gebhart/patrepeval huggingface dataset:
Up‐regulation of muscle‐specific transcription factors during embryonic somitogenesis of zebrafish (Danio rerio) by knock‐down of myostatin‐1 (2004)

Myostatin, a secreted growth and differentiation factor (GDF-8) belongs to transforming growth factor (TGF-beta) superfamily that plays as a negative regulator of skeletal muscle development and growth. Recently, myostatin has been isolated from fish; however, its role in muscle development and growth remains unknown. Here, we present the expression of myostatin during development and the effects of its knock-down on various genes such as muscle regulatory transcription factors (MRFs), muscle-specific proteins (MSP), and insulin-like growth factors (IGFs). The myostatin expression was found to be maternal as it starts in one-cell stage onward. The reverse transcription-polymerase chain reaction (RT-PCR), in situ hybridization, and Southern and Northern blots demonstrated that the myostatin expression is not only restricted to skeletal muscle, but it expressed all the tested tissues. Expression of myostatin was effected by using antisense morpholinos resulted in significant phenotypic difference in stages 18 and 20 hours postfertilization (hpf). To confirm the specificity of myostatin morpholino, furthermore, a rescue experiment was conducted. The length as well as width of somites was increased with almost no gap in between the somites. In addition, it deserves to mention that this is a first animal model that shows changes in the size of the somites. Moreover, analyses of MRFs, MSP, and IGFs in the knock-down embryos by RT-PCR revealed the up-regulation of MyoD, Myogenin, and Mck transcription, whereas IGF-2 transcription showed mild response with no effect on IGF-1, Desmin, and Myf5. In situ hybridization showed that there was an increase in the number of somites from 3 to 4 at 13 and 22 hpf. Taken together, these data suggest that myostatin plays a major role during myogenesis, apart from inhibition of proliferation as well as differentiation.
Factorial study of the effects of atorvastatin and fish oil on dyslipidaemia in visceral obesity (2002)

Atorvastatin and fish oil have independent and additive effects in correcting dyslipidaemia in viscerally obese men. Improvement in abnormalities in remnant lipoproteins may occur only with use of atorvastatin. Combination treatment with statin and fish oil may, however, offer an optimal therapeutic approach for globally correcting dyslipidaemia in obesity.
A Survey of Cyclic Replacements for the Central Diamide Moiety of Inhibitors of Inosine Monophosphate Dehydrogenase (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Design and high power operation of a stress-induced single-polarization single-transverse mode LMA Yb-doped photonic crystal fiber (2006)

Photonic crystal fibers consisting of a solid fused silica core surrounded by a regular array of sub-micron air-holes have been shown to operate with single mode core well above 30 &#956;m in active laser geometries as well as passive beam delivery fibers. Novel designs based on the combination of stress applying elements that are index matched to the holey cladding have recently been emerged. In this report we summarize the properties of these polarization maintaining photonic crystal fibers. Beside the characterization of the polarizing window and birefringence, high power laser and amplifier configurations using these fibers are demonstrated and first experiments concerning the temperature sensitivity of the polarizing properties are presented.
Poly(N-isopropylacrylamide)-based semi-interpenetrating polymer networks for tissue engineering applications. Effects of linear poly(acrylic acid) chains on rheology (2004)

Semi-interpenetrating polymer networks (semi-IPNs), comprised of poly(N-isopropylacrylamide-co-acrylic acid) (p(NIPAAm-co-AAc)) hydrogels and linear p(AAc) chains, were synthesized, and the effects of the p(AAc) chains on semi-IPN rheology were examined. Oscillatory shear rheometry studies were performed and the rheological data were analyzed as a function of temperature, frequency, and p(AAc) chain amount (weight average molecular weight (Mw) 4.5 x 10(5) g/mol). At 22 degrees C, the semi-IPNs, as well as control p(NIPAAm-co-AAc) hydrogels, demonstrated rheological data that were representative of soft, loosely cross-linked solids. Furthermore, only the highest p(AAc) chain amount tested affected the rigidity of the p(NIPAAm-co-AAc)-based semi-IPNs, as compared to the p(NIPAAm-co-AAc) hydrogels. At 37 degrees C, the complex shear moduli (G*) demonstrated by the p(NIPAAm-co-AAc)-based semi-IPNs were significantly greater than G* exhibited by the p(NIPAAm-co-AAc) hydrogels, and the semi-IPN G* values significantly increased with increasing p(AAc) chain amount. These results can be used to develop p(NIPAAm)-based semi-IPNs with tailored mechanical properties that may function as scaffolds in tissue engineering initiatives.
Rapid Hybridoma Screening Method for the Identification of Monoclonal Antibodies to Low-Abundance Cytoplasmic Proteins (1998)

