gebhart/patrepeval huggingface dataset:
Bayesian networks (1995)

This brief tutorial on Bayesian networks serves to introduce readers to some of the concepts, terminology, and notation employed by articles in this special section. In a Bayesian network, a variable takes on values from a collection of mutually exclusive and collective exhaustive states. A variable may be discrete, having a finite or countable number of states, or it may be continuous. Often the choice of states itself presents an interesting modeling question. For example, in a system for troubleshooting a problem with printing, we may choose to model the variable “print output” with two states—“present” and “absent”—or we may want to model the variable with finer distinctions such as “absent,” “blurred ,” “cut off,” and “ok.”
Immunization with antigen and interleukin 2 in vivo overcomes Ir gene low responsiveness. (1985)

We studied the effect of purified interleukin 2 (IL-2), made by recombinant DNA techniques, on the serum antibody response to myoglobin in high- and low-responder mice. Previous studies (6, 7) have shown that this response is controlled by H-2-linked Ir genes. The IL-2 was emulsified with the antigen in complete Freund's adjuvant to provide a sustained high local concentration. In low-responder B10.BR mice, a single dose (optimum 50,000 U) resulted in a consistent 10-50-fold increase in specific serum antibody throughout the time course of the response, from 10 d to 46 d after immunization. In contrast, no effect of IL-2 was seen in congenic high-responder B10.D2 mice. With IL-2, the low-responder mice achieved specific antibody levels comparable to those of high responders. Vehicle alone had no effect, and IL-2 alone, without antigen, did not induce myoglobin-specific antibody. No effect of IL-2 was seen in athymic nude mice of high-responder H-2 haplotype. The effect of IL-2 may be on a small number of responding T cells in the low responder mice, but it is possible that IL-2 also acts directly on B cells in a response that remains T-dependent, and therefore is not observed in athymic mice. We suggest that IL-2 may enhance suboptimal T cell help in the low responder, whereas help is not limiting in the high responder. This approach may enable the study of antibody responses in low responders otherwise too weak to analyze, and may be useful in producing antibodies to poorly immunogenic antigens. Potential clinical uses include immunization with weak antigens in normal patients, or with any antigen in certain immunodeficient patients.
Identification of novel prostate‐specific antigen‐binding peptides modulating its enzyme activity (2000)

Prostate-specific antigen (PSA) is a serine protease with highly prostate-specific expression. Measurement of PSA in serum is widely used for diagnosis and monitoring of prostate cancer. PSA dissolves the seminal gel forming after ejaculation. It has been suggested to mediate invasion and metastasis of prostate cancer but also to exert antiangiogenic activity. We have identified peptides specific for PSA by screening cyclic phage display peptide libraries. PSA-binding peptides were isolated from four different libraries and produced as a fusion protein with glutathione S-transferase (GST). The phage and fusion proteins were shown to bind to PSA specifically as indicated by lack of binding to other serine proteinases. A peptide with four cysteines showed the highest affinity for PSA. Zn2+, an inhibitor of PSA activity, increased the affinity of the peptides to PSA. The binding specificity was characterized by cross-inhibition using monoclonal anti-PSA antibodies of known epitope specificities. The peptides bound to the same region as mAbs specific for free PSA indicating that they bind close to the active site of the enzyme. The peptides enhanced the enzyme activity of PSA against a chromogenic substrate. These results show that peptides binding to PSA and modulating its enzyme activity can be developed by phage display technique. The peptides have the potential to be used for identification of PSA variants and for imaging and targeting of prostatic tumors.
Rethinking on Challenging “Ricardo Law” and Construct Innovative and Harmonious China (2009)

Developed countries, heading by the United States, have been trying to break away from the “Ricardo law” circle, while the US financial crisis has once again declared its failure. As the biggest developing country, China is now challenging the “Ricardo Law”. This paper has a brief rethinking on the western conflictive and harmonious thoughts of World development in order to probe on our ongoing harmonious socialist development. 


