gebhart/patrepeval huggingface dataset:
Progenitor Cells From Dental Follicle Are Able to Form Cementum Matrix In Vivo (2002)

To address the molecular mechanisms of cementogenesis, we have isolated dental follicle cells and examined them to see if they contain cementoblast progenitors. Dental follicle tissue was dissected from the root surface of bovine tooth germ and cells were released by digestion with bacterial collagenase. The released cells were maintained as a bovine dental follicle cells (BDFC). To elucidate the differentiation capacity of BDFC, they were transplanted into severe combined immunodeficiency (SCID) mice for 4 weeks. Transplanted BDFC formed cementumlike matrix; in contrast, bovine alveolar osteoblast (BAOB) transplants formed bonelike matrix, and bovine periodontal ligament cells (BPDL) formed a small amount of the cementumlike matrix. Immunohistochemical analysis showed that cementumlike matrix was positive for anti-cementum attachment protein monoclonal antibody, whereas bone-like matrix was negative. These results indicated that the BDFC contained cementoblast progenitors that were able to differentiate to cementoblasts in vivo. They also indicated that the BDFC are phenotypically distinct from BAOB and BPDL, and provide a useful model for investigating molecular mechanisms of cementogenesis.
Human let-7 stem-loop precursors harbor features of RNase III cleavage products (2003)

The bidentate RNase III Dicer cleaves microRNA precursors to generate the 21-23 nt long mature RNAs. These precursors are 60-80 nt long, they fold into a characteristic stem-loop structure and they are generated by an unknown mechanism. To gain insights into the biogenesis of microRNAs, we have characterized the precise 5' and 3' ends of the let-7 precursors in human cells. We show that they harbor a 5'-phosphate and a 3'-OH and that, remarkably, they contain a 1-4 nt 3' overhang. These features are characteristic of RNase III cleavage products. Since these precursors are present in both the nucleus and the cytoplasm of human cells, our results suggest that they are generated in the nucleus by the nuclear RNase III. Additionally, these precursors fit the minihelix export motif and are thus likely exported by this pathway.
Protein Kinase C βII Specifically Binds to and Is Activated by F-actin (1996)

The two most closely related isoenzymes of protein kinase C (PKC), PKC betaI and betaII, are distinct but highly homologous isoenzymes derived via alternative splicing of the same gene product. In this study, PKC betaII, but not PKC betaI, translocated to the actin cytoskeleton upon stimulation of cells with phorbol esters. In cells, antibodies to PKC betaII, but not to PKC betaI, co-immunoprecipitated actin. Using an actin-binding co-sedimentation assay, we show in vitro that PKC betaII, but not PKC betaI, binds to actin specifically. This binding was inhibited by peptides based on sequences unique to PKC betaII; thus defining an actin-binding site in PKC betaII that is not present in PKC betaI. The binding of PKC betaII to actin was not inhibited by kinase inhibitors of PKC (sphingosine and staurosporine), suggesting that prior activation and/or substrate phosphorylation are not required for the interaction of PKC betaII with actin. On the other hand, the interaction of PKC betaII with actin resulted in marked enhancement of autophosphorylation of PKC betaII and in an alteration in substrate specificity. These studies serve to define a novel functional domain in the carboxyl-terminal region of PKC beta, which is involved in directing isoenzyme-specific protein-protein interactions, and consequently, isoenzyme-specific functions in vivo.
Centrosome and microtubules behavior in the cytoplasts. (1995)

After enucleation of PK (pig kidney embryo) cells using cytochalasin D centrioles remained approximately in 80% of cytoplasts. Some cytoplasts retained a single centriole. 14-16 h after enucleation large secondary lysosomes and lipid droplets were evident around the centrosome of many cytoplasts. In part of the cytoplasts replicating centrioles were found 16 h after enucleation. Ouabain treatment (1 mM, 30 min) of the cytoplasts resulted in the appearance of mainly perpendicular orientation of mother centrioles relative to the substrate surface. Reconstruction of microtubule pattern around the centrosome showed that a total of approximately 15 microtubules were attached in the centrosome of normal cells and twice more than that in cytoplasts. Microtubules in the cytoplasts were more resistant to nocodazole induced depolymerization. We suggest that microtubule instability is modulated by regulatory effector that is under direct nucleus control.
ChemInform Abstract: PREPARATIVE CARBOCATION CHEMISTRY PART 6, ADVANTAGEOUS STABLE AND SOLUBLE FLUOROPHOSPHATE SALTS, TRIALKYLOXONIUM, TRIALKYLCARBOXONIUM, AND DIALKOXYCARBENIUM HEXAFLUOROPHOSPHATES (1973)

