gebhart/patrepeval huggingface dataset:
Isolation of Markers for Chondro-osteogenic Differentiation Using cDNA Library Subtraction (1996)

To identify novel marker molecules associated with chondro-osteogenic differentiation, we have set up a differential screening system based on a cDNA library subtraction in organ cultures of prenatal mouse mandibular condyles. Differential screening of a cDNA library constructed from in vitro cultured condyles allowed the isolation of a novel gene, named E25. Full-length E25 cDNA is predicted to encode a type II integral membrane protein of 263 amino acid residues. In situ hybridization experiments show that E25 is expressed in the outer perichondrial rim of the postnatal mandibular condyle, which contains the proliferating progenitor cells, but not in the deeper layers of the condyle containing the more differentiated chondroblasts and chondrocytes. Other cartilagenous tissues and their perichondrium were negative. Strong in situ hybridization signals were also detected on bone trabeculae of mature bone in tooth germs and in hair follicles. Northern blot analysis showed strong expression in osteogenic tissues, such as neonatal mouse calvaria, paws, tail, and in skin. This expression profile suggests that E25 could be a useful marker for chondro-osteogenic differentiation. Homology searches of DNA databanks showed that E25 belongs to a novel multigene family, containing three members both in man and mouse. The mouse E25 gene locus (Itm2) was mapped to the X chromosome.
Development of transgenic rats producing human β-amyloid precursor protein as a model for Alzheimer's disease: Transgene and endogenous APP genes are regulated tissue-specifically (2008)

This manuscript describes the generation of APP-transgenic inbred Fischer 344 rats. These are the first human AD model rat lines generated by lentiviral infection. The APP21 rat line expresses high levels of human APP and could be a useful model for AD. Tissue-specific expression in the two transgenic rat lines and in wild-type rats contradicts our current understanding of APP gene regulation. Determination of the elements that are responsible for tissue-specific expression of APP may enable new treatment options for AD.
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing (2011)

Copy number variation (CNV) in the genome is a complex phenomenon, and not completely understood. We have developed a method, CNVnator, for CNV discovery and genotyping from read-depth (RD) analysis of personal genome sequencing. Our method is based on combining the established mean-shift approach with additional refinements (multiple-bandwidth partitioning and GC correction) to broaden the range of discovered CNVs. We calibrated CNVnator using the extensive validation performed by the 1000 Genomes Project. Because of this, we could use CNVnator for CNV discovery and genotyping in a population and characterization of atypical CNVs, such as de novo and multi-allelic events. Overall, for CNVs accessible by RD, CNVnator has high sensitivity (86%-96%), low false-discovery rate (3%-20%), high genotyping accuracy (93%-95%), and high resolution in breakpoint discovery (<200 bp in 90% of cases with high sequencing coverage). Furthermore, CNVnator is complementary in a straightforward way to split-read and read-pair approaches: It misses CNVs created by retrotransposable elements, but more than half of the validated CNVs that it identifies are not detected by split-read or read-pair. By genotyping CNVs in the CEPH, Yoruba, and Chinese-Japanese populations, we estimated that at least 11% of all CNV loci involve complex, multi-allelic events, a considerably higher estimate than reported earlier. Moreover, among these events, we observed cases with allele distribution strongly deviating from Hardy-Weinberg equilibrium, possibly implying selection on certain complex loci. Finally, by combining discovery and genotyping, we identified six potential de novo CNVs in two family trios.
Trichome Distribution in Arabidopsis thaliana and its Close Relative Arabidopsis lyrata: Molecular Analysis of the Candidate Gene GLABROUS1 (2001)

GLABROUS1 (GL1) belongs to the large family of MYB transcription factors and is known to play a central role in trichome initiation. We studied trichome distribution and the molecular variation of GL1 in 28 A. thaliana accessions. Trichome density on rosette leaves was highly variable among those accessions. On the molecular level, we detected substantial sequence variation in a 3-kb fragment which included the complete coding region of the GL1 locus (pi = 0.01). Phylogenetic analysis of GL1 indicates the presence of two diverged clades among 28 accessions. Using ANOVA, we show that the phenotypic variation in trichome density cannot be explained by the sequence divergence between the two phylogenetic lineages. Sequence analysis of wild-type Arabidopsis thaliana and Arabidopsis lyrata accessions indicates that all amino acid substitutions are located outside of the conserved helix-turn-helix DNA-binding domains R2 and R3. Using plants of A. thaliana and A. lyrata with either naturally occurring or ethyl methane sulfonate--induced glabrous phenotypes, we demonstrate that the last 14 C-terminal amino acids of the GL1 gene have no major impact on the initiation of trichomes.
Novel Mechanism for Gonadotropin-Releasing Hormone Neuronal Migration Involving Gas6/Ark Signaling to p38 Mitogen-Activated Protein Kinase (2002)

