gebhart/patrepeval huggingface dataset:
Three differentiation states risk-stratify bladder cancer into distinct subtypes (2012)

Current clinical judgment in bladder cancer (BC) relies primarily on pathological stage and grade. We investigated whether a molecular classification of tumor cell differentiation, based on a developmental biology approach, can provide additional prognostic information. Exploiting large preexisting gene-expression databases, we developed a biologically supervised computational model to predict markers that correspond with BC differentiation. To provide mechanistic insight, we assessed relative tumorigenicity and differentiation potential via xenotransplantation. We then correlated the prognostic utility of the identified markers to outcomes within gene expression and formalin-fixed paraffin-embedded (FFPE) tissue datasets. Our data indicate that BC can be subclassified into three subtypes, on the basis of their differentiation states: basal, intermediate, and differentiated, where only the most primitive tumor cell subpopulation within each subtype is capable of generating xenograft tumors and recapitulating downstream populations. We found that keratin 14 (KRT14) marks the most primitive differentiation state that precedes KRT5 and KRT20 expression. Furthermore, KRT14 expression is consistently associated with worse prognosis in both univariate and multivariate analyses. We identify here three distinct BC subtypes on the basis of their differentiation states, each harboring a unique tumor-initiating population.
Conductivity switching characteristics and reset currents in NiO films (2005)

Conductivity switching phenomena controlled by external voltages have been investigated for various NiO films deposited by dc reactive sputtering methods. Pt∕NiO∕Pt capacitor structures with top electrodes of different diameters have showed increasing off-state current with the diameter of a top electrode and nearly the same on-state current independent of the diameter. Local conductivity switching behaviors have been observed in a series structure consisting of two Pt∕NiO∕Pt capacitors with different resistance values. By reasoning out conductivity switching mechanisms from the switching characteristics and introducing multilayers consisting of NiO layers with different resistance values, we have reduced the reset current by two orders of magnitude.
Compensation of Hysteresis Nonlinearity in Magnetostrictive Actuators With Inverse Multiplicative Structure for Preisach Model (2013)

Compensation of hysteresis nonlinearities in smart material based actuators presents a challenging task for their applications. Many approaches have been proposed in the literature, including the inverse multiplicative scheme. The advantage for such a scheme is to avoid direct model inversions. However, the approach is mainly developed for the Bouc-Wen model. Focusing on the Preisach model which is utilized to describe magnetostrictive actuators, in this paper an inverse compensation approach for Preisach model using the inverse multiplicative structure is developed. Since the input signal is implicitly involved in the Preisach model, it imposes a great challenge to construct the inverse function of the model. To obtain an explicit expression of the input signal from its implicit form so that the inverse multiplicative technique can be applied, the Preisach model is decomposed into a non-memory part and memory part. Using this separation, it only requires to solve the inverse of the non-memory part to obtain an explicit expression of the input signal, thus avoiding constructing the inverse for entire complex dual integral formulation of the Preisach model. Experimental results for a magnetostrictive actuator demonstrate the effectiveness of the proposed approach.
Aqueous Tracers for Oilfield Applications (1991)

ABSTRACT As an oil field matures, the need for reservoir information increases. Improved geological descriptions are frequently necessary for the implementation of numerical modelling or improved oil recovery techniques. Frequently this description can be enhanced by tracer studies. Detecting the location of faults between wells is one specific use for tracing fluid flow. Tracer studies have also been used to complement the information provided by other reservoir characterization methods such as pulse and interference testing. The primary importance of tracer testing is that it provides direct proof that fluid flow has progressed from point A to point B, showing that communication paths exist. In addition, measured tracer breakthrough times are quite useful for inferring the flow characteristics of the reservoir. If the tracer program is poorly designed, the apparent absence of tracer detection at point B may lead to incorrect decisions affecting the management of the reservoir. We will discuss the proper selection and usage of chemicals for tracer testing. Limitations and precautions for individual chemicals will be demonstrated with test data from several field tests. The objective of a tracer test design must be known before a proper test can be implemented. Environmental aspects and analysis of certain tracer materials will also be addressed.
Preservation media, durations and cell concentrations of short-term storage affect key features of human adipose-derived mesenchymal stem cells for therapeutic application (2017)

