gebhart/patrepeval huggingface dataset:
Scoring System for Tumor-Infiltrating Lymphocytes and Its Prognostic Value for Gastric Cancer (2019)

The tumor microenvironment (TME) is the internal environment of malignant tumor progression, and the host antitumor immune response and normal tissue destruction occur in the TME. Tumor-infiltrating lymphocytes (TIL) is a crucial component of the TME and reflect the host antitumor immune response. The purpose of this study was to discuss the methodology for TIL evaluation and assess the prognostic value of TIL in gastric cancer. In total, we reviewed 1,033 gastrectomy cases between 2002 and 2008 at the Third Affiliated Hospital of Soochow University. To understand the prognostic value of TIL in gastric cancer (GC), TIL were assessed by optical microscopy, and verified by immunohistochemistry. There is no current consensus on TIL scoring in GC. In this study, we discussed a TIL evaluation system that includes an analysis of the amount and percentage of TIL in a tumor. Ultimately, 439 (52.7%) cases showed high levels of TIL and 394 (47.3%) cases had low levels. There was a statistically significant relationship among TIL, tumor size, histological grade, LN metastasis, nerve invasion, tumor thrombus, pTN stage, and WHO subtypes (<i>p</i> < 0.001, respectively). TIL<sup>hi</sup> was a positive significant predictor of overall survival (OS) in Kaplan-Meier survival analysis (<i>P</i> < 0.001) and multivariate Cox regression analysis (<i>HR</i> = 0.431, 95% CI: 0.347-0.534, <i>P</i> < 0.001). After surgery, patients with malignant tumors underwent chemoradiotherapy according to standard therapeutic guidelines based on TNM stage. The TNM scoring system cannot reflect the full information of TME; therefore, TIL can be used as a diagnostic supplement. We constructed a nomogram model that showed more predictive accuracy for OS than pTN stage. In summary, this study proves that high levels of TIL are associated with a positive prognosis and that TIL reflect the protective host antitumor immune response.
Enzymatic activities of activated and zymogen forms of human Hageman factor (factor XII) (1982)

Pro-Phe-Arg chloromethylketone (PPACMK) at 5.26 microM inactivated the amidolytic activity of native human Hageman factor with an apparent first-order rate constant of 0.75 min-1. The activated forms of Hageman factor, Hfa and HFf, were also inactivated by PPACMK with rate constants 0.82 and 0.72 min-1. These numbers indicate that the activity detectable in native Hageman factor is due to contamination with activated species. Uncleaved Hageman factor reacts slowly with 40 mM diisopropyl fluorophosphate with concomitant loss of its procoagulant activity. Incubation of native Hageman factor with PPACMK does not destroy its procoagulant activity, even in the presence of the activator dextran sulphate, but PPACMK inhibits autoactivation of Hageman factor, suggesting that no active site is formed in uncleaved, surface-bound Hageman factor. The activation of prekallikrein by Hageman factor under initial-rate conditions occurs after a lag and is prevented by an inhibitor of Hageman factor from corn. The kinetics of prekallikrein activation and the effects of inhibitors provide evidence that the amidolytic and proteolytic activities of human Hageman factor reside in the activated forms derived by limited proteolysis of the native molecule.
Nanomechanical Characterization of the Tensile Modulus of Rupture for Kerogen-Rich Shale (2017)

