gebhart/patrepeval huggingface dataset:
Immunohistochemical analysis of beta3 integrin (CD61): expression in pig tissues and human tumors. (2002)

CD61 is a membrane glycoprotein that associates with CD41 (alphaIIb) to form the heterodimeric complex gpIIb/IIIa (CD41/CD61), predominantly expressed in platelets and megakariocytes. CD61 or beta3 integrin also associates with alpha v (CD51) to form the vitronectin receptor, which is expressed in many tissues. We have used a monoclonal antibody against the porcine gpIIIa or CD61 (JM2E5) to study the distribution of this molecule in different normal pig tissues. As in humans, CD61 was broadly expressed in all tissues examined. In the kidney, strong expression of CD61 was observed in epithelial cells from renal tubules. In the testis, CD61 expression was detected in the Leydig cells. However, in liver, CD61 was weak or not detected. Many integrins are particularly involved in tumogenicity and in tumor progression mediating cell-cell interaction. Immunofluorescence experiments using cultured human tumor HeLa cells showed nuclear and cytoplasmic staining of mAb JM2E5. Immunohistochemical analysis of human tumor sections from several organs showed a heterogeneus distribution in metastatic cases from colon and breast carcinoma. However, no staining was found in metastasis from melanoma.
On the DNA binding protein II from Bacillus stearothermophilus. II. The amino acid sequence and its relation to those of homologous proteins from other prokaryotes. (1983)

The complete amino acid sequence of DNA binding protein II from Bacillus stearothermophilus has been determined. The protein contains 90 amino acid residues and has a calculated Mr of 9716. The sequence is compared to homologous molecules from Escherichia coli, Thermoplasma acidophilum, and Pseudomonas aeruginosa (where only a partial sequence is available). The B. stearothermophilus molecule has 58% and 59% residues identical with the two forms of the E. coli protein and 32% with the T. acidophilum protein. There are totally conserved residues at positions 46-48 and 61-65 with an intervening cluster of basic amino acids in all four proteins.
Neutralization Synergy of Human Immunodeficiency Virus Type 1 Primary Isolates by Cocktails of Broadly Neutralizing Antibodies (2001)

Several reports have described the existence of synergy between neutralizing monoclonal antibodies (MAbs) against human immunodeficiency virus type 1 (HIV-1). Synergy between human MAbs b12, 2G12, 2F5, and 4E10 in neutralization of primary isolates is of particular interest. Neutralization synergy of these MAbs, however, has not been studied extensively, and the mechanism of synergy remains unclear. We investigated neutralization synergy among this human antibody set by using the classical approach of titrating antibodies mixed at a fixed ratio as well as by an alternative, variable ratio approach in which the neutralization curve of one MAb is assessed in the presence and absence of a fixed, weakly neutralizing concentration of a second antibody. The advantage of this second approach is that it does not require mathematical analysis to establish synergy. No neutralization enhancement of any of the MAb combinations tested was detected for the T-cell-line-adapted molecular HIV-1 clone HxB2 using both assay formats. Studies of primary isolates (89.6, SF162, and JR-CSF) showed neutralization synergy which was relatively weak, with a maximum of two- to fourfold enhancement between antibody pairs, thereby increasing neutralization titers about 10-fold in triple and quadruple antibody combinations. Analysis of b12 and 2G12 binding to oligomeric envelope glycoprotein by using flow cytometry failed to demonstrate cooperativity in binding between these two antibodies. The mechanism by which these antibodies synergize is, therefore, not yet understood. The results lend some support to the notion that an HIV-1 vaccine that elicits moderate neutralizing antibodies to multiple epitopes may be more effective than hereto supposed, although considerable caution in extrapolating to a vaccine situation is required.
Basement Membrane and Repair of Injury to Peripheral Nerve: Defining a Potential Role for Macrophages, Matrix Metalloproteinases, and Tissue Inhibitor of Metalloproteinases-1 (1996)

