gebhart/patrepeval huggingface dataset:
Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication (2006)

Chromatin methylation is necessary for stable repression of gene expression during mammalian development. During cell division, DNMT1 maintains the DNA methylation pattern of the newly synthesized daughter strand, while G9a methylates H3K9. Here, DNMT1 is shown to directly bind G9a both in vivo and in vitro and to colocalize in the nucleus during DNA replication. The complex of DNMT1 and G9a colocalizes with dimethylated H3K9 (H3K9me2) at replication foci. Similarly, another H3K9 histone methyltransferase, SUV39H1, colocalizes with DNMT1 on heterochromatic regions of the nucleoli exclusively before cell division. Both DNMT1 and G9a are loaded onto the chromatin simultaneously in a ternary complex with loading factor PCNA during chromatin replication. Small interfering RNA (siRNA) knockdown of DNMT1 impairs DNA methylation, G9a loading, and H3K9 methylation on chromatin and rDNA repeats, confirming DNMT1 as the primary loading factor. Additionally, the complex of DNMT1 and G9a led to enhanced DNA and histone methylation of in vitro assembled chromatin substrates. Thus, direct cooperation between DNMT1 and G9a provides a mechanism of coordinated DNA and H3K9 methylation during cell division.
Gene expression profiling spares early breast cancer patients from adjuvant therapy: derived and validated in two population-based cohorts (2005)

We have identified discriminatory gene expression signatures working both on untreated and systematically treated primary breast cancer patients with the potential to spare them from adjuvant therapy.
Hypothalamic control of energy metabolism via the autonomic nervous system (2010)

The hypothalamic control of hepatic glucose production is an evident aspect of energy homeostasis. In addition to the control of glucose metabolism by the circadian timing system, the hypothalamus also serves as a key relay center for (humoral) feedback information from the periphery, with the important role for hypothalamic leptin receptors as a striking example. The hypothalamic biological clock uses its projections to the preautonomic hypothalamic neurons to control the daily rhythms in plasma glucose concentration, glucose uptake, and insulin sensitivity. Euglycemic, hyperinsulinemic clamp experiments combined with either sympathetic-, parasympathetic-, or sham-denervations of the autonomic input to the liver have further delineated the hypothalamic pathways that mediate the control of the circadian timing system over glucose metabolism. In addition, these experiments clearly showed both that next to the biological clock peripheral hormones may "use" the preautonomic neurons in the hypothalamus to affect hepatic glucose metabolism, and that similar pathways may be involved in the control of lipid metabolism in liver and white adipose tissue.
The surface glycoprotein Thy-1 is excluded from growing axons during development: a study of the expression of Thy-1 during axogenesis in hippocampus and hindbrain (1991)

Thy-1 is a developmentally regulated surface glycoprotein expressed on a number of tissues, including nerve where it is a major surface component of mature neurons. During neural development in the rat and mouse, expression of Thy-1 protein does not necessarily follow appearance of its mRNA, but additionally requires completion of the initial phase of axonal growth. Where there is a substantial lag phase between initial elongation and final axonal outgrowth into a terminal field (e.g. pontine projection to the cerebellum), Thy-1 protein appears at the cell body and dendrites of the neurons, but is excluded from their axons until the terminal phase of axonal growth is completed. In the more complex case of the vestibular ganglion neurons, whose axons project primarily to the vestibular nuclei in the brainstem before birth, and then 1-2 weeks later into the cerebellum, Thy-1 enters the proximal axonal regions where growth is completed, but not the distal growing ends. Thus complex controls govern the initial expression and distribution of Thy-1 so as to exclude it from growing regions of axons.
The Translation Initiation Factor eIF-4E Binds to a Common Motif Shared by the Translation Factor eIF-4γ and the Translational Repressors 4E-Binding Proteins (1995)

