gebhart/patrepeval huggingface dataset:
Cardiac and Extracardiac Expression of Csx/Nkx2.5 Homeodomain Protein (1998)

Csx/Nkx2.5 is an evolutionary conserved homeobox gene related to the Drosophila tinman gene, which is essential for the dorsal mesoderm formation. Expression of Csx/Nkx2.5 mRNA is the earliest marker for heart precursor cells in all vertebrates so far examined. Previous studies have demonstrated that Csx/Nkx2.5 mRNA is highly expressed in the heart and at lower levels in the spleen, tongue, stomach, and thyroid in the murine embryo. Since some developmental genes are regulated by posttranscriptional mechanisms, we analyzed the developmental pattern of Csx protein expression at the single-cell level using Csx-specific antibodies. Immunohistochemical analysis of murine embryos at 7.8 days post coitum revealed that Csx protein is strongly expressed in the nucleus of endodermal and mesodermal cells in the cardiogenic plate. Subsequently, in the heart, Csx protein was detected only in the nucleus of myocytes of the atrium and the ventricle through the adult stage. During the fetal period, Csx protein expression in the nucleus was also noted in the spleen, stomach, liver, tongue, and anterior larynx. Unexpectedly, confocal microscopy revealed that Csx immunoreactivity was detected only in the cytoplasm of a subset of cranial skeletal muscles. Csx protein was not detected in the thyroid glands. The expression of Csx protein in all organs was markedly downregulated after birth except in the heart. These results raise the possibility that Csx/Nkx2.5 may play a role in the early developmental process of multiple tissues in addition to its role in early heart development.
Practical Flow Cytometry (2003)

List of Tables and Figures. Preface to the Fourth Edition: Why You Should Read the Book - Or Not. Foreword to the Third Edition. Preface to the Third Edition. Preface to the Second Edition. Foreword to the First Edition. Preface to the First Edition. 1. Overture. 2. Learning Flow Cytometry. 3. History. 4. How Flow Cytometers Work. 5. Data Analysis. 6. Flow Sorting. 7. Parameters and Probes. 8. Buying Flow Cytometers. 9. Building Flow Cytometers. 10. Using Flow Cytometers: Applications, Extensions, and Alternatives. 11. Sources of Supply. 12. Afterword.
In vitro models for liver toxicity testing. (2013)

Over the years, various liver-derived <i>in vitro</i> model systems have been developed to enable investigation of the potential adverse effects of chemicals and drugs. Liver tissue slices, isolated microsomes, perfused liver, immortalized cell lines, and primary hepatocytes have been used extensively. Immortalized cell lines and primary isolated liver cells are currently most widely used <i>in vitro</i> models for liver toxicity testing. Limited throughput, loss of viability, and decreases in liver-specific functionality and gene expression are common shortcomings of these models. Recent developments in the field of <i>in vitro</i> hepatotoxicity include three-dimensional tissue constructs and bioartificial livers, co-cultures of various cell types with hepatocytes, and differentiation of stem cells into hepatic lineage-like cells. In an attempt to provide a more physiological environment for cultured liver cells, some of the novel cell culture systems incorporate fluid flow, micro-circulation, and other forms of organotypic microenvironments. Co-cultures aim to preserve liver-specific morphology and functionality beyond those provided by cultures of pure parenchymal cells. Stem cells, both embryonic- and adult tissue-derived, may provide a limitless supply of hepatocytes from multiple individuals to improve reproducibility and enable testing of the individual-specific toxicity. This review describes various traditional and novel <i>in vitro</i> liver models and provides a perspective on the challenges and opportunities afforded by each individual test system.
MPEG-4 video encoder based on DSP-FPGA techniques (2005)

With the development of video encoding techniques, video compression algorithms become more complicated. A real-time high resolution video encoder cannot be implemented with a single CPU or DSP. We design and implement a MPEG-4 video encoder based on coordinated DSP-FPGA techniques. The FPGA module takes the tasks of video acquisition, YUV separation and data I/O functions, while the DSP is dedicated for video compression. We optimize the data flow scheme of the MPEG-4 video compression to utilize the DSP's on-chip memory. A MB (macro block) type judging algorithm is proposed based on MB's space complexity. It effectively reduces the computational complexity of the video compression. The experimental results indicate that our MPEG-4 video encoder implementation can encode 39.2 fps in CIF resolution.
Computation of elementary functions on the IBM RISC System/6000 processor (1990)