Key words: financial crisis; western economics; Ricardo Law; conflictive and harmonious thoughts; harmonious society
Anti-herpesvirus activity of the acyclic nucleoside 9-(1,3-dihydroxy-2-propoxymethyl)guanine (1983)

The antiherpetic effects of a novel purine acyclic nucleoside, 9-(1,3-dihydroxy-2-propoxymethyl)guanine (DHPG), were compared with those of acyclovir in cell cultures and in mice. The modes of action of DHPG and acyclovir were similar in that herpes thymidine kinase phosphorylated each compound, and both agents selectively inhibited viral over host cell DNA synthesis. In 50% plaque reduction assays in Vero cells, the drugs inhibited herpes simplex virus types 1 and 2 thymidine kinase-positive strains at 0.2 to 2.4 microM. DHPG was markedly more active than acyclovir against human cytomegalovirus (50% inhibitory doses were 7 and 95 microM, respectively). Each nucleoside inhibited uninfected cell macromolecule synthesis and cell proliferation at concentrations far above those required to inhibit herpes simplex virus replication. Although the two compounds had many similarities in their behavior in vitro, the important difference was the superior performance of DHPG against herpesvirus-induced encephalitis and vaginitis in vivo. Thus, mortality in mice infected with herpesvirus type 2 was reduced 50% by daily doses of 7 to 10 mg of DHPG/kg, whereas an equally effective daily dose of acyclovir was approximately 500 mg/kg. DHPG at a daily dose of 50 mg/kg was also superior to acyclovir at 100 mg/kg per day in its inhibition of herpetic vaginal lesions in mice.
Aflibercept in wet age-related macular degeneration: a perspective review (2012)

In the treatment of neovascular age-related macular degeneration (AMD), vascular endothelial growth factor (VEGF) has emerged as a key target of therapy. Currently, patients with neovascular AMD are treated with monthly intravitreal injections of anti-VEGF medications. Aflibercept is a novel recombinant fusion protein engineered to bind all isoforms of VEGF-A, VEGF-B, and placental growth factor. It is the latest medication to receive US Federal Drug Administration (FDA) approval for the treatment of neovascular AMD. Theoretical models suggest this molecule may have a longer duration of action compared with current treatments. The results of the VEGF Trap-Eye: Investigation of Efficacy and Safety in wet Age-related Macular Degeneration studies (VIEW 1 and VIEW 2) support this by demonstrating that aflibercept, dosed every 2 months after a monthly loading dose for 3 months, was noninferior in the proportion of patients who maintained or improved vision at 52 weeks compared with monthly injections of ranibizumab. These results were maintained over the 2 years of the studies. Aflibercept (Eylea; Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA and Bayer, Basel, Switzerland) was approved by the FDA for the treatment of neovascular AMD on 18 November 2011.
Structural and Functional Studies of the Tryptic Core of the Human Chorionic Gonadotropin β-Subunit* (1987)

The beta-subunit of hCG was digested with trypsin to produce a modified form of the subunit for structure-function and immunological studies. After digestion of hCG beta with trypsin, the residual disulfide-linked core was isolated and found to be lacking the carboxy-terminal peptide (residues 115-145) and to contain bond cleavages between residues 2-3, 43-44, 74-75, and 95-96. The locations of these bond cleavages within the disulfide-bridged core were identified by isolation of the following peptides after reduction and S-carboxymethylation of the trypsin beta-core: beta 1-43, beta 3-43, beta 44-74, beta 44-95, beta 75-95, and beta 96-114. The circular dichroic spectrum of the tryptic beta-core over the wavelength region of about 200-320 nm was similar to that of the native subunit. In addition, the tryptic beta-core retained nearly full immunopotency in both polyclonal and monoclonal competitive RIAs and could combine with complementary native alpha-subunit. The hybrid, composed of the tryptic beta-core and native alpha, was purified and displayed a molar potency of about 0.1% relative to intact hCG in both a radioreceptor assay and an adenylate cyclase assay. Thus, the hybrid retained little biological activity. Although the extensive bond cleavages in the tryptic beta-core did not appear to change its secondary and tertiary structure sufficiently to significantly alter the circular dichroic spectrum, the immunoreactivity, or the capability to combine with its alpha-subunit complement, the biological functional integrity of the tryptic beta-core-containing hybrid was essentially abolished. Hence, the tryptic beta-core provides a useful derivative for detailed structure-function studies aimed at defining the necessary determinants for subunit association, receptor binding, and subsequent biological actions.
An influenza N1 neuraminidase-specific monoclonal antibody with broad neuraminidase inhibition activity against H5N1 HPAI viruses (2011)