Gonadotropin-releasing hormone (GnRH) is the central regulator of the reproductive axis. Normal sexual maturation depends on the migration of GnRH neurons from the olfactory placode to the hypothalamus during development. Previously, we showed restricted expression of the membrane receptor adhesion-related kinase (Ark) in immortalized cell lines derived from migratory but not postmigratory GnRH neurons. In addition, Ark and GnRH transcripts were detected along the GnRH neuron migratory route in the E13 mouse cribriform plate. In the present study, we examined the role of Ark and its ligand, Gas6 (encoded by growth arrest-specific gene 6), in GnRH neuron migration. Gas6 stimulated lamellipodial extension, membrane ruffling, and chemotaxis of immortalized NLT GnRH neuronal cells via the Ark receptor. Gas6/Ark signaling promoted activation of the Rho family GTPase Rac, and adenoviral-mediated expression of dominant negative N17Rac abolished Gas6/Ark-induced actin cytoskeletal reorganization and migration of GnRH neuronal cells. In addition, p38 MAPK was activated downstream of Ark and Rac, and inhibition of p38 MAPK with either SB203580 or adenoviral dominant negative p38alpha also blocked Gas6/Ark-mediated migration. Finally, downstream of Rac and p38 mitogen-activated protein kinase (MAPK), Gas6/Ark signaling promoted activation of MAPK-activated protein kinase 2 and induced phosphorylation of HSP25, a known regulator of cortical actin remodeling. The data are the first to demonstrate a migratory signaling pathway downstream of Ark/Axl family receptors and suggest a previously unidentified role for p38 MAPK in neuronal migration. Furthermore, these studies support a potential role for Ark in the regulation of GnRH neuronal migration.
Do Measures of Body Fat Distribution Provide Information on the Risk of Type 2 Diabetes in Addition to Measures of General Obesity? (2003)

Throughout its range, BMI was an excellent predictor of type 2 diabetes risk in Pima Indians and was not significantly improved by combining it with other measures of general adiposity or body fat distribution.
[Genotypes of merozoite surface protein 2 of Plasmodium falciparum in different malaria endemic areas]. (2001)

There were obvious differences in the distribution and frequencies of MSP2 alleles between Yunnan and Hainan endemic areas. MSP2 is suitable to be used as a marker gene for the genotyping of P. falciparum infection.
Direct Measurement of a Tethered Ligand-Receptor Interaction Potential (1997)

Many biological recognition interactions involve ligands and receptors that are tethered rather than rigidly bound on a cell surface. A surface forces apparatus was used to directly measure the force-distance interaction between a polymer-tethered ligand and its receptor. At separations near the fully extended tether length, the ligands rapidly lock onto their binding sites, pulling the ligand and receptor together. The measured interaction potential and its dynamics can be modeled with standard theories of polymer and colloidal interactions.
Polymyxins facilitate entry into mammalian cells (2016)

Polymyxin B is an antibiotic used against multi-resistant gram negative infections, despite observed nephrotoxicity. Here we report the synthesis of functionalized derivatives of polymyxin B and its per-guanidinylated derivative in order to further explore the structural requirements necessary to facilitate uptake of the antibiotic into mammalian cells. We also investigate the possibility of using these novel scaffolds as molecular transporters. At nanomolar concentrations, both are capable of delivering large cargo (>300 kDa) into living cells. Their uptake depends exclusively on cell surface heparan sulfate. Mechanistic studies indicate these novel transporters are internalized through caveolae-mediated pathways and confocal microscopy show colocalization with lysosomes. The polymyxin-based transporters demonstrate cytosolic delivery through the delivery of a ribosome-inactivating toxin. Furthermore, the natural polymyxin scaffold can be incorporated into liposomes and enhance their intracellular uptake. In addition to demonstrating the ability of the polymyxin scaffold to facilitate internalization into mammalian cells, these observations suggest the potential use of polymyxin and guanidinopolymyxin for intracellular delivery.
T-cell recognition of ovarian cancer. (1993)