Eukaryotic translation initiation factor 4E (eIF-4E), which possesses cap-binding activity, functions in the recruitment of mRNA to polysomes as part of a three-subunit complex, eIF-4F (cap-binding complex). eIF-4E is the least abundant of all translation initiation factors and a target of growth regulatory pathways. Recently, two human cDNAs encoding novel eIF-4E-binding proteins (4E-BPs) which function as repressors of cap-dependent translation have been cloned. Their interaction with eIF-4E is negatively regulated by phosphorylation in response to cell treatment with insulin or growth factors. The present study aimed to characterize the molecular interactions between eIF-4E and the other subunits of eIF-4F and to similarly characterize the molecular interactions between eIF-4E and the 4E-BPs. A 49-amino-acid region of eIF-4 gamma, located in the N-terminal side of the site of cleavage by Picornaviridae protease 2A, was found to be sufficient for interacting with eIF-4E. Analysis of deletion mutants in this region led to the identification of a 12-amino-acid sequence conserved between mammals and Saccharomyces cerevisiae that is critical for the interaction with eIF-4E. A similar motif is found in the amino acid sequence of the 4E-BPs, and point mutations in this motif abolish the interaction with eIF-4E. These results shed light on the mechanisms of eIF-4F assembly and on the translational regulation by insulin and growth factors.
Downregulation of CD1 Marks Acquisition of Functional Maturation of Human Thymocytes and Defines a Control Point in Late Stages of Human T Cell Development (1997)

We have investigated whether in the human thymus transition of CD4+CD8+ double positive (DP) to CD4+ or CD8+ single positive (SP) cells is sufficient for generation of functional immunocompetent T cells. Using the capacity of thymocytes to expand in vitro in response to PHA and IL-2 as a criterion for functional maturity, we found that functional maturity of both SP and DP thymocytes correlates with downregulation of CD1a. CD1a- cells with a persistent DP phenotype were also found in neonatal cord blood, suggesting that at least a proportion of mature DP cells can emigrate from the thymus. The requirements for generating functional T cells were investigated in a hybrid human/mouse fetal thymic organ culture. MHC class II-positive, but not MHC class II-negative, mouse thymic microenvironments support differentiation of human progenitors into TCR alpha beta+CD4+ SP cells, indicating that mouse MHC class II can positively select TCR alpha beta +CD4+ SP human cells. Strikingly, these SP are arrested in the CD1a+ stage and could not be expanded in vitro with PHA and IL-2. CD1a+CD4+ SP thymocytes do not represent an end stage population because purified CD1a+CD4+ SP thymocytes differentiate to expandable CD1a- cells upon cocultivation with human thymic stromal cells. Taken together these data indicate that when CD1a+ DP TCR alpha beta low cells mature, these cells interact with MHC, but that an additional, apparently species-specific, signal is required for downregulation of CD1a to generate functional mature TCR alpha beta + cells.
Cytogenetic analysis of 363 consecutively ascertained diffuse large B-cell lymphomas (1999)

Cytogenetic analysis was performed on 363 biopsy specimens with histologically confirmed diffuse large B-cell lymphoma (DLBCL), consecutively ascertained at the Memorial Sloan-Kettering Cancer Center, New York, between 1984 and 1994. Among 248 samples successfully karyotyped, clonal chromosomal abnormalities were noted in 215 (87%). The salient cytogenetic features of DLBCL from this analysis comprised the following. Breakpoints clustered, in decreasing frequency, at 10 recurring sites: 14q32, 18q21, 1q21, 3q27, 1p36, 8q24, 3p21, 6q21, 1p22, and 22q11. Of these, deletion breaks affecting bands 3p2 and 1p22 and translocation breaks affecting bands 14q32, 3q27, and 1q2 were frequent and distinctive for this subset of lymphomas. Translocations affecting band 14q32 were noted in 110 cases (51%) of which 42 (20%) had t(14;18)(q32;q21), 21 (10%) had t(8;14)(q24;q32) or t(8;22)(q24;q11), 14 (6.5%) had t(3;14)(q27;q32) or t(3;22)(q27;q11), and 33 (15%) had other rearrangements of 14q32. Among 144 new translocations detected in the entire group, the breakpoints in 19 were recurrent and clustered at three sites: 1q21, 3q27, and 14q32. Regions of common cytogenetic deletions were identified at 11 sites, 1p36, 1p33-34, 1p31, 1q32, 3p25-26, 3p21, 3q21, 6q15, 6q21, 6q23-24, and 7q32, suggesting possible loss of candidate tumor suppressor genes associated with DLBCL development. Of these, only those at 6q21, 6q23, and 7q32 have previously been described in lymphoid neoplasms. The group of DLBCL with translocations affecting band 14q32 showed a significantly different pattern of additional cytogenetic changes compared to the group lacking such translocation. This new comprehensive cytogenetic characterization provides the basis for investigations aimed at identifying molecular mechanisms as well as the clinical impact of cytogenetic changes in DLBCL.
Soybean oil, blackcurrant seed oil, medium-chain triglycerides, and plasma phospholipid fatty acids of stressed patients. (1993)