H5N1 avian influenza continues to be a potential pandemic threat. Several vaccine candidates based on potentially pandemic influenza strains and antiviral drugs have been tested in preclinical and clinical studies. The data obtained so far have shown some promise, but have also revealed some shortcomings with both of these approaches. We have identified and characterized an H5N1 neuraminidasespecific monoclonal antibody which specifically inhibits N1 neuraminidase activity of highly pathogenic avian influenza (HPAI) strains from clades 1 and 2. We have also shown the protective efficacy of this antibody in animal challenge models using homologous virus. Specific and effective inhibition of N1 NA could make this mAb a useful therapeutic tool in the treatment of human infection, in particular with oseltamivirand zanamivir-resistant strains of HPAI.
In Vitro Effect of Penetration Enhancers on Sodium Nonivamide Acetate in Rat Skin. (1995)

Sodium nonivamide acetate (SNA) is a newly synthetic analogue of capsaicin which produces no overt pungent sensation or irritation. In this present study, the effects and roles of penetration enhancers for SNA through rat skin were investigated by in vitro skin penetration experiment and differential scanning calorimeter (DSC) determination. The penetration fluxes of SNA after the incorporation of enhancers increased in the order of Polysorbate 20 < sodium laurylsulfate < or = benzalkonium chloride. This result was consistent with that of DSC profiles which indicated the disruptive effects of surfactants on the rat stratum corneum increased in the order of Polysorbate 20 < sodium laurylsulfate < benzalkonium chloride. The information gained is particularly helpful in the development of SNA transdermal drug delivery system.
Low-Tube-Voltage, High-Tube-Current Multidetector Abdominal CT: Improved Image Quality and Decreased Radiation Dose with Adaptive Statistical Iterative Reconstruction Algorithm—Initial Clinical Experience (2009)

Compared with standard FBP reconstruction, an ASIR algorithm improves image quality and has the potential to decrease radiation dose at low-tube-voltage, high-tube-current multidetector abdominal CT during the late hepatic arterial phase.
The Identification of Uncultured Microbial Pathogens (1993)

Clinicians have long been aware of human diseases that are associated with visible but uncultured microorganisms. Without the ability to cultivate these organisms, they have remained unidentified. Environmental microbiologists have also discovered on the basis of recent advances in the field of molecular phylogeny that culture-based methods for detecting microorganisms are biased and insensitive. A culture-independent experimental approach is described for the identification of microbial pathogens. This approach incorporates fundamental aspects of 16S rRNA-based molecular phylogeny as well as nucleic acid amplification technology. From its application to Whipple's disease, one can speculate as to the potential insights a highly sensitive, culture-independent method may provide into the diversity and natural ecology of human microbial pathogens.
Molecular selection of human antibodies with an unconventional bacterial B cell antigen. (1993)

Unconventional Ag for B cells that are comparable to known superantigens for T lymphocytes have not been well characterized. However, the bacterial membrane protein, Staphylococcal protein A (SpA), has sites that interact with the Fab of many IgM, IgA, IgG, and IgE, and in recent reports we have provided evidence of VH restriction in Fab that bind SpA. To investigate the molecular basis for this Fab binding specificity, we have selected monoclonal Fab from a phage-display combinatorial Ig library, based on the ability to bind SpA. By this approach, in an unselected human polyclonal IgG Fab library, about 17% of antibody-expressing clones were found to bind SpA. SpA binding was completely restricted to Fab with VH3 H chains, and about 60% of VH3 Fab in the unselected library had SpA binding capacity. Analysis of 21 VH sequences and 6 VL sequences demonstrated that Fab that bind SpA use diverse VH3 genes, while the L chains derive from a variety of V kappa and V lambda gene families. By creation of antibodies with differential H-L chain pairing, the global capacity to bind SpA was shown to be dictated by VH3 usage, but different L chain usage could result in up to a fourfold change in binding affinity. The apparent KD of the SpA binding by different Fab ranged from 2.5 x 10(-7) to > 10(-5) M. Furthermore, repeated rounds of in vitro panning selected for antibodies based on higher binding affinity. These data indicate that the pattern of VH family restriction of Ig reactive with SpA is comparable to known superantigens, and there is a hierarchy within the binding affinities of VH3 Fab based on V gene usage.
Identification of Critical Staphylococcal Genes Using Conditional Phenotypes Generated by Antisense RNA (2001)

