gebhart/patrepeval huggingface dataset:
Hematopoietic Stem Cells (2009)

Hematopoietic stem cells (HSCs) are the most well-characterized tissue-specific stem cell. Over 50 years of basic research and clinical application has provided insight into the molecular and cellular mechanisms of HSC biology. HSC undergo self-renewal by symmetric or asymmetric division, or differentiation to common myeloid progenitors and progressively more differentiated myeloid and lymphoid progeny. The chemokine SDF-1/ CXCL12 produced by marrow reticular cells plays a central role in regulating HSC migration and homing. HSC reside within a three-dimensional multicellular signaling unit or "niche" within the bone marrow. Within the niche HSC can be sustained in a dormant G0 state. Accumulating genetic and functional data indicate molecular cross-talk between HSCs and osteoblasts, endothelial cells, and perivascular reticular cells that compose the endosteal and vascular niches. This involves large number of molecules (cytokines, chemokines, integrins, morphogens, and their receptors). The cytokines c-Kit ligand and thrombopoietin in particular are critical for HSC maintenance and self-renewal. The morphogens (Notch ligands, Wnt, Hedgehog, TGFβ, and BMP) also have variable and overlapping roles in supporting HSC self-renewal. Many of these secreted signaling molecules bind to the extracellular matrix and do not diffuse far or are presented by niche cells in transmembrane form (e.g., Jagged-Notch, Kit Ligand-c-Kit, Angiopoietin1-Tie2). Increased understanding of the molecular basis of HSC regulation will ultimately lead to protocols for maintenance and expansion of HSCs in vitro for clinical use in cell and gene therapies.
Comparative Study of Circulating MMP-7, CCL18, KL-6, SP-A, and SP-D as Disease Markers of Idiopathic Pulmonary Fibrosis (2016)

Background. Recent reports indicate that matrix metalloproteinase-7 (MMP-7) and CC-chemokine ligand 18 (CCL18) are potential disease markers of idiopathic pulmonary fibrosis (IPF). The objective of this study was to perform direct comparisons of these two biomarkers with three well-investigated serum markers of IPF, Krebs von den Lungen-6 (KL-6), surfactant protein-A (SP-A), and SP-D. Methods. The serum levels of MMP-7, CCL18, KL-6, SP-A, and SP-D were evaluated in 65 patients with IPF, 31 patients with bacterial pneumonia, and 101 healthy controls. The prognostic performance of these five biomarkers was evaluated in patients with IPF. Results. The serum levels of MMP-7, KL-6, and SP-D in patients with IPF were significantly elevated compared to those in patients with bacterial pneumonia and in the healthy controls. Multivariate survival analysis showed that serum MMP-7 and KL-6 levels were independent predictors in IPF patients. Moreover, elevated levels of both KL-6 and MMP-7 were associated with poorer survival rates in IPF patients, and the combination of both markers provided the best risk discrimination using the C statistic. Conclusions. The present results indicated that MMP-7 and KL-6 were promising prognostic markers of IPF, and the combination of the two markers might improve survival prediction in patients with IPF.
Tactile/Kinesthetic Stimulation Effects on Preterm Neonates (1986)

Tactile/kinesthetic stimulation was given to 20 preterm neonates (mean gestational age, 31 weeks; mean birth weight, 1,280 g; mean time in neonatal intensive care unit, 20 days) during transitional ("grower") nursery care, and their growth, sleep-wake behavior, and Brazelton scale performance was compared with a group of 20 control neonates. The tactile/kinesthetic stimulation consisted of body stroking and passive movements of the limbs for three, 15-minute periods per day for a 10 days. The stimulated neonates averaged a 47% greater weight gain per day (mean 25 g v 17 g), were more active and alert during sleep/wake behavior observations, and showed more mature habituation, orientation, motor, and range of state behavior on the Brazelton scale than control infants. Finally, their hospital stay was 6 days shorter, yielding a cost savings of approximately $3,000 per infant. These data suggest that tactile/kinesthetic stimulation may be a cost effective way of facilitating growth and behavioral organization even in very small preterm neonates.
The role of cell-derived oligomers of Aβ in Alzheimer's disease and avenues for therapeutic intervention (2005)