Thirty-six adult severe head injury and cerebral stroke patients in four intensive-care units were randomized to receive one of three enteral diets for 21 days. These diets, which supplied 45% of calories from fat, differed only in lipid composition. Diet A was comprised of 100% soybean oil, diet B contained a 50:50 (wt/wt) mixture of soybean oil and medium-chain triglycerides (MCTs), and diet C contained 42.5% MCT, 50% soybean oil, and 7.5% blackcurrant seed oils. Plasma phosphatidylcholine and fatty acid composition of plasma total phospholipids were determined before initiating treatment (day 0) and weekly throughout the study. Results indicated that at the start of the study, all patients had low linoleic acid (18:2 omega 6) levels compared with healthy subjects. Emulsion A disturbed the balance between several fatty acids of the omega 6 series, as exemplified by the significant increase in 18:2 omega 6 proportions. In contrast, both emulsions B and C introduced a less-pronounced rise in 18:2 omega 6 associated for emulsion C with a significant increase in dihomo-gamma-linolenic acid (20:3 omega 6) and docosapentaenoic acid (22:5 omega 3) in plasma phospholipids. Furthermore, 18:3 omega 6 change was significantly different between groups A and C and that of 20:3 omega 6 between group A and both groups B and C. Throughout the study, arachidonic acid (20:4 omega 6) exhibited remarkable steady-state levels regardless of the diet. This study shows that providing the injured body with high amounts of 18:2 omega 6 does not lead to high levels of its upper derivatives in plasma phospholipids.(ABSTRACT TRUNCATED AT 250 WORDS)
Efficacy of Severe Acute Respiratory Syndrome Vaccine Based on a Nonhuman Primate Adenovirus in the Presence of Immunity Against Human Adenovirus (2006)

Replication-deficient human adenovirus type 5 (AdH5) vectors can induce strong transgene product-specific cellular and humoral responses. However, many adult humans have neutralizing antibodies (NAbs) against AdH5 as a result of natural infection with this virus. Therefore, a chimpanzee adenovirus C7 (AdC7) vector was developed to circumvent interference by preexisting immunity to AdH5. This study evaluated the impact of preexisting immunity to human adenovirus on the efficacy of adenovirus-based vaccines against the coronavirus that causes severe acute respiratory syndrome (SARS-CoV). Efficacy was assessed after intramuscular injection of the vector into mice and was measured as the frequency of SARS-CoV-specific T cells and NAbs against SARS-CoV. Immunogenicity of the AdH5-based vaccine was significantly attenuated or completely abolished when the preexisting anti-AdH5 NAb titer was higher than 40. Because 27% of human serum samples from the United States tested so far have an anti-AdH5 NAb titer higher than 40, our results suggested that a significant percentage of humans with preexisting anti-AdH5 immunity would not be candidates for vaccination with an AdH5-based genetic vaccine. In contrast, preexisting anti-AdH5 NAbs have a minimal effect on the potency of the AdC7-based genetic vaccine. Taken together, our studies warrant the further development of AdC7 as a vaccine carrier for human trials.
The Pulmonary Collectins and Surfactant Metabolism (2001)

Lung surfactant covers and stabilizes a large, delicate surface at the interface between the host and the environment. The surfactant system is placed at risk by a number of environmental challenges such as inflammation, infection, or oxidant stress, and perhaps not surprisingly, it demonstrates adaptive changes in metabolism in response to alterations in the alveolar microenvironment. Recent experiments have shown that certain components of the surfactant system are active participants in the regulation of the alveolar response to a wide variety of environmental challenges. These components are capable not only of maintaining a low interfacial surface tension but also of amplifying or dampening inflammatory responses. These observations suggest that regulatory molecules are capable of both sensing the environment of the alveolus and providing feedback to the cells regulating surfactant synthesis, secretion, alveolar conversion, and clearance. In this review we examine the evidence from in vitro systems and gene-targeted mice that two surfactant-associated collectins (SP-A and SP-D) may serve in these roles and help modify surfactant homeostasis as part of a coordinated host response to environmental challenges.
Survival and Chipping of Zirconia‐Based and Metal–Ceramic Implant‐Supported Single Crowns (2011)