Comprehensive genomic analysis of the important human pathogen Staphylococcus aureus was achieved by a strategy involving antisense technology in a regulatable gene expression system. In addition to known essential genes, many genes of unknown or poorly defined biological function were identified. This methodology allowed gene function to be characterized in a comprehensive, defined set of conditionally growth-defective/lethal isogenic strains. Quantitative titration of the conditional growth effect was performed either in bacterial culture or in an animal model of infection. This genomic strategy offers an approach to the identification of staphylococcal gene products that could serve as targets for antibiotic discovery.
Affinity depletion versus relative protein enrichment: a side-by-side comparison of two major strategies for increasing human cerebrospinal fluid proteome coverage (2019)

Cerebrospinal fluid (CSF) is in direct contact with the central nervous system. This makes human CSF an attractive source of potential biomarkers for neurologic diseases. Similarly to blood plasma, proteomic analysis of CSF is complicated by a high dynamic range of individual protein concentrations and by the presence of several highly abundant proteins. To deal with the abundant human CSF proteins, methods developed for blood plasma/serum are routinely used. Multiple affinity removal systems and protein enrichment of less abundant proteins using a combinatorial peptide ligand library are among the most frequent approaches. However, their relative impact on CSF proteome coverage has never been evaluated side-by-side in a single study. Therefore, we explored the effect of CSF depletion using MARS 14 cartridge and ProteoMiner ligand library on the number of CSF proteins identified in subsequent LC-MS/MS analysis. LC-MS/MS analysis of crude (non-treated) CSF provided roughly 500 identified proteins. Depletion of CSF by MARS 14 cartridge increased the number of identifications to nearly 800, while treatment of CSF using ProteoMiner enabled identification of 600 proteins. To explore the potential losses of CSF proteins during the depletion process, we also analyzed the "waste" fractions generated by both methods, i.e., proteins retained by the MARS 14 cartridge, and the molecules present in the flow-through fraction from ProteoMiner. More than 250 proteins were bound to MARS 14 cartridge, 100 of those were not identified in the corresponding depleted CSF. Similarly, analysis of the waste fraction in ProteoMiner workflow provided almost 70 unique proteins not found in the CSF depleted by the ligand library. Both depletion strategies significantly increased the number of identified CSF proteins compared to crude CSF. However, MARS 14 depletion provided a markedly higher number of identified proteins (773) compared to ProteoMiner (611). Further, we showed that CSF proteins are lost due to co-depletion (MARS 14) or exclusion (ProteoMiner) during the depletion process. This suggests that the routinely discarded "waste" fractions contain proteins of potential interest and should be included in CSF biomarker studies.
<title>A Stereophotogrammetric Method For The Measurement Of Body Surfaces Using A Projected Grid</title> (1980)

A simplified stereophotogrammetric method for the measurement of body surfaces is presented. The advantage of this method in comparison with common stereophotogrammetry is that only one photograph has be evaluated. The technical equipment consists of a projector with a grid slide and a camera. This is equivalent to the common arrangement for stereophotography, if the directions of the light rays emerging from the projector are thought of having been reversed. So the grid slide and the photograph form some sort of a stereo image pair. The grid is projected on the surface to be measured. The evaluation of the photographs is accomplished by the identification of corresponding points. The correspondance can easily be established by counting the crosspoints of the grid. The coordinates of the grid points in the slide can be calculated by this count, whereas those in the photograph have to be measured. Thus a correlation of two images by stereoscopic vision is not necessary. The measurement can be performed with a simple di-gitizer.The calibration of the apparatus is done by using landmarks and solving the normal equations for the orientation elements of the camera and of the projector. With a slight modification the method can be employed for quasi-continuous measurements of the body surface along projected grid lines.
IL-2 administration increases CD4+CD25hi Foxp3+ regulatory T cells in cancer patients (2005)

