gebhart/patrepeval huggingface dataset:
The human microglial HMC3 cell line: where do we stand? A systematic literature review (2018)

Microglia, unique myeloid cells residing in the brain parenchyma, represent the first line of immune defense within the central nervous system. In addition to their immune functions, microglial cells play an important role in other cerebral processes, including the regulation of synaptic architecture and neurogenesis. Chronic microglial activation is regarded as detrimental, and it is considered a pathogenic mechanism common to several neurological disorders. Microglial activation and function have been extensively studied in rodent experimental models, whereas the characterization of human cells has been limited due to the restricted availability of primary sources of human microglia. To overcome this problem, human immortalized microglial cell lines have been developed. The human microglial clone 3 cell line, HMC3, was established in 1995, through SV40-dependent immortalization of human embryonic microglial cells. It has been recently authenticated by the American Type Culture Collection (ATCC®) and distributed under the name of HMC3 (ATCC®CRL-3304). The HMC3 cells have been used in six research studies, two of which also indicated by ATCC® as reference articles. However, a more accurate literature revision suggests that clone 3 was initially distributed under the name of CHME3. In this regard, several studies have been published, thus contributing to a more extensive characterization of this cell line. Remarkably, the same cell line has been used in different laboratories with other denominations, i.e., CHME-5 cells and C13-NJ cells. In view of the fact that "being now authenticated by ATCC®" may imply a wider distribution of the cells, we aimed at reviewing data obtained with the human microglia cell line clone 3, making the readers aware of this complicated nomenclature. In addition, we also included original data, generated in our laboratory with the HMC3 (ATCC®CRL-3304) cells, providing information on the current state of the culture together with supplementary details on the culturing procedures to obtain and maintain viable cells.
Lasing characteristics of low-threshold oxide confinement InGaAs-GaAlAs vertical-cavity surface-emitting lasers (1995)

Some lasing characteristics of index-guided InGaAs-GaAlAs vertical-cavity surface-emitting lasers (VCSEL's) with a native oxide confinement structure, which produced a low threshold current of 70 μA, are presented. It was found that nonradiative recombination was reduced and the estimated surface recombination velocity was almost negligible. The oxidation process was uniform to produce low threshold devices while the oxidation rate was dependent on the doping or composition of DBR's.
Analysis of Functional Conservation in the Surface and Transmembrane Glycoprotein Subunits of Human T-Cell Leukemia Virus Type 1 (HTLV-1) and HTLV-2 (1998)

Human T-cell leukemia virus types 1 and 2 (HTLV-1 and HTLV-2) are closely related retroviruses with nucleotide sequences that are 65% identical. To determine whether their envelope glycoproteins function similarly and to define the molecular determinants of HTLV-2 envelope-mediated functions, we have used pseudotyped viruses and have introduced mutations into regions of the HTLV-2 glycoproteins homologous to those known to be important for HTLV-1 glycoprotein functions. The envelopes of the two viruses could be exchanged with no loss of infectivity, suggesting that the glycoproteins function in broadly similar ways. However, comparative analysis of the HTLV-1 and HTLV-2 glycoproteins showed subtle differences in the structure-function relationships of the two surface glycoprotein (SU) subunits, even though they recognize the same receptor. Indeed, mutations introduced at equivalent positions in the two SU glycoproteins resulted in different phenotypes in the two viruses. The scenario is the opposite for the transmembrane glycoprotein (TM) subunits, in which the functional domains of the two viruses are strictly conserved, confirming the involvement of the TM ectodomain in postfusion events required for full infectivity of the HTLVs. Thus, although they recognize the same receptor, the HTLV-1 and HTLV-2 SU subunits have slightly different ways of transducing the conformational information that primes a common fusion mechanism effected by similar TM subunits.
Lytic Activity of LysH5 Endolysin Secreted by Lactococcus lactis Using the Secretion Signal Sequence of Bacteriocin Lcn972 (2012)

