aneuploidies are hampered by low sensitivities and high false positive rates. Attempts to redress this situation include the enrichment of fetal cells from maternal blood, or the use of fetal DNA in the plasma of pregnant women. By the use of real-time quantitative polymerase chain reaction (PCR) it has recently been shown that circulatory male fetal DNA in maternal plasma is elevated in pregnancies with trisomy 21 fetuses. In this independent study we confirm and extend upon these results by showing that the levels of fetal DNA are also elevated in pregnancies with other chromosomal aneuploidies (mean=185.8 genome equivalents/ml; range=62.2-471.7) when compared to pregnancies with normal male fetuses (mean=81.9 genome equivalents/ml; range=28.8-328.9), p=0.005. This elevation was greatest for fetuses with trisomy 21, whereas it was not significant for fetuses with trisomy 18, p=0.356. These data suggest that a quantitative analysis of such fetal DNA levels may serve as an additional marker for certain fetal chromosomal abnormalities, in particular for trisomy 21.
Source Parameters and Rupture Velocities of Microearthquakes in Western Nagano, Japan, Determined Using Stopping Phases (2004)

We use an inversion method based on stopping phases (Imanishi and Takeo, 2002) to estimate the source dimension, ellipticity, and rupture velocity of microearthquakes and investigate the scaling relationships between source parameters. We studied 25 earthquakes, ranging in size from M 1.3 to M 2.7, that occurred between May and August 1999 at the western Nagano prefecture, Japan, which is characterized by a high rate of shallow earthquakes. The data consist of seismograms recorded in an 800-m borehole and at 46 surface and 2 shallow borehole seismic stations whose spacing is a few kilometers. These data were recorded with a sampling frequency of 10 kHz. In particular, the 800-m-borehole data provide a wide frequency bandwidth with greatly reduced ground noise and coda wave amplitudes compared with surface recordings. High-frequency stopping phases appear in the body waves in Hilbert transform pairs and are readily detected on seismograms recorded in the 800-m borehole. After correcting both borehole and surface data for attenuation, we also measure the rise time, which is defined as the interval from the arrival time of the direct wave to the timing of the maximum amplitude in the displacement pulse. The differential time of the stopping phases and the rise times were used to obtain source parameters. We found that several microearthquakes propagated unilaterally, suggesting that all microearthquakes cannot be modeled as a simple circular crack model. Static stress drops range from approximately 0.1 to 2 MPa and do not vary with seismic moment. It seems that the breakdown in stress drop scaling seen in previous studies using surface data is simply an artifact of attenuation in the crust. The average value of rupture velocity does not depend on earthquake size and is similar to those reported for moderate and large earthquakes. It is likely that earthquakes are self-similar over a wide range of earthquake size and that the dynamics of small and large earthquakes are similar.
Engagement of CD14 on human monocytes terminates T cell proliferation by delivering a negative signal to T cells (1991)

We have recently shown that engagement of the human monocytic Ag CD14 by murine mAb induces lymphocyte function-associated antigen-1/intercellular adhesion molecule-1-dependent homotypic adhesion. To determine whether CD14 plays a role in monocyte-T cell interactions, we tested the effect of anti-CD14 mAb on the proliferation of human T cells. Our results show that anti-CD14 mAb strongly inhibited T cell proliferation induced by Ag, anti-CD3 mAb, and mitogenic lectins. Inhibition by anti-CD14 mAb was epitope-dependent and required physical contact between monocytes and T cells. CD14 engagement did not affect IL-2R expression or IL-2 synthesis but induced a state of unresponsiveness that was not IL-2 specific; proliferation of anti-CD3-activated T cell blasts in response to both IL-2 and IL-4 was abrogated by addition of monocytes preincubated with anti-CD14 mAb. Inhibition of T cell proliferation after engagement of CD14 on monocytes was likely to result from delivery of a negative signal to T cells, rather than from disruption of a costimulatory monocyte-derived signal, because incubation of monocytes with anti-CD14 mAb also inhibited monocyte-independent T cell proliferation induced by PMA and ionophore. These results, together, point to a role of CD14 in the monocyte-dependent regulation of T cell proliferation.
Tumour-targeted delivery of TRAIL using Salmonella typhimurium enhances breast cancer survival in mice (2009)

These results show the pre-clinical utility of S. typhimurium as a TRAIL expression vector that effectively reduces tumour growth and extends host survival.