gebhart/patrepeval huggingface dataset:
The purification of shikimate dehydrogenase from Escherichia coli (1985)

A procedure was developed for the purification of shikimate dehydrogenase from Escherichia coli. Homogeneous enzyme with specific activity 1100 units/mg of protein was obtained in 21% overall yield. The subunit Mr estimated by polyacrylamide-gel electrophoresis in the presence of sodium dodecyl sulphate was 32 000. The native Mr, estimated by gel-permeation chromatography on a TSK G2000SW column, was also 32 000. E. coli shikimate dehydrogenase is therefore a monomeric NADP-linked dehydrogenase.
Role of neutrophils in induction of acute inflammation in T‐cell‐mediated immune dermatosis, psoriasis: A neutrophil‐associated inflammation‐boosting loop (2000)

A growing body of evidence has indicated that T-cell-mediated immunity plays an important role in triggering and maintenance of psoriatic lesions. In this review we present our own experimental results as well as those from the literature related to the pathomechanism of the development of inflammatory changes in psoriatic lesions. First of all it is important to acknowledge the fact that psoriatic lesions are not uniform as assumed by many authors but that they are actually rather heterogeneous both clinically and histologically even within the same plaques. Lymphokines produced by activated T cells in psoriatic lesions have a strong influence on the proliferation of the epidermis, whose stimulated kertinocytes released several cytokines, which in turn enhance the activation state of T cells. Thus, they form a vicious cycle, a T-cell-mediated inflammation-sustaining loop. Although the interaction between T-cell-mediated immunity and epidermal keratinocytes may well explain the maintenance of background "chronic" inflammatory changes diffusely observed throughout psoriatic lesions, it is not enough to explain the island-like, "acute" inflammatory changes observed within and at the border of the plaque lesions. Characteristic neutrophil accumulation under the stratum corneum can be observed in the highly inflamed and therapeutically recalcitrant areas of psoriatic lesions. They are chemotactically attracted and activated there by synergistic action of chemokines, IL-8 and Gro-a released by the stimulated keratinocytes, and particularly C5a/C5a des arg produced via the alternative complement pathway activation possibly on the surface of corneocytes. In this review, we emphasize that the accumulation of neurophils is not simply a passive event. We think that those stimulated neutrophils are able to influence not only the growth and differentiation of epidermal keratinocytes but also the activation-state of T cells by aberrant expression of HLA-DR on their surfaces as well as by their effects. These T cells in turn influence the transepidermal neutrophil migration through the effect of their lymphokines on the keratinocyte production of pro-inflammatory mediators including C3. Therefore, we propose a neutrophil-associated inflammation-boosting loop that may well explain the localized "acute" inflammatory changes scattered over the "chronic" psoriatic plaques as well as in the acutely inflamed lesions of pustular psoriasis.
Tumor Eradication by Cisplatin Is Sustained by CD80/86-Mediated Costimulation of CD8+ T Cells (2016)

Certain cytotoxic chemotherapeutic drugs are immunogenic, stimulating tumor immunity through mechanisms that are not completely understood. Here we show how the DNA-damaging drug cisplatin modulates tumor immunity. At the maximum tolerated dose (MTD), cisplatin cured 50% of mice with established murine TC-1 or C3 tumors, which are preclinical models of human papillomavirus (HPV)-associated cancer. Notably, the curative benefit of cisplatin relied entirely upon induction of tumor-specific CD8<sup>+</sup> T cells. Mechanistic investigations showed that cisplatin stimulated tumor infiltration of inflammatory antigen-presenting cells (APC) expressing relatively higher levels of the T-cell costimulatory ligands CD70, CD80, and CD86. Cell death triggered by cisplatin was associated with the release of at least 19 proteins in the tumor environment that could act as damage-associated molecular patterns and upregulate costimulatory molecules, either alone or in concert, but the responsible proteins remain unknown. Essentially, the curative effect of cisplatin was abrogated in mice lacking expression of CD80 and CD86 on APCs. Furthermore, cisplatin treatment was improved by CTLA-4 blockade, which increases the availability of CD80/86 to bind to CD28. In contrast, there was no effect of CD27 stimulation, which replaces CD70 interaction. At the cisplatin MTD, cure rates could also be increased by vaccination with synthetic long peptides, whereas cures could also be achieved at similar rates at 80% of the MTD with reduced side effects. Our findings reveal an essential basis for the immunogenic properties of cisplatin, which are mediated by the induction of costimulatory signals for CD8<sup>+</sup> T-cell-dependent tumor destruction. Cancer Res; 76(20); 6017-29. ©2016 AACR.
PAX8-PPARγ Rearrangement in Thyroid Tumors (2002)