Bacteriophage endolysins have an interesting potential as antimicrobials. The endolysin LysH5, encoded by Staphylococcus aureus phage vB_SauS-phi-IPLA88, was expressed and secreted in Lactococcus lactis using the signal peptide of bacteriocin lactococcin 972 and lactococcal constitutive and inducible promoters. Up to 80 U/mg of extracellular active endolysin was detected in culture supernatants, but most of the protein (up to 323 U/mg) remained in the cell extracts.
Rheological and cohesive properties of hyaluronic acid (2005)

Hyaluronic acid (HA) is a naturally occurring polysaccharide with unique biomedical applications. We have studied the cohesive and rheological properties of HA of three molecular weights (0.35 x 10(6) -1.80 x 10(6) Da) and found that the cohesive nature of HA was highly dependent on molecular weight and solution concentration. To a first approximation, the cohesive nature of HA in solution correlates with concentration, independent of molecular weight. Several rheological parameters correlated with molecular weight: zero shear viscosity, complex viscosity, and the complex viscosity at the crossover point. The cohesive properties of the HA solutions, measured by dynamic aspiration (Poyer et al, J Cataract Refract Surg 1998;24:1130-1135), were found to decrease as the zero shear viscosity increases. The cohesive properties of HA polymer in solution were found to correlate with the high frequency complex viscosity and high frequency loss modulus independent of molecular weight.
RCS: a reference model architecture for intelligent control (1992)

The real-time control system (RCS), a reference model architecture for intelligent real-time control systems, is described. It partitions the control problem into four basic elements: task decomposition, world modeling, sensory processing and value judgment. RCS clusters these elements into computational nodes that control specific subsystems, and arranges these nodes in hierarchical layers so that each layer has characteristic functionality and timing. The RCS architecture has a systematic regularity and recursive structure that suggests a canonical form. Four versions of RCS have been developed. The application of one of the versions to machining workstation consisting of a part buffer, a machine tool and a robot is examined. The functionality of each of the levels in the control hierarchy is discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Accurate Three-Dimensional Registration of CT, PET, and/or MR Images of the Brain (1989)

A surface matching technique has been developed to register multiple imaging scans of the brain in three dimensions, with accuracy on the order of the image pixel sizes. Anatomic information visualized in X-ray CT and magnetic resonance images may be integrated with each other and with functional information from positron emission tomography. Anatomical structures and other volumes of interest may be mapped from one scan to another, and corresponding sections through multiple scans may be directly compared. This capability provides a novel quantitative method to address the fundamental problem of relating structure to function in the brain. Applications include basic and clinical problems in the neurosciences and delivery and assessment of brain tumor therapy.
Optical interconnection using ShuffleNet multihop networks in multi-connected ring topologies (1988)

In many applications, such as metropolitan area, campus, and local area networks, multicomputer interconnection networks, and the interconnection of cabinets, shelves, and boards, optical interconnection is increasingly favored over electrical. Recently, ShuffleNet multihop lightwave networks were proposed as a way to tap the vast bandwidth potential of optical fiber for multiuser packet communications. We consider the use of ShuffleNet multihop networks for optical interconnection, and study their implementation in ring topologies with each node connected to several other nodes of the ring (i.e., multi-connected ring topologies). To minimize fiber cabling congestion, the design procedure uses a new representation of the ShuffleNet connectivity graph and a generalization of Gray code patterns. As an example, only six fibers (without wavelength-division multiplexing) are required to interconnect 24 Network Interface Units (NIUs), providing a total network throughput of 1.47 Gb/s for an optical transmission rate of 100 Mb/s. The design also provides for easy, modular growth of multi-connected rings.
Characterization and Immunogenicity of a Novel Mosaic M HIV-1 gp140 Trimer (2014)

The development of an HIV-1 vaccine remains a formidable challenge due to multiple circulating strains of HIV-1 worldwide. This study describes a candidate HIV-1 Env protein vaccine whose sequence has been designed by computational methods to address HIV-1 diversity. The characteristics and immunogenicity of this Env protein, both alone and mixed together with a clade C Env protein vaccine, are described.
Salmonella typhi does not inhibit phagosome-lysosome fusion in human monocyte-derived macrophages (1995)