In this study, ME + HSA was found to be the best medium, most likely due to the supplement of HSA which could protect cells, the physiological pH (7.4) of ME and sodium gluconate ingredient in ME which could provide energy for cells. Duration should be limited to 24 h because of reduced nutrient supply and increased waste and lactic acid accumulation during prolonged storage. To keep cell proliferation and limit lactic acid accumulation, the proper cell concentration is 5× 10<sup>6</sup> cells/ml. Surface markers, cell cycle and immunosuppressive capacity did not change significantly after storage using the optimized condition, which confirmed our results that this optimized short-term storage condition of MSCs has a great potential for the application of cell therapy.
Molecular, functional, and evolutionary analysis of sequences specific to Salmonella. (1993)

In that salmonellae have been implicated in an unprecedented array of diseases, sequences found to be specific to this species are often thought to be involved in the virulence attributes not seen in other enteric bacteria. To identify the molecular, genetic, and phenotypic characteristics that differentiate bacterial species, we analyzed five cloned DNA fragments that were originally described as being confined to Salmonella. Most of these segments mapped to unique positions on the Salmonella typhimurium chromosome indicative of independent evolutionary events, and three had G+C contents considerably lower than that of the Salmonella genome, suggesting that they arose through horizontal transfer. The nucleotide sequence was determined for one of the clones exhibiting an atypical base composition. This 4.9-kb fragment contained an open reading frame with structural similarity to the LysR family of transcriptional regulators. Strains harboring deletions in this region were tested for > 120 phenotypic characteristics including the effects on a collection of environmentally regulated lac gene fusions. In addition, all deletion strains behaved like the wild-type parent when tested for virulence in mice.
Natural history and prognosis of diarrhoea of unknown cause in patients with acquired immunodeficiency syndrome (AIDS). (1995)

This paper is a prospective study of patients with advanced human immunodeficiency virus infection and chronic diarrhoea for which no cause could be found after extensive investigations, including examination of multiple stool specimens for all known faecal pathogens and the histological examination of small and large bowel biopsy specimens. Of 39 such patients recruited from 155 prospectively investigated patients, eight had a possible cause of diarrhoea identified on follow up investigations, including small bowel neoplasms in three and cytomegalovirus in two. In 17 of the remaining 31 the diarrhoea resolved completely in a mean of seven months from its onset. Eleven had continuing mild or intermittent diarrhoea and three had more than 1 litre of diarrhoea daily for which no cause could be found. The median survival for patients with 'pathogen negative' diarrhoea was 48.7 months, which is similar to that of control patients with no diarrhoea and significantly longer than that of matched patients with a gastrointestinal pathogen (9.6 months).
Recombinant Human Interleukin-11 Directly Promotes Megakaryocytopoiesis In Vitro (1997)

We have investigated the mechanism of action of the thrombopoietic cytokine, recombinant human interleukin-11 (rhIL-11), on megakaryocytopoiesis in vitro. We have shown that rhIL-11-induced murine and human megakaryocytopoiesis are not mediated by thrombopoietin (Tpo). Murine megakaryocytes (MKs) were produced from bone marrow (BM) mononuclear cells cultured with rhIL-11, IL-3, and a combination of the two cytokines. Conditioned media (CM) were collected and assayed for the presence of biologically active Tpo. Tpo activity was not detected in any of the CMs tested. Next, human BM CD34+ cells were cultured in serum-free fibrin clot medium with rhIL-11, IL-3, or rhIL-11 plus IL-3 and an antibody that neutralizes human Tpo activity. No inhibition of either burst-forming unit-MK- or colony-forming unit-MK-derived colony formation was observed. The antibody did partially inhibit steel factor-induced MK-colony formation, suggesting that the actions of this cytokine are mediated, in part, by Tpo. We determined that MKs can be direct targets of rhIL-11 by showing the expression of functional IL-11 receptor on these cells. Total RNA was prepared from cultured human BM CD41+CD14- cells (MKs) and IL-11 receptor alpha chain mRNA was detected in the MKs by reverse transcription-polymerase chain reaction. Analysis of single-sorted CD41+CD14- cells confirmed that the observed IL-11 receptor expression was not due to contaminating CD41- cells in the pool. The presence of rhIL-11 receptor alpha chain protein in the cells was established by Western blot analysis. After a short exposure of purified BM MKs to rhIL-11, enhanced phosphorylation of both its signal transduction subunit, gp130, and the transcription factor, STAT3 was detected, showing a direct activation of receptor signaling by the cytokine. Consistent with the lack of effect of rhIL-11 on platelets in vivo, IL-11 receptor alpha chain mRNA and protein were not detected in isolated human platelets. These data indicate that rhIL-11 acts directly on MKs and MK progenitors but not on platelets.
Stimuli-Responsive Core–Shell Microcapsules with Tunable Rates of Release by Using a Depolymerizable Poly(phthalaldehyde) Membrane (2013)