Chipping was found to be more frequent for all-ceramic implant-supported single crowns. If the reasons for the vulnerability of all-ceramic crowns remain unknown, implants with all-ceramic single crowns should generally be recommended with care.
Roles of MCP-1 in development of HIV-dementia (2008)

The encephalopathy caused by HIV, known clinically as HIV-associated dementia (HAD) and pathologically as HIV encephalitis (HIVE), results from intense infiltration of mononuclear cells, productive replication of the virus in monocyte-derived macrophages/microglia, abortive replication in astrocytes and activation of macrophages/microglia and astrocytes leading to neuronal degeneration in the brains of infected persons. Recent findings have suggested that development of HAD is based more on the activation process than on direct evidence of virus replication in the brain. Since HAD is based on the encephalitic process, major studies have been directed to the mechanisms regulating the inflammatory process. Monocyte chemoattractant protein 1, MCP-1, is a chemokine that is implicated in this process and also in the development of activation in the brain. In this review, we have attempted to identify mechanisms that induce expression of MCP-1 in the brain and the role that it plays in recruitment of mononuclear cells from blood to brain and in the activation processes of inflammatory and neural cells that lead to development of degenerative changes in the neuronal population.
A chemical‐regulated inducible RNAi system in plants (2003)

Constitutive expression of an intron-containing self-complementary 'hairpin' RNA (ihpRNA) has recently been shown to efficiently silence target genes in transgenic plants. However, this technique cannot be applied to genes whose silencing may block plant regeneration or result in embryo lethality. To obviate these potential problems, we have used a chemical-inducible Cre/loxP (CLX) recombination system to trigger the expression of an intron-containing inverted-repeat RNA (RNAi) in plants. A detailed characterization of the inducible RNAi system in transgenic Arabidopsis thaliana and Nicotiana benthamiana plants demonstrated that this system is stringently controlled. Moreover, it can be used to induce silencing of both transgenes and endogenous genes at different developmental stages and at high efficiency and without any detectable secondary affects. In addition to inducing complete silencing, the RNAi can be produced at various times after germination to initiate and obtain different degrees of gene silencing. Upon induction, transgenic plants with genetic chimera were obtained as demonstrated by PCR analysis. Such chimeric plants may provide a useful system to study signaling mechanisms of gene silencing in Arabidopsis as well as other cases of long-distance signaling without grafting. The merits of using the inducible CLX system for RNAi expression are discussed.
Stereospecific Ring-Opening Metathesis Polymerization of Cycloolefins Using Novel Molybdenum and Tungsten Complexes Having Biphenolate Ligands. Development of Crystalline Hydrogenated Poly(endo-dicyclopentadiene) and Poly(norbornene) (2003)

Novel molybdenum- and tungsten-based catalysts induced stereospecific ring-opening metathesis polymerization (ROMP) of cycloolefins to produce a new class of crystalline polymers. Various monomeric molybdenum(VI) and tungsten(VI) complexes of the general formula M(=O)(O−Ar)4 (M = Mo or W; (O−Ar)4 is two biphenolate or four phenolate ligands) were prepared. These catalysts exhibited moderate ROMP activity in the presence of cocatalyst such as n-BuLi and Et3Al. The molybdenum and tungsten complexes bearing substituted biphenolate ligands such as oxomolybdenum(VI) bis(racemic-5,5‘,6,6‘-tertamethyl-3,3‘-di-tert-butyl-1,1‘-biphenyl-2,2‘-diolate) promoted cis and isospecific ROMP of endo-dicyclopentadiene (cis > 90% and meso > 95%). The novel ternary and quarternary catalysts such as MoOCl4−biphenolate−n-BuLi (1:2:2) were developed as a new useful methodology to control the stereoselectivity of the ROMP. Hydrogenation of the cis-isotactic poly(endo-dicyclopentadiene)s and poly(norbornene)s provided novel crystalline polymers with high melting points (295 °C, ΔH = 50 J/g; 175 °C, ΔH = 60 J/g, respectively), which can be regarded as a new class of crystalline polymers.
Gel electrophoresis (2007)