We examined phagosome-lysosome fusion in Salmonella typhi-infected human monoeyte-derived macrophages and its relevance to the intracellular survival of this bacterium in vitro.S. typhi was found to survive and multiply in human monoeyte-derived macrophages, whereas S. typhimurium was killed easily, indicating that the survival of Salmonella serovars is host-specific.Neither S. typhi nor S. typhimurium inhibited phagosome-lysosome fusion in human monocyte-derived macrophages.No difference between the phagosome-lysosome fusibilities of freshly prepared human monocytes and monocyte-derived macrophages was observed.These results suggest that S. typhi may survive by adapting to the conditions within fused phagolysosomes of human monocyte-derived macrophages.
The Regioselective Synthesis of Tepoxalin, 3-[5-(4-Chlorophenyl)-1-(4-methoxyphenyl)-3-pyrazolyl]-N-hydroxy-N-methylpropanamide and Related 1,5-Diarylpyrazole Anti-inflammatory Agents (1991)

Tepoxalin, a potent anti-inflammatory agent, and its analogs can be synthesized by condensing an appropriate arylhydrazine hydrochloride and a 6-aryl-4,6-dioxohexanoic acid in alcohol with a base catalyst. These diarylpyrazolylpropanoic acids can be converted to their N-methylhydroxamic acids by generating the requisite acid chloride, and allowing it to react with N-methylhydroxylamine.
A quantitation method for mass spectrometry imaging (2011)

A new quantitation method for mass spectrometry imaging (MSI) with matrix-assisted laser desorption/ionization (MALDI) has been developed. In this method, drug concentrations were determined by tissue homogenization of five 10 µm tissue sections adjacent to those analyzed by MSI. Drug levels in tissue extracts were measured by liquid chromatography coupled to tandem mass spectrometry (LC/MS/MS). The integrated MSI response was correlated to the LC/MS/MS drug concentrations to determine the amount of drug detected per MSI ion count. The study reported here evaluates olanzapine in liver tissue. Tissue samples containing a range of concentrations were created from liver harvested from rats administered a single dose of olanzapine at 0, 1, 4, 8, 16, 30, or 100 mg/kg. The liver samples were then analyzed by MALDI-MSI and LC/MS/MS. The MALDI-MSI and LC/MS/MS correlation was determined for tissue concentrations of ~300 to 60,000 ng/g and yielded a linear relationship over two orders of magnitude (R(2) = 0.9792). From this correlation, a conversion factor of 6.3 ± 0.23 fg/ion count was used to quantitate MSI responses at the pixel level (100 µm). The details of the method, its importance in pharmaceutical analysis, and the considerations necessary when implementing it are presented.
The Sec61 complex is located in both the ER and the ER-Golgi intermediate compartment (1999)

The heteromeric Sec61 complex is composed of (alpha), beta and (gamma) subunits and forms the core of the mammalian ER translocon. Oligomers of the Sec61 complex form a transmembrane channel where proteins are translocated across and integrated into the ER membrane. We have studied the subcellular localisation of the Sec61 complex using both wild-type COS1 cells and cells transfected with GFP-tagged Sec61(alpha). By double labelling immunofluorescence microscopy the GFP-tagged Sec61(alpha) was found in both the ER and the ER-Golgi intermediate compartment (ERGIC) but not in the trans-Golgi network. Immunofluorescence studies of endogenous Sec61beta and Sec61(gamma) showed that these proteins are also located in both the ER and the ERGIC. Using the alternative strategy of subcellular fractionation, we have shown that wild-type Sec61(alpha), beta and (gamma), and GFP-tagged Sec61(alpha), are all present in both the ER and the ERGIC/Golgi fractions of the gradient. The presence of the Sec61 subunits in a post-ER compartment suggests that these proteins can escape the ER and be recycled back, despite the fact that none of them contain any known membrane protein retrieval signals such as cytosolic di-lysine or di-arginine motifs. We also found that another translocon component, the glycoprotein TRAM, was present in post-ER compartments as demonstrated by subcellular fractionation. Our data indicate that the core components of the mammalian ER translocon are not permanently resident in the ER, but rather that they are maintained in the ER by a specific retrieval mechanism.
Optical reversibility theorems for polarization: application to remote control of polarization (1993)