Interleukin-2 (IL-2) is historically known as a T-cell growth factor. Accumulating evidence from knockout mice suggests that IL-2 is crucial for the homeostasis and function of CD4+ CD25+ regulatory T cells in vivo. However, the impact of administered IL-2 in an immune intact host has not been studied in rodents or humans. Here, we studied the impact of IL-2 administration on the frequency and function of human CD4+ CD25(hi) T cells in immune intact patients with melanoma or renal cancer. We found that the frequency of CD4+ CD25(hi) T cells was significantly increased after IL-2 treatment, and these cells expressed phenotypic markers associated with regulatory T cells. In addition, both transcript and protein levels of Foxp3, a transcription factor exclusively expressed on regulatory T cells, were consistently increased in CD4 T cells following IL-2 treatment. Functional analysis of the increased number of CD4+ CD25(hi) T cells revealed that this population exhibited potent suppressive activity in vitro. Collectively, our results demonstrate that administration of high-dose IL-2 increased the frequency of circulating CD4+ CD25(hi) Foxp3+ regulatory T cells. Our findings suggest that selective inhibition of IL-2-mediated enhancement of regulatory T cells may improve the therapeutic effectiveness of IL-2 administration.
Modification of inflammatory response to implanted biomedical materialsin vivo by surface bound superoxide dismutase mimics (2000)

The healing response to implanted biomedical materials involves varying degrees and stages of inflammation and healing which in some cases leads to device failure. In this article, we describe synthetic methods and in vivo results of a novel surface treatment for biomedical materials involving covalent conjugation of a low molecular weight superoxide dismutase mimic (SODm), which imparts anti-inflammatory character to the material. SODm investigated in this study are a new class of anti-inflammatory drugs consisting of a Mn(II) complex of a macrocyclic polyamine ring that catalyze the dismutation of superoxide at rates equivalent to that of native enzyme. The SODms were covalently linked to small disks of ultra-high molecular weight polyethylene, poly(etherurethane urea), and tantalum metal at two concentrations and implanted in a subcutaneous rat implant model for 3, 7, 14, and 28 days. Histological examination of the implant tissue performed at 3 and 28 days revealed striking anti-inflammatory effects on both acute and chronic inflammatory responses. At 3 days, the formation of a neutrophil-rich acute inflammatory infiltrate seen in control implants was inhibited for all three materials treated with SODm. At 28 days, foreign body giant cell formation (number of FBGCs per field) and fibrous capsule formation (mean thickness of implant capsule) were also significantly inhibited over untreated control implants. A mechanism based on our current understanding of superoxide as an inflammatory mediator at implanted biomedical materials is proposed.
Measurement of the Intensity of Cell Surface Antigen Expression in B-Cell Chronic Lymphocytic Leukemia (1994)

Immunophenotyping of peripheral blood lymphocytes from 95 patients with B-cell chronic lymphocytic leukemia (B-CLL) was performed to estimate surface membrane intensity of the HLA-DR, CD20, and light-chain antigens. Cases were classified as having weak, moderate, or strong intensity by a standard slide immunocytochemical method, and the fluorescence intensity (FI) was measured by flow cytometry in molecules of equivalent soluble fluorescence (MESF). Staining intensity was strongest for HLA-DR; with both methods, 94 cases were classified as strong. For CD20, 67% were weak, 27% moderate, and 6% strong; the mean MESF values were 31.7, 66.4, and 177.4 x 10(3), respectively (P < .001). Thirty-nine percent had weak surface light-chain staining, 50% moderate, and 11% strong; the mean MESF values were 4.9, 7.5, and 16 x 10(3), respectively (P = .005). These results indicate that the FI of cell surface antigens can be estimated and quantified by flow cytometry. Because of the wide overlap of FI values among the three groups, an exact correlation was not found between the two methods of classifying intensity of surface antigen expression. The usefulness of these quantitative measurements needs further analysis in clinical trials.
A Novel Method to Capture Methylated Human DNA from Stool: Implications for Colorectal Cancer Screening (2007)

MBD capture increases assay sensitivity for detecting methylated DNA markers in stool. Applied clinical studies for stool cancer screening are indicated.