A PAX8-PPARgamma rearrangement has been recently identified in follicular thyroid carcinomas, but not in follicular adenomas or other thyroid tumors. We report here the analyses of PAX8-PPARgamma in a series of 118 thyroid tumors using a newly developed RT-PCR assay to detect this rearrangement in frozen and paraffin-embedded tissues and using immunostaining with a PPARgamma antibody. PAX8-PPARgamma was detected by RT-PCR in eight of 15 (53%) follicular carcinomas and two of 25 (8%) follicular adenomas but not in 35 papillary carcinomas (including 12 follicular variants), 12 Hurthle cell carcinomas, 12 Hurthle cell adenomas, two anaplastic carcinomas, one poorly differentiated carcinoma, or 16 hyperplastic nodules. The prevalence was higher in follicular carcinomas from patients with a history of radiation exposure (three of three). Strong, diffuse nuclear immunostaining with the PPARgamma antibody correlated with the presence of PAX8-PPARgamma detected by RT-PCR. Most sporadic follicular carcinomas positive for PAX8-PPARgamma were overtly invasive, whereas tumors lacking the rearrangement were predominantly minimally invasive. The two follicular adenomas positive for PAX8-PPARgamma had trabecular growth pattern and thick capsule, but no invasion, and thus may represent "pre-invasive" follicular carcinomas. The absence of PAX8-PPARgamma rearrangements in Hurthle cell tumors and papillary thyroid carcinomas highlights the differences in the molecular pathogenesis of these thyroid tumors.
Nearest Neighbour Classification with Monotonicity Constraints (2008)

Abstract. In many application areas of machine learning, prior knowledge concerning the monotonicity of relations between the response variable and predictor variables is readily available. Monotonicity may also be an important model requirement with a view toward explaining and justifying decisions, such as acceptance/rejection decisions. We propose a modified nearest neighbour algorithm for the construction of monotone classifiers from data. We start by making the training data monotone with as few label changes as possible. The relabeled data set can be viewed as a monotone classifier that has the lowest possible error-rate on the training data. The relabeled data is subsequently used as the training sample by a modified nearest neighbour algorithm. This modified nearest neighbour rule produces predictions that are guaranteed to satisfy the monotonicity constraints. Hence, it is much more likely to be accepted by the intended users. Our experiments show that monotone kNN often outperforms standard kNN in problems where the monotonicity constraints are applicable. 1
Dihedral angle and secondary structure database of short amino acid fragments (2006)

DASSD can be accessed and downloaded from http://www.cs.rmit.edu.au/dassd/
Plasma leakage through glomerular basement membrane ruptures triggers the proliferation of parietal epithelial cells and crescent formation in non‐inflammatory glomerular injury (2012)

Glomerular crescents are most common in rapidly progressive glomerulonephritis but also occur in non-inflammatory chronic glomerulopathies; thus, factors other than inflammation should trigger crescent formation, eg vascular damage and plasma leakage. Here we report that Alport nephropathy in Col4A3-deficient Sv129 mice is complicated by diffuse and global crescent formation in which proliferating parietal epithelial cells are the predominant cell type. Laminin staining and transmission and acellular scanning electron microscopy of acellular glomeruli documented disruptions and progressive disintegration of the glomerular basement membrane in Col4A3-deficient mice. FITC-dextran perfusion further revealed vascular leakage from glomerular capillaries into Bowman's space, further documented by fibrin deposits in the segmental crescents. Its pathogenic role was validated by showing that the fibrinolytic activity of recombinant urokinase partially prevented crescent formation. In addition, in vitro studies confirmed an additional mitogenic potential of serum on murine and human parietal epithelial cells. Furthermore, loss of parietal cell polarity and unpolarized secretion of extracellular matrix components were evident within fibrocellular crescents. Among 665 human Alport nephropathy biopsies, crescent formation was noted in 0.4%. We conclude that glomerular vascular injury and GBM breaks cause plasma leakage which triggers a wound healing programme involving the proliferation of parietal cells and their loss of polarity. This process can trigger cellular and fibrocellular crescent formation even in the absence of cellular inflammation and rupture of the Bowman's capsule.
Artificial microfluidic skin for in vitro perspiration simulation and testing (2013)

