gebhart/patrepeval huggingface dataset:
Cathepsin cysteine proteases in cardiovascular disease (2007)

Extracellular matrix (ECM) remodeling is one of the underlying mechanisms in cardiovascular diseases. Cathepsin cysteine proteases have a central role in ECM remodeling and have been implicated in the development and progression of cardiovascular diseases. Cathepsins also show differential expression in various stages of atherosclerosis, and in vivo knockout studies revealed that deficiency of cathepsin K or S reduces atherosclerosis. Furthermore, cathepsins are involved in lipid metabolism. Cathepsins have the capability to degrade low-density lipoprotein and reduce cholesterol efflux from macrophages, aggravating foam cell formation. Although expression studies also demonstrated differential expression of cathepsins in cardiovascular diseases like aneurysm formation, neointima formation, and neovascularization, in vivo studies to define the exact role of cathepsins in these processes are lacking. Evaluation of the feasibility of cathepsins as a diagnostic tool revealed that serum levels of cathepsins L and S seem to be promising as biomarkers in the diagnosis of atherosclerosis, whereas cathepsin B shows potential as an imaging tool. Furthermore, cathepsin K and S inhibitors showed effectiveness in (pre) clinical evaluation for the treatment of osteoporosis and osteoarthritis, suggesting that cathepsin inhibitors may also have therapeutic effects for the treatment of atherosclerosis.
http://www.HIVmedicine.com (2007)

Abstract Free Medical Information http://www.freemedicalinformation.com by Bernd Sebastian Kamps is an online book that seeks to show physicians how to produce and market their own books. Under the aegis of his publishing house (Flying Publisher), this text is part of a project to publish free online books that cover the most important fields in medicine by the year 2010. Here Dr. Kamps addresses fundamental issues pertaining to the role of publishers in an information environment that is dominated by the Internet and the role of physicians in the dissemination of medical information. HIV Medicine (2005) is the pilot text in Kamps' movement to disseminate high quality free medical information via the Internet. This paper reviews HIV Medicine in the context of Free Medical Information in order to discern if this is a viable publishing model. doi:10.1300/ J383v04n01_15
The acylated form of protein D of Haemophilus influenzae is more immunogenic than the nonacylated form and elicits an adjuvant effect when it is used as a carrier conjugated to polyribosyl ribitol phosphate (1997)

The nonacylated form of protein D (PDm) of Haemophilus influenzae has been shown to induce the production of antibodies that are bactericidal to homologous and heterologous nontypeable H. influenzae (NTHi) strains. In this study, immunization of rats with lipoprotein D (LPD) induced higher levels of anti-protein D immunoglobulin G and A serum antibodies than immunization with PDm, and the bactericidal activities of sera from LPD-immunized rats were greater than those of sera from PDm-immunized rats. Immunization with LPD or PDm did not prevent the development of acute otitis media (AOM) when rats were challenged with 10(4) CFU of an NTHi strain. However, on the eighth day of bacterial challenge, 50% (5 of 10) of LPD-immunized rats had recovered from otitis media and 30% (3 of 10) had negative middle ear cultures, whereas only 30% (3 of 10) of PDm-immunized rats had recovered, though none was culture positive. Immunization with an inactivated homologous bacterial strain elicited 70% protection (i.e., 7 of 10 rats) in the rat otitis media model. LPD and PDm were also conjugated to the H. influenzae type b (Hib) capsular polysaccharide, polyribosyl ribitol phosphate (PRP), to test protein D-conjugated PRP vaccine's potential for protection against Hib infection. When two LPD-conjugated and two PDm-conjugated PRP vaccines, each containing a different protein concentration, and a tetanus toxoid-conjugated vaccine (ACT-HIB) were tested in the experimental model of rat otitis induced with a Hib strain (Minn A), both of the LPD-conjugated and one of the PDm-conjugated vaccines induced significant protection from AOM, the level of protection being highest in animals given the vaccine with the highest LPD content. Sera from these rats also manifested the highest anti-PRP and anti-LPD antibody levels and the highest bactericidal activities against a Hib strain and an NTHi strain.
Controlled n-Type Doping of Carbon Nanotube Transistors by an Organorhodium Dimer (2016)