The aim of this project is to develop a simple system for the teaching and demonstration of DNA gel electrophoresis. DNA gel electrophoresis requires the use of specialized apparatus, toxic reagents, expensive agarose gel, and DNA samples, as well as a considerable amount of valuable classroom time to complete. A systematic evaluation of suitable alternative materials and components for the simulation of DNA gel electrophoresis was undertaken. A tried and tested set of combinations is presented here for educators to use in hands-on classroom teaching, which does not require DNA, agarose, or Tris-borate-EDTA buffer. The use of common biological stains in place of DNA samples, agar-agar-based gels, and weak electrolyte solutions provides a simple, inexpensive, and highly reproducible system that is adaptable to instructional needs. The migration of multicolored bands during electrophoresis provides an intuitive, compelling demonstration of the concept of electrophoresis.
Load-sensitive measures may overestimate global systolic function in the presence of left ventricular hypertrophy: a comparison with load-insensitive measures (2005)

Transgenic animal models have provided a vital insight into the pathogenesis of cardiovascular disease, but functional cardiac assessment is often limited by high heart rates and small heart size. We hypothesized that in the presence of concentric left ventricular (LV) hypertrophy (LVH), load-sensitive measures of contractility may be misinterpreted as overestimating global cardiac function, because the normal function of excess sarcomeres may displace a greater volume of blood during contraction. Conductance catheter technology was used to evaluate pressure-volume (P-V) relationships as a load-insensitive method of assessing cardiac function in vivo in 18-wk-old heterozygous (mRen-2)27 transgenic rats (a model of LVH), compared with age-matched Sprague-Dawley (SD) controls. Anesthetized animals underwent echocardiography followed by P-V loop analysis. Blood pressure, body weight, and heart rate were higher in the Ren-2 rats (P < 0.05). Load-sensitive measures of systolic function, including fractional area change, fractional shortening, ejection fraction, and positive peak rate of LV pressure development, were greater in the Ren-2 than control animals (P < 0.05). Load-insensitive measures of systolic function, including the preload recruitable stroke work relationship and the end-systolic P-V relationship, were not different between Ren-2 and SD rats. Regional wall motion assessed by circumferential shortening velocity suggested enhanced circumferential fiber contractility in the Ren-2 rats (P = 0.02), but tissue Doppler imaging, used to assess longitudinal function, was not different between groups. Although conventional measures suggested enhanced systolic function in the Ren-2 rat, load-insensitive measures of contractility were not different between Ren-2 and SD animals. These findings suggest that the normal range of values for load-sensitive indexes of contractility needs to be altered according to the degree of LVH. To accurately identify changes in systolic function, we suggest that a combination of echocardiography with assessment of load-insensitive measures be used routinely.
Mitotic recombination of chromosome 17 in astrocytomas. (1989)

Allelic combinations at seven loci on human chromosome 17 defined by restriction fragment length polymorphisms were determined in tumor and normal tissues from 35 patients with gliomas. Loss of constitutional heterozygosity at one or more of these loci was observed in 8 of the 24 tumors displaying astrocytic differentiation and in the single primitive neuroectodermal tumor examined. The astrocytomas showing these losses included examples of each adult malignancy grade of the disease, including glioblastoma (malignancy grade IV), and seven of them demonstrated concurrent maintenance of heterozygosity for at least one chromosome 17 locus. Determination of allele dosage together with the genotypic data indicated that the tumor chromosomes 17 were derived by mitotic recombination in 7 of the 9 cases with shared homozygosity of the region 17p11.2-pter in all cases. In contrast, tumors of oligodendrocytic, ependymal, or mixed cellular differentiation did not exhibit loss of alleles at any of the loci examined. These data suggest that the somatic attainment of homozygosity for loci on chromosome 17p is frequently associated with the oncogenesis of central nervous system tumors, particularly those showing solely astrocytic differentiation, and that mitotic recombination mapping is a useful approach towards the subregional localization of a locus whose rearrangement is involved in this disease.