To expedite development of any skin wearable material, product, or device, an artificial perspiration (sweat) simulator can provide improved ease, cost, control, flexibility, and reproducibility in comparison to human or animal tests. Reported here is a human perspiration mimicking device including microreplicated skin-texture. A bottom 0.2 μm track etched polycarbonate membrane layer provides flow-rate control while a top photo-curable layer provides skin-like features such as sweat pore density, hydrophobicity, and wetting hysteresis. Key capabilities of this sweat simulator include: constant 'sweat' rate density without bubble-point variation even down to ~1 L h(-1) m(-2); replication of the 2 pores mm(-2) pore-density and the ~50 μm texture of human skin; simple gravity-fed flow control; low-cost and disposable construction.
Thermal imaging to detect physiological indicators of stress in humans (2013)

Real-time, stand-off sensing of human subjects to detect emotional state would be valuable in many defense, security and medical scenarios. We are developing a multimodal sensor platform that incorporates high-resolution electro-optical and mid-wave infrared (MWIR) cameras and a millimeter-wave radar system to identify individuals who are psychologically stressed. Recent experiments have aimed to: 1) assess responses to physical versus psychological stressors; 2) examine the impact of topical skin products on thermal signatures; and 3) evaluate the fidelity of vital signs extracted from thermal imagery and radar signatures. Registered image and sensor data were collected as subjects (n=32) performed mental and physical tasks. In each image, the face was segmented into 29 non-overlapping segments based on fiducial points automatically output by our facial feature tracker. Image features were defined that facilitated discrimination between psychological and physical stress states. To test the ability to intentionally mask thermal responses indicative of anxiety or fear, subjects applied one of four topical skin products to one half of their face before performing tasks. Finally, we evaluated the performance of two non-contact techniques to detect respiration and heart rate: chest displacement extracted from the radar signal and temperature fluctuations at the nose tip and regions near superficial arteries to detect respiration and heart rates, respectively, extracted from the MWIR imagery. Our results are very satisfactory: classification of physical versus psychological stressors is repeatedly greater than 90%, thermal masking was almost always ineffective, and accurate heart and respiration rates are detectable in both thermal and radar signatures.
Modeling optical and thermal distributions in tissue during laser irradiation (1987)

The propagation of light energy in tissues is an important problem in phototherapy, especially with the increased use of lasers as light sources. Often a slight difference in delivered energy separates a useless, efficacious, or disastrous treatment. Methods are presented for experimental characterization of the optical properties of a tissue and computational prediction of the distribution of light energy within a tissue. A standard integrating sphere spectrophotometer measured the total transmission, Tt, total reflectance, Rt, and the on-axis transmission, Ta, for incident collimated light that propagated through the dermis of albino mouse skin, over the visible spectrum. The diffusion approximation solution to the one-dimensional (1-D) optical transport equation computed the expected Tt and Rt for different combinations of absorbance, k, scattering, s, and anisotropy, g, and by iterative comparison of the measured and computed Tt and Rt values converged to the intrinsic tissue parameters. For example, mouse dermis presented optical parameters of 2.8 cm-1, 239 cm-1, and 0.74 for k, s, and g, respectively, at 488 nm wavelength. These values were used in the model to simulate the optical propagation of the 488-nm line of an argon laser through mouse skin in vivo. A 1-D Green's function thermal diffusion model computed the temperature distribution within the tissue at different times during laser irradiation. In vitro experiments showed that the threshold temperature range for coagulation was 60 degrees-70 degrees C, and the kinetics were first order, with a temperature-dependent rate constant that obeyed an Arrhenius relation (molar entropy 276 cal/mol-degrees K, molar enthalpy 102 kcal/mol). The model simulation agreed with the corresponding in vivo experiment that a 2-s pulse at 55 W/cm2 irradiance will achieve coagulation of the skin.
Isolation and characterization of a spontaneously immortalized human breast epithelial cell line, MCF-10. (1990)