Injury to a peripheral nerve is followed by a remodeling process consisting of axonal degeneration and regeneration. It is not known how Schwann cell-derived basement membrane is preserved after injury or what role matrix metalloproteinases (MMPs) and their inhibitors play in axonal degeneration and regeneration. We showed that the MMPs gelatinase B (MMP-9), stromelysin-1 (MMP-3), and the tissue inhibitor of MMPs (TIMP)-1 were induced in crush and distal segments of mouse sciatic nerve after injury. TIMP-1 inhibitor activity was present in excess of proteinase activity in extracts of injured nerve. TIMP-1 protected basement membrane type IV collagen from degradation by exogenous gelatinase B in cryostat sections of nerve in vitro. In vivo, during the early phase (1 d after crush) and later phase (4 d after crush) after injury, induction of TNF-alpha and TGF-beta 1 mRNAs, known modulators of TIMP-1 expression, were paralleled by an upregulation of TIMP-1 and gelatinase B mRNAs. At 4 days after injury, TIMP-1, gelatinase B, and TNF-alpha mRNAs were localized to infiltrating macrophages and Schwann cells in the regions of nerve infiltrated by elicited macrophages. TIMP-1 and cytokine mRNA expression was upregulated in undamaged nerve explants incubated with medium conditioned by macrophages or containing the cytokines TGF-beta 1, TNF-alpha, and IL-1 alpha. These results show that TIMP-1 may protect basement membrane from uncontrolled degradation after injury and that cytokines produced by macrophages may participate in the regulation of TIMP-1 levels during nerve repair.
Inhibition of Human HT29 Colon Carcinoma Growth In Vitro and In Vivo by Swainsonine and Human Interferon-α2 (1989)

Swainsonine, a plant alkaloid and potent inhibitor of Asn-linked oligosaccharide processing, has previously been shown to inhibit organ colonization by metastatic murine tumor cells and to inhibit the growth of transformed fibroblasts in soft agar. In this report, we show that swainsonine has antiproliferative activity against human tumor cells growing in tissue culture and as tumor xenografts in nude mice. The antiproliferative activity of swainsonine was additive with that of human interferon-alpha 2 (HuIFN-alpha 2) in cultures of HT29 colon carcinoma, SN12 renal carcinoma, and A375 melanoma cells. In vivo, the growth rate of HT29m human colon carcinoma tumors in athymic nude mice was reduced by supplementing their drinking water with swainsonine (49%) or by administering HuIFN-alpha 2 systemically (53%); combining these treatments reduced tumor growth by 78%. Combining swainsonine and HuIFN-alpha 2 treatments enhanced the activity of the interferon-inducible enzyme 2',5'-oligoadenylate [2',5'-oligo(A)] synthetase in HT29m tumors compared to that observed in tumors from mice treated with interferon alone. In vitro, swainsonine enhanced interferon-dependent induction of 2',5'-oligo(A) synthetase activity in low-density cultures of HT29m cells. However, swainsonine alone did not stimulate 2',5'-oligo(A) synthetase activity in vivo or in vitro, indicating that the antiproliferative effect of swainsonine is independent of interferon production. The results suggest that in addition to the previously reported antimetastatic activity of swainsonine, the plant alkaloid has antiproliferative activity that is independent from, but additive with, that of interferon in vivo and in vitro.
Monocular visual localization using road structural features (2014)

Precise localization is an essential issue for autonomous driving applications, where GPS-based systems are challenged to meet requirements such as lane-level accuracy. This paper introduces a new visual-based localization approach in dynamic traffic environments, focusing on and exploiting properties of structured roads like straight roads or intersections. Such environments show several line segments on lane markings, curbs, poles, building edges, etc., which demonstrate the road's longitude, latitude and vertical directions. Based on this observation, we define a Road Structural Feature (RSF) as sets of segments along three perpendicular axes together with feature points. At each video frame, the proper road structure (or multiple road structures in case of an intersection) is predicted based on the geometric information given by a 2D map. The RSF is then detected from line segments and points extracted from the image, and used to estimate the pose of the vehicle. Experiments are conducted using video streams collected on major roads in downtown Beijing, which are structured and with intense dynamic traffic. GPS/IMU data have been collected and synchronized with the video streams as a reference in validation. The results show good performance compared with that of a more traditional visual odometry method. Future work will be addressed on using visual approach to improve GPS localization accuracy.
Depth-based target segmentation for intelligent vehicles: fusion of radar and binocular stereo (2002)