Burgeoning evidence suggests that soluble oligomers of Aβ (amyloid β-protein) are the earliest effectors of synaptic compromise in Alzheimer's disease. Whereas most other investigators have employed synthetic Aβ peptides, we have taken advantage of a β-amyloid precursor protein-overexpressing cell line (referred to as 7PA2) that secretes sub-nanomolar levels of low-n oligomers of Aβ. These are composed of heterogeneous Aβ peptides that migrate on SDS/PAGE as dimers, trimers and tetramers. When injected into the lateral ventricle of rats in vivo, these soluble oligomers inhibit hippocampal long-term potentiation and alter the memory of a complex learned behaviour. Biochemical manipulation of 7PA2 medium including immunodepletion with Aβ-specific antibodies and fractionation by size-exclusion chromatography allowed us to unambiguously attribute these effects to low-n oligomers. Using this paradigm we have tested compounds directed at three prominent amyloid-based therapeutic targets: inhibition of the secretases responsible for Aβ production, inhibition of Aβ aggregation and immunization against Aβ. In each case, compounds capable of reducing oligomer production or antibodies that avidly bind Aβ oligomers also ameliorate the synaptotoxic effects of these natural, cell-derived oligomers.
Biochemical and Molecular Characterization of a Mutation That Confers a Decreased Raffinosaccharide and Phytic Acid Phenotype on Soybean Seeds (2002)

Abstract A single, recessive mutation in soybean (Glycine max L. Merr.), which confers a seed phenotype of increased inorganic phosphate, decreased phytic acid, and a decrease in total raffinosaccharides, has been previously disclosed (S.A. Sebastian, P.S. Kerr, R.W. Pearlstein, W.D. Hitz [2000] Soy in Animal Nutrition, pp 56–74). The genetic lesion causing the multiple changes in seed phenotype is a single base change in the third base of the codon for what is amino acid residue 396 of the mature peptide encoding a seed-expressed myo-inositol 1-phospate synthase gene. The base change causes residue 396 to change from lysine to asparagine. That amino acid change decreases the specific activity of the seed-expressed myo-inositol 1-phosphate synthase by about 90%. Radio tracer experiments indicate that the supply ofmyo-inositol to the reaction, which converts UDP-galactose and myo-inositol to galactinol is a controlling factor in the conversion of total carbohydrate into the raffinosaccharides in both wild-type and mutant lines. That same decrease in myo-inositol 1-phosphate synthetic capacity leads to a decreased capacity for the synthesis ofmyo-inositol hexaphosphate (phytic acid) and a concomitant increase in inorganic phosphate.
A Simple and Effective Method for Phosphoryl Transfer Using TiCl4 Catalysis (2002)

[reaction: see text] A number of Lewis acids have been evaluated as catalysts for the phosphoryl transfer, the most efficient being TiCl(4). Application of this methodology to the phosphorylation of a number of representative target alcohols is presented
Oxidative Stress Induced Lipocalin 2 Gene Expression: Addressing its Expression under the Harmful Conditions (2007)

Lipocalin 2/H 2 O 2 /oxidative stress/radiation/liver.
Vulnerable Atherosclerotic Plaque: Clinical Implications (2003)

Coronary Artery Disease (CAD) remains globally the leading cause of death and long-term morbidity. Among the many manifestations of CAD, acute coronary syndrome (ACS), ranging from unstable angina to acute myocardial infarction, is the most catastrophic event due to our inability to predict its occurrence. Despite improved treatments of CAD, ACS results in sudden death or permanent disability in a substantial percentage of patients. If we could predict the timing of ACS or better yet prevent its occurrence, we could alter the otherwise unfavorable course of CAD. Several studies have convincingly demonstrated that majority of all ACS develops from previously mild to moderate stenoses. Thus, based on these and autopsy studies, sudden disruption or rupture of the non-obstructive "vulnerable" atherosclerotic lesion is currently considered the cause of ACS. Recent clinical studies have substantiated earlier autopsy observations that plaque vulnerability is a systemic process, involving multiple locations concurrently. Although the exact inciting factors of the vulnerable plaque rupture are unknown, inflammation is accepted to be a pivotal event. The possibility of stabilizing the vulnerable plaques has strongly been supported by the lipid lowering trials, in which dramatic reduction of the acute coronary events was noted despite subtle improvements in luminal diameter. Furthermore, antiplatelet therapies have become an important preventative therapy due to the essential role of platelets in the aftermath of plaque rupture. Finally, various imaging modalities to diagnose the plaque vulnerability could help prevent the acute coronary events in the future.
Influence of novel MOS varactors on the performance of a fully integrated UMTS VCO in standard 0.25-μm CMOS technology (2002)