Two sublines of a breast epithelial cell culture, MCF-10, derived from human fibrocystic mammary tissue exhibit immortality after extended cultivation in low calcium concentrations (0.03-0.06 mM) and floating transfers in low calcium (MCF-10F), or by trypsin-Versene passages in the customary (normal) calcium levels, 1.05 mM (MCF-10A). Both sublines have been maintained as separate entities after 2.3 years (849 days) in vitro and at present have been in culture for longer than 4 years. MCF-10 has the characteristics of normal breast epithelium by the following criteria: (a) lack of tumorigenicity in nude mice; (b) three-dimensional growth in collagen; (c) growth in culture that is controlled by hormones and growth factors; (d) lack of anchorage-independent growth; and (e) dome formation in confluent cultures. Cytogenetic analysis prior to immortalization showed normal diploid cells; although later passages showed minimal rearrangement and near-diploidy, the immortal cells were not karyotypically normal. The emergence of an immortal culture in normal calcium media was not an inherent characteristic of the original tissue from which MCF-10 was derived since reactivated cryo-preserved cells from cultures grown for 0.3 and 1.2 years in low calcium were incapable of sustained growth in normal calcium.
Stroma-derived factor (SDF-1/CXCL12) and human tumor pathogenesis (2006)

The chemokine stroma-derived factor (SDF-1/CXCL12) plays multiple roles in tumor pathogenesis. It has been demonstrated that CXCL12 promotes tumor growth and malignancy, enhances tumor angiogenesis, participates in tumor metastasis, and contributes to immunosuppressive networks within the tumor microenvironment. Therefore, it stands to reason that the CXCL12/CXCR4 pathway is an important target for the development of novel anti-cancer therapies. In this review, we consider the pathological nature and characteristics of the CXCL12/CXCR4 pathway in the tumor microenvironment. Strategies for therapeutically targeting the CXCL12/CXCR4 axis also are discussed.
Gcg-XTEN: An Improved Glucagon Capable of Preventing Hypoglycemia without Increasing Baseline Blood Glucose (2010)

The data show that Gcg-XTEN is effective in preventing hypoglycemia without the associated hyperglycemia expected for unmodified glucagon. While the plasma clearance of this Gcg-XTEN has been optimized for overnight dosing, specifically for the treatment of nocturnal hypoglycemia, constructs with significantly longer exposure profiles are feasible. Such constructs may have multiple applications such as allowing for more aggressive insulin treatment regimens, treating hypoglycemia due to insulin-secreting tumors, providing synergistic efficacy in combination therapies with long-acting GLP1 analogs, and as an appetite suppressant for treatment of obesity. The improved physical properties of the Gcg-XTEN molecule may also allow for novel delivery systems not currently possible with native glucagon.
ChemInform Abstract: SYNTHESIS, PROPERTIES, AND SPECTRAL STUDIES OF 1‐PHENYLSULFINYL‐2‐ARYLOXYETHENES (1984)

Abstract Durch Persäureoxidation der Phenylthioaryloxyethene (I) werden die Titelverbindungen (II) dargestellt.
Development and Optimization of a Novel Immunomagnetic Separation- Bacteriophage Assay for Detection of Salmonella enterica Serovar Enteritidis in Broth (2001)

Salmonella is the second-leading cause of food-borne illness in most developed countries, causing diarrhea, cramps, vomiting, and often fever. Many rapid methods are available for detection of Salmonella in foods, but these methods are often insensitive or expensive or require a high degree of technical ability to perform. In this paper we describe development and characterization of a novel assay that utilizes the normal infection cycle of bacteriophage SJ2 for detection of Salmonella enterica serovar Enteritidis in broth. The assay consists of four main stages: (i) capture and concentration of target cells by using immunomagnetic separation (IMS); (ii) infection of the target bacterium with phage; (iii) amplification and recovery of progeny phage; and (iv) assay of progeny phage on the basis of their effect on a healthy population of host cells (signal-amplifying cells). The end point of the assay can be determined by using either fluorescence or optical density measurements. The detection limit of the assay in broth is less than 10(4) CFU/ml, and the assay can be performed in 4 to 5 h. The results of this study demonstrate that the IMS-bacteriophage assay is a rapid, simple, and sensitive technique for detection of Salmonella serovar Enteritidis in broth cultures which can be applied to preenriched food samples.
Interleukin 1 signaling occurs exclusively via the type I receptor. (1993)

