gebhart/patrepeval huggingface dataset:
Circulating MicroRNAs as Biomarkers for Hepatocellular Carcinoma (2011)

The addition of miR-16 to conventional serum markers improved sensitivity and specificity for HCC. Use of miR-16 for second-line testing in cases considered negative on the basis of conventional HCC markers should be explored in larger, prospective studies.
Control of Nanoparticle Location in Block Copolymers (2005)

A simple procedure is described to incorporate gold nanoparticles and control their location within symmetric poly(styrene-b-2 vinyl pyridine) (PS-PVP) diblock copolymers. Gold nanoparticles coated with thiol-terminated PS and/or PVP homopolymer chains (Mn approximately 1300 and 1500 g/mol, respectively) are incorporated into alternating lamellar layers of PS and PVP (total Mn approximately 196 500 g/mol). The location of the particles is controlled by varying the composition of ligands on the particle surfaces. In particular, gold particles coated with 100% PS or PVP reside near the center of the respective polymer domains, while particles coated with a mixture of both homopolymers reside at the interfaces between the two blocks.
Cantharidin, another natural toxin that inhibits the activity of serine/threonine protein phosphatases types 1 and 2A (1993)

Cantharidin, a natural toxicant of blister beetles, is a strong inhibitor of protein phosphatases types 1 (PP1) and 2A (PP2A). Like okadaic acid, cantharidin inhibits the activity of the purified catalytic subunit of PP2A (IC50 = 0.16 microM) at a lower concentration than that of PP1 (IC50 = 1.7 microM) and only inhibits the activity of protein phosphatase type 2B (PP2B) at high concentrations. Dose-inhibition studies conducted with whole cell homogenates indicate that cantharidin also inhibits the native forms of these enzymes. Thus, cantharidin, which is economical and readily available, may be useful as an additional probe for studying the functions of serine/threonine protein phosphatases.
Ethics and Methodology in Legal Theory a (Personal) Research Anti-Manifesto (2002)

The attitude of the critical researcher, as opposed to the traditional researcher into 'objective' knowledge, lies in the conviction that the theorist-researcher is no mere observer or discoverer of knowledge, but is herself embedded in the social, historical, political context in which knowledge is formed (Horkheimer 1968). The critical researcher therefore aims to be self-reflective, and attentive to the conventional dimensions of scholarship. Some methodological questions for the critical researcher might be -- what are the norms of 'good' scholarship, where do these derive from in cultural or political terms, on what basis can they be defended, and how should they be challenged or re-formed? Another question of some significance is -- how do ethical and political beliefs influence the substance and methodology of research? This is the issue which I want to focus upon in this brief article, focusing particularly upon methodology.
Three-dimensional photoacoustic imaging of blood vessels in tissue (1998)

We applied photoacoustics as a tissue tomography technique for the detection of blood concentrations, e.g., angiogenesis around tumors. We imaged blood vessels in highly scattering samples, using 532-nm light, to depths of ~1 cm . The samples were real tissue (chicken breast) or 10% dilutions of Intralipid-10%. The blood flowed through nylon capillaries. Polyvinylidene difluoride (PVdF) piezoelectric detectors were used in a surface-scanning mode. We demonstrate the sensitivity of the technique by photoacoustic detection of single red blood cells upon a glass plate. Lateral resolution is limited by the detector diameter (200 microm). The depth resolution is ~10 microm.
The blood volumes of the primary and secondary circulatory system in the Atlantic codGadus morhuaL., using plasma bound Evans Blue and compartmental analysis (2003)

The volume of the primary (PCS) and secondary (SCS) circulatory system in the Atlantic cod Gadus morhua was determined using a modified dye dilution technique. Cod (N=10) were chronically cannulated in the second afferent branchial artery with PE-50 tubing. Evans Blue dye was bound to harvested fish plasma at a concentration of 1 mg dye ml(-1) plasma, and injected at a concentration of 1 mg kg(-1) body mass. Serial sampling from the cannula produced a dye dilution curve, which could be described by a double exponential decay equation. Curve analysis enabled the calculation of the primary circulatory and total distribution volume. The difference between these volumes is assumed to be the volume of the SCS. From the dilution curve, it was also possible to calculate flow rates between and within the systems. The results of these experiments suggest a plasma volume in the PCS of 3.42+/-0.89 ml 100 g(-1) body mass, and in the SCS of 1.68+/-0.35 ml 100 g(-1) body mass (mean +/- S.D.) or approximately 50% that of the PCS. Flow rates to the SCS were calculated as 2.7% of the resting cardiac output. There was an allometric relationship between body mass and blood volumes. Increasing condition factor showed a tendency towards smaller blood volumes of the PCS, expressed as percentage body mass, but this was not evident for the volume of the SCS.
MAD analyses of yeast 5-aminolaevulinate dehydratase: their use in structure determination and in defining the metal-binding sites (2000)