Dynamic environment interpretation is of special interest for intelligent vehicle systems. It is expected to provide lane information, target depth, and the image positions of targets within given depth ranges. Typical segmentation algorithms cannot solve the problems satisfactorily, especially under the high-speed requirements of a real-time environment. Furthermore, the variation of image positions and sizes of targets creates difficulties for tracking. In this paper, we propose a sensor-fusion method that can make use of coarse target depth information to segment target locations in video images. Coarse depth ranges can be provided by radar systems or by a vision-based algorithm introduced in the paper. The new segmentation method offers more accuracy and robustness while decreasing the computational load.
Neuroinflammation in Alzheimer's disease: chemokines produced by astrocytes and chemokine receptors. (2014)

Chemokines secreted by astrocytes play multiple roles in the pathology of Alzheimer’s disease, a chronic inflammation disorder of central nervous system. The level of chemokines in serum, cerebrospinal fluid and brain tissue and their receptors both significantly changed in patients with Alzheimer’s disease. In this review, we briefly summarized the involvement of astrocytes and chemokines in Alzheimer’s disease, and the role of chemokine/chemokine receptors in the occurrence and development of Alzheimer’s disease. Clarification of the involvement of chemokines and their receptors, such as MCP-1/CCR2, fractalkine/CX3CR1, SDF-1α/CXCR4, MIP-1α/CCR5, IP-10/CXCR3, IL-8/CXCR1, CXCR2, and RANTES/CCR1, CCR3, CCR5, will provide a new strategy and more specific targets for the treatment of Alzheimer’s disease.
Biodegradable therapeutic MOFs for the delivery of bioactive molecules (2010)

A new metal organic framework (MOF) built up from non-toxic iron and the therapeutically active linker nicotinic acid, with pellagra-curative, vasodilating, and antilipemic properties, has been isolated and characterised via single crystal methods. The release of the therapeutic agent, which is a constituent of the framework, is achieved through the degradation of the hybrid phase, under simulated physiological conditions, allowing for the delivery of the bioactive molecule.
Intracellular and extracellular processing of human apolipoprotein A-I: secreted apolipoprotein A-I isoprotein 2 is a propeptide. (1983)

We have recently proposed that the major secreted isoprotein form of human apolipoprotein A-I (designated apo A-I2) is modified extracellularly to become the predominant apo A-I form seen in plasma (designated apo A-I4). In the current report we demonstrate that the primary translation product of human apo A-I (designated apo A-I2p) has a 24-amino-acid NH2-terminal extension with a sequence of Met-Lys-Ala-Ala-Val-Leu-Thr-Leu-Ala-Val-Leu-Phe- Leu-Thr-Gly-Ser-Gln-Ala-Arg-His-Phe-Trp-Gln-Gln. The first 18 amino acids of this NH2-terminal extension are cleaved intracellularly by the signal peptidase, resulting in the formation of apo A-I2, which is the secreted form of apo A-I. Sequence analysis of apo A-I2 confirmed that it contains a hexapeptide extension at its NH2 terminus compared to apo A-I4. This observation demonstrates that apo A-I2 is a propeptide and that the apo A-I2 to apo A-I4 conversion involves the removal of the NH2-terminal hexapeptide of apo A-I2 by a protease in plasma, lymph, or both. Our findings indicate that apo A-I is synthesized as a prepropeptide, which undergoes intracellular and extracellular proteolysis to attain the major plasma apo A-I4 isoprotein form.
Comparison of Hemorrhage Control Agents Applied to Lethal Extremity Arterial Hemorrhages in Swine (2005)

FSD was superior to other currently utilized hemostatic products in controlling lethal arterial hemorrhage in this model of a fatal extremity wound. CD showed some hemostatic benefit. The exothermic reaction of QC was significant and resulted in gross and histologic tissue changes of unknown clinical significance. Controlled human studies with the promising products are required.
Spread of HTLV-I Between Lymphocytes by Virus-Induced Polarization of the Cytoskeleton (2003)