Screening assays are the most time-consuming and labor-intensive part of generating monoclonal antibodies (MAbs). Antibodies identified by enzyme-linked immunosorbent assay (ELISA) screening often are not suitable for their intended application such as immunofluorescence staining. We describe here a rapid and efficient flow cytometric screening procedure for the identification of MAbs directed against low-abundance cytoplasmic proteins, in our case, the pro-apoptotic molecule Bim. Cells from an equal mixture of a parental cell line and a subline expressing Bim were fixed, permeabilized and incubated with hybridoma supernatants. The supernatants were derived from a fusion of Sp2/0 plasmacytoma cells and spleen cells from a rat immunized with recombinant glutathione-S-transferase (GST)-BimL fusion protein. Secondary staining with fluorochrome-labeled anti-rat Ig antibodies allowed detection of clones expressing Bim-specific antibodies. The screening procedure was rapid and efficient, and most monoclonal antibodies identified were proven to be useful for immunofluorescence staining and other applications.
Whole-genome DNA sequencing (1999)

Computation is integrally and powerfully involved with the DNA sequencing technology that promises to reveal the complete human DNA sequence in the next several years. After introducing the latest DNA sequencing methods, this article describes three current approaches for completing the sequencing.
Myeloid-derived suppressor cells express the death receptor Fas and apoptose in response to T cell-expressed FasL (100.18) (2010)

Abstract Myeloid-derived suppressor cells (MDSC) accumulate to high levels in individuals with a variety of conditions including cancer, chronic inflammation, and stress, where they are potent inhibitors of adaptive and innate immunity. Some of the factors that induce their accumulation are known; however, physiological conditions that regulate their turn-over have not been identified. Mass spectrometry analysis revealed prominent expression of apoptosis pathway proteins by MDSC and led us to hypothesize that Fas/FasL-mediated apoptosis may be a key mechanism that regulates MDSC turn-over. This hypothesis was confirmed by the findings that MDSC levels significantly regress after removal of primary mammary tumors from STAT6-deficient or CD-1-deficient mice, but do not regress in mice doubly deficient for FasL and STAT6 or CD-1. Flow cytometry and confocal microscopy studies examining activated caspase 3 expression and cytochrome C localization revealed that MDSC apoptosis is triggered via the extrinsic, and not the intrinsic, pathway. Surprisingly, activated FasL+ T cells mediated MDSC apoptosis in vivo, demonstrating a retaliatory relationship between these two cell populations, and suggesting that Fas-FasL interactions could be exploited as a strategy to reduce in vivo levels of MDSC.
Purification of intact and nicked forms of a zinc-containing, Mg2+-dependent, low Km cyclic AMP phosphodiesterase from bakers' yeast. (1984)

A low Km cyclic AMP phosphodiesterase was purified to homogeneity from microsomes of bakers' yeast. "Intact" enzyme, purified from microsomes prepared in the presence of the protease inhibitor phenylmethylsulfonyl fluoride, had a specific activity of 0.6 mumol/min/mg of protein (30 degrees C, pH 8.0, 1 microM cyclic AMP), a pI of 6.65 +/- 0.15, and a molecular weight of 61,000 determined by gel electrophoresis in the presence of sodium dodecyl sulfate. Gel filtration of native enzyme suggested it is a monomer. When phenylmethylsulfonyl fluoride was omitted, a product ("nicked" enzyme) was obtained with a specific activity of 1.2 mumol/min/mg of protein, the same pI, and a similar amino acid composition; but gel electrophoresis now showed two bands, with molecular weights of 45,000 and about 17,000, together with a small amount of the 61,000 band. Apart from the higher specific activity of the nicked enzyme, no difference was found between the catalytic properties of the two enzyme forms. Between 40 nM and 1 microM cyclic AMP, an apparent Km of 170 nM was observed at pH 8.0, but at higher cyclic AMP concentrations (2-30 microM), Hofstee plots curved upwards. Cyclic deoxy-AMP was a substrate, but cyclic GMP was not and did not affect the activity towards cyclic AMP. Both enzyme forms contained tightly bound zinc. The metal chelators, 8-hydroxyquinoline and orthophenanthroline , caused progressive partial inactivation of the enzyme and a decrease in its affinity for cyclic AMP. Dialysis against Zn2+, Cu2+, Co2+, or Mn2+ (but not Mg2+ or Ni2+) reversed these changes.
Mediation of Staphylococcal Adherence to Mucosal Cells by Lipoteichoic Acid (1983)