MAD experiments attempting to solve the structure of 5--aminolaevulinic acid dehydratase using Zn and Pb edges are described. The data obtained proved insufficient for a complete structure solution but were invaluable in subsequent identification of metal-binding sites using anomalous difference Fourier analyses once the structure of the enzyme had been solved. These sites include the highly inhibitory substitution of an enzymic cofactor Zn(2+) ion by Pb(2+) ions, which represents a major contribution towards understanding the molecular basis of lead poisoning. The MAD data collected at the Pb edge were also used with isomorphous replacement data from the same Pb co-crystal and a Hg co-crystal to provide the first delineation of the enzyme's quaternary structure. In this MADIR analysis, the Hg co-crystal data were treated as native data. Anomalous difference Fouriers were again used, revealing that Hg(2+) had substituted for the same Zn(2+) cofactor ion as had Pb(2+), a finding of fundamental importance for the understanding of mercury poisoning. In addition, Pt(2+) ions were found to bind at the same place in the structure. The refined structures of the Pb- and the Hg-complexed enzymes are presented at 2.5 and 3.0 A resolution, respectively.
Multicomponent Polymers of Poly(Lactic Acid) Macromonomers with Methacrylate Terminal and Copolymers of Poly(2-Hydroxyethyl Methacrylate) (1996)

Abstract Poly(lactic acid) macromonomers with methacrylate terminal functionality have been synthesized from the cyclic dimer of lactic acid (referred to as lactide) with 2-hydroxyethyl methacrylate (HEMA) as initiator and stannous 2-ethyl hexanoate as catalyst. The macromonomers were characterized with FT-IR, NMR, GPC, DSC, WAXS, and CD. The molecular weights of the macromonomers ranging from M n 1425 to 19,169 are predictable from the lactide/HEMA ratio in the polymerization feeds. The properties of the macromonomers vary with the stereochemistry of the lactide and the composition. Circular dichroism measurements demonstrate that there is little racemization during polymerization.
N,N′‐Dialkyl‐ and N‐Alkyl‐N‐mesityl‐Substituted N‐Heterocyclic Carbenes as Ligands in Grubbs Catalysts (2006)

Various symmetrically and asymmetrically substituted N-heterocyclic carbene (NHC) ligands bearing aliphatic nitrogen-containing side groups have been synthesised. In our attempts to isolate the corresponding second-generation Grubbs catalysts, we were unsuccessful when using the symmetrical aliphatic NHC ligands. For the asymmetrical ligands bearing an aliphatic moiety on one side and an aromatic mesityl group on the other side, substitution of a phosphine ligand was achieved. The performance of a so-formed series of Ru-based metathesis initiators has been evaluated for the ring-opening metathesis polymerisation (ROMP) of cycloocta-1,5-diene and the ring-closing metathesis (RCM) of diethyl diallylmalonate.
The Chondroitin Sulfate Proteoglycans Neurocan and Phosphacan Are Expressed by Reactive Astrocytes in the Chronic CNS Glial Scar (1999)

Chondroitin sulfate proteoglycans (CS-PGs) expressed by reactive astrocytes may contribute to the axon growth-inhibitory environment of the injured CNS. The specific potentially inhibitory CS-PGs present in areas of reactive gliosis, however, have yet to be thoroughly examined. In this study, we used immunohistochemistry, combined immunohistochemistry-in situ hybridization, immunoblot analysis, and reverse transcription-PCR to examine the expression of specific CS-PGs by reactive astrocytes in an in vivo model of reactive gliosis: that is, the glial scar, after cortical injury. Neurocan and phosphacan can be localized to reactive astrocytes 30 d after CNS injury, whereas brevican and versican are not expressed in the chronic glial scar. Neurocan is also expressed by astrocytes in primary cell culture. Relative to the amount present in cultured astrocytes or uninjured cortex, neurocan expression increases significantly in the glial scar resulting from cortical injury, including the re-expression of the neonatal isoform of neurocan. In contrast, phosphacan protein levels are decreased in the glial scar compared with the uninjured brain. Because these CS-PGs are capable of inhibiting neurite outgrowth in vitro, our data suggest that phosphacan and neurocan in areas of reactive gliosis may contribute to axonal regenerative failure after CNS injury.
Approved Antiviral Drugs over the Past 50 Years (2016)