Single-walled carbon nanotube (SWCNT) transistors are among the most developed nanoelectronic devices for high-performance computing applications. While p-type SWCNT transistors are easily achieved through adventitious adsorption of atmospheric oxygen, n-type SWCNT transistors require extrinsic doping schemes. Existing n-type doping strategies for SWCNT transistors suffer from one or more issues including environmental instability, limited carrier concentration modulation, undesirable threshold voltage control, and/or poor morphology. In particular, commonly employed benzyl viologen n-type doping layers possess large thicknesses, which preclude top-gate transistor designs that underlie high-density integrated circuit layouts. To overcome these limitations, we report here the controlled n-type doping of SWCNT thin-film transistors with a solution-processed pentamethylrhodocene dimer. The charge transport properties of organorhodium-treated SWCNT thin films show consistent n-type behavior when characterized in both Hall effect and thin-film transistor geometries. Due to the molecular-scale thickness of the organorhodium adlayer, large-area arrays of top-gated, n-type SWCNT transistors are fabricated with high yield. This work will thus facilitate ongoing efforts to realize high-density SWCNT integrated circuits.
Electrochemical Methods: Fundamentals and Applications (1980)

Major Symbols. Standard Abbreviations. Introduction and Overview of Electrode Processes. Potentials and Thermodynamics of Cells. Kinetics of Electrode Reactions. Mass Transfer by Migration and Diffusion. Basic Potential Step Methods. Potential Sweep Methods. Polarography and Pulse Voltammetry. Controlled--Current Techniques. Method Involving Forced Convention--Hydrodynamic Methods. Techniques Based on Concepts of Impedance. Bulk Electrolysis Methods. Electrode Reactions with Coupled Homogeneous Chemical Reactions. Double--Layer Structure and Adsorption. Electroactive Layers and Modified Electrodes. Electrochemical Instrumentation. Scanning Probe Techniques. Spectroelectrochemistry and Other Coupled Characterization Methods. Photoelectrochemistry and Electrogenerated Chemiluminescence. Appendix A: Mathematical Methods. Appendix B: Digital Simulations of Electrochemical Problems. Appendix C: Reference Tables. Index.
Processing of the carboxyl 15-amino acid extension in the alpha-chain of fibrinogen (1993)

The cDNA for the alpha-chain of human fibrinogen codes for 15 amino acids at the carboxyl terminus that are not found in the native protein circulating in plasma. In the present studies, experiments were designed to test whether the carboxyl extension was required for fibrinogen assembly or was simply the result of limited proteolysis and maturation of the protein during or following secretion. Baby hamster kidney cells were transfected with cDNAs coding for the alpha-, beta-, and gamma-chains, and the recombinant fibrinogen secreted into the cell culture medium was identified either with an antibody against the mature molecule or with an antibody directed toward the carboxyl extension of the alpha-chain. The secreted protein contained primarily two species of alpha-chains, including one with the carboxyl extension and one that was the same as that in plasma fibrinogen. A mutant fibrinogen, in which Arg-611 at the putative cleavage site in the alpha-chain was converted to Gly, was also readily assembled, and, in this case, the protein was secreted with the alpha-chain carboxyl extension. Similarly, a mutant fibrinogen that completely lacked the carboxyl extension of the alpha-chain was assembled and secreted from the transfected baby hamster kidney cells. These two mutants with modified alpha-chains were readily clotted by thrombin and cross-linked by factor XIIIa. These results indicate that the alpha-chain carboxyl extension in fibrinogen is not required for assembly or secretion of the molecule. Accordingly, it was concluded that the cleavage of the alpha-chain removing the carboxyl-terminal 15 amino acids is a normal and specific processing event occurring during the maturation of the protein.
Kinase Inhibitors:  Not Just for Kinases Anymore (2003)

