gebhart/patrepeval huggingface dataset:
Human antibody derivatives against the fibroblast activation protein for tumor stroma targeting of carcinomas (2001)

The fibroblast activation protein (FAP) is selectively expressed on activated fibroblasts of the tumor stroma on more than 90% of lung, breast and colon carcinomas. The high prevalence and abundance of FAP(+) stroma make it a promising target for in vivo diagnosis and therapy of a variety of carcinomas. We describe the humanization of the murine FAP-specific MAb, F19, which has already been clinically used for in vivo diagnostic purposes. Using phage display technology and human V-repertoires, VL and VH regions of F19 were replaced by analogous human V-regions while retaining the original HCDR3 sequence in order to maintain F19 epitope specificity. The resulting human single-chain fragments of immunoglobulin variable regions (scFv 34, scFv 18) showed affinities of 6 nM on cell membrane-bound FAP. scFv 34 was expressed as a bivalent minibody (Mb 34). The antigen-binding characteristics of Mb 34 were comparable to the parental and a complementarity-determining region (CDR)-grafted version of F19. This was revealed by binding competition studies, FACS analyses and immunohistochemistry on various tumor samples including breast, colon and lung carcinomas. Importantly, compared with the CDR-grafted humanized scFv version of F19, the V-regions of the selected human scFv 34 showed sequence identity with the parental antibody (Ab) only over the short, 15-amino acid long HCDR3. Thus, a largely reduced xenoantigenic potential is expected. These human Ab derivatives are suitable to develop novel therapeutic concepts with broad applicability for a wide variety of histological carcinomas based on tumor stroma targeting.
Origin of Plasma Cell-free DNA after Solid Organ Transplantation (2003)

Despite current interest in the biology and diagnostic application of plasma cell-free DNA (1), there is little knowledge regarding the cellular origin of this DNA. Recently, we have used a sex-mismatched bone marrow transplantation model to study the relative contributions of hematopoietic and nonhematopoietic cells to circulating DNA (2). We have demonstrated that the predominant proportion of plasma DNA originates from the hematopoietic system (2). However, the proportions of cell-free plasma DNA originating from other organs (e.g., heart, liver, and kidneys) remain unknown. We therefore investigated the contribution of the heart, liver, and kidneys to circulating DNA with use of sex-mismatched heart, liver, and renal transplantation models, respectively.

Sex-mismatched heart, liver, and renal transplantation patients were recruited for the study. Twenty-one patients who had received heart transplants were recruited from the Grantham Hospital, Hong Kong. Fourteen of these heart transplantation patients were females with male donors, whereas the remaining 7 were males with female donors. Four sex-mismatched liver transplantation patients at the Pediatric Surgical Unit of the Department of Surgery, Prince of Wales Hospital were recruited; two of these patients were females with male donors and the other two were males with female donors. Six sexmismatched renal transplantation patients were recruited from the Department of Medicine and Therapeutics of …
Synthesis and Characterization of Chelator-Lipids for Reversible Immobilization of Engineered Proteins at Self-Assembled Lipid Interfaces (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and Characterization of Chelator-Lipids for Reversible Immobilization of Engineered Proteins at Self-Assembled Lipid InterfacesLutz Schmitt, Christian Dietrich, and Robert TampeCite this: J. Am. Chem. Soc. 1994, 116, 19, 8485–8491Publication Date (Print):September 1, 1994Publication History Published online1 May 2002Published inissue 1 September 1994https://pubs.acs.org/doi/10.1021/ja00098a008https://doi.org/10.1021/ja00098a008research-articleACS PublicationsRequest reuse permissionsArticle Views1750Altmetric-Citations188LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Mesenchymal Stem Cells and Bone Regeneration (2006)

These techniques can be employed clinically to regenerate bone and serve as an alternative to autogenous cancellous bone.
Therapeutic implications of variable expression of CD52 on clonal cytotoxic T cells in CD8+ large granular lymphocyte leukemia (2009)

While alemtuzumab may be highly effective in large granular lymphocytic leukemia, prospective serial monitoring for the presence of CD52-deficient clonal cytotoxic T-lymphocytes should be a component of clinical trials investigating the efficacy of this drug. CD52 deficiency may explain lack of response to alemtuzumab, and such therapy may confer a survival advantage to glycophosphatidylinositol-negative clonal cytotoxic T-lymphocytes.
Induction Machine Fault Diagnostic Analysis With Wavelet Technique (2004)

