gebhart/patrepeval huggingface dataset:
TLR4 related to CXCR4 and CCR5 expression in HIV (2008)

In the present investigation, flow cytometric techniques were utilized to evaluate 20 cases of HIV for CXCR4, CCR5, and TLR4 expression in CD4 positive T cells, CD8 positive T cells, regulatory T cells, and Th17 cells, and mean fluorescence intensities (MFI) were determined. RT‐PCR was utilized to measure gene expression of CXCR4, CCR5, and TLR4. CD4+ T cells positively expressed CXCR4 in 16 cases, CCR5 in all 20, and TLR4 in 17. CD8+ T cells were positive for CXCR4 expression in 15 cases, CCR5 in all cases, and TLR4 in 18. Regulatory T cells positively expressed CXCR4 and CCR5 in 12 cases, and TLR4 in 11 cases. Th17 cells were positive for CXCR4 expression in 19 cases and TLR4 in 17. When compared to stage of disease, receptor expression by all cell types increased greatly as infection progressed from acute to chronic phase, but decreased only slightly as infection progressed from chronic phase to AIDS. Results reveal a positive correlation between CXCR4, CCR5, and TLR4 expression which may indicate that TLR4 also serves as a co‐receptor for HIV. In addition, these data suggest that TLR4 up‐regulation is not limited to gram‐negative bacterial infection nor is expression limited to myeloid cells.
Midbrain dopaminergic neuronal degeneration in a transgenic mouse model of familial amyotrophic lateral sclerosis (1997)

Familial amyotrophic lateral sclerosis has been linked in 15% of families to mutations in the gene encoding for copper-zinc superoxide dismutase (Cu/Zn-SOD), a key enzyme in the cellular defense mechanisms against free radical attack. We used a transgenic mouse model of familial amyotrophic lateral sclerosis (transgenic G1H mice) based on expression of mutant human Cu/Zn-SOD to examine the influence of the transgene expression on midbrain dopaminergic neurons, cells that contain conspicuous amounts of this enzyme. At the time that 50% of motor neurons of the spinal cord were lost, we observed concurrent reductions in dopamine levels in the caudate-putamen and the nucleus accumbens of transgenic G1H mice. In addition, numbers of tyrosine hydroxylase-immunostained neurons were significantly reduced in both the substantia nigra (26%) and the ventral tegmental area (16%) compared to those in their nontransgenic littermates. Similar abnormalities were not observed in the brains of transgenic mice overexpressing wild-type Cu/Zn-SOD. These findings indicate that overexpression of the mutated Cu/Zn-SOD protein caused a significant loss of midbrain dopaminergic neurons in addition to the loss of spinal motor neurons. The potential of the mutated enzyme to induce cell death extending beyond the motor neurons is consistent with the description of substantia nigra degeneration in some patients with familial amyotrophic lateral sclerosis. Furthermore, if mutated Cu/Zn-SOD is conclusively shown to kill cells by oxidative stress, such an observation would be in keeping with the known sensitivity of dopaminergic neurons to free radical attack.
High-frequency network oscillation in the hippocampus (1992)

Pyramidal cells in the CA1 hippocampal region displayed transient network oscillations (200 hertz) during behavioral immobility, consummatory behaviors, and slow-wave sleep. Simultaneous, multisite recordings revealed temporal and spatial coherence of neuronal activity during population oscillations. Participating pyramidal cells discharged at a rate lower than the frequency of the population oscillation, and their action potentials were phase locked to the negative phase of the simultaneously recorded oscillatory field potentials. In contrast, interneurons discharged at population frequency during the field oscillations. Thus, synchronous output of cooperating CA1 pyramidal cells may serve to induce synaptic enhancement in target structures of the hippocampus.
Spontaneous Homologous Recombination Is Induced by Collapsed Replication Forks That Are Caused by Endogenous DNA Single-Strand Breaks (2005)