Kinase inhibitors are widely employed as biological reagents and as leads for drug design. Their use is often complicated by their lack of specificity. Although binding conserved ATP sites accounts for some of their nonspecificity, some compounds inhibit proteins not known to bind ATP. It has been found that promiscuous hits from high-throughput screening may act as aggregates. To explore whether this mechanism might explain the action of widely used nonspecific kinase inhibitors, 15 such compounds were studied. Eight of these, rottlerin, quercetin, K-252c, bisindolylmaleimide I, bisindolylmaleimide IX, U0126, indirubin, and indigo, inhibited three diverse non-kinase enzymes. Inhibition was time-dependent and sensitive to enzyme concentration; by light scattering, the compounds formed particles of 100-1000 nm diameter. These observations suggest that these eight kinase inhibitors, at least at micromolar concentrations, are promiscuous and act as aggregates. Results obtained from the use of these compounds at micromolar or higher concentrations against individual enzymes should be interpreted cautiously.
Characterization of Human DNase I Family Endonucleases and Activation of DNase γ during Apoptosis (2000)

We describe here the characterization of the so far identified human DNase I family DNases, DNase I, DNase X, DNase gamma, and DNAS1L2. The DNase I family genes are found to be expressed with different tissue specificities and suggested to play unique physiological roles. All the recombinant DNases are shown to be Ca(2+)/Mg(2+)-dependent endonucleases and catalyze DNA hydrolysis to produce 3'-OH/5'-P ends. High activities for DNase I, DNase X, and DNase gamma are observed under neutral conditions, whereas DNAS1L2 shows its maximum activity at acidic pH. These enzymes have also some other peculiarities: different sensitivities to G-actin, aurintricarboxylic acid, and metal ions are observed. Using a transient expression system in HeLa S3 cells, the possible involvement of the DNases in apoptosis was examined. The ectopic expression of each DNase has no toxic effect on the host cells; however, extensive DNA fragmentation is observed only in DNase gamma-transfected cells after the induction of apoptosis. Furthermore, DNase gamma is revealed to be located at the perinuclear region in living cells, and to translocate into the nucleus during apoptosis. Our results demonstrate that DNase I, DNase X, DNase gamma, and DNAS1L2 have similar but unique endonuclease activities, and that among DNase I family DNases, DNase gamma is capable of producing apoptotic DNA fragmentation in mammalian cells.
Housekeeping and tissue-specific genes in mouse tissues (2007)

These identified housekeeping genes could represent appropriate controls for RT-PCR and northern blot when comparing the expression levels of genes in several tissues. The results reveal several tissue-specific genes highly expressed in testis and pituitary gland. Furthermore, the main function of tissue-specific genes expressed in liver, lung and bone is the cell defence, whereas several keratins involved in cell structure function are exclusively detected in skin and vagina. The results from this study can be used for example to target a tissue for agent delivering by using the promoter of tissue-specific genes. Moreover, this study could be used as basis for further researches on physiology and pathology of these tissues.
Academic Library Outreach to Minority Students: The Role the Library Plays in Meeting the Needs of Minority Students at Francis Marion University (2014)

As college student populations nationwide become more racially and ethnically diverse, it is imperative that academic libraries provide services and resources to meet the changing needs. In a span of nearly 20 years, Francis Marion University’s student population has shifted from 74% white and 24% black to nearly 50% black. Because of this, James A. Rogers Library at FMU is challenged with meeting these changing needs. In efforts to diversify its services, James A. Rogers Library gives biennial surveys to FMU students to assess student needs and perception of the library and in 2010, the library created an African-American collection.
Java 3D Programming (2002)

Java 3D Programming is a roadmap for application developers. It shows a path through the design issues and pitfalls they will face. The book starts by introducing the basic 3D graphics concepts and terminology, and proceeds, through a comprehensive set of programming examples, to illustrate the techniques, features, work-arounds, and bug fixes for practical Java 3D work.
Evidence that APC regulates survivin expression: a possible mechanism contributing to the stem cell origin of colon cancer. (2001)

Because colorectal cancers (CRCs) frequently display APC mutation, inhibition of apoptosis, and increased expression of the antiapoptotic protein survivin, we hypothesized that APC mutation inhibits apoptosis by allowing constitutive survivin expression. Using HT-29 CRC cell lines having inducible wild-type APC (wt-APC) or transfected dominant-negative TCF-4, we show that wt-APC down-regulates survivin expression via APC/beta-catenin/TCF-4 signaling. Using normal colonic epithelium, we found survivin by immunostaining/reverse transcription-PCR to be preferentially expressed in the lower crypt (which inversely correlates with wt-APC's expression pattern). Thus, wt-APC, by progressively decreasing survivin and increasing apoptosis from crypt bottom to top, may limit the population size of stem cells and other proliferative cells in the lower crypt; mutant APC may allow expansion of these populations, thereby initiating tumorigenesis.
Measurement of Soluble and Membrane‐Bound Interleukin 1 Using a Fibroblast Bioassay (2000)