A wavelet transform based method was developed for diagnosing machine faults operating at different rotating speeds. This paper shows that machine fault diagnosis can be effectively performed when an appropriate narrow-band filter is used to extract the required spectra components. A wavelets-transform-based technique is used to design specified narrow filter banks. This enables effective machine fault diagnostic analysis to be performed in the frequency domain. Gaussian-enveloped oscillation-type wavelet is employed. By matching the wavelet basis functions with the associated faulty signals, the required narrow filter banks are obtained. As a result, the detection and diagnosis of machine faults operating at different rotating speeds are made possible. The proposed technique was thoroughly tested at different rotating speeds.
Psychopathology of Frontal Lobe Syndromes (1990)

In this review, some basic aspects of frontal lobe functioning have been discussed and methods of testing for frontal lobe abnormalities outlined. It has been emphasized that the frontal lobes are affected in a number of diseases, which cover a broad spectrum of neuropsychiatric problems. Furthermore, it is suggested that the frontal lobes are involved in syndromes not traditionally thought to be related to frontal lobe dysfunction, for example, schizophrenia, and rarer presentations such as misidentification syndromes. Frontal lobe dysfunction often goes unrecognized, especially in patients who have normal neurologic testing and apparently intact IQ when routine methods of investigation are employed. Although marked disturbances of behavior following frontal lobe dysfunction have now been described for well over 120 years, these large areas of the human brain, and their links with some of the highest attributes of mankind, have been relatively neglected and are worthy of much further exploration by those interested in neuropsychiatric problems.
Phase 1 Clinical Study of siRNA Targeting Carbohydrate Sulphotransferase 15 in Crohn’s Disease Patients with Active Mucosal Lesions (2016)

Local application of STNM01 is safe and well tolerated in CD patients with active mucosal lesions.
Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis (2020)

Recent advances in mass spectrometry (MS)-based proteomics have enabled tremendous progress in the understanding of cellular mechanisms, disease progression, and the relationship between genotype and phenotype. Though many popular bioinformatics methods in proteomics are derived from other omics studies, novel analysis strategies are required to deal with the unique characteristics of proteomics data. In this review, we discuss the current developments in the bioinformatics methods used in proteomics and how they facilitate the mechanistic understanding of biological processes. We first introduce bioinformatics software and tools designed for mass spectrometry-based protein identification and quantification, and then we review the different statistical and machine learning methods that have been developed to perform comprehensive analysis in proteomics studies. We conclude with a discussion of how quantitative protein data can be used to reconstruct protein interactions and signaling networks.
Cyber Security Risks Assessment with Bayesian Defense Graphs and Architectural Models (2009)

To facilitate rational decision making regarding cyber security investments, decision makers need to be able to assess expected losses before and after potential investments. This paper presents a model based assessment framework for analyzing the cyber security provided by different architectural scenarios. The framework uses the Bayesian statistics based extended influence diagrams to express attack graphs and related countermeasures. In this paper it is demonstrated how this structure can be captured in an abstract model to support analysis based on architectural models. The approach allows calculating the probability that attacks will succeed and the expected loss of these given the instantiated architectural scenario. Moreover, the framework can handle the uncertainties that are accompanied to the analyses. In architectural analysis there are uncertainties acquainted both to the scenario and its properties, as well as to the analysis framework that stipulates how security countermeasures contribute to cyber security.
Array electrode design for transcutaneous electrical stimulation: A simulation study (2009)

Array electrodes are a promising technology that is likely to bring transcutaneous electrical stimulation (TES) a step forward. The dynamic adaptation of electrode size and position helps to simplify the use of electrical stimulation systems and to increase their clinical efficacy. However, up to now array electrodes were built by trial and error and it is unclear how, for example. the gaps between the array elements or the resistivity of the electrode-skin interface material influence the current distribution. A TES model that comprises a finite element model and a nerve model has been used to analyze the influence of array electrode gaps and gel resistivities on nerve activation. Simulation results indicate that the resistivity of the electrode-skin interface layer should be adapted depending on the size of the gaps between the array elements Furthermore, the gap sizes should be smaller than 3 mm in order to keep losses small. (C) 2009 IPEM. Published by Elsevier Ltd. All rights reserved.
3-D characterization of high-permeability zones in a gravel aquifer using 2-D crosshole GPR full-waveform inversion and waveguide detection (2013)