The additional speed and precision of the IBM RISC System/6000* floating-point unit have motivated reexamination of algorithms to perform division, square root, and the elementary functions. New results are obtained which avoid the necessity of doing special testing to get the last bit rounded correctly in accordance with all of the IEEE rounding modes in the case of division and square root. For the elementary function library, a technique is described for always getting the last bit rounded correctly in the selected IEEE rounding mode.
Pruning and Grouping Discovered Association Rules (1995)

Association rules are statements of the form &amp;quot;for 90 % of the rows of the relation, if the row has value 1 in the columns in set X, then it has 1 also in the columns in set Y &amp;quot;. Efficient methods exist for discovering association rules from large collections of data. The number of discovered rules can, however, be so large that the rules cannot be presented to the user. We show how the set of rules can be pruned by forming rule covers. A rule cover is a subset of the original set of rules such that for each row in the relation there is an applicable rule in the cover if and only if there is an applicable rule in the original set. We also discuss grouping of association rules by clustering, and present some experimental results of both pruning and grouping. Keywords: data mining, association rules, covers, clustering. 1 Introduction Association rules are an interesting class of database regularities, introduced by Agrawal, Imielinski, and Swami [AIS93]. An association rule is an expres...
Designer Gene Delivery Vectors: Molecular Engineering and Evolution of Adeno-Associated Viral Vectors for Enhanced Gene Transfer (2007)

Gene delivery vectors based on adeno-associated virus (AAV) are highly promising due to several desirable features of this parent virus, including a lack of pathogenicity, efficient infection of dividing and non-dividing cells, and sustained maintenance of the viral genome. However, several problems should be addressed to enhance the utility of AAV vectors, particularly those based on AAV2, the best characterized AAV serotype. First, altering viral tropism would be advantageous for broadening its utility in various tissue or cell types. In response to this need, vector pseudotyping, mosaic capsids, and targeting ligand insertion into the capsid have shown promise for altering AAV specificity. In addition, library selection and directed evolution have recently emerged as promising approaches to modulate AAV tropism despite limited knowledge of viral structure-function relationships. Second, pre-existing immunity to AAV must be addressed for successful clinical application of AAV vectors. "Shielding" polymers, site-directed mutagenesis, and alternative AAV serotypes have shown success in avoiding immune neutralization. Furthermore, directed evolution of the AAV capsid is a high throughput approach that has yielded vectors with substantial resistance to neutralizing antibodies. Molecular engineering and directed evolution of AAV vectors therefore offer promise for generating 'designer' gene delivery vectors with enhanced properties.
Stem Cell Factor Is a Potent Synergistic Factor in Hematopoiesis (1994)

Stem cell factor (SCF), a ligand for c-kit, has a broad range of activities including effects on cells at or near the level of the multipotential stem cell as well as on committed cells. Preclinical studies show that SCF can protect against lethal irradiation, elicit multilineage responses in peripheral blood and bone marrow cellularity, and increase circulating peripheral blood progenitor cells (PBPC) in a dose-dependent manner. Recombinant human SCF has major clinical potential through its synergy with other factors, especially recombinant human granulocyte colony-stimulating factor, to enhance mobilization of PBPC.
Phase III Randomized Clinical Trial Comparing Tremelimumab With Standard-of-Care Chemotherapy in Patients With Advanced Melanoma (2013)

This study failed to demonstrate a statistically significant survival advantage of treatment with tremelimumab over standard-of-care chemotherapy in first-line treatment of patients with metastatic melanoma.
Surface modification of the biomedical polymer poly(ethylene terephthalate) (1993)

X-ray photoelectron spectroscopy was used to characterize modified surfaces of a biomedically important polymer, poly(ethylene terephthalate). Several modification schemes were investigated and direct silanization with 3-aminopropyltriethoxysilane was found to be the optimum procedure, resulting in an aminated surface. Surface coverage of up to 100% was achieved with retention of the polymeric structural integrity. Further activation of the silanized surface was accomplished with two cross-linkers, glutaraldehyde and sebacoyl chloride. A simple biomolecule, L-cysteine, was successfully immobilized onto a surface pre-treated with 3-aminopropyltriethoxysilane and glutaraldehyde, with a coverage of 42%.
Increased expression of insulin-like growth factor I receptor in malignant cells expressing aberrant p53: functional impact. (2000)