Since the first antiviral drug, idoxuridine, was approved in 1963, 90 antiviral drugs categorized into 13 functional groups have been formally approved for the treatment of the following 9 human infectious diseases: (i) HIV infections (protease inhibitors, integrase inhibitors, entry inhibitors, nucleoside reverse transcriptase inhibitors, nonnucleoside reverse transcriptase inhibitors, and acyclic nucleoside phosphonate analogues), (ii) hepatitis B virus (HBV) infections (lamivudine, interferons, nucleoside analogues, and acyclic nucleoside phosphonate analogues), (iii) hepatitis C virus (HCV) infections (ribavirin, interferons, NS3/4A protease inhibitors, NS5A inhibitors, and NS5B polymerase inhibitors), (iv) herpesvirus infections (5-substituted 2'-deoxyuridine analogues, entry inhibitors, nucleoside analogues, pyrophosphate analogues, and acyclic guanosine analogues), (v) influenza virus infections (ribavirin, matrix 2 protein inhibitors, RNA polymerase inhibitors, and neuraminidase inhibitors), (vi) human cytomegalovirus infections (acyclic guanosine analogues, acyclic nucleoside phosphonate analogues, pyrophosphate analogues, and oligonucleotides), (vii) varicella-zoster virus infections (acyclic guanosine analogues, nucleoside analogues, 5-substituted 2'-deoxyuridine analogues, and antibodies), (viii) respiratory syncytial virus infections (ribavirin and antibodies), and (ix) external anogenital warts caused by human papillomavirus infections (imiquimod, sinecatechins, and podofilox). Here, we present for the first time a comprehensive overview of antiviral drugs approved over the past 50 years, shedding light on the development of effective antiviral treatments against current and emerging infectious diseases worldwide.
The aliasing problem in computer-generated shaded images (1977)

Certain defects, such as jagged edges and disappearing detail, have long been an annoyance in digitally generated shaded images. Although increasing the resolution or defocusing the display can attenuate them, an understanding of these defects leads to more effective methods. This paper explains the observed defects in terms of the aliasing phenomenon inherent in sampled signals and discusses prefiltering as a recognized cure. A method for evaluating filters is presented, the application of prefiltering to hidden-surface algorithms is discussed, and an implementation of a filtering tiler is shown accompanied by examples of its effectiveness.
An isochore map of human chromosomes (2006)

Isochores are large DNA segments (>>300 kb on average) that are characterized by an internal variation in GC well below the full variation seen in the mammalian genome. Precisely defining in terms of size and composition as well as mapping the isochores on human chromosomes have, however, remained largely unsolved problems. Here we used a very simple approach to segment the human chromosomes de novo, based on assessments of GC and its variation within and between adjacent regions. We obtain a complete coverage of the human genome (neglecting the remaining gaps) by approximately 3200 isochores, which may be visualized as the ultimate chromosomal bands. Isochores visibly belong to five families characterized by different GC levels, as expected from previous investigations. Since we previously showed that isochores are tightly linked to basic biological properties such as gene density, replication timing, and recombination, the new level of detail provided by the isochore map will help the understanding of genome structure, function, and evolution.
<title>Correlation between aluminum alloy sputtering target metallurgical characteristics, arc initiation, and in-film defect intensity</title> (1997)

Increasing levels of metallization, shrinking device geometries, and stringent defect density requirements have led to a continuous focus in the semiconductor manufacturing community to reduce defects generated during metal deposition by PVD techniques. Of particular interest in the metallization community is the reduction in in-film defect density in sputtered aluminum films. Pareto analysis of in-film defects in currently used interconnect metallization schemes suggest that a considerable portion of the in-film defects (up to 50%) are caused by unipolar arcing during aluminum deposition. Due to their unusual molten appearance, these defects are commonly referred to as splats. These defects can be as large as 500 micrometers , and due to their frequency of occurrence and size can significantly impact device yield in a manufacturing environment. Systematic investigations have revealed that the formation of splats, due to unipolar arcing, can be strongly correlated to the metallurgy of the aluminum alloy targets used during aluminum sputter deposition. The presence of undesirable metallurgical attributes such as alumina inclusions, porosity, oxygen content etc. are the primary causes for the occurrence of unipolar arcing. These undesirable metallurgical attributes appear to be the result of the manufacturing processes used to manufacture the aluminum alloy targets. The results of this study indicate that significant improvement in defect generation due to unipolar arcing during sputter deposition of aluminum films, and hence an improvement in device yield, is possible by reduction/elimination of the various undesirable metallurgical attributes in the aluminum alloy targets.
Patterns of chemokines and chemokine receptors expression in different forms of human periodontal disease (2003)