Staphylococcal lipoteichoic acid markedly reduced adherence by Staphylococcus aureus to buccal cells in vitro, suggesting that lipoteichoic acid mediates adherence by that bacterium. Adherence inhibition by lipoteichoic acid was lost after deacylation of the preparation, suggesting that fatty acids on the molecule are essential to binding.
A Mechanism for the Specific Immunogenicity of Heat Shock Protein-Chaperoned Peptides (1995)

Endogenously synthesized antigenic determinants are generally presented on major histocompatibility complex (MHC) class I molecules, whereas exogenous determinants are presented by MHC class II molecules. Here, it is shown that exogenous antigens chaperoned by a heat shock protein can be channeled into the endogenous pathway, presented by MHC class I molecules, and recognized by CD8+ T lymphocytes. This pathway is functional only in a subset of macrophages among the cell types tested. These observations provide a basis for the tumor-specific and virus-specific immunogenicity of cognate heat shock protein preparations and offer a mechanism for the classical phenomenon of cross-priming.
Was the Human Genome Project Worth the Effort? (2005)

The Human Genome Project is much more than the genetic map of our species. It is also a powerful set of integrated tools for solving problems in medicine and biology. Application of these tools to a common cause of human blindness, age-related macular degeneration, implicates a common variant in the gene encoding complement factor H as a major contributor to the risk of developing this disease (
 Klein
 et al.,
 Haines
 et al.,
 Edwards
 et al.). The new findings raise hopes for better diagnosis and treatment of macular degeneration and further validate the importance of the Human Genome Project
The CMV early enhancer/chicken β actin (CAG) promoter can be used to drive transgene expression during the differentiation of murine embryonic stem cells into vascular progenitors (2008)

Vectors containing the CAG promoter offer a valuable tool for the long term expression of transgenes during stem cell differentiation towards mesoderm, while the CMV and beta-actin promoters lead to very poor transgene expression during this process.
Molecular basis of hereditary fructose intolerance: Mutations and polymorphisms in the human aldolase B gene (1995)

Mutations in the human aldolase B gene that result in hereditary fructose intolerance have been characterized extensively. Although the majority of subjects have been from northern Europe, subjects from other geographical regions and ethnic groups have been identified. At present 21 mutations have been reported; 15 of these are single base substitutions, resulting in nine amino acid replacements, four nonsense codons, and two putative splicing defects. Two large deletions, two four-base deletions, a single-base deletion, and a seven-base deletion/one-base insertion have been found. This last mutation leads to a defect in splicing and it is likely that one of the small deletions does as well. Regions of the enzyme where mutations have been observed recurrently are encoded by exons 5 and 9. Indeed, the three most common mutations are found in these exons. Two of these prevalent HFI mutations arose from a common ancestor and spread throughout the population by genetic drift. This finding was based on linkage to two sequence polymorphisms, which are among very few informative polymorphic markers that have been identified within the aldolase B gene. Because of the prevalence of a few HFI alleles, and the recent advances in molecular methods for identifying and screening for mutation, the diagnosis of HFI by molecular screening methods should become routine. These molecular diagnostic methods will be extremely beneficial for this often difficult to diagnose and sometimes fatal disease.
Conversion of metal carbides to carbide derived carbon by reactive ion etching in halogen gas (2006)