We investigated the functional impact of p53 on insulin-like growth factor I receptor (IGF-IR) expression in malignant cells. Using the BL-41tsp53-2 cell line, a transfectant carrying temperature-sensitive (ts) p53 and endogenous mutant p53 (codon 248), we demonstrated a drastic down-regulation of plasma membrane-bound IGF-IRs on induction of wild-type p53. However, a similar response was obtained by treatment of BL-41tsp53-2 cells expressing mutant ts p53 with a p53 antisense oligonucleotide. Thus, even if the negative effect of wild-type p53 predominates under a competitive condition, these data indicate that mutant p53 may be important for up-regulation of IGF-IR. To further elucidate this issue, three melanoma cell lines (BE, SK-MEL-5, and SK-MEL-28) that overexpressed p53 were investigated. The BE cell line has a "hot spot" mutation (codon 248) and expresses only codon 248-mutant p53. SK-MEL-28 has a point mutation at codon 145. SK-MEL-5 cells did not exhibit any p53 mutations, but the absence of p21Waf1 expression suggested functionally aberrant p53. Our data suggest that interaction with Mdm-2 may underlie p53 inactivation in these cells. Using p53 antisense oligonucleotides, we demonstrated a substantial down-regulation of cell surface expression of IGF-IR proteins in all melanoma cell lines after 24 h. This was paralleled by decreased tyrosine phosphorylation of IGF-IR and growth arrest, and, subsequently, massive cell death was observed (this was also seen in BL-41tsp53-2 cells with mutant conformation of ts p53). Taken together, our results suggest that up-regulation of IGF-IR as a result of expression of aberrant p53 may be important for the growth and survival of malignant cells.
Adeno-associated virus type 2-mediated transfer of ecotropic retrovirus receptor cDNA allows ecotropic retroviral transduction of established and primary human cells (1997)

The cellular receptors that mediate binding and internalization of retroviruses have recently been identified. The concentration and accessibility of these receptors are critical determinants in accomplishing successful gene transfer with retrovirus-based vectors. Murine retroviruses containing ecotropic glycoproteins do not infect human cells since human cells do not express the receptor that binds the ecotropic glycoproteins. To enable human cells to become permissive for ecotropic retrovirus-mediated gene transfer, we have developed a recombinant adeno-associated virus type 2 (AAV) vector containing ecotropic retroviral receptor (ecoR) cDNA under the control of the Rous sarcoma virus (RSV) long terminal repeat (LTR) promoter (vRSVp-ecoR). Established human cell lines, such as HeLa and KB, known to be nonpermissive for murine ecotropic retroviruses, became permissive for infection by a retroviral vector containing a bacterial gene for resistance to neomycin (RV-Neo(r)), with a transduction efficiency of up to 47%, following transduction with vRSVp-ecoR, as determined by the development of colonies that were resistant to the drug G418, a neomycin analog. No G418-resistant colonies were present in cultures infected with either vRSVp-ecoR or RV-Neo(r) alone. Southern and Northern blot analyses revealed stable integration and long-term expression, respectively, of the transduced murine ecoR gene in clonal isolates of HeLa and KB cells. Similarly, ecotropic retrovirus-mediated Neo(r) transduction of primary human CD34+ hematopoietic progenitor cells from normal bone marrow was also documented, but only following infection with vRSVp-ecoR. The retroviral transduction efficiency was approximately 7% without prestimulation and approximately 14% with prestimulation of CD34+ cells with cytokines, as determined by hematopoietic clonogenic assays. No G418-resistant progenitor cell colonies were present in cultures infected with either vRSVp-ecoR or RV-Neo(r) alone. These results suggest that sequential transduction of primary human cells with two different viral vectors may overcome limitations encountered with a single vector. Thus, the combined use of AAV- and retrovirus-based vectors may have important clinical implications for ex vivo and in vivo human gene therapy.
Quantitation of zidovudine-resistant human immunodeficiency virus type 1 in the blood of treated and untreated patients. (1993)