A novel MOS varactor design is compared to standard MOS varactors and its influence on the tuning range, phase noise, and pushing of a CMOS voltage-controlled oscillator (VCO) for UMTS is presented. Three fully integrated CMOS VCOs have been fabricated in standard 0.25-/spl mu/m technology, two with different versions of a novel device, and one with a conventional nMOSFET as the tuning element. All of the fully integrated VCOs fulfill UNITS tuning and phase noise specifications with a power consumption of only 7.5 mW at a 2.5-V power supply. The new varactors outperform the nMOSFET by increasing the frequency tuning from /spl plusmn/7% to /spl plusmn/11% or /spl plusmn/13%, while the measured phase noise of all three VCOs is -117 dBc/Hz at a 1 MHz offset from a 4-GHz carrier.
Preservation of viable bone marrow cells by freezing (1960)

In a study of low-temperature preservation, mouse bone marrow cells were slow-frozen and fast-thawed. A number of additives, including glycerol and other polyhydric alcohols, were tested for their ability to protect the cells against freezing and thawing damage. Effectiveness of thawed cells to promote recovery in lethally irradiated (900 r) mice was used as a measure of viability. Tyrode's solution, mouse serum, glucose, polyvinylpyrrolidone, dextran and bovine serum albumin gave little or no protection at the concentrations tested. Polyhydric alcohols and some sugars and other organic compounds were effective at certain concentrations. Results of tests of marrow frozen in 15% glycerol made after storage at various temperatures for various times indicate that liquid nitrogen temperatures give the best long-term storage. The eosin uptake test was found to be a poor assay of the effectiveness of thawed marrow samples. Submitted on November 13, 1959
PPAR and Oxidative Stress: Con() Catenating NRF2 and FOXO (2012)

Peroxisome-proliferator activator receptor γ (PPARγ) is a nuclear receptor of central importance in energy homeostasis and inflammation. Recent experimental pieces of evidence demonstrate that PPARγ is implicated in the oxidative stress response, an imbalance between antithetic prooxidation and antioxidation forces that may lead the cell to apoptotic or necrotic death. In this delicate and intricate game of equilibrium, PPARγ stands out as a central player devoted to the quenching and containment of the damage and to foster cell survival. However, PPARγ does not act alone: indeed the nuclear receptor is at the point of interconnection of various pathways, such as the nuclear factor erythroid 2-related factor 2 (NRF2), Wnt/β-catenin, and forkhead box proteins O (FOXO) pathways. Here we reviewed the role of PPARγ in response to oxidative stress and its interaction with other signaling pathways implicated in this process, an interaction that emerged as a potential new therapeutic target for several oxidative-related diseases.
Distinct roles for CD4 and CD8 as co‐receptors in T cell receptor signalling (1994)

We demonstrate that CD4 and CD8 modify signals induced through the T cell receptor for antigen (TCR alpha beta) in distinct fashions. Pretreatment of CD4+ lymph node T cells with CD4-specific monoclonal antibody results in a tenfold inhibition of DNA synthesis induced by anti-TCR alpha beta. In contrast, pretreatment of CD8+ T cells with CD8-specific mAb has no effect on DNA synthesis subsequently induced through TCR alpha beta. While inhibiting late activation signals, pretreatment with anti-CD4 does not detectably alter the pattern of anti-TCR alpha beta-induced tyrosine phosphorylation of cellular proteins, nor subsequent Ca2+ mobilization. The distinct biological consequences of anti-CD4 and anti-CD8 pretreatment correlate with the differential association of their respective ligands with the cellular protein tyrosine kinase, p56lck. While both T cell lineages contain similar levels of cellular p56lck, tenfold more is associated with CD4 than with CD8. This difference is associated with the differential effects of pretreatment with anti-CD4 and anti-CD8 on the distribution and activity of p56lck. Further, antibody-mediated aggregation of TCR alpha beta on CD4+ T cells induces the appearance of a p56lck species with decreased mobility in sodium dodecylsulfate-polyacrylamide gel electrophoresis. This effect is observed in CD4+ T cells exclusively and involves the fraction of p56lck which is not associated with CD4. The results presented here demonstrate that the signalling elements which couple the antigen receptor to second messenger-generating systems are under distinct physical and/or functional constraints in the two T cell lineages.
Photonic nanojet-enabled optical data storage (2008)