Using Jones’s formalism, we prove three optical reversibility theorems that relate the polarization ellipticity at the output of an optical system to the polarization of the retroreflected light at the input. We describe how these theorems can be used to measure the ellipticity of a polarization remotely and thus to control it remotely. As an example, we use this method to create a linear or a circular polarization after a total internal reflection inside a prism, and the impurity of polarization is found to be better than 10−3. Finally we describe the use of this remote control to create polarization configurations that are useful for laser cooling of atoms.
Regulation of the Cdk inhibitor p27 and its deregulation in cancer (2000)

p27 is a cell cycle inhibitor whose cellular abundance increases in response to many antimitogenic stimuli. In this review, we summarize the current knowledge on p27 function and its regulation by synthesis and by ubiquitin-mediated degradation. Importantly, p27 degradation is enhanced in many aggressive human tumors. The frequency with which this is observed suggests that loss of p27 may confer a growth advantage to these cancers. From a practical point of view, immunodetection of p27 in tumors may prove to be useful in the assessment of prognosis and may ultimately influence the therapy of this disease.
Total Synthesis of Complex Cyclotryptamine Alkaloids: Stereocontrolled Construction of Quaternary Carbon Stereocenters (2007)

Our ability to access the more complex members of the cyclotryptamine family of alkaloids, and to exploit their disparate biological activities, is limited by the synthetic challenge posed by their oligomeric, polyindoline structures. A recurring structural theme within these molecules is the presence of multiple quaternary stereocenters in close proximity to one another. Over the last decade, we have developed a set of transformations that allow rapid access to polyindolines, a number of which exploit the ability of catalytic levels of palladium to orchestrate carbon-carbon bond formation with impressive levels of regio- and stereocontrol. This review tells the story behind the development of this toolbox of synthetic methods, and their validation through the total synthesis of a number of structurally complex cyclotryptamine alkaloids. It also highlights an aspect of asymmetric catalysis that has received little attention, the ability of catalytic asymmetric reactions to selectively elaborate complex, polyfunctional molecules.
Compiler-Directed Soft Error Detection and Recovery to Avoid DUE and SDC via Tail-DMR (2016)

This article presents Clover, a compiler-directed soft error detection and recovery scheme for lightweight soft error resilience. The compiler carefully generates soft-error-tolerant code based on idempotent processing without explicit checkpoints. During program execution, Clover relies on a small number of acoustic wave detectors deployed in the processor to identify soft errors by sensing the wave made by a particle strike. To cope with DUEs (detected unrecoverable errors) caused by the sensing latency of error detection, Clover leverages a novel selective instruction duplication technique called tail-DMR (dual modular redundancy) that provides a region-level error containment. Once a soft error is detected by either the sensors or the tail-DMR, Clover takes care of the error as in the case of exception handling. To recover from the error, Clover simply redirects program control to the beginning of the code region where the error is detected. The experimental results demonstrate that the average runtime overhead is only 26%, which is a 75% reduction compared to that of the state-of-the-art soft error resilience technique. In addition, this article evaluates an alternative technique called tail-wait, comparing it to Clover. According to the evaluation with the different processor configurations and the various error detection latencies, Clover turns out to be a superior technique, achieving 1.06 to 3.49 × speedup over the tail-wait.
Normal incident SiGe/Si multiple quantum well infrared detector (2002)