Current knowledge states that periodontal diseases are chronic inflammatory reactions raised in response to periodontopathogens. Many cell types and mediators, including Th1 and Th2 lymphocytes, cytokines and chemokines, appear to be involved in the immunopathogenesis of periodontal diseases. Chemokines, a family of chemotactic cytokines, bind to specific receptors and selectively attract different cell subsets to the inflammatory site. They can also interact with classical cytokines and modulate the local immune response. In order to study the role of chemokines in periodontal diseases, we examined the expression of chemokines, chemokine receptors and cytokines by means of reverse transcription-polymerase chain reaction (RT-PCR) techniques. Characteristic patterns of such factors' expression were found in gingival biopsies from patients presenting with aggressive periodontitis and chronic periodontitis. The expression of the chemokines macrophage inflammatory protein-1 alpha (MIP-1alpha) and interferon-gamma inducible protein 10 (IP-10) and of their respective receptors, CCR5 and CXCR3, were more prevalent and higher in aggressive periodontitis, and associated with higher interferon-gamma (IFN-gamma) expression and lower interleukin-10 (IL-10) expression. In contrast, chronic periodontitis patients exhibited a more frequent and higher expression of monocyte chemoattractant protein-1 (MCP-1) and its receptor CCR4, and higher expression of IL-10. It is possible that chemokines, in addition to the classical cytokines, are involved in the immunopathogenesis of periodontal disease, driving the migration and the maintenance of several inflammatory cell types such as polymorphonuclear leukocytes, dendritic cells (DCs), natural killer cells, macrophages, and subsets of lymphocytes in the gingival tissues. These cells are thought to participate in the inflammatory and immune reaction that takes place in periodontal disease, killing pathogens, presenting antigens, and producing cytokines. The selective recruitment of polarized lymphocyte subsets could result in differential cytokine production at the site of response, which is supposed to determine the stable or progressive nature of the lesion. Besides, the role of chemokines as activators and chemoattracts of osteclasts may be involved in the determination of disease severity.
Combined Treatment of Intrapancreatic Autologous Bone Marrow Stem Cells and Hyperbaric Oxygen in Type 2 Diabetes Mellitus (2008)

The objective of this study was to determine whether the combination therapy of intrapancreatic autologous stem cell infusion (ASC) and hyperbaric oxygen treatment (HBO) before and after ASC can improve islet function and metabolic control in patients with type 2 diabetes mellitus (T2DM). This prospective phase 1 study enrolled 25 patients with T2DM who received a combination therapy of intrapancreatic ASC and peri-infusion HBO between March 2004 and October 2006 at Stem Cells Argentina Medical Center Buenos Aires, Argentina. Clinical variables (body mass index, oral hypoglycemic drugs, insulin requirement) and metabolic variables (fasting plasma glucose, C-peptide, HbA1c, and calculation of C-peptide/glucose ratio) were assessed over quartile periods starting at baseline and up to 1 year follow-up after intervention. Means were calculated in each quartile period and compared to baseline. Seventeen male and eight female patients were enrolled. Baseline variables expressed as means +/- SEs were: age 55 +/- 2.14 years, diabetes duration 13.2 +/- 1.62 years, insulin dose 34.8 +/- 2.96 U/day, and BMI 27.11 +/- 0.51. All metabolic variables showed significant improvement when comparing baseline to 12 months follow-up, respectively: fasting glucose 205.6 +/- 5.9 versus 105.2 +/- 14.2 mg/dl, HbAlc 8.8 +/- 0.2 versus 6.0 +/- 0.4%, fasting C-peptide 1.5 +/- 0.2 versus 3.3 +/- 0.3 ng/ml, C-peptide/glucose ratio 0.7 +/- 0.2 versus 3.5 +/- 0.3, and insulin requirements 34.8 +/- 2.9 versus 2.5 +/- 6.7 U/day. BMI remained constant over the 1-year follow-up. Combined therapy of intrapancreatic ASC infusion and HBO can improve metabolic control and reduce insulin requirements in patients with T2DM. Further randomized controlled clinical trials will be required to confirm these findings.
Brief report: CD24 and CD44 mark human intestinal epithelial cell populations with characteristics of active and facultative stem cells (2013)