We show that our recently reported microwave photonic jet technique for detection of deeply subwavelength pits in a metal substrate can be extended to optical wavelengths for purposes of high-density data storage. Three-dimensional finite-difference time-domain computational solutions of Maxwell's equations are used to optimize the photonic nanojet and pit configuration to account for the Drude dispersion of an aluminum substrate in the spectral range near lambda= 400 nm. Our results show that nanojet-illuminated pits having lateral dimensions of only 50 nm x 80 nm yield a contrast ratio 27 dB greater than previously reported using a lens system for pits of similar area. Such pits are much smaller than BluRay features. The high detection contrast afforded by the photonic nanojet could potentially yield significant increases in data density and throughput relative to current commercial optical data-storage systems while retaining the basic geometry of the storage medium.
An Adaptive Method for Subband Decomposition ICA (2005)

Subband decomposition ICA (SDICA), an extension of ICA, assumes that each source is represented as the sum of some independent subcomponents and dependent subcomponents, which have different frequency bands. In this article, we first investigate the feasibility of separating the SDICA mixture in an adaptive manner. Second, we develop an adaptive method for SDICA, namely band-selective ICA (BS-ICA), which finds the mixing matrix and the estimate of the source independent subcomponents. This method is based on the minimization of the mutual information between outputs. Some practical issues are discussed. For better applicability, a scheme to avoid the high-dimensional score function difference is given. Third, we investigate one form of the overcomplete ICA problems with sources having specific frequency characteristics, which BS-ICA can also be used to solve. Experimental results illustrate the success of the proposed method for solving both SDICA and the over-complete ICA problems.
Direct derivation of conditionally immortal cell lines from an H-2Kb-tsA58 transgenic mouse. (1991)

Studies on cell lines have greatly improved our understanding of many important biological questions. Generation of cell lines is facilitated by the introduction of immortalizing oncogenes into cell types of interest. One gene known to immortalize many different cell types in vitro encodes the simian virus 40 (SV40) large tumor (T) antigen (TAg). To circumvent the need for gene insertion in vitro to generate cell lines, we created transgenic mice harboring the SV40 TAg gene. Since previous studies have shown that TAg expression in transgenic mice is associated with tumorigenesis and aberrant development, we utilized a thermolabile TAg [from a SV40 strain, tsA58, temperature sensitive (ts) for transformation] to reduce the levels of functional TAg present in vivo. To direct expression to a broad range of tissues, we used the mouse major histocompatibility complex H-2Kb promoter, which is both widely active and can be further induced by interferons. tsA58 TAg mRNA was expressed in tissues of all animals harboring the hybrid construct. Development of all tissues was macroscopically normal except for thymus, which consistently showed hyperplasia. Fibroblast and cytokeratin+ thymic epithelial cultures from these mice were readily established without undergoing crisis and were conditionally immortal in their growth; the degree of conditionality was correlated with the levels of tsA58 TAg detected. One strain of H-2Kb-tsA58 mice has been bred through several generations to homozygosity and transmits a functional copy of the transgene.
Labeling of fusion proteins with synthetic fluorophores in live cells (2004)

A general approach for the sequential labeling of fusion proteins of O(6)-alkylguanine-DNA alkyltransferase (AGT) with different fluorophores in mammalian cells is presented. AGT fusion proteins with different localizations in the cell can be labeled specifically with different fluorophores, and the fluorescence labeling can be used for applications such as multicolor analysis of dynamic processes and fluorescence resonance energy transfer measurements. The facile access to a variety of different AGT substrates as well as the specificity of the labeling reaction should make the approach an important tool to study protein function in live cells.
Phage Display of Adenovirus Type 5 Fiber Knob as a Tool for Specific Ligand Selection and Validation (2001)