Homologous recombination is vital to repair fatal DNA damage during DNA replication. However, very little is known about the substrates or repair pathways for homologous recombination in mammalian cells. Here, we have compared the recombination products produced spontaneously with those produced following induction of DNA double-strand breaks (DSBs) with the I-SceI restriction endonuclease or after stalling or collapsing replication forks following treatment with thymidine or camptothecin, respectively. We show that each lesion produces different spectra of recombinants, suggesting differential use of homologous recombination pathways in repair of these lesions. The spontaneous spectrum most resembled the spectra produced at collapsed replication forks formed when a replication fork runs into camptothecin-stabilized DNA single-strand breaks (SSBs) within the topoisomerase I cleavage complex. We found that camptothecin-induced DSBs and the resulting recombination repair require replication, showing that a collapsed fork is the substrate for camptothecin-induced recombination. An SSB repair-defective cell line, EM9 with an XRCC1 mutation, has an increased number of spontaneous gammaH2Ax and RAD51 foci, suggesting that endogenous SSBs collapse replication forks, triggering recombination repair. Furthermore, we show that gammaH2Ax, DSBs, and RAD51 foci are synergistically induced in EM9 cells with camptothecin, suggesting that lack of SSB repair in EM9 causes more collapsed forks and more recombination repair. Furthermore, our results suggest that two-ended DSBs are rare substrates for spontaneous homologous recombination in a mammalian fibroblast cell line. Interestingly, all spectra showed evidence of multiple homologous recombination events in 8 to 16% of clones. However, there was no increase in homologous recombination genomewide in these clones nor were the events dependent on each other; rather, we suggest that a first homologous recombination event frequently triggers a second event at the same locus in mammalian cells.
Effect of nanoparticle-bound ampicillin on the survival of Listeria monocytogenes in mouse peritoneal macrophages (1992)

The efficacy of ampicillin bound to polyisohexylcyanoacrylate nanoparticles was studied in vitro in mouse peritoneal macrophages infected with Listeria monocytogenes. Nanoparticles containing ampicillin 1 mg/L were more effective after 30 h than free ampicillin at the same concentration, with viable counts of 3.68 and 5.43 log10 cfu/mL, respectively. The nanoparticles acted on the intracellular bacteria after a lag period of 6-9 h; this time was apparently required for the degradation of the polymer. At the doses used in these experiments, empty nanoparticles had neither an anti-listeria nor a cytotoxic effect.
Genetic and Environmental Relationships Among Somatic Cell Count, Bacterial infection, and Clinical Mastitis (1992)

Incidence of bacterial infection in 9784 lactations of 7763 cows in 31 herds, SCC in 32,448 lactations of 19,764 cows from 54 herds, and incidence of first parity mastitis recorded in the first lactations of 148,143 cows in 828 herds were analyzed. Bacterial infection was analyzed dichotomously by both threshold and linear models. The effects of parity, season, stage of lactation, and parity by stage of lactation interaction on SCC were estimated. Heritability of mean lactation log SCC--corrected for the effects of parity, season, and stage of lactation--varied from .13 to .27 for all parities in different data sets. Heritability of bacterial infection was .04 for the threshold model and .02 for the linear models. Heritability of field-recorded mastitis was .01. The genetic correlation between bacterial infection and SCC was near unity, but the genetic correlation between SCC and mastitis was .3. Selection for lowered SCC should reduce incidence of bacterial infection by 2% per unit of selection intensity.
Techniques For Characterizing Optical System Fabrication (1984)

A theory has been developed for representing fabricated optical components by a set of easily identified local coordinate systems linked by physically relevant stationary pivot points. The use of stationary pivot modeling has many advantages when attempting to make performance predictions on complex optical systems during the fabrication and assembly process. In this paper, the basic techniques for modeling fabricated optical components by stationary pivots are developed and some applications discussed.
An overview of the OmniTRACS: The first operational mobile Ku-band satellite communications (1988)

The service features of the OmniTRACS system developed by Omninet Communications Services of Los Angeles, California are described. This system is the first operational mobile Ku-band satellite communications system that provides two-way messaging and position determination and reporting services to mobile users on a nationwide basis. The system uses existing Ku-band satellites under a secondary international allocation for mobile satellite services.
Vasoactive intestinal peptide protects against β‐amyloid‐induced neurodegeneration by inhibiting microglia activation at multiple levels (2008)