Summary In the past decade, chemical, physical, and mechanical characterization of source-rock reservoirs has moved toward micro- and nanoscale testing and analyses. Nanoindentation is now widely used in many industrial and university laboratories to measure stiffness and strength as well as other mechanical properties of shales. However, to date, tensile failures of shales have not been studied at the micro- or nanoscale. In this work, a scanning electron microscope (SEM) coupled with a focused ion beam (FIB) and a special nanoindenter (NI) testing configuration (SEM-FIB-NI) is used to bring organic-rich shale samples (preserved Woodford shale from a wellsite in Ada, Oklahoma, USA) to failure in tension. Microcantilever beam geometries were milled and loaded to failure in tension while monitoring in situ with SEM. The force-displacement curves were generated while videos recording in-situ real-time displacements and failures were collected simultaneously. The microcantilever beam tests of this composite natural material demonstrate linear elastic behavior followed by elastic/plastic yield before complete failure. This behavior was clearly observed to correlate with the amount of organic matter (OM) at the fractured surface of the microcantilever beam supports. Energy-dispersive X-ray spectroscopy (EDS) analyses were conducted along the prepared microbeam samples before loading. In addition, post-failure EDS analysis was performed on the resulting fractured faces of the failed microbeams, and the correlation between tensile behavior and shale OM content was shown. Large tensile moduli of rupture, or moduli of toughness, were associated with high OM, or kerogen, present at the failed supports of the kerogen-rich-shale (KRS) microcantilever beams. The moduli of toughness as a measure of work or energy needed to bring these samples into tensile failure were ten times less when OM was missing or barely present at the support, in terms of shale microbeam volume.
The Baculovirus Display Technology - An Evolving Instrument for Molecular Screening and Drug Delivery (2008)

High throughput screening is a core technology in drug discovery. During the past decade, several strategies have been developed to screen (poly)peptide libraries for diverse applications including disease diagnosis and profiling, imaging, as well as therapy. The recently established baculovirus display vector system (BDVS) represents a eukaryotic screening platform that combines the positive attributes of both cell and virus-based display approaches, allowing presentation of complex polypeptides on cellular and viral surfaces. Compared to microbial display systems, the BDVS has the advantage of correct protein folding and post-translational modifications similar to those in mammals, facilitating expression and analysis of proteins with therapeutic interest. The applicability of the system is further expanded by the availability of genetically engineered insect cell lines capable of performing e.g. mammalianized glycosylation in combination with high level of expression. In addition to insect cells, baculovirus can mediate delivery and expression of heterologous genes in a broad spectrum of primary and established mammalian cells. Currently, a variety of baculovirus-based assays aiming at routine high throughput identification of agents targeting cell surface receptors or studies on ligand-receptor interactions are under construction. Here, the advancements and future prospects of the baculovirus display technologies with emphasis on molecular screening and drug delivery applications using insect cell display, mammalian cell display, and virion display are described.
Activity and Deletion Analysis of Recombinant Human Cathepsin L Expressed in Escherichia coli (1989)

A cDNA clone encoding the human cysteine protease cathepsin L was expressed at high levels in Escherichia coli in a T7 expression system. The insoluble recombinant enzyme was solubilized in urea and refolded at alkaline pH. 38-kDa procathepsin L was purified by gel filtration at pH 8.0, and a 29-kDa form of the enzyme was purified by gel filtration after autoprocessing of the proenzyme at pH 6.5. The kinetic properties of the 29-kDa species of recombinant cathepsin L were similar to those published for the human liver enzyme (Mason, R. W., Green, G. D. J., and Barrett, A.J. (1985) Biochem. J. 226, 233-241), using benzyloxycarbonyl-Phe-Arg-7-(4-methyl)coumarylamide as substrate. However, the stability of the recombinant enzyme, and its pH optimum for this substrate was shifted to a higher pH. Structure-function studies of cathepsin L were performed by constructing mutations in either the propeptide portion or the carboxyl-terminal light chain portion of the protein. These constructions were expressed in the E. coli system, and enzymatic activities were assayed following solubilization, renaturation, and gel filtration chromatography of the mutated proteins. Deletions of increasing size in the propeptide resulted in large proportional losses of activity, indicating that the propeptide is essential for proper enzyme folding and/or processing in this renaturation system. Deletion of part of the light chain containing a disulfide-forming cysteine residue or a single amino acid substitution of alanine for this cysteine residue resulted in almost complete loss of activity. These data suggest that the disulfide bond joining the heavy and light chains of cathepsin L is essential for enzymatic activity.
Motility induced changes in viscosity of suspensions of swimming microbes in extensional flows (2015)