Reliable high-resolution 3-D characterization of aquifers helps to improve our understanding of flow and transport processes when small-scale structures have a strong influence. Crosshole ground penetrating radar (GPR) is a powerful tool for characterizing aquifers due to the method's high-resolution and sensitivity to porosity and soil water content. Recently, a novel GPR full-waveform inversion algorithm was introduced, which is here applied and used for 3-D characterization by inverting six crosshole GPR cross-sections collected between four wells arranged in a square configuration close to the Thur River in Switzerland. The inversion results in the saturated part of this gravel aquifer reveals a significant improvement in resolution for the dielectric permittivity and electrical conductivity images compared to ray-based methods. Consistent structures where acquisition planes intersect indicate the robustness of the inversion process. A decimetre-scale layer with high dielectric permittivity was revealed at a depth of 5–6 m in all six cross-sections analysed here, and a less prominent zone with high dielectric permittivity was found at a depth of 7.5–9 m. These high-permittivity layers act as low-velocity waveguides and they are interpreted as high-porosity layers and possible zones of preferential flow. Porosity estimates from the permittivity models agree well with estimates from Neutron–Neutron logging data at the intersecting diagonal planes. Moreover, estimates of hydraulic permeability based on flowmeter logs confirm the presence of zones of preferential flow in these depth intervals. A detailed analysis of the measured data for transmitters located within the waveguides, revealed increased trace energy due to late-arrival elongated wave trains, which were observed for receiver positions straddling this zone. For the same receiver positions within the waveguide, a distinct minimum in the trace energy was visible when the transmitter was located outside the waveguide. A novel amplitude analysis was proposed to explore these maxima and minima of the trace energy. Laterally continuous low-velocity waveguides and their boundaries were identified in the measured data alone. In contrast to the full-waveform inversion, this method follows a simple workflow and needs no detailed and time consuming processing or inversion of the data. Comparison with the full-waveform inversion results confirmed the presence of the waveguides illustrating that full-waveform inversion return reliable results at the highest resolution currently possible at these scales. We envision that full-waveform inversion of GPR data will play an important role in a wide range of geological, hydrological, glacial and periglacial studies in the critical zone.
Electronic spin detection in molecules using scanning-tunneling- microscopy-assisted electron-spin resonance (2002)

By combining the spatial resolution of a scanning-tunneling microscope (STM) with the electronic spin sensitivity of electron-spin resonance, we show that it is possible to detect the presence of localized spins on surfaces. The principle is that a STM is operated in a magnetic field, and the resulting component of the tunnel current at the Larmor (precession) frequency is measured. This component is nonzero whenever there is tunneling into or out of a paramagnetic entity. We have succeeded in obtaining spectra from free radical molecules from which the g factor of a spin entity may be inferred. For the molecules studied here, α,γ-bisdiphenylene-β-phenylallyl, g was found to be 2±0.1.
Overexpression of a kinase‐deficient form of the EDR1 gene enhances powdery mildew resistance and ethylene‐induced senescence in Arabidopsis (2002)

The EDR1 gene of Arabidopsis has previously been reported to encode a Raf-like mitogen-activated protein kinase kinase (MAPKK) kinase, and to function as a negative regulator of disease resistance. A phylogenetic analysis of plant and animal protein kinases revealed, however, that plant Raf-like kinases are more closely related to animal mixed lineage kinases (MLKs) than Raf-like kinases, and are deeply divergent from both classes of animal kinases, making inferences of substrate specificity questionable. We, therefore, assayed the kinase activity of recombinant EDR1 protein in vitro. The EDR1 kinase domain displayed autophosphorylation activity and phosphorylated the common MAP kinase substrate myelin basic protein. The EDR1 kinase domain also phosphorylated a kinase-deficient EDR1 protein, indicating that EDR1 autophosphorylation can occur via an intermolecular mechanism. Overexpression of a kinase-deficient full-length EDR1 gene (35S::dnEDR1) in wild-type Arabidopsis plants caused a dominant negative phenotype, conferring resistance to powdery mildew (Erysiphe cichoracearum) and enhancing ethylene-induced senescence. RNA-gel blot analyses showed that the 35S::dnEDR1 transgene was highly transcribed in transgenic plants. Western blot analysis, however, revealed that neither the wild-type nor mutant EDR1 protein could be detected in these lines, indicating that the dominant negative phenotype may be caused by a translational inhibition mechanism rather than by a protein level effect. Overexpression of orthologous dnEDR1 constructs may provide a novel strategy for controlling powdery mildew disease in crops.
T Cells Activated by Zwitterionic Molecules Prevent Abscesses Induced by Pathogenic Bacteria (2000)

Immunologic paradigms classify bacterial polysaccharides as T cell-independent antigens. However, these models fail to explain how zwitterionic polysaccharides (Zps) confer protection against intraabdominal abscess formation in a T cell-dependent manner. Here, we demonstrate that Zps elicit a potent CD4+ T cell response in vitro that requires available major histocompatibility complex class II molecules on antigen-presenting cells. Specific chemical modifications to Zps show that: 1) the activity is specific for carbohydrate structure, and 2) the proliferative response depends upon free amino and carboxyl groups on the repeating units of these polysaccharides. Peptides synthesized to mimic the zwitterionic charge motif associated with Zps also exhibited these biologic properties. Lysine-aspartic acid (KD) peptides with more than 15 repeating units stimulated CD4+ T cells in vitro and conferred protection against abscesses induced by bacteria such as Bacteroides fragilis and Staphylococcus aureus. Evidence for the biologic importance of T cell activation by these zwitterionic polymers was provided when human CD4+ T cells stimulated with these molecules in vitro and adoptively transferred to rats in vivo conferred protection against intraabdominal abscesses induced by viable bacterial challenge. These studies demonstrate that bacterial polysaccharides with a distinct charge motif activate T cells and that this activity confers immunity to a distinct pathologic response to bacterial infection.
A report of an outbreak of postoperative endophthalmitis. (2000)