A nonselective ex vivo assay was used to directly detect and quantify zidovudine (AZT)-resistant human immunodeficiency virus type 1 (HIV-1) in the blood of treated and untreated patients. In contrast to previous reports, drug-resistant virus was detected in peripheral blood mononuclear cells of a few of the patients who had never received AZT. The AZT resistance of HIV-1 isolates from one untreated individual was confirmed by further susceptibility studies in vitro and by the finding of a characteristic mutation (Lys-->Arg at codon 70) in the reverse transcriptase. In patients who were clinically stable while on AZT, HIV-1 titers in plasma and mononuclear cells were generally low but resistant viruses already predominated. In those individuals who were deteriorating despite AZT administration, high levels of viremia were observed, and the resistance phenotype was nearly universal. These findings serve to emphasize the magnitude of the AZT-resistance problem in patients on drug treatment.
Clinical presentation and treatment of type 2 diabetes in children (2007)

Type 2 diabetes mellitus (T2DM) has dramatically increased throughout the world in many ethnic groups and among people with diverse social and economic backgrounds. This increase has also affected the young such that over the past decade, the increase in the number of children and youth with T2DM has been labeled an 'epidemic'. Before the 1990s, it was rare for most pediatric centers to have significant numbers of patients with T2DM. However, by 1994, T2DM patients represented up to 16% of new cases of diabetes in children in urban areas and by 1999, depending on geographic location, the range of percentage of new cases because of T2DM was 8-45% and disproportionately represented among minority populations. Although the diagnosis was initially regarded with skepticism, T2DM is now a serious diagnostic consideration in all young people who present with signs and symptoms of diabetes in the USA.
Framework design: a role modeling approach (2000)

Role modeling for framework design, as developed in this dissertation, makes designing,learning, and using object-oriented frameworkseasicr than possible with traditional class-based approaches.Object-oriented frameworks promisehigher productivity and shorter time-to-market for the develop ment of object-orientedapplications.These goals are achieved through design and code reuse.While many projects show that these promises can be met, failed projects also show that they are not always easy to reach.This dissertation addresses three pertinent technical problems of designing, learning, and using object-oriented frameworks: complexity of classes, complexity of objeet collaboration, and lack of clarity of requirements put upon use-clients of a framework.Role modeling for framework design is an evolutionary extension of class-based modeling of frame works.The method enhancesclass-based modeling with role modeling concepts.In this method, ob jeets play roles that are described by role types.An objeet typically plays several roles, so that the class of an objeet composes several role types.Moreover, objeets collaboratefor several different pur- poses, each of which is called an objeet collaborationtask.Such a task is described by a role model.A class model composes all relevant role models to describe how instances of its classes collaborate.De
Anterior cruciate ligament reconstruction using cryopreserved irradiated bone‐ACL‐bone‐allograft transplants (1994)

Bone-ACL-bone allograft transplantation has been investigated as a potential solution to reconstruction of the anterior cruciate ligament (ACL). To minimize disease transmission (e.g. the acquired immuno deficiency syndrome), bony and collagenous tissues should be sterilized. Recent animal studies indicate that gamma irradiation and ethylene oxide sterilization result in diminished histological and biomechanical properties. The purpose of the present study was biomechanical and histological determination of the fate of deep-frozen gamma-irradiated (2.5 Mrad) canine bone-ACL-bone allografts with argon gas protection. Particular attention was paid to collagenous and neuroanatomical morphology 3, 6 and 12 months after implantation, by comparison to a non-irradiated control group. Sixty skeletally mature foxhounds were operated on in this study, divided up in two groups of 30 dogs each. In group A animals the ACL was replaced by a deep-frozen (-80 degrees C) bone-ACL-bone LAD-augmented allograft subjected to 2.5 Mrad gamma irradiation with argon gas protection. The animals in group B received an LAD-augmented ACL-allograft transplant without gamma irradiation. All knees from both groups were evaluated 3, 6 and 12 months after implantation in regard to biomechanical properties, collagen morphology and routine histology (haematoxylin and eosin stain, polarization microscopy), neuroanatomical morphology (silver and gold chloride stain) and microvasculature (modified Spalteholz technique). The irradiated ACL allografts withstood a maximum load that was 63.8% (718.3 N) of the maximum load of normal ACLs after 12 months. By contrast, the non-irradiated allografts failed at 69.1% (780.1 N) of the maximum load of normal control ACLs.(ABSTRACT TRUNCATED AT 250 WORDS)
Virus-Encoded Serine Proteinase Inhibitor SERP-1 Inhibits Atherosclerotic Plaque Development After Balloon Angioplasty (1996)