Suspensions of motile cells are model systems for understanding the unique mechanical properties of living materials which often consist of ensembles of self-propelled particles. We present here a quantitative comparison of theory against experiment for the rheology of such suspensions in extensional flows. The influence of motility on viscosities of cell suspensions is studied using a novel acoustically-driven microfluidic capillary-breakup extensional rheometer. Motility increases the extensional viscosity of suspensions of algal pullers, but decreases it in the case of bacterial or sperm pushers. A recent model [Saintillan, Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys., 2010, 81, 56307] for dilute active suspensions is extended to obtain predictions for higher concentrations, after independently obtaining parameters such as swimming speeds and diffusivities. We show that details of body and flagellar shape can significantly determine macroscale rheological behaviour.
The role of stem cell factor and of alternative c-kit gene products in the establishment, maintenance and function of germ cells (2000)

The c-kit gene plays a fundamental role during the establishment, the maintenance and the function of germ cells. In the embryonal gonad the c-kit tyrosine kinase receptor and its ligand Stem Cell Factor (SCF) are required for the survival and proliferation of primordial germ cells. In the postnatal animal, c-kit/SCF are required for the production of the mature gametes in response to gonadotropic hormones, i.e. for the survival and/or proliferation of the only proliferating germ cells of the testis, the spermatogonia, and for the growth and maturation of the oocytes. Finally, a truncated c-kit product, tr-kit, specifically expressed in post-meiotic stages of spermatogenesis and present in mature spermatozoa, causes parthenogenetic activation when microinjected into mouse eggs, suggesting that it might play a role in the final function of the gametes, fertilization.
Neuroinflammation in Sepsis: Sepsis Associated Delirium (2015)

Sepsis-associated delirium (SAD) is a clinical manifestation of the involvement of the central nervous system (CNS) during sepsis. The purpose of this review is to provide a concise overview of SAD including the epidemiology and current diagnostic criteria for SAD. We present in detail the pathophysiology with regards to blood-brain-barrier breakdown, cytokine activation and neurotransmitter deregulation. Treatment and prognosis for SAD are also briefly discussed. SAD is the most common form of delirium acquired in the ICU (Intensive Care Unit), and is described in about 50% of septic patients. Clinical features include altered level of consciousness, reduced attention, change in cognition and perceptual disturbances. Symptoms can reversible, but prolonged deficits can be observed in older patients. Pathophysiology of SAD is poorly understood, but involves microvascular, metabolic and, not least, inflammatory mechanisms leading to CNS dysfunction. These mechanisms can be different in SAD compared to ICU delirium associated with other conditions. SAD is diagnosed clinically using validated tools such as CAM-ICU (Confusion Assessment Method for the Intensive Care Medicine) or ICDSC (The Intensive Care Delirium Screening Checklist), which have good specificity but low sensitivity. Neuroimaging studies and EEG (Electroencephalography) can be useful complement to clinical evaluation to define the severity of the condition. Prompt diagnosis and eradication of septic foci whenever possible is vital. Preventive measures for SAD in the critically ill patient requiring long-term sedation include maintaining light levels of sedation using non-benzodiazepine sedatives (either propofol or dexmedetomidine). Early mobilization of patients in the ICU is also recommended. Antipsychotic drugs (haloperidol and atypical antipsychotics) are widely used to treat SAD, but firm evidence of their efficacy is lacking.
Immune complex hyperlipidemia induced by an apolipoprotein-reactive immunoglobulin A paraprotein from a patient with multiple myeloma. Characterization of this immunoglobulin. (1985)