We report an outbreak of endophthalmitis following cataract extraction or secondary intraocular lens (IOL) implantation in a 400-bed general hospital in northern Thailand. From December 1997 to September 1998, of 329 patients who had undergone cataract extraction or secondary IOL implantation in the hospital, 31 (9.4%) developed postoperative endophthalmitis. The interval between the operation and the clinical diagnosis of endophthalmitis ranged from 5 to 74 days with a median of 15 days. Of the 31 cases of endophthalmitis, 18 occurred in phacoemulsification (PE) with IOL, 11 in extracapsular cataract extraction (ECCE) with IOL, and 2 in secondary IOL implantation. Patients who had undergone PE with IOL had a significantly higher rate (12.4%) than those of ECCE with IOL (6.3%). The infection rates also increased with the order of the operations within each operation period (morning or afternoon); later operations were at higher risk. Our findings detected defects in sterilization for the surgeries including possible inadequacy in the autoclave sterilization of surgical instruments, insufficient exposure time with 2 per cent activated glutaraldehyde solution (about 15-30 minutes) for sterilizing some surgical instruments, and the use of multiple-dose intraocular irrigating solution. This outbreak of endophthalmitis emphasizes the necessity to monitor regularly the practice of sterilization/disinfection in hospitals for prevention and control of nosocomial infections.
Alternative Securities Trading Systems: Tests and Regulatory Implications of the Adoption of Technology (1996)

Reasons for the mixed reactions to today's electronic off-exchange trading systems are examined, and regulatory implications are explored. Information technology (IT) could provide more automated markets, which have lower costs. Yet for an electronic trading system to form a liquid and widely used market, a sufficient number of traders would need to make a transition away from established trading venues and to this alternative way of trading. This transition may not actually occur for a variety of reasons. Two tests are performed of the feasibility and the desirability of transitions to new markets. In the first test, traders in a series of economic experiments demonstrate an ability to make a transition and develop a critical mass of trading activity in a newly opened market. In the second test, simulation is used to compare the floor-based specialist auction in place in most U.S. stock exchanges today to a disintermediated alternative employing screen-based order matching. The results indicate that reducing the role of dealer-intermediaries can actually diminish important measures of market quality. Our findings suggest that the low trading volumes on many off-exchange systems do not result from traders' inability to break away from established trading floors. Rather, today's off-exchange trading systems are not uniformly superior to the trading mechanisms of traditional exchanges. Thus, regulatory actions favoring off-exchange trading systems are not warranted; but, improved designs for IT-based trading mechanisms are needed, and when these are available, they are likely to win significant trading volume from established exchanges.
Expression of the Complement Anaphylatoxin C3a and C5a Receptors on Bronchial Epithelial and Smooth Muscle Cells in Models of Sepsis and Asthma (2001)

The presence of the complement-derived anaphylatoxin peptides, C3a and C5a, in the lung can induce respiratory distress characterized by contraction of the smooth muscle walls in bronchioles and pulmonary arteries and aggregation of platelets and leukocytes in pulmonary vessels. C3a and C5a mediate these effects by binding to their specific receptors, C3aR and C5aR, respectively. The cells that express these receptors in the lung have not been thoroughly investigated, nor has their expression been examined during inflammation. Accordingly, C3aR and C5aR expression in normal human and murine lung was determined in this study by immunohistochemistry and in situ hybridization. In addition, the expression of these receptors was delineated in mice subjected to LPS- and OVA-induced models of inflammation. Under noninflamed conditions, C3aR and C5aR protein and mRNA were expressed by bronchial epithelial and smooth muscle cells of both human and mouse lung. C3aR expression increased significantly on both bronchial epithelial and smooth muscle cells in mice treated with LPS; however, in the OVA-challenged animals only the bronchial smooth muscle cells showed increased C3aR expression. C5aR expression also increased significantly on bronchial epithelial cells in mice treated with LPS, but was not elevated in either cell type in the OVA-challenged mice. These results demonstrate the expression of C3aR and C5aR by cells endogenous to the lung, and, given the participation of bronchial epithelial and smooth muscle cells in the pathology of diseases such as sepsis and asthma, the data suggest a role for these receptors during lung inflammation.