Interleukin 1 (IL-1) is both a major mediator of inflammation and an important signal for activation and differentiation of lymphoid cells. IL-1 is produced by a large variety of cell types, but in most immunologic systems, activated macrophages are its major cellular source. This unit describes a bioassay for testing biological fluids based on the ability of IL-1 to induce IL-8 or IL-6 in fibroblasts. Also listed are sources of commercially available kits (ELISAs, immunoassays) to measure IL-1, and antibodies useful in setting up these assays.
Low-coherent quantitative phase microscope for nanometer-scale measurement of living cells morphology (2008)

We have developed a Linnik-type interference microscope provided with a low-coherent light source to obtain topographic images of an intact cellular membrane on a nanometer scale. Our technique is based on measurement of the interference between light reflected from the cell surface and a reference beam. The results show full field surface topography of cultured cells and reveal an intrinsic membrane motion of tens of nanometers.
Regulation of human immunodeficiency virus type 1 and cytokine gene expression in myeloid cells by NF-kappa B/Rel transcription factors (1995)

CD4+ macrophages in tissues such as lung, skin, and lymph nodes, promyelocytic cells in bone marrow, and peripheral blood monocytes serve as important targets and reservoirs for human immunodeficiency virus type 1 (HIV-1) replication. HIV-1-infected myeloid cells are often diminished in their ability to participate in chemotaxis, phagocytosis, and intracellular killing. HIV-1 infection of myeloid cells can lead to the expression of surface receptors associated with cellular activation and/or differentiation that increase the responsiveness of these cells to cytokines secreted by neighboring cells as well as to bacteria or other pathogens. Enhancement of HIV-1 replication is related in part to increased DNA-binding activity of cellular transcription factors such as NF-kappa B. NF-kappa B binds to the HIV-1 enhancer region of the long terminal repeat and contributes to the inducibility of HIV-1 gene expression in response to multiple activating agents. Phosphorylation and degradation of the cytoplasmic inhibitor I kappa B alpha are crucial regulatory events in the activation of NF-kappa B DNA-binding activity. Both N- and C-terminal residues of I kappa B alpha are required for inducer-mediated degradation. Chronic HIV-1 infection of myeloid cells leads to constitutive NF-kappa B DNA-binding activity and provides an intranuclear environment capable of perpetuating HIV-1 replication. Increased intracellular stores of latent NF-kappa B may also result in rapid inducibility of NF-kappa B-dependent cytokine gene expression. In response to secondary pathogenic infections or antigenic challenge, cytokine gene expression is rapidly induced, enhanced, and sustained over prolonged periods in HIV-1-infected myeloid cells compared with uninfected cells. Elevated levels of several inflammatory cytokines have been detected in the sera of HIV-1-infected individuals. Secretion of myeloid cell-derived cytokines may both increase virus production and contribute to AIDS-associated disorders.
Role of lipooligosaccharides in experimental dermal lesions caused by Haemophilus ducreyi (1991)

The mouse and rabbit intradermal injection models have been used to define factors that may be important in Haemophilus ducreyi pathogenesis. We used H. ducreyi strains with diverse geographic origins and phenotypic characteristics to evaluate the experimental models. Injection of live and heat-killed bacteria caused skin abscesses in both models. Semiquantitative cultures of skin injected with live bacteria showed that H. ducreyi failed to replicate in animal tissue. These data suggested that the experimental lesions were caused by a heat-stable substance such as lipooligosaccharide (LOS). In mice, injection of H. ducreyi and Haemophilus influenzae LOS and Escherichia coli lipopolysaccharide caused mild to moderate inflammation. In rabbits, injection of H. ducreyi LOS caused intradermal abscesses that were histologically similar to those caused by live and heat-killed bacteria. H. ducreyi and Neisseria gonorrhoeae LOS caused significantly larger lesions than equivalent amounts of H. influenzae LOS and E. coli lipopolysaccharide in the rabbit model. We conclude that the intradermal injection models are not valid models to study the growth of H. ducreyi in vivo. However, these data indicate that H. ducreyi LOS may play an important role in the pathogenesis of chancroid and that the rabbit model should be useful in studying H. ducreyi LOS toxicity at the cellular level.
The relationship between trinucleotide (GAA) repeat length and clinical features in Friedreich ataxia. (1996)