Two receptors for the proinflammatory cytokine interleukin 1 (IL-1) have been cloned and characterized biochemically. While it has been well established that the type I (80-kDa) IL-1 receptor can mediate responses to IL-1, the function of the type II (60-kDa) IL-1 receptor has been unknown. In this manuscript we describe experiments designed to ask whether the type II receptor is capable of delivering a biological signal. We have examined two types of experimental situation: responses to IL-1 in cells which express predominantly the type II receptor, and responses to IL-1 which have been suggested previously in the literature to be mediated by type II receptors. In both situations we find that the responses instead are mediated via type I receptors. A blocking antibody against the type II receptor never inhibits, and in fact sometimes enhances, the responses. We conclude that a very small number of type I receptors is sufficient to mediate all of the actions of IL-1 which we have examined here and that the function of the type II receptor may not be to transduce signals.
A Monte Carlo based three‐dimensional dose reconstruction method derived from portal dose images (2006)

The verification of intensity-modulated radiation therapy (IMRT) is necessary for adequate quality control of the treatment. Pretreatment verification may trace the possible differences between the planned dose and the actual dose delivered to the patient. To estimate the impact of differences between planned and delivered photon beams, a three-dimensional (3-D) dose verification method has been developed that reconstructs the dose inside a phantom. The pretreatment procedure is based on portal dose images measured with an electronic portal imaging device (EPID) of the separate beams, without the phantom in the beam and a 3-D dose calculation engine based on the Monte Carlo calculation. Measured gray scale portal images are converted into portal dose images. From these images the lateral scattered dose in the EPID is subtracted and the image is converted into energy fluence. Subsequently, a phase-space distribution is sampled from the energy fluence and a 3-D dose calculation in a phantom is started based on a Monte Carlo dose engine. The reconstruction model is compared to film and ionization chamber measurements for various field sizes. The reconstruction algorithm is also tested for an IMRT plan using 10 MV photons delivered to a phantom and measured using films at several depths in the phantom. Depth dose curves for both 6 and 10 MV photons are reconstructed with a maximum error generally smaller than 1% at depths larger than the buildup region, and smaller than 2% for the off-axis profiles, excluding the penumbra region. The absolute dose values are reconstructed to within 1.5% for square field sizes ranging from 5 to 20 cm width. For the IMRT plan, the dose was reconstructed and compared to the dose distribution with film using the gamma evaluation, with a 3% and 3 mm criterion. 99% of the pixels inside the irradiated field had a gamma value smaller than one. The absolute dose at the isocenter agreed to within 1% with the dose measured with an ionization chamber. It can be concluded that our new dose reconstruction algorithm is able to reconstruct the 3-D dose distribution in phantoms with a high accuracy. This result is obtained by combining portal dose images measured prior to treatment with an accurate dose calculation engine.
Structural and Functional Analysis of a C3b-specific Antibody That Selectively Inhibits the Alternative Pathway of Complement (2009)

Amplification of the complement cascade through the alternative pathway can lead to excessive inflammation. Targeting C3b, a component central to the alternative pathway of complement, provides a powerful approach to inhibit complement-mediated immune responses and tissue injury. In the present study, phage display technology was employed to generate an antibody that selectively recognizes C3b but not the non-activated molecule C3. The crystal structure of C3b in complex with a Fab fragment of this antibody (S77) illustrates the structural basis for this selectivity. Cleavage of C3 to C3b results in a plethora of structural changes within C3, including the rearrangement of macroglobulin domain 6 enabling binding of S77 to the adjacent macroglobulin domain 7 domain. S77 blocks binding of factor B to C3b inhibiting the first step in the formation of the alternative pathway C3 convertase. In addition, S77 inhibits C5 binding to C3b. This results in significantly reduced formations of anaphylatoxins and membrane-attack complexes. This study for the first time demonstrates the structural basis for complement inhibition by a C3b-selective antibody and provides insights into the molecular mechanisms of alternative pathway complement activation.