A long-wavelength ( approximately 10- mu m) quantum-well (QW) infrared detector with normal incident detection was fabricated using p-type Si/sub 1-x/Ge/sub x//Si multiple QWs. Photocurrent is measured as a function of the incident beam polarization. With a beam polarized parallel to the growth plane (90 degrees polarization, normal incidence), a photocurrent peak is observed at near 7.2 mu m with a full width at half maximum (FWHM) of about 80 meV. On the other hand, when the beam is polarized along the growth direction (0 degrees polarization), a peak is observed at near 8.6 mu m with FWHM of about 80 meV. With the non-optimized detector, the peak photoresponsivity of 0.3 A/W and detectivity of D* approximately 1.0*10/sup 9/cm square root Hz/W at 77 K are obtained for both polarizations. The results of normal incident detection demonstrate the feasibility of Si-based long-wavelength IR detectors and focal plane arrays with the advantage of monolithic integration with Si integrated circuits.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Arabidopsis Homologs of a c-Jun Coactivator Are Present Both in Monomeric Form and in the COP9 Complex, and Their Abundance Is Differentially Affected by the Pleiotropic cop/det/fus Mutations (1998)

Shing F. Kwok, Roberto Solano, Tomohiko Tsuge, Daniel A. Chamovitz, Joseph R. Ecker, Minami Matsui, Xing-Wang Deng, Arabidopsis Homologs of a c-Jun Coactivator Are Present Both in Monomeric Form and in the COP9 Complex, and Their Abundance Is Differentially Affected by the Pleiotropic cop/det/fus Mutations, The Plant Cell, Vol. 10, No. 11 (Nov., 1998), pp. 1779-1790
Human PAD4 Regulates Histone Arginine Methylation Levels via Demethylimination (2004)

Methylation of arginine (Arg) and lysine residues in histones has been correlated with epigenetic forms of gene regulation. Although histone methyltransferases are known, enzymes that demethylate histones have not been identified. Here, we demonstrate that human peptidylarginine deiminase 4 (PAD4) regulates histone Arg methylation by converting methyl-Arg to citrulline and releasing methylamine. PAD4 targets multiple sites in histones H3 and H4, including those sites methylated by coactivators CARM1 (H3 Arg17) and PRMT1 (H4 Arg3). A decrease of histone Arg methylation, with a concomitant increase of citrullination, requires PAD4 activity in human HL-60 granulocytes. Moreover, PAD4 activity is linked with the transcriptional regulation of estrogen-responsive genes in MCF-7 cells. These data suggest that PAD4 mediates gene expression by regulating Arg methylation and citrullination in histones.
An Anchor-Free Localization Scheme with Kalman Filtering in ZigBee Sensor Network (2013)

A localization scheme for wireless sensor networks is proposed and its performances are investigated in this paper. The proposed scheme is an anchor-free scheme, in which no geometrical information of sensor nodes is required for their localization. Thus, only local interaction among sensor nodes is used to estimate their locations. This scheme employs the link quality indicator and hop count between sensor nodes for location estimation. A weighted averaging and Kalman filtering schemes are incorporated in order to reduce the effects of the measurement errors in the obtained values of the link quality indicator. We performed experiments by implementing the proposed scheme on ZigBee sensor modules. The results of our experiments indicate that estimation could be successfully performed for networks comprising four sensor nodes.
Efficient fax transmission of halftone images (1992)

The efficient encoding and transmission of information for facsimile communication relies on redundancy in the scanned pixels. Halftone images, especiaily those rendered by high-quality dispersed dot techniques, are "busy" with alternative black and white pixels and shorter run lengths as compared to text information. Because of this, it is desirable to increase the redundancy and decrease the entropy of those images for efficient encoding and transmission. We propose a novel technique whereby both transmiffing and receiving fax devices have in memory a halftone screen such as the "blue noise mask" (BNM). The BNM is a halftone screen that produces a visuaily appealing dispersed dot pattern with an unstructured, isotropic pattern. When both the transmitting and receiving fax devices have the same halftone screen in ROM, the problem of halftone image encoding can be reduced to that of transmitting the mean gray value of blocks, or subimages, followed by a sparse halftone error image with increased redundancy and run-lengths compared to the original halftone. Examples show that by using the proposed technique, image entropy can be reduced to 0.2 bits/pixel, and typical run-lengths can increase by a factor of 5. The increase in image quality, combined with increased transmission speed, could add considerably to the utilization and acceptance of halftone fax images.