Abstract Trimethyloxonium‐ (IIIa) und Triäthyloxonium‐hexafluorophosphat (IIIb), die im Vergleich zu den Meerwein′schen Tetrafluoroboraten stabiler und löslicher sind, können in guten Ausbeuten aus den Orthoameisensäureestern (I) und den entsprechenden Dialkyläther‐Phosphorpentafluorid‐Komplexen (II) gewonnen werden.
Production of Human Monoclonal and Polyclonal Antibodies in TransChromo Animals (2002)

We have developed TransChromo (TC) technology, which enables the introduction of megabase-sized segments of DNA into cells. We have used this approach to derive mice that carry megabases of human DNA by the use of a human chromosome fragment (HCF) as a vector. TC technology has been applied to the construction of the TC Mouse,trade mark which incorporates entire human immunoglobulin (hIg) loci. TC Mouse expresses a fully diverse repertoire of hIgs, including all the subclasses of IgGs (IgG1-G4). Immunization of the TC Mouse with various human antigens produced antibody responses comprised of human antibodies. Furthermore, it was possible to obtain hybridoma clones expressing fully human antibodies specific for the target human antigen. However, because of the instability of the Igkappa locus-bearing HCF2, the efficiency of hybridoma production was less than one-tenth of that observed in normal mice. An instant solution to this problem was to cross-breed the Kirin TC Mouse carrying the HCF14, which was stable in mouse cells, with the Medarex YAC-transgenic mouse carrying about 50% of the hIgVkappa gene segments as a region that is stably integrated into the mouse genome. The resulting mouse, dubbed the KM Mouse, performed as well as normal mice with regard to immune responsiveness and efficiency of hybridoma production. Another application of TC technology is the production of polyclonal antibodies in large animals such as chickens and cows. To test the efficacy of human polyclonal antibodies derived from TC animals, feasibility studies were performed using antisera and purified gamma-globulin from TC mice immunized with Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus (MRSA), or Japanese encephalitis virus (JEV). The TC mouse-derived antisera and gamma-globulin showed a much higher titer and efficacy in terms of the neutralizing activity of the pathogens in vitro and in vivo than either human serum or gamma-globulin prepared from human blood.
Trading and Exchanges: Market Microstructure for Practitioners (2002)

Describes in plain words how markets work; how governments and exchanges regulate them; and how traders create liquidity,volatility, informative prices, trading profits, and transaction costs. It identifies the trading strategies that make markets liquid, produce prices that reflect information about fundamental values, and allow some traders to consistently profit while others lose. Since the success of trading strategies depends on the trading rules that markets use, the text also considers the regulatory forces that create and enforce trading rules.
Information systems research at George Mason University (1997)