The excellent tribological properties, very low friction coefficient, ~0.05, of the recently discovered carbide derived carbon (CDC) films have shown them to be excellent candidates in many applications where friction and wear are dominating issues in performance. In this work we examine the feasibility of employing a reactive ion etching process (RIE) with chlorine gas at low temperature, as opposed to the current high temperature chlorination process, in achieving the conversion of metal carbide films into amorphous carbon films. The overall goal is develop a process that is friendlier to microfabricated devices towards employing the tribological properties of CDC films in such devices. We examine this RIE processing using both bulk scale and thin film specimens. These metal-carbide specimens are subjected to a halogen containing ion plasma at reduced pressure in order to leach out the metal, resulting in an amorphous carbon film, a so-called carbide-derived carbon (CDC) process. This reactive ion etching process has been used to produce carbon layers on multiphase carbide materials containing silicon and titanium. The resulting carbon layers have been characterized using a variety of techniques. The results on the bulk scale specimens, via Raman spectrometry, indicated that RIE processing can indeed achieve conversion, while results of the thin films indicated that although conversion occurred poor adhesion of the films to the substrate resulted spallation during friction testing attempts.
Primer design for automated DNA sequencing utilizing T7 DNA polymerase and internal labeling with fluorescein-15-dATP. (1995)

We have identified additional criteria for the walking primer design that improve the success rate of automated fluorescent DNA sequencing using the internal labeling technique and T7 DNA polymerase. These criteria resulted from the evaluation of over 220 sequences generated with walking primers and fluorescein-15-dATP as internal label in the course of the European Community (EC) yeast genome sequencing project. In this project primers were designed using standard commercial software. Intensities of sequencing signals varied over a broad range from very strong to very weak, depending on the primers used. This led us to evaluate primer performance relative to (i) the template sequence immediately downstream of the primer binding site and (ii) the primer sequence itself. Our experiments show that the position of the first labeled dATP to be incorporated downstream of the primer into the growing strand is substantial for the signal intensity of the sequence. The closer to the primer that the first 'A' is incorporated, the stronger the peak intensities are. An additional feature of sequencing with native T7 DNA polymerase is its ability to remove a 3'-terminal 'A' of the primer by the 3'-->5' exonuclease activity and to exchange the nucleotide with a labeled dATP by the polymerase activity.
Common co‐lipids, in synergy, impart high gene transfer properties to transfection‐incompetent cationic lipids (2005)

Efficacious cationic transfection lipids usually need either DOPE or cholesterol as co-lipid to deliver DNA inside the cell cytoplasm in non-viral gene delivery. If both of these co-lipids fail in imparting gene transfer properties, the cationic lipids are usually considered to be transfection inefficient. Herein, using both the reporter gene assay in CHO, COS-1 and HepG2 cells and the whole cell histochemical X-gal staining assay in representative CHO cells, we demonstrate that common co-lipids DOPE, Cholesterol and DOPC, when act in synergy, are capable of imparting improved gene transfer properties to a novel series of cationic lipids (1-5). Contrastingly, lipids 1-5 became essentially transfection-incompetent when used in combination with each of the pure co-lipid components alone.
Introduction to Quantum Algorithms (2000)

These notes discuss the quantum algorithms we know of that can solve problems significantly faster than the corresponding classical algorithms. So far, we have only discovered a few techniques which can produce speed up versus classical algorithms. It is not clear yet whether the reason for this is that we do not have enough intuition to discover more techniques, or that there are only a few problems for which quantum computers can significantly speed up the solution.
Evidence That a Defective Spindle Assembly Checkpoint Is Not the Primary Cause of Maternal Age-Associated Aneuploidy in Mouse Eggs1 (2009)