An antibodylike paraprotein has been isolated from a patient with multiple myeloma and autoimmune hyperlipoproteinemia. The paraprotein bound to apolipoprotein B (apo B)-containing lipoproteins that formed macromolecular aggregates, and globules thought to be aggregated complexes of lipoproteins and reactive immunoglobulins were observed circulating within the retinal blood vessels of this patient. This binding specificity permitted purification of the paraprotein from both the agglutinated immune complexes and from the plasma. The protein is an IgA, kappa-immunoglobulin which exists primarily in a polymeric state. Capillary immunoprecipitation demonstrated reactivity with very low density lipoproteins (VLDL) and low density proteins (LDL), but not with high density lipoproteins (HDL). Delipidated apo B and apo E, but not apo A or apo C, formed precipitates with this immunoglobulin. In using a radioimmunoassay format, the affinity of the immunoglobulin was greatest for VLDL and decreases sequentially for intermediate density lipoproteins and LDL. No binding occurred with a dispersion of LDL lipids or with HDL. Deglycosylation did not change the binding to LDL. The apolipoproteins B and E bound with similar affinity, but no binding occurred with apo A-I or apo A-II. Weak binding appeared to occur with apo C. This paraprotein immunoprecipitated apo B-containing lipoproteins from all classes of vertebrates tested. Displacement of the lipids of LDL by Triton X-100 resulted in the formation of an apo B-Triton complex which, however, did not bind to the immunoglobulin; apparently the binding site on apo B was lost. Upon enzymatic digestion with the IgA-specific protease from Streptococcus sanguis the immunoglobulin was cleaved into Fc and Fab fragments, and the binding of LDL occurred only with the latter, consistent with the behavior of an immunoglobulin. The immunoreactivity of this paraprotein with apo B and apo E raises the interesting possibility that it may be binding to a site on these apolipoproteins which is reactive with the apo B, E receptor of the plasma membrane, a site which is conserved throughout the vertebrate phylum.
An interactive driver assistance system monitoring the scene in and out of the vehicle (2004)

This paper presents a framework for interactive driver assistance systems including techniques for fast speed sign detection and classification, car detection and tracking, and lane departure warning. In addition, the driver's actions are monitored. The integrated system uses information extracted from the road scene (speed signs, position within the lane, relative position to other cars, etc.) together with information about the driver's state such as eye gaze and head pose, to issue adequate warnings. A touch screen monitor presents relevant information and allows the driver to interact with the system. The research is focused around robust on-line algorithms. Initial results of online speed sign detection and car tracking are presented in the context of a driver assistance system.
CD43 is a ligand for E-selectin on CLA+ human T cells (2005)

The recruitment of memory T cells from blood into tissues is a central element of immune surveillance and adaptive immune responses and a key feature of chronic cutaneous inflammatory diseases such as psoriasis and atopic dermatitis. Human memory T cells that infiltrate skin express the carbohydrate epitope cutaneous lymphocyte-associated antigen (CLA). Expression of the CLA epitope on T cells has been described on P-selectin glycoprotein ligand-1 (PSGL-1) and associated with the acquisition of both E-selectin and P-selectin ligand functions. In this report, we show that CD43, a sialomucin expressed constitutively on T cells, can also be decorated with the CLA epitope and serve as an E-selectin ligand. CLA expressed on CD43 was found exclusively on the high-molecular-weight (125 kDa) glycoform bearing core-2-branched O-linked glycans. CLA+ CD43 purified from human T cells supported tethering and rolling in shear flow via E-selectin but did not support binding of P-selectin. The identification and characterization of CD43 as a T-cell E-selectin ligand distinct from PSGL-1 expands the role of CD43 in the regulation of T-cell trafficking and provides new targets for the modulation of immune functions in skin.
Object Migration and Authentication (1979)

When typed objects migrate in virtual memory, onto off-ine storage, or among the nodes of a network, the type managers must relinguish control over the object representation and state. In this paper we present a mechanism which allows a type manager to authenticate and reinstantiate migrated objects. This mechanism also solves some problems stemming from the hierarchical structure of the system itself. The mechanism is based on a combination of cryptographic techniques using (nondistributable) centralized, secret keys, and data redundancy which characterizes the object representation and state.
Role of organ selectivity in the determination of metastatic patterns of B16 melanoma. (1980)