Tumor-specific cytotoxic T lymphocytes can be expanded from both TAL and TIL. However, TAL do not kill solid tumor as efficiently as TIL. This suggests the requirement of TIL, or a combination of TIL and TAL, for effective immunotherapy.
An Architecture for Wearable, Wireless, Smart Biosensors: The MoteCare Prototype (2006)

Part of designing any system requires the development of an architecture on which the system and subsequent implementations are based. The architecture will vary depending on the requirements. For a healthcare monitoring application the researchers developed a four-tiered architecture that consists of the following layers: user interface, process management, database and sensor network. In this paper, the authors present their layered architecture for remote healthcare monitoring of aged and infirm persons and illustrate its advantages by describing their latest prototype which is called MoteCare. They also discuss the direction the researchers intend to take for the development of their fourth prototype, paying particular attention to the use of open source databases, the issue of security in the development of mote sensor networks (MSN) and the advantages of linking such systems with wireless broadband to enable potential users to achieve more mobility options.
N-terminal connective tissue growth factor is a marker of the fibrotic phenotype in scleroderma (2005)

These results support a role for CTGF in scleroderma-associated fibrosis and the utility of N-terminal CTGF as a marker of fibrosis.
Conversion of a proton pair para order into 13C polarization by rf irradiation, for use in MRI (2005)

We describe the theory of production of hyperpolarized 13 C in small organic molecules, for use as molecular contrast agents in MRI, by a two-step process. The first is a catalyzed hydrogenation with para-hydrogen in a small dc magnetic field under rf irradiation, resulting in a molecular proton pair in the pure para state. The second step converts this para order into net hyperpolarization of a nearby carbon 13 through a sequence of rf pulses at the resonance frequencies of both spin species. The final theoretical polarization is close to unity. The whole process, which was successfully implemented, takes a few seconds.
Recent Progress in Studies on Autoantigens for Various Autoimmune Blistering Skin Diseases. (1995)

Autoimmune blistering skin diseases develop separation either between epidermal keratinocytes or dermo-epidermal junction. Recent studies have revealed that the autoantigens for these diseases are components of either the desmosome, the cell adhesion junction between keratinocytes, or the hemidesmosome complex, cell adhesion machinery at the dermo-epidermal junction. Thus, the major pemphigus antigens are desmogleins, one of desmosomal cadherins. Both the 230 kD and 180 kD bullous pemphigoid antigens are present in the hemidesmosome, and epidermal basement membrane zone-specific extracellular matrices, epiligrin and type VII collagen, are detected by sera of cicatricial pemphigoid and epidermolysis bullosa acquisita, respectively. Furthermore, animal model studies using newborn mice have revealed that these autoantibodies are really pathogenic and can induce blister formation by passive transfer into mice. Therefore, these skin diseases seem to be a typical model for various autoimmune diseases, for most of which the role of autoantibodies has not yet been revealed.
Peripheral Blood-Derived Mesenchymal Stromal Cells Promote Angiogenesis via Paracrine Stimulation of Vascular Endothelial Growth Factor Secretion in the Equine Model (2014)

Mesenchymal stromal cells (MSCs) have received much attention as a potential treatment of ischemic diseases, including ischemic tissue injury and cardiac failure. The beneficial effects of MSCs are thought to be mediated by their ability to provide proangiogenic factors, creating a favorable microenvironment that results in neovascularization and tissue regeneration. To study this in more detail and to explore the potential of the horse as a valuable translational model, the objectives of the present study were to examine the presence of angiogenic stimulating factors in the conditioned medium (CM) of peripheral blood-derived equine mesenchymal stromal cells (PB-MSCs) and to study their in vitro effect on angiogenesis-related endothelial cell (EC) behavior, including proliferation and vessel formation. Our salient findings were that CM from PB-MSCs contained significant levels of several proangiogenic factors. Furthermore, we found that CM could induce angiogenesis in equine vascular ECs and confirmed that endothelin-1, insulin growth factor binding protein 2, interleukin-8, and platelet-derived growth factor-AA, but not urokinase-type plasminogen activator, were responsible for this enhanced EC network formation by increasing the expression level of vascular endothelial growth factor-A, an important angiogenesis stimulator.
An endogenous peptide signal in Arabidopsis activates components of the innate immune response (2006)