Cell contact is required for efficient transmission of human T cell leukemia virus- type 1 (HTLV-I) between cells and between individuals, because naturally infected lymphocytes produce virtually no cell-free infectious HTLV-I particles. However, the mechanism of cell-to-cell spread of HTLV-I is not understood. We show here that cell contact rapidly induces polarization of the cytoskeleton of the infected cell to the cell-cell junction. HTLV-I core (Gag protein) complexes and the HTLV-I genome accumulate at the cell-cell junction and are then transferred to the uninfected cell. Other lymphotropic viruses, such as HIV-1, may similarly subvert normal T cell physiology to allow efficient propagation between cells.
Sequence-specific DNA primer effects on telomerase polymerization activity. (1993)

The ribonucleoprotein enzyme telomerase synthesizes one strand of telomeric DNA by copying a template sequence within the RNA moiety of the enzyme. Kinetic studies of this polymerization reaction were used to analyze the mechanism and properties of the telomerase from Tetrahymena thermophila. This enzyme synthesizes TTGGGG repeats, the telomeric DNA sequence of this species, by elongating a DNA primer whose 3' end base pairs with the template-forming domain of the RNA. The enzyme was found to act nonprocessively with short (10- to 12-nucleotide) primers but to become processive as TTGGGG repeats were added. Variation of the 5' sequences of short primers with a common 3' end identified sequence-specific effects which are distinct from those involving base pairing of the 3' end of the primer with the RNA template and which can markedly induce enzyme activity by increasing the catalytic rate of the telomerase polymerization reaction. These results identify an additional mechanistic basis for telomere and DNA end recognition by telomerase in vivo.
The T cell-B cell interaction via OX40-OX40L is necessary for the T cell-dependent humoral immune response. (1996)

Recent in vitro studies have established that activated B cells express OX40 ligand (L), a member of the tumor necrosis factor/nerve growth factor family of cytokines, and become stimulated to proliferate and secrete immunoglobulin (Ig) after cross-linking of OX40L by its counterreceptor OX40, which is expressed on activated T cells. In the present study we investigated the in vivo role of this receptor-ligand pair for the interaction of T and B cells in the course of the T-dependent B cell response against 2,4,6 trinitro-phenyl-keyhole limpet hemocyanin. First, we showed that OX40 is maximally expressed by T cells in the periarteriolar lymphoid sheath (PALS) 3 d after primary immunization. These OX40+ cells are located in close proximity to antigen-specific, activated B cells. Second, we demonstrated that blocking of OX40-OX40L interaction with polyclonal anti-OX40 antibody or with antibodies against certain peptide sequences within its extracellular domain resulted in a profound decrease of the anti-hapten IgG response, whereas the antihapten IgM response was grossly unchanged. Third, we showed that this antibody treatment leads to an inhibition of the development of PALS-associated B cell foci, whereas the formation of germinal centers remained intact. Finally, our data suggest that, whereas B cell memory development was not impaired by anti-OX40 administration, OX40-OX40L interaction seems to be crucial in the secondary immune response. We conclude from these data that the OX40-OX40L interaction in vivo is necessary for the differentiation of activated B cells into highly Ig-producing cells, but is not involved in other pathways of antigen-driven B cell differentiation such as memory cell development in the germinal centers.
Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes (2012)

Deep sequencing of transcriptomes allows quantitative and qualitative analysis of many RNA species in a sample, with parallel comparison of expression levels, splicing variants, natural antisense transcripts, RNA editing and transcriptional start and stop sites the ideal goal. By computational modeling, we show how libraries of multiple insert sizes combined with strand-specific, paired-end (SS-PE) sequencing can increase the information gained on alternative splicing, especially in higher eukaryotes. Despite the benefits of gaining SS-PE data with paired ends of varying distance, the standard Illumina protocol allows only non-strand-specific, paired-end sequencing with a single insert size. Here, we modify the Illumina RNA ligation protocol to allow SS-PE sequencing by using a custom pre-adenylated 3' adaptor. We generate parallel libraries with differing insert sizes to aid deconvolution of alternative splicing events and to characterize the extent and distribution of natural antisense transcription in C. elegans. Despite stringent requirements for detection of alternative splicing, our data increases the number of intron retention and exon skipping events annotated in the Wormbase genome annotations by 127% and 121%, respectively. We show that parallel libraries with a range of insert sizes increase transcriptomic information gained by sequencing and that by current established benchmarks our protocol gives competitive results with respect to library quality.
Polychromatic transfer functions in stellar speckle interferometry (1989)