George Mason University began as an independent state university in 1972. Its development has been marked by rapid growth and innovative planning, resulting in an enrollment of more than 24,000 students in 1997. It is located in Fairfax, Virginia—about fifteen miles southwest of Washington, DC—near many governmental agencies and industrial firms specializing in information-intensive products and services. Information and Software Systems Engineering (ISSE) is one of six departments in GMU's School of Information Technology and Engineering (SITE). Established in 1985, SITE has approximately 90 faculty and ISSE has 13 full time faculty. ISSE is a rapidly growing department with wide-ranging teaching and research interests. The department offers no undergraduate degree programs and Master of Science degrees in Information Systems (MSIS) and Software Engineering (SWSE). MSIS has about 800 students and the SWSE has approximately 400 students enrolled. The MSIS program graduates about 120 students and the SWSE program awards 40 degrees per year. ISSE faculty participate in the SITE doctoral program in Information Technology. ISSE Faculty chair the committees of more than one third of the doctoral students in the SITE program, which currently graduates about 30 PhDs per year. Two research centers are associated with the department: The Center for Secure Information Systems (Sushil Jajodia, Director) and the Center for Information Systems Integration and Evolution (Larry Kerschberg, Director). Departmental research in information systems is supported by grants and contracts from several sources. The following awards have been received so far for the academic year 1997-1998 and beyond: Knowledge Rovers: A Family of Intelligent Software Agents for Logistics for the Warrior. Defense Advanced Research Projects Agency (co-PIs: Kerschberg, Gomaa, Jajodia, Motro) Electronic Commerce for Logistics, Teaming Agreement with American Management Systems for DARPA BAA 95-25 Logistics Research and Development (co-PIs: Kerschberg, Gomaa, Jajodia, Motro) Linear Constraint Databases, NSF Research Initiation Award (PI: Brodsky) Linear Constraint Programming, ONR (co-PI: Brodsky with late Kannelakis (PI), Van Hentenryck, and Lassez) Towards Expressive and Efficient Queries on Sequenced Data, NSF Research Initiation Award (PI: Wang) Supporting Multiple time granularities in Query Evaluation and Data Mining, NSF (co-PIs: Jajodia, Wang) Fine Granularity Access Controls in World Wide Web, NSA (PI: Jajodia) Information Flow Control in Object-Oriented Systems NSA (PI: Jajodia) Exploring Steganography: Seeing the Unseen, NSA (PI: Jajodia) Trusted Recovery from Information Attacks, Rome Laboratory (co-PIs: Jajodia, Ammann) A Unified Framework for Supporting Multiple Access Control Policies, DARPA (PI: Jajodia) The remainder of this article provides a brief overview of our research followed by a selected list of publications. More detailed information is available at www.isse.gmu.edu.
A meta-analysis of constraint-induced movement therapy after stroke (2014)

Constraint-induced movement therapy can improve arm motor function and improve arm motor activities and may have a lasting effect on arm motor activity.
A combined PET/CT scanner: the path to true image fusion (2002)

Software-based image fusion is used routinely for the alignment of functional and anatomical images of the brain. For other parts of the body, image registration is more problematic owing to differences in patient positioning, scanner bed profiles and the involuntary movement of internal organs. An alternative to the software approach is a scanner that acquires both function and anatomy during a single imaging session: a fusion of the technologies rather than a fusion of the images post hoc. Consequently, we designed and built a prototype combined PET and CT scanner comprising a clinical CT and a clinical PET scanner mounted together in a single gantry. Over 300 cancer patients have been imaged in the scanner to establish the clinical value of the combined PET/CT approach. The CT images were used to provide essentially noiseless attenuation correction factors for the PET data. The widespread interest created by the patient studies acquired with the prototype PET/CT stimulated commercial activity and several major vendors of medical imaging equipment now offer combined PET/CT designs. This paper reviews the development of the combined PET/CT scanner, and illustrates the clinical aspects with some typical studies in cancer patients. The potential impact on medical practice of the commercial availability of PET/CT scanner technology at affordable cost is assessed.
Fragment recruitment on metabolic pathways: comparative metabolic profiling of metagenomes and metatranscriptomes (2013)

The sheer scale of the metagenomic and metatranscriptomic datasets that are now available warrants the development of automated protocols for organizing, annotating and comparing the samples in terms of their metabolic profiles. We describe a user-friendly java program FROMP (Fragment Recruitment on Metabolic Pathways) for mapping and visualizing enzyme annotations onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways or custom-made pathways and comparing the samples in terms of their Pathway Completeness Scores, their relative Activity Scores or enzyme enrichment odds ratios. This program along with our fully configurable PERL-based annotation organization pipeline Meta2Pro (METAbolic PROfiling of META-omic data) offers a quick and accurate standalone solution for metabolic profiling of environmental samples or cultures from different treatments. Apart from pictorial comparisons, FROMP can also generate score matrices for multiple meta-omics samples, which can be used directly by other statistical programs.
Pharmacological profile of BIBN4096BS, the first selective small molecule CGRP antagonist (2000)