Advanced maternal age is unequivocally associated with increased aneuploidy in human eggs and infertility, but the molecular basis for this phenomenon is unknown. An age-dependent deterioration of the spindle assembly checkpoint (SAC) has been proposed as a probable cause of aneuploidy. Accurate chromosome segregation depends on correct chromosome attachment to spindle microtubules, and the SAC provides time for this process by delaying anaphase onset until all chromosomes are stably attached. If SAC function decreases with age, oocytes from reproductively old mice would enter anaphase of meiosis I (AI) prematurely, leading to chromosome segregation errors and aneuploid eggs. Although intuitively appealing, this hypothesis is largely untested. We used a natural reproductive aging mouse model to determine if a defective SAC is the primary cause of aneuploidy in eggs. We tracked the progress of individual oocytes from young and old mice through meiosis I by time-lapse microscopy and counted chromosomes in the resulting eggs. This data set allowed us to correlate the timing of AI onset with aneuploidy in individual oocytes. We found that oocytes from old mice do not enter AI prematurely compared to young counterparts despite a 4-fold increase in the incidence of aneuploidy. Moreover, we did not observe a correlation between the timing of AI onset and aneuploidy in individual oocytes. When SAC function was challenged with a low concentration of the spindle toxin nocodazole, oocytes from both young and old mice arrested at meiosis I, which is indicative of a functional checkpoint. These findings indicate that a defective SAC is unlikely the primary cause of aneuploidy associated with maternal age.
Expression of the Epstein Barr virus transforming protein LMP1 causes a rapid and transient stimulation of the Bcl-2 homologue Mcl-1 levels in B-cell lines. (1996)

The EBV-encoded latent membrane protein 1 (LMP1) suppresses apoptosis in B lymphocytes through up-regulation of Bcl-2. However, the maximum induction of Bcl-2 by LMP1 takes about 48-72 h. We show in this report that up-regulation of the Bcl-2 homologue Mcl-1 by LMP1 preceded the induction of Bcl-2 and that the up-regulation was transient; therefore, Mcl-1 levels decreased when Bcl-2 levels started to increase. This finding supports the hypothesis that Mcl-1 functions as a rapidly inducible, short-term effector of cell viability. LMP1 also blocked the decline in the Mcl-1 levels in response to apoptotic stimulation triggered by elevated cyclic AMP. This effect of LMP1 was associated with a delayed cell death in the EBV-negative Burkitt lymphoma cell line BL41. The maintenance of Mcl-1 expression by LMP1 is likely to be a crucial immediate-early response that enables cells to survive until Bcl-2 can be up-regulated.
Outcome of pregnancy in diabetic women in northeast England and in Norway, 1994-7 (2000)

In northeast England, perinatal mortality is five times higher and congenital malformation is four times higher for pregnancies in diabetic women than for those in women who do not have diabetes.1 The same is true in other regions in the United Kingdom, 2 3 but this is not the case in Norway.4 Why is the outcome of pregnancy in diabetic women better in Norway? Does Norway use the same definitions and record the same outcome data as the United Kingdom? If the data are standardised will these differences disappear? If not, what is causing the difference in the outcome of pregnancy in diabetic women?

The methodology for data collection needs to be standardised between the two countries to determine whether differences in outcome are real before looking for explanations in the healthcare systems of the two countries. We compare the …
Efficient Synthesis of α-C-Galactosyl Ceramide Immunostimulants: Use of Ethylene-Promoted Olefin Cross-Metathesis (2004)

[reaction: see text] Olefin cross-metathesis has been used to prepare alpha-C-galactosylceramide derivatives. The metathesis process merged vinyl and propenyl glycosides with vinyl derivatives of phytosphingosine. The use of ethylene enhanced the yield of the methathesis step.
Analytical analysis of finite cache penalty and cycles per instruction of a multiprocessor memory hierarchy using miss rates and queuing theory (2001)

Advances in technology have provided a continuing improvement in processor speed and capacity of attached main memory. The increasing gap between main memory and processor cycle times has required increasingly more levels of caching to prevent performance degradation. The net result is that the inherent delay of a memory hierarchy associated with any computing system is becoming the major performance-determining factor and has inspired many types of analysis methods. While an accurate performance-evaluation tool requires the use of trace-driven simulators, good approximations and significant insight can be obtained by the use of analytical models to evaluate finite cache penalties based on miss rates (or miss ratios) and queuing theory combined with empirical relations between various levels of a memory hierarchy. Such tools make it possible to readily determine trends in performance vs. changes in input parameters. This paper describes such an analysis approach—one which has been implemented in a sp readsheet and used successfully to perform early engineering tradeoffs for many uniprocessor and multiprocessor memory hierarchies.