Adenovirus (Ad) vectors are most potent for use as gene delivery vehicles to infect human cells in vitro and in vivo with high efficiency. The main limitation in utilization of Ad as a gene transfer vector is the lack of specificity. Genetic modifications of Ad capsid proteins resulting in incorporation of foreign polypeptide ligand sequences can redirect the vector towards target cells. However, in many cases the incorporated ligands lose specificity or lead to conformational changes influencing virion integrity. In order to select target-specific ligands a priori structurally compatible with Ad, we propose a system for displaying polypeptide sequences in the context of the Ad fiber knob on the surfaces of filamentous bacteriophages. To establish this concept, we displayed the wild-type Ad serotype 5 knob and knobs containing c-Myc epitopes and six-histidine sequences in the pJuFo phage system. The knobs remained trimeric and bound the coxsackievirus-Ad receptor, and the phage knob-displayed ligands recognized and bound their cognates in the phage-displayed knob context. Further development of this system may be useful for candidate ligand fidelity and Ad structural compatibility validation prior to Ad modification.
Mesoporous Colloidal Superparticles of Platinum‐Group Nanocrystals with Surfactant‐Free Surfaces and Enhanced Heterogeneous Catalysis (2015)

Synthesis of colloidal superparticles (CSPs) of nanocrystals, a class of assembled nanocrystals in the form of colloidal particles, has been emerging as a new frontier in the field of nanotechnology because of their potential novel properties originated from coupling of individual nanocrystals in CSPs. Here, a facile approach is reported for the controlled synthesis of mesoporous CSPs made of various platinum‐group nanocrystals that exhibit high colloidal stability and ligand‐free surfaces to significantly benefit their applications in solution‐phase heterogeneous catalysis. The synthesis relies on self‐limiting growth of composite particles through coprecipitation of both Pt‐group nanocrystals (or their precursor compounds) and silver halides on sacrificial substrates of colloidal silver particles. The intermediate silver halides in the composite particles play the critical role in limiting the continuous growth (and/or coalescence) of individual Pt‐group nanocrystals and they can be selectively dissolved to create nanoscale pores in the resulting CSPs.
Effect of liposomes on mineralization in rat osteoblast-enriched cultures. (1999)

Liposomes, artificial membranous lipid vesicles, have been used as model structures for biological calcification processes. However, there is no definite conclusion that liposomes can be like matrix vesicles for inducing bone calcification and bone-like tissue formation on primary cultured cells. To determine whether liposomes can promote bone cell growth and mineralization by inducing crystal nucleation, liposomes composed of egg phosphatidylcholine, cholesterol, and bovine brain phosphatidylserine were added to 21-day-old Sprague-Dawley fetal rat calvarial cell cultures from day 1. The aims were to observe proliferation and the phenotype of osteoblasts by measuring cell numbers and alkaline phosphatase (ALP) activity and, when added at confluence, to observe calcification. The data were analyzed with two-way ANOVA. During the 16-day culture period, cell numbers were not significantly affected by liposomes (100 mumol/L). However, ALP activity was significantly inhibited by liposomes (p < 0.05) at day 16 and thereafter. Calcified particles were detected by von Kossa's method, and were larger and more abundant (p < 0.05) in the liposomes groups than in the control from days 12-24. This response depended on liposomes dose. These findings suggest that liposomes promote calcification and accelerate the formation of bone-like tissue. Liposomes slightly reduce the expression of the osteoblast phenotype and do not affect cell growth in primary rat osteoblast-enriched cultures.
An introduction to the free radical hypothesis in Parkinson's disease (1992)

Iron-induced oxidant stress has been implicated in the pathogenesis of Parkinson's disease. An increasing body of evidence now indicates that in Parkinson's disease the environment within the substantia nigra is conducive to the formation of cytotoxic free radicals and cell degeneration. Dopamine neurons may be particularly vulnerable because of the oxidative metabolism of dopamine and the potential of neuromelanin to promote the site-specific accumulation and reduction of iron. This hypothesis has attracted considerable attention because it opens the way for employing antioxidant strategies as possible neuroprotective treatment for Parkinson's disease. Although the concept is appealing, free radicals have not yet been proven to play a role in Parkinson's disease, and many important issues remain to be resolved before the oxidative hypothesis can ultimately be confirmed or refuted.