A general expression has been derived for the dichromatic speckle cross spectrum (DCS), using as a unique assumption Korff’s log-normal model for the complex wave amplitude at the telescope pupil. For a given spectral bandwidth, it is shown that the attenuation of the DCS with respect to the monochromatic spectrum is strongly seeing dependent. A high-frequency asymptotic form is derived for the rapid numerical computation of the DCS, thus making it possible to estimate with ease the allowable spectral bandwidth for any given speckle experiment. The performance of the instrumental achromatization technique is analyzed and shown to be useful only with good seeing and narrow bandwidths.
Mouse 4T1 Breast Tumor Model (2000)

The 4T1 mammary carcinoma is a transplantable tumor cell line that is highly tumorigenic and invasive and, unlike most tumor models, can spontaneously metastasize from the primary tumor in the mammary gland to multiple distant sites including lymph nodes, blood, liver, lung, brain, and bone The 4T1 tumor has several characteristics that make it a suitable experimental animal model for human mammary cancer. First, tumor cells are easily transplanted into the mammary gland so that the primary tumor grows in the anatomically correct site, as described in this unit. Second, as in human breast cancer, 4T1 metastatic disease develops spontaneously from the primary tumor. Also, the progressive spread of 4T1 metastases to the draining lymph nodes and other organs is very similar to that of human mammary cancer. In this unit, a protocol describes surgical removal of the primary tumor, so that metastatic disease can be studied in an animal setting comparable to the clinical situation where the primary tumor is surgically removed, and metastatic foci remain intact. Another advantage of 4T1 is its resistance to 6-thioguanine. This property enables precise quantitation of metastatic cells, even when they are disseminated and at sub-microscopic levels in distant organs, as described here.
Properties of MEKs, the kinases that phosphorylate and activate the extracellular signal-regulated kinases. (1993)

Activation of extracellular signal-regulated kinase (ERK) or mitogen-activated protein kinase by MEK (mitogen-activated protein kinase or extracellular signal-regulated kinase kinase) is an essential event in the mitogenic growth factor signal transduction. We now demonstrate that three recombinant MEKs (MEK1, MEK2, MEK3) show remarkably different activity toward recombinant ERK1 and ERK2. MEK2 is the most active ERK activator. The recombinant MEK1 has an activity approximately seven times lower than that of MEK2. MEK3, which is identical to MEK1 except for missing an internal 26-amino acid residue and probably represents an alternative splicing product of MEK1, shows neither autophosphorylation nor ERK-activating activity. Recombinant MEK1 and MEK2 can be activated by epidermal growth factor-stimulated SWISS3T3 cell lysate. MEK1 and MEK2 can also be activated by autophosphorylation. Autophosphorylation of MEKs correlates with their ability to phosphorylate and activate ERKs. Phosphorylation of MEK is also stimulated by ERK. Phosphoamino acid analysis showed that ERK1 preferentially phosphorylated threonine residue of MEKs. MEKs complex with ERKs in vitro. Interestingly, MEK3 also forms a complex with ERK1, although it is totally inactive as an ERK activator.
Analysis of time-interleaved delta-sigma analog to digital converter (2003)

Although /spl Delta//spl Sigma/ modulators are widely used for low to moderate rate analog-to-digital conversion, the time oversampling requirement has limited their application to higher rate converters. This paper presents an architecture wherein multiple /spl Delta//spl Sigma/ modulators are combined with time-interlacing. Indeed, the system achieves the effect of oversampling from the multiplicity of /spl Delta//spl Sigma/ modulators. For a system containing M L/sup th/ order /spl Delta//spl Sigma/ modulators, approximately L bits of accuracy are gained for every doubling of M. A major benefit of the architecture is that it retains much of the robustness to non-ideal circuit behavior of individual /spl Delta//spl Sigma/ modulators. As a result, the architecture offers the potential of integrating high-precision, high-speed ADC together with digital signal processing functions using VLSI processes optimized for digital circuitry. Because of the parallelism, the performance of the architecture is hugely degraded by channel mismatches. A digital technique is used to overcome this problem. The paper presents the general architecture and provides a performance analysis closely supported by computer simulations.