Friedreich ataxia (FA) is associated with the expansion of a GAA trinucleotide repeat in the first intron of the X25 gene. We found both alleles expanded in 67 FA patients from 48 Italian families. Five patients from three families were compound heterozygotes with expansion on one allele and an isoleucine-->phenylalanine change at position 154 on the other one. We found neither expansions nor point mutations in three patients. The length of FA alleles ranged from 201 to 1,186 repeat units, with no overlap with the normal range, and showed a negatively skewed distribution with a peak between 800 and 1,000 repeats. The FA repeat showed meiotic instability with a median variation of 150 repeats. The lengths of both larger and smaller alleles in each patient inversely correlated with age at onset of the disorder. Smaller alleles showed the best correlation, accounting for approximately 50% of the variation of age at onset. Mean allele length was significantly higher in patients with diabetes and in those with cardiomyopathy.
Congenital aneurysmal dilatation of the left auricle demonstrated by sequential cardiac blood-pool scintiscanning. (1978)

Congenital aneurysmal dilatation of the left auricle is a rare condition often associated with cardiac arrhythmias and systemic emboli. The diagnosis is made often by surgical exploration or presurgically by contrast angiography. A case is reported in which the dilated left auricle did not fill during contrast angiography but was demonstrated by sequential cardiac blood-pool scintiscanning.
The role of MLL in hematopoiesis and leukemia (2002)

The MLL gene, also called HRX or ALL-1, was originally identified as a recurrent chromosomal translocation in particular subtypes of acute lymphocytic leukemia (ALL) and acute myelogenous leukemia (AML). Reciprocal rearrangements of the MLL gene are most common in infant ALL and secondary AML. Because of the unique association with infant leukemia and the intriguingly immature and mixed lineage phenotype of leukemic cells, the authors speculate that the wild-type MLL gene plays an important role early in the development of the hematopoietic system. This article reviews recent progress in understanding the function of the wild-type MLL protein, with particular consideration of potential functions within the developing hematopoietic system. Murine gain- and loss-of-function models have provided clues to the normal functions of MLL and altered functions of oncogenic MLL fusion proteins. Biochemical and genetic approaches using other model organisms have also elucidated mechanisms by which these functions are achieved.
Rodent Models of Amyotrophic Lateral Sclerosis (2015)

Amyotrophic Lateral Sclerosis (ALS) is a motor neuron disease affecting upper and lower motor neurons in the central nervous system. Patients with ALS develop extensive muscle wasting and atrophy leading to paralysis and death 3 to 5 years after disease onset. The condition may be familial (fALS 10%) or sporadic ALS (sALS, 90%). The large majority of fALS cases are due to genetic mutations in the Superoxide dismutase 1 gene (SOD1, 15% of fALS) and repeat nucleotide expansions in the gene encoding C9ORF72 (∼ 40% to 50% of fALS and ∼ 10% of sALS). Studies suggest that ALS is mediated through aberrant protein homeostasis (i.e., ER stress and autophagy) and/or changes in RNA processing (as in all non-SOD1-mediated ALS). In all of these cases, animal models suggest that the disorder is mediated non-cell autonomously, i.e., not only motor neurons are involved, but glial cells including microglia, astrocytes, and oligodendrocytes, and other neuronal subpopulations are also implicated in the pathogenesis. Provided in this unit is a review of ALS rodent models, including discussion of their relative advantages and disadvantages. Emphasis is placed on correlating the model phenotype with the human condition and the utility of the model for defining the disease process. Information is also presented on RNA processing studies in ALS research, with particular emphasis on the newest ALS rodent models.