Innate immunity is initiated in animals and plants through the recognition of a variety of pathogen-associated molecules that in animals are called pathogen-associated molecular patterns and in plants are called elicitors. Some plant pathogen-derived elicitors have been identified as peptides, but peptide elicitors derived from the plant itself that activate defensive genes against pathogens have not been previously identified. Here, we report the isolation and characterization of a 23-aa peptide from Arabidopsis, called AtPep1, which activates transcription of the defensive gene defensin (PDF1.2) and activates the synthesis of H(2)O(2), both being components of the innate immune response. The peptide is derived from a 92-aa precursor encoded within a small gene that is inducible by wounding, methyl jasmonate, and ethylene. Constitutive expression of the AtPep1 precursor gene PROPEP1 in transgenic Arabidopsis plants causes a constitutive transcription of PDF1.2. When grown in soil, the transgenic plants exhibited an increased root development compared with WT plants and an enhanced resistance toward the root pathogen Pythium irregulare. Six paralogs of PROPEP1 are present in Arabidopsis, and orthologs have been identified in species of several agriculturally important plant families, where they are of interest for their possible use in crop improvement.
Low field magnetic resonance images of polarized noble gases obtained with a dc superconducting quantum interference device (1998)

Using a low transition temperature superconducting quantum interference device as a detector, we have obtained magnetic resonance images of laser-polarized He3 gas and solid Xe129 at 4.2 K in magnetic fields as low as 0.54 mT (3He) and 1 mT (129Xe), corresponding to Larmor frequencies of 17.6 and 11.8 kHz, respectively. The experimental resolution of the images is ∼500 μm for He3 in the gas phase and ∼950 μm for Xe129 in the solid state.
Evaluation of Microbiological Screening Systems Using Dental Plaque Specimens from Young Children Aged 6–36 Months (2006)

Using cotton swab specimens of dental plaque from children aged 6-36 months, four commercial chairside tests for oral bacteria were evaluated by comparison with conventional selective culture: mitis salivarius kanamycin bacitracin agar for mutans streptococci and Rogosa SL agar for lactobacilli. Representative colonies of all isolates were identified by commercial identification kits. According to qualitative evaluations, all chairside tests for mutans streptococci were effective in our population. Those for lactobacilli were not as effective, due mainly to a high recovery of yeast contaminants.
Down-regulation of cdc2 in senescent human and hamster cells. (1991)

Senescent cells fail to respond to serum-induced signals for DNA synthesis. Because a central role for the p34cdc2 protein kinase is postulated in control of the cell cycle, we examined the status of this kinase in senescent cells and other growth-arrested cells. In growing human and Syrian hamster fibroblasts, three 35S-labeled proteins of 34-36 kDa were immunoprecipitated with p34cdc2 antiserum. Only the two slower migrating forms were phosphorylated as determined by 32P labelling. In senescent cells, which failed to incorporate [3H]thymidine, no p34cdc2 protein was synthesized and very little or no cdc2 mRNA was observed. When maintained for 48 h in 0.5% serum, young cells also retained only marginal cdc2 expression. After stimulation of low serum-arrested cells by addition of 10% serum, a time-dependent increase of cdc2 mRNA was observed, whereas serum stimulation of senescent cells did not increase cdc2 mRNA. In contrast to senescent and low serum-arrested cells, cdc2 mRNA was expressed at normal levels in cells partially growth arrested by isoleucine deficiency in G1, by aphidicolin at G1-S, by etoposide in G2, or by Colcemid in the M phase of the cell cycle, indicating that cdc2 down-regulation does not always occur upon growth arrest. Following transfection of a plasmid containing the human CDC2 gene into hamster cells, expression of human cdc2 failed to overcome the block to DNA synthesis in senescent cells. Although p34cdc2 was synthesized in the transfected cells, the multiple phosphorylated forms of the proteins were not observed. Taken together, these data support the concept that a chain of events leads to senescence. While p34cdc2 kinase may be one of the critical elements, other cell cycle controls are also involved.
Facile meso to rac Isomerization of the Bis-Planar Chiral Ferrocenyldiphosphine Bis(1-(diphenylphosphino)-η5-indenyl)iron(II) (2002)