Calcitonin gene-related peptide (CGRP) is one of the most potent endogenous vasodilators known. This peptide is increased during migraine attacks and has been implicated in the pathogenesis of migraine headache. Here we report on the first small molecule selective CGRP antagonist: BIBN4096BS. In vitro, this compound is extremely potent at primate CGRP receptors exhibiting an affinity (Ki) for human CGRP receptors of 14.4 +/- 6.3 (n = 4) pM. In an in vivo model, BIBN4096BS in doses between 1 and 30 micrograms kg-1 (i.v.) inhibited the effects of CGRP, released by stimulation of the trigeminal ganglion, on facial blood flow in marmoset monkeys. It is concluded that BIBN4096BS is a potent and selective CGRP antagonist.
Dynamic element matching for high-accuracy monolithic D/A converters (1976)

A novel way to obtain a very high accuracy in the bit weighting required for bipolar monolithic digital-to-analog (D/A) converters is described. The new method combines passive division using matched elements with a time division concept, needs no trimming, and is insensitive to element aging. A 12-bit monolithic D/A network with internal reference sources, built as a test circuit, demonstrates the versatility of this new technique.
Altered plastidic ATP/ADP‐transporter activity influences potato (Solanum tuberosumL.) tuber morphology, yield and composition of tuber starch (1998)

Summary The metabolic function of the plastidic ATP/ADP transporter (AATP) in heterotrophic plastids was examined in transgenic potato plants that exhibited increased or decreased amounts of the protein. Altered mRNA levels correlated with activities of the plastidic ATP/ADP transporter. Potato tubers with decreased plastidic ATP/ADP transporter activities exhibited reduced starch contents whereas sense lines accumulated increased amounts of tuber starch. Starch from wild‐type tubers had an amylose content of 18.8%, starch from antisense plants contained 11.5–18.0% amylose, whereas starch from sense plants had levels of 22.7–27.0%. The differences in physiological parameters were accompanied with altered tuber morphology. These changes are discussed with respect to the stromal ATP supply during starch biosynthesis.
Emr, an Escherichia coli locus for multidrug resistance. (1992)

An Escherichia coli chromosomal DNA fragment cloned on a multicopy plasmid conferred resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. The sequence of the cloned emr locus located at minute 57.5 of the chromosome revealed two open reading frames, emrA and emrB. emrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. The peptide is homologous to QacA, a multidrug-resistant pump from Staphylococcus aureus, and belongs to a gene family that includes tetracycline-resistant pumps of Gram-positive bacteria and the galactose/H+ symporter of E. coli. emrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain. An active pho-fusion to the C domain suggested that EmrA is a membrane protein. Disruption of emrB significantly increased sensitivity of cells to uncouplers. The cellular content of uncoupler increased in the order: overexpressed emrB cells greater than wild type greater than emrB-.
Evaluating Software Deployment Languages and Schema (1998)

Software distribution is evolving from a physical media approach to one where it is practical and advantageous to leverage the connectivity of networks. Network distribution of software systems provides timeliness and continuity of evolution not possible with physical media distribution methods. To support network-based software distribution, companies and organizations such as Microsoft, Marimba, and the Desktop Management Task Force (DMTF) are strengthening their efforts to package software systems in a way that is conducive to network distribution and management. The result of these efforts has led to the creation of software description languages and schema such as the Open Software Description format created by Microsoft and Marimba and the Management Information Format created by DMTF. While these efforts are steps in the right direction, they do not address deployment issues in a complete and systematic fashion. The contribution of this paper is to evaluate these leading software description technologies.
Milk Fat Content Measurement by a Simple UV Spectrophotometric Method: An Alternative Screening Method (2005)

We developed a simple microtechnique to measure lipids in milk by UV spectrophotometry. This technique is based upon the property of fatty acids to absorb UV light proportional to their concentration. Samples of powdered or fluid milk (30 or 60 muL) were added to 3 mL of analytic grade ethanol and stored at -20 degrees C for at least 1 h. This procedure precipitates proteins and hydrophobic peptides that interfere with UV measurement. Sample absorbances are then measured at 208 nm in an UV-Vis spectrophotometer. This technique correlated very well against Milko-Scan, a device that measures milk fat by IR spectroscopy, with an r(2) >0.982. Accuracy and precision, evaluated by recovery and replicate assays, are also very acceptable. This method is suitable as a fast, cost-effective alternative screening method to estimate milk fat content in small samples without prior lipid extraction.
A novel BEOL transistor (BETr) with InGaZnO embedded in Cu-interconnects for on-chip high voltage I/Os in standard CMOS LSIs (2011)