Recent seminal studies have rapidly advanced the understanding of intestinal epithelial stem cell (IESC) biology in murine models. However, the lack of techniques suitable for isolation and subsequent downstream analysis of IESCs from human tissue has hindered the application of these findings toward the development of novel diagnostics and therapies with direct clinical relevance. This study demonstrates that the cluster of differentiation genes CD24 and CD44 are differentially expressed across LGR5 positive "active" stem cells as well as HOPX positive "facultative" stem cells. Fluorescence-activated cell sorting enables differential enrichment of LGR5 (CD24-/CD44+) and HOPX (CD24+/CD44+) cells for gene expression analysis and culture. These findings provide the fundamental methodology and basic cell surface signature necessary for isolating and studying intestinal stem cell populations in human physiology and disease.
Scanning electron microscopy and immunohistochemical observations of the vascular nerve plexuses in the dental pulp of rat incisor (1998)

It has become evident that the large terminal arterioles in the rat incisors receive a dense nerve supply and provide well-developed wall architecture, suggesting an important role of neuronal regulation on the vessels.
Characterization of a new human lymphoma cell line (RC-K8) with t(11;14) chromosome abnormality (1986)

A human cell line (RC-K8) that produces plasminogen activator was established from the peritoneal effusion of a patient with histiocytic lymphoma. The RC-K8 cell line grew mainly in single cell suspension and consisted of primitive cells with pleomorphic morphology. RC-K8 cells were positive for alpha-naphthyl butyrate esterase, acid phosphatase and periodic acid-Schiff stainings. Immunologic and molecular biological studies showed that RC-K8 cells reacted with monoclonal antibodies to B cell antigens (B1 and Leu12) and Ia antigen (OKIa1) and possessed immunoglobulin gene rearrangement in the absence of surface and cytoplasmic immunoglobulin. Neither Epstein-Barr virus nuclear antigen nor terminal deoxynucleotidyl transferase was detected in the cells. Chromosome analysis of RC-K8 disclosed 46 XY with complex abnormalities including t(11;14)(q23;q32). Intraperitoneal inoculation of RC-K8 cells to immunosuppressed newborn hamsters produced massive metastatic tumors in the lungs. The RC-K8 cell line will be of considerable value for the study of lymphomagenesis associated with t(11;14) and pulmonary metastasis of lymphoma cells.
Multiple domains in endoglucanase B (CenB) from Cellulomonas fimi: functions and relatedness to domains in other polypeptides (1991)

Endoglucanase B (CenB) from the bacterium Cellulomonas fimi is divided into five discrete domains by linker sequences rich in proline and hydroxyamino acids (A. Meinke, C. Braun, N. R. Gilkes, D. G. Kilburn, R. C. Miller, Jr., and R. A. J. Warren, J. Bacteriol. 173:308-314, 1991). The catalytic domain of 608 amino acids is at the N terminus. The sequence of the first 477 amino acids in the catalytic domain is related to the sequences of cellulases in family E, which includes procaryotic and eucaryotic enzymes. The sequence of the last 131 amino acids of the catalytic domain is related to sequences present in a number of cellulases from different families. The catalytic domain alone can bind to cellulose, and this binding is mediated at least in part by the C-terminal 131 amino acids. Deletion of these 131 amino acids reduces but does not eliminate activity. The catalytic domain is followed by three domains which are repeats of a 98-amino-acid sequence. The repeats are approximately 50% identical to two repeats of 95 amino acids in a chitinase from Bacillus circulans which are related to fibronectin type III repeats (T. Watanabe, K. Suzuki, K. Oyanagi, K. Ohnishi, and H. Tanaka, J. Biol. Chem. 265:15659-15665, 1990). The C-terminal domain of 101 amino acids is related to sequences, present in a number of bacterial cellulases and xylanases from different families, which form cellulose-binding domains (CBDs). It functions as a CBD when fused to a heterologous polypeptide. Cells of Escherichia coli expressing the wild-type cenB gene accumulate both native CenB and a stable proteolytic fragment of 41 kDa comprising the three repeats and the C-terminal CBD. The 41-kDa polypeptide binds to cellulose but lacks enzymatic activity.