Alzheimer's disease (AD) is characterized by extracellular deposits of fibrillar beta-amyloid (Abeta) in the brain, increased microglial-mediated inflammatory reactions in senile plaques, selective neuronal death, and cognitive deficits. The use of agents that limit microglial activation and inflammation in AD has recently emerged as an attractive therapeutic strategy for this disease. The vasoactive intestinal peptide (VIP), a widely distributed neuropeptide, has shown neuroprotective effects in acute brain damage in vivo and potent anti-inflammatory actions in central nervous system. Here, we report that VIP inhibits Abeta-induced neurodegeneration by indirectly inhibiting the production of a wide panel of inflammatory and neurotoxic agents by activated microglia cells. The inhibitory effect of VIP is mediated by blocking signaling through the p38 MAPK, p42/p44 MAPK, and NFkB cascades, the three major transduction pathways involved in the transcription of inflammatory mediators and the production of free radicals by Abeta-activated microglia cells. Based on its neuroprotective action and its efficacy in inhibiting a broad range of inflammatory responses, VIP may provide a novel therapeutic approach to AD.
A Fast Quartet tree heuristic for hierarchical clustering (2010)

The Minimum Quartet Tree Cost problem is to construct an optimal weight tree from the 3(n4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologies is optimal (so it can be the case that the optimal tree embeds all quartets as nonoptimal topologies). We present a Monte Carlo heuristic, based on randomized hill-climbing, for approximating the optimal weight tree, given the quartet topology weights. The method repeatedly transforms a dendrogram, with all objects involved as leaves, achieving a monotonic approximation to the exact single globally optimal tree. The problem and the solution heuristic has been extensively used for general hierarchical clustering of nontree-like (non-phylogeny) data in various domains and across domains with heterogeneous data. We also present a greatly improved heuristic, reducing the running time by a factor of order a thousand to ten thousand. All this is implemented and available, as part of the CompLearn package. We compare performance and running time of the original and improved versions with those of UPGMA, BioNJ, and NJ, as implemented in the SplitsTree package on genomic data for which the latter are optimized.
Studies on toxinogenesis in Vibrio cholerae. III. Characterization of nontoxinogenic mutants in vitro and in experimental animals. (1975)

Spontaneous and chemically induced mutants with reduced ability to produce cholera enterotoxin (choleragen) as an extracellular protein were isolated from Vibrio cholerae strains 569B Inaba, a classical cholera vibrio, and 3083-2 Ogawa, an El Tor vibrio. By qualitative and quantitative immunological assay in vitro such mutants could be separated into different classes characterized either by production of no detectable choleragen (tox minus), or of small quantities of extracellular choleragen, or of large quantities of cell-associated choleragen but little extracellular choleragen. Analysis of proteins in concentrated culture supernates by electrophoresis in polyacrylamide gels showed that cultures from tox minus strains lacked proteins with electrophoretic mobilities corresponding with choleragen or the spontaneously formed toxoid (choleragenoid). Infant rabbits infected with the tox minus strains remained asymptomatic or developed milder symptoms than rabbits infected with the tox+ parental strains. When symptoms of cholera developed after inoculation with tox minus mutants, detectable numbers of tox+ revertants could be isolated from the intestines of the infected animals. Two tox minus strains, designated M13 and M27, caused no sumptoms and showed no evidence of reversion to tox+ during single passage in infant rabbits, and mutant M13 also remained avirulent and stably tox minus during six cycles of serial passage in infant rabbits. Strains M13 and M27 were also noncholeragenic in acult rabbit ileal loops. Quantitative cultures of the intestines from infected infant rabbits demonstrated that the avirulent mutant M13 can multiply in vivo and can persist in the intestinal tract for at least 48 h.
OLAP Solutions - Building Multidimensional Information Systems (1997)

From the Publisher:
Although many commercial OLAP products are readily available -- as stand-alone tools and, increasingly, in close association with relational databases -- OLAP remains a difficult and complex technology to master. The second edition of Thomsen's classic OLAP Solutions provides a clear and comprehensive explanation of the concepts and best techniques for deploying OLAP -- no matter what tools you're using. This edition is thoroughly revised, offering expanded coverage of logical issues such as dimensional hierarchies, as well as physical issues of data storage, access, and calculation. Thomsen has also created an entirely new application section that provides a computational cross-value chain model of ten interconnected business processes within the context of a manufacturing company. The practical methods and formulas you'll learn are useful no matter what commercial OLAP tool(s) you use.
Oximes and Hydrazones in Bioconjugation: Mechanism and Catalysis (2017)