A novel BEOL transistor (BETr) is developed in Cu interconnects with wide band-gap InGaZnO (IGZO) film for on-chip high voltage I/Os in standard CMOS LSIs only by one additional mask. Underlying Cu interconnect and SiN barrier-dielectric on the Cu are utilized as the gate stack in a unique reverse-type thin-film-transistor (TFT) structure. Thickness control of both the IGZO channel and gate SiN is a key to achieve high on-current (I on ) with low leakage (I off ). Ability of high voltage operation (much higher than 3V) with small feature size is expected as an interface bridge for signal conversion between CMOS core-logics with low-voltages and peripheral devices driven with high-voltages.
Inhibition of C5a-induced inflammation with preserved C5b-9-mediated bactericidal activity in a human whole blood model of meningococcal sepsis (2003)

The complement system plays an important role in the initial defense against Neisseria meningitidis. In contrast, uncontrolled activation in meningococcal sepsis contributes to the development of tissue damage and shock. In a novel human whole blood model of meningococcal sepsis, we studied the effect of complement inhibition on inflammation and bacterial killing. Monoclonal antibodies (mAbs) blocking lectin and alternative pathways inhibited complement activation by N meningitidis and oxidative burst induced in granulocytes and monocytes. Oxidative burst was critically dependent on CD11b/CD18 (CR3) expression but not on Fc gamma-receptors. Specific inhibition of C5a using mAb 137-26 binding the C5a moiety of C5 before cleavage prohibited CR3 up-regulation, phagocytosis, and oxidative burst but had no effect on C5b-9 (TCC) formation, lysis, and bacterial killing. An mAb-blocking cleavage of C5, preventing C5a and TCC formation, showed the same effect on CR3, phagocytosis, and oxidative burst as the anti-C5a mAb but additionally inhibited TCC formation, lysis, and bacterial killing, consistent with a C5b-9-dependent killing mechanism. In conclusion, the anti-C5a mAb 137-26 inhibits the potentially harmful effects of N meningitidis-induced C5a formation while preserving complement-mediated bacterial killing. We suggest that this may be an attractive approach for the treatment of meningococcal sepsis.
The development of computer simulations of the geometries and thermodynamics of biological molecules. (1990)

The historical development of computer simulations of molecular geometry and thermodynamics (molecular mechanics, force field method) is outlined. The advantages and disadvantages of techniques such as energy minimization, molecular dynamics and free energy perturbation are discussed. An example is included that shows how energy minimization studies of dopamine D-2 antagonists have been used to develop an understanding of the three-dimensional pharmacophore necessary for this pharmacological activity.
HDAC Inhibitors Correct Frataxin Deficiency in a Friedreich Ataxia Mouse Model (2008)

Lack of acute toxicity, normalization of frataxin levels and of the transcription profile changes resulting from frataxin deficiency provide strong support to a possible efficacy of this or related compounds in reverting the pathological process in Friedreich ataxia, a so far incurable neurodegenerative disease.
The JAK2/STAT3 signaling pathway is required for growth of CD44+CD24– stem cell–like breast cancer cells in human tumors (2011)

Intratumor heterogeneity is a major clinical problem because tumor cell subtypes display variable sensitivity to therapeutics and may play different roles in progression. We previously characterized 2 cell populations in human breast tumors with distinct properties: CD44+CD24- cells that have stem cell-like characteristics, and CD44-CD24+ cells that resemble more differentiated breast cancer cells. Here we identified 15 genes required for cell growth or proliferation in CD44+CD24- human breast cancer cells in a large-scale loss-of-function screen and found that inhibition of several of these (IL6, PTGIS, HAS1, CXCL3, and PFKFB3) reduced Stat3 activation. We found that the IL-6/JAK2/Stat3 pathway was preferentially active in CD44+CD24- breast cancer cells compared with other tumor cell types, and inhibition of JAK2 decreased their number and blocked growth of xenografts. Our results highlight the differences between distinct breast cancer cell types and identify targets such as JAK2 and Stat3 that may lead to more specific and effective breast cancer therapies.