The meso isomer of the ferrocenyldiphosphine bis(1-(diphenylphosphino)-η5-indenyl)iron(II) isomerizes to the rac isomer overnight in tetrahydrofuran at room temperature. The isomerization is accelerated by salts but does not occur in chloroform solvent.
Effect of Combined Immune Checkpoint Inhibition vs Best Supportive Care Alone in Patients With Advanced Colorectal Cancer (2020)

ClinicalTrials.gov Identifier: NCT02870920.
Planning Wildfire Protection for the Santa Monica Mountains: An Economic Analysis of Alternatives (1978)

This paper demonstrates how formal quantitative methods can be used in planning fire protection policy for a particular geographical area. As an example, it presents an economic analysis of three wildland fire protection policies for the Santa Monica Mountains, northwest of Los Angeles. The alternatives are augmented programs of (1) fire prevention and initial attack; (2) fuel break systems; and (3) fire-resistance roofs and brush clearance around homes. Quantitative models are developed to determine the various fire-related costa and losses that would be incurred under each policy. It is shown that the most attractive alternative fronithe standpoint of minimising total expected cost plus loss to society is the implementation of fire resis?tant roofs and brush clearance around homes. Economic incentives are suggested for carrying out such a policy.
Infusion of CD133+ Bone Marrow–Derived Stem Cells After Selective Portal Vein Embolization Enhances Functional Hepatic Reserves After Extended Right Hepatectomy (2011)

Promising data from this survival analysis suggest that PVE, together with CD133+ BMSC pretreatment, could positively impact overall outcomes after extended right hepatectomy.
Two-stage power conversion architecture for an LED driver circuit (2013)

This paper presents a merged-two-stage circuit topology suitable for efficient LED drivers operating from either wide-range dc input voltage or ac line voltage. This two-stage topology is based on a soft-charged switched-capacitor pre-regulator/transformation stage and a high-frequency magnetic regulator stage. Soft charging of the switched capacitor circuit, zero voltage switching of the high-frequency regulator circuit, and time-based indirect scale current control are used to maintain high efficiency, high power density, and high power factor. Two implementations of the proposed architecture are demonstrated: a wide input voltage range dc-dc converter and a line interfaced ac-dc converter. The dc-dc converter shows 85-95% efficiency at 20 W power across 25-200 V input voltage range, and the ac-dc converter achieves 88% efficiency with 0.93 power factor at 8.4 W average power.
Changes in DNA Methylation in Neoplasia: Pathophysiology and Therapeutic Implications (2001)

Methylation of DNA is a biochemical modification that can influence gene expression and is involved in inactivating one of the two X chromosomes in women. Evidence that has accumulated in the past 10 years suggests that cancer cells usurp this physiologic mechanism and use it to their benefit by inactivating tumor suppressor genes and related proteins. However, the primary structure of the affected proteins remains intact; reversal of abnormalities in DNA methylation may therefore restore the tumor-suppressive function of these genes and provide a novel approach to cancer therapy. Two demethylating drugs, 5-azacytidine and 5-aza-deoxycytidine, are currently being tested in clinical trials, and several others are in preclinical development. In this article, the biological rationale for targeting aberrant methylation in cancer therapy is reviewed and completed phase I and II trials of this approach, some of which show promise for treatment of hematologic malignancies, are summarized.
The roles of oxidation state, Lewis acid cocatalyst and solvent polarity in activating titanium compounds for olefin polymerization (1995)

Abstract The polymerization activity of the following three catalyst systems towards ethylene has been investigated and compared: 1) methyltitanocene chloride‐Me 2 AlCl 2) η 3 ‐allyltitanocene‐Me 2 AlCl and 3) titanium dichloride tetrahydrofuranate‐Me 2 AlCl. The first two catalysts formed homogeneous phases and produced linear polymer; the last catalyst functioned in a heterogeneous medium and formed crosslinked polymer. The titanium(IV) catalyst was about 30 times more active than the titanium(III) system and the titanium(II) catalyst on MgCl 2 could be made 8 times more active than the titanium(IV) system. A novel mechanism is proposed to explain the behavior and activity of the titanium(II) system.