The formation of oximes and hydrazones is employed in numerous scientific fields as a simple and versatile conjugation strategy. This imine-forming reaction is applied in fields as diverse as polymer chemistry, biomaterials and hydrogels, dynamic combinatorial chemistry, organic synthesis, and chemical biology. Here we outline chemical developments in this field, with special focus on the past ∼10 years of developments. Recent strategies for installing reactive carbonyl groups and α-nucleophiles into biomolecules are described. The basic chemical properties of reactants and products in this reaction are then reviewed, with an eye to understanding the reaction's mechanism and how reactant structure controls rates and equilibria in the process. Recent work that has uncovered structural features and new mechanisms for speeding the reaction, sometimes by orders of magnitude, is discussed. We describe recent studies that have identified especially fast reacting aldehyde/ketone substrates and structural effects that lead to rapid-reacting α-nucleophiles as well. Among the most effective new strategies has been the development of substituents near the reactive aldehyde group that either transfer protons at the transition state or trap the initially formed tetrahedral intermediates. In addition, the recent development of efficient nucleophilic catalysts for the reaction is outlined, improving greatly upon aniline, the classical catalyst for imine formation. A number of uses of such second- and third-generation catalysts in bioconjugation and in cellular applications are highlighted. While formation of hydrazone and oxime has been traditionally regarded as being limited by slow rates, developments in the past 5 years have resulted in completely overturning this limitation; indeed, the reaction is now one of the fastest and most versatile reactions available for conjugations of biomolecules and biomaterials.
Characterization of the Glycosylation Sites in Cyclooxygenase-2 Using Mass Spectrometry (2001)

Cyclooxygenase is involved in the biosynthesis and function of prostaglandins. It is a glycoprotein located in the endoplasmic reticulum and in the nuclear envelope, and it has been found to have two isoforms termed COX-1 and COX-2. This paper reports on the glycosylation site analysis of recombinant COX-2 using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) and nanoelectrospray (nanoESI) quadrupole-TOF (Q-TOF) MS. The nanoESI MS analysis of COX-2 revealed the presence of three glycoforms at average molecular masses of 71.4, 72.7, and 73.9 kDa. Each glycoform contained a number of peaks differing by 162 Da indicating heterogeneity and suggesting the presence of high-mannose sugars. The masses of the glycoforms indicate that oligosaccharides occupy two to four sites and a single N-acetylglucosamine (GlcNAc) residue occupied up to two sites. The MALDI MS analysis of a tryptic digest of the protein showed a number of potential glycopeptides. The peptides differed by 162 Da which further suggested high-mannose sugars. Nanoelectrospray MS/MS experiments confirmed glycosylation at the Asn 53 and Asn 130 sites and confirmed the presence of the peptides Asn 396-Arg 414 + GlcNAc and Thr 576-Arg 587 + GlcNAc containing Asn 580. It was not possible to conclusively determine whether the Asn 396 site was glycosylated via an MS/MS experiment, so the tryptic digest was deglycosylated to confirm the presence of the glycopeptides. Finally, a non-glycosylated tryptic peptide was observed containing the Asn 592.
A Single Rate Three Color Marker (1999)

This document defines a Single Rate Three Color Marker (srTCM), which can be used as component in a Diffserv traffic conditioner [RFC2475, RFC2474]. The srTCM meters a traffic stream and marks its packets according to three traffic parameters, Committed Information Rate (CIR), Committed Burst Size (CBS), and Excess Burst Size (EBS), to be either green, yellow, or red. A packet is marked green if it doesn't exceed the CBS, yellow if it does exceed the CBS, but not the EBS, and red otherwise.
5.6 ps Gate Delay All Refractory Josephson OR Gate with Modified Variable Threshold Logic (1985)

The modified variable threshold logic (MVTL) OR gate has a wide operating margin of ±43% and occupies a small area of 45×65 µm 2 . We made this gate with all refractory material including Nb/Al-AlO x /Nb junctions and Mo resistors. A chain of 5-stage MVTL OR gate was fabricated. The junction diameters were 4 µm and 7 µm, and critical current density was 1400 A/cm 2 . The minimum gate delay of 5.6 ps/gate was measured using a Josephson sampler.
Abnormalities of CD4+ T cell subpopulations in ANCA-associated vasculitis (2005)