Purified SERP-1, a virus-encoded secreted glycoprotein, reduces plaque growth after primary balloon-mediated injury. Plaque development is decreased by inhibition of serine proteinase activity and is associated with a focal reduction in macrophage infiltration immediately after injury. Investigation of serine proteinase inhibitors may provide new insight into the regulation of arterial responses to injury.
Activation of the HIV-1 enhancer by the LEF-1 HMG protein on nucleosome-assembled DNA in vitro. (1995)

Lymphoid enhancer-binding factor 1 (LEF-1) is a regulatory high mobility group (HMG) protein that activates the T cell receptor alpha (TCR alpha) enhancer in a context-restricted manner in T cells. In this paper we demonstrate that the distal region of the human immunodeficiency virus-1 (HIV-1) enhancer, which contains DNA-binding sites for LEF-1 and Ets-1, also provides a functional context for activation by LEF-1. First, we show that mutations in the LEF-1-binding site inhibit the activity of multimerized copies of the HIV-1 enhancer in Jurkat T cells, and that LEF-1/GAL4 can activate a GAL4-substituted HIV-1 enhancer 80- to 100-fold in vivo. Second, recombinant LEF-1 is shown to activate HIV-1 transcription on chromatin-assembled DNA in vitro. By using a nucleosome-assembly system derived from Drosophila embryos, we find that the packaging of DNA into chromatin in vitro strongly represses HIV-1 transcription and that repression can be counteracted efficiently by preincubation of the DNA with LEF-1 (or LEF-1 and Ets-1) supplemented with fractions containing the promoter-binding protein, Sp1. Addition of TFE-3, which binds to an E-box motif upstream of the LEF-1 and Ets-1 sites, further augments transcription in this system. Individually or collectively, none of the three enhancer-binding proteins (LEF-1, Ets-1, and TFE-3) could activate transcription in the absence of Sp1. A truncation mutant of LEF-1 (HMG-88), which contains the HMG box but lacks the trans-activation domain, did not activate transcription from nucleosomal DNA, indicating that bending of DNA by the HMG domain is not sufficient to activate transcription in vitro. We conclude that transcription activation by LEF-1 in vitro is a chromatin-dependent process that requires a functional trans-activation domain in addition to the HMG domain.
Stem cell-based therapies in inflammatory bowel disease: promises and pitfalls (2016)

Inflammatory bowel disease (IBD) is a chronic, often relapsing, condition that deeply impacts the quality of life for many patients. Although there have been significant advances in medical treatments, a large proportion of patients become refractory to available therapeutic options. Stem-cell therapy through hematopoietic stem cells (HSCs) or mesenchymal stem (stromal) cells (MSCs) is a promising therapeutic option for severe refractory cases especially when surgery is not feasible. In HSC transplantation, the objective is to destroy the 'autoreactive' immune cells responsible for disease chronicity, and to re-establish gut tolerance to gut microbes. In perianal Crohn's disease (CD), the objective is to deposit MSCs locally in fistulizing tracts to down-regulate the local immune response and induce wound healing. Results from upcoming and ongoing clinical trials will set the path of these novel therapeutic options that have the capability to successfully treat severe refractory Crohn's patients.
2-Phenylhydroxypropynyladenosine Derivatives as High Potent Agonists at A2BAdenosine Receptor Subtype (2003)

Adenosine derivatives bearing in 2-position the (R,S)-phenylhydroxypropynyl chain were evaluated for their potency at human A2B adenosine receptor, stably transfected on CHO cells, on the basis that (R,S)-2-phenylhydroxy-propynyl-5'-N-ethylcarboxyamidoadenosine [(R,S)-PHPNECA] was found to be a good agonist at the A2B receptor subtype. Biological studies demonstrated that the presence of small alkyl groups in N6-position of these molecules are well tolerated, whereas large groups abolished A2B potency. On the other hand, the presence of an ethyl group in the 4'-carboxamido function seems to be optimal, the (S)-PHPNECA resulting the most potent agonist at A2B receptor reported so far.