The preferential growth of B16 melanoma metastases in specific organs was studied. Following the i.v. injection of B16 melanoma cells into syngeneic C57BL/6 mice, tumor growths developed in the in situ lungs and in grafts of pulmonary or ovarian tissue implanted either s.c. or i.m. In contrast, neoplastic lesions failed to develop in control grafts of similarly implanted renal tissue or at the site of a surgical trauma. Parabiosis experiments suggested that the growth of the B16 melanoma in ectopic lung or ovary tissue was due to the immediate arrest of circulating neoplastic cells and not to shedding of malignant cells from foci growing in the in situ lungs. Quantitative analysis of tumor cell arrest and distribution using cells labeled with [125I]-5-iodo-2'-deoxyuridine indicated that the growth of tumors in the implanted organs was not due to an enhanced initial arrest of B16 cells. No significant differences in immediate tumor cell arrest were detected between implanted fragments of lungs (tumor positive) and kidney (tumor negative) or between organ-bearing and contralateral control limbs. We conclude that the outcome of metastasis is dependent on both tumor cell properties and host factors. This conclusion supports the "seed and soil" hypothesis to explain the nonrandom pattern of cancer metastasis.
Sensor Network Optimization for a Passive Sensing Impact Detection Technique (2009)

An investigation was performed to develop a sensor placement method to maximize the performance of a structural health monitoring (SHM) system with a minimal number of sensors for detection of impact in structures, particularly for structures made of fiber-reinforced composite materials. The performance of the SHM system is evaluated based on the probability of detection (POD). This optimization problem was formulated to maximize the POD through selection of optimal sensor locations for a given sensor network. A genetic algorithm was adopted and integrated with the SHM system to perform the optimization process. Numerical simulations on two composite panels showed that the selection of sensor network configuration is crucial for the performance of the SHM system. For a targeted POD, the proposed method can be used to configure an SHM system with a minimal number of sensors to identify impact forces that are greater than a pre-defined critical value.
A comparative autoradiographic study demonstrating differential intratumor localization of monoclonal antibodies to cell surface (Lym-1) and intracellular (TNT-1) antigens. (1990)

Autoradiography was utilized to explore the patterns of distribution of two different monoclonal antibodies (Lym-1 and TNT-1) in tumor-bearing nude mice. Lym-1 is an antibody against a cell surface B-cell antigen. In comparison, TNT-1 represents a novel approach and is an antibody against an intracellular (nuclear) antigen that is selectively revealed in degenerating tumor cells. Experimentally iodine-125-(125I) labeled Lym-1 or TNT-1 was injected intravenously into nude mice bearing either the Raji lymphoma or the ME-180 human cervical carcinoma. Qualitative autoradiographic analyses performed after injection revealed that Lym-1 accumulated at the periphery of the target tumor where vascular permeability is marked and where Lym-1 positive cells are first encountered. By contrast, TNT-1 lost its initial peripheral distribution and demonstrated progressive concentration in the center of the tumor where binding to its nuclear antigen is facilitated by the presence of cell degeneration and necrosis. These studies confirm the ability of TNT-1 to bind areas deep within tumor that traditionally are considered inaccessible to antibodies administered for imaging and therapy.
In vivo measurement of T2 distributions and water contents in normal human brain (1997)

Using a 32-echo imaging pulse sequence, T2 relaxation decay curves were acquired from five white- and six gray-matter brain structures outlined in 12 normal volunteers. The water contents of white and gray matter were 0.71 (0.01) and 0.83 (0.03) g/ml, respectively. All white-matter structures had significantly higher myelin water percentages (signal percentage with T2 between 10 and 50 ms) than all gray-matter structures. The range in geometric mean T2 of the main peak for both white and gray matter was from 70 to 86 ms. T2 distributions from the posterior internal capsules and splenium of the corpus callosum were significantly wider (width is related to water environment inhomogeneity) than those from any other white- or gray-matter structures. Thus, quantitative measurement and analysis of T2 relaxation reveals differences in brain tissue water environments not discernible on conventional MR images. These differences may make short T2 components reliable markers for normal myelin.