In patients with ANCA-associated vasculitis (AAV), CD25 expression is increased on circulating T cells. Although in animal experiments the role of CD4(+) CD25(+) T-regulatory-cells (T(reg)) in protection against autoimmunity is well established, the role of these cells in AAV is unknown. To investigate the hypothesis that an increased expression of CD25 on T cells is related to persistent T cell activation and not to disturbances in T(reg) cells in AAV (34 patients, six of them after renal transplantation), we investigated CD25 expression in different subpopulations of CD4(+) cells and FOXP3 mRNA expression by reverse transcription-polymerase chain reaction (RT-PCR). In addition, T cell proliferation and cytokine secretion after stimulation with anti-CD3 and anti-CD28 and intracellular cytokine production after stimulation with phorbol myristate acetate (PMA)-ionomycin was determined. Controls were non-vasculitic renal transplant patients (n = 9) and healthy controls (HC) (n = 13). In AAV the total number of lymphocytes, CD4(+) lymphocytes and the percentage of naive T cells are lower than in HC and RTX. An increased percentage of CD25(+) cells was found in AAV and AAV/RTX, irrespective of disease activity, but not in HC or RTX. This was confined to the naive (CD4(+) CD45RB(high)) population only. FOXP3 mRNA expression in CD4(+) T cells did not differ between AAV patients and healthy controls. In vitro T cell proliferation was enhanced in AAV patients compared to HC (P < 0.01). PBMC of AAV patients produced significantly less interleukin (IL)-10 and interferon (IFN)-gamma after anti-CD3/CD28 stimulation. The percentage of IL-10 and IL-12, but not IFN-gamma, IL-4 or tumour necrosis factor (TNF)-alpha-producing cells was significantly higher in patients compared to HC. These findings were confined to the memory population of CD4(+) cells. We conclude that AAV patients are lymphopenic and have low numbers of CD4(+) T cells, which seem to be in a persistent state of activation.
Guided visibility sampling (2006)

This paper addresses the problem of computing the triangles visible from a region in space. The proposed aggressive visibility solution is based on stochastic ray shooting and can take any triangular model as input. We do not rely on connectivity information, volumetric occluders, or the availability of large occluders, and can therefore process any given input scene. The proposed algorithm is practically memoryless, thereby alleviating the large memory consumption problems prevalent in several previous algorithms. The strategy of our algorithm is to use ray mutations in ray space to cast rays that are likely to sample new triangles. Our algorithm improves the sampling efficiency of previous work by over two orders of magnitude.
Multi-antenna testbeds for research and education in wireless communications (2004)

Wireless communication systems present unique challenges and trade-offs at various levels of the system design process. Since a variety of performance measures are important in wireless communications, a family of testbeds becomes essential to validate the gains reported by the theory. Wireless testbeds also play a very important role in academia for training students and enabling research. In this article we discuss a classification scheme for wireless testbeds and present an example of the testbeds developed at UCLA for each of these cases. We present the unique capabilities of these testbeds, provide the results of the experiments, and discuss the role they play in an educational environment.
Fast computation of shadow boundaries using spatial coherence and backprojections (1994)

This paper describes a fast, practical algorithm to compute the shadow boundaries in a polyhedral scene illuminated by a polygonal light source. The shadow boundaries divide the faces of the scene into regions such that the structure or “aspect” of the visible area of the light source is constant within each region. The paper also describes a fast, practical algorithm to compute the structure of the visible light source in each region. Both algorithms exploit spatial coherence and are the most efficient yet developed.
Requirement for CD4 T Cell Help in Generating Functional CD8 T Cell Memory (2003)

Although primary CD8 responses to acute infections are independent of CD4 help, it is unknown whether a similar situation applies to secondary responses. We show that depletion of CD4 cells during the recall response has minimal effect, whereas depletion during the priming phase leads to reduced responses by memory CD8 cells to reinfection. Memory CD8 cells generated in CD4+/+ mice responded normally when transferred into CD4-/- hosts, whereas memory CD8 cells generated in CD4-/- mice mounted defective recall responses in CD4+/+ adoptive hosts. These results demonstrate a previously undescribed role for CD4 help in the development of functional CD8 memory.