Flow-focusing microfluidic techniques were used to provide access to core–shell microcapsules in which the shell is composed of end-capped poly(phthalaldehydes) that depolymerize completely from head-to-tail in response to fluoride. Microcapsules made from these depolymerizable polymers provide an amplified response to the applied chemical signal, where the rate of the response can be tuned both by varying the length of the polymer and the thickness of the shell wall.
Two-frame 3D particle tracking (2006)

A whole-field three-dimensional (3D) particle tracking velocimetry (PTV) tool for diagnostics in fluid mechanics is presented. Specifically, it is demonstrated why and when PTV is the natural choice in 3D applications compared to particle image velocimetry (PIV). Three different tracking methods are investigated, namely the nearest neighbour, the neural network and the relaxation method. In order to demonstrate the use of PTV for 3D applications, the selected tracking schemes are implemented for use with the defocusing digital particle image velocimetry (DDPIV) technique. The performance of the tracking algorithms is evaluated based on synthetic 3D information. Furthermore, the potential benefit of a merging between the PIV and PTV approaches is explored within the DDPIV framework. The results show that the relaxation tracking method is the most robust and efficient, while the combined PIV/PTV analysis brings significant improvements solely with the neural network scheme. In terms of errors, PTV is found to be more sensitive to particle reconstruction errors than the DDPIV cross-correlation analysis.
The synthesis and biological activity of certain pentaazaacenaphthylenes, hexaazaacenaphthylenes and their corresponding nucleosides. (1986)

Synthesis of the tricyclic nucleoside 8-amino-6-N-methyl-2-(beta-D-ribo-furanosyl)-1,2,3,5,6,7-hexaazaacena phthylene (5) has been accomplished by the ring closure of an appropriately substituted pyrazolo[3,4-d]-pyrimidine nucleoside followed by the requisite chemical conversions. The formation, isolation and structural elucidation of two unexpected nucleosides formed by a reductive ring cleavage of the hexaazaacenaphthylene ring system is discussed. A comparison of the antitumor and biological activity of 5 with the structurally related tricyclic pentaazaacenaphthylene nucleoside which is currently in phase II clinical trials at the 5'-phosphate pro-drug is also presented.
Correlations of receptor binding and metabolic and mitogenic potencies of insulin analogs designed for clinical use. (2000)

In recent years, analogs of human insulin have been engineered with the aim of improving therapy for people with diabetes. To ensure that the safety profile of the human hormone is not compromised by the molecular modifications, the toxico-pharmacological properties of insulin analogs should be carefully monitored. In this study, we compared the insulin and IGF-I receptor binding properties and metabolic and mitogenic potencies of insulin aspart (B28Asp human insulin), insulin lispro (B28Lys,B29Pro human insulin), insulin glargine (A21Gly,B31Arg,B32Arg human insulin), insulin detemir (NN304) [B29Lys(epsilon-tetradecanoyl), desB30 human insulin], and reference insulin analogs. Receptor affinities were measured using purified human receptors, insulin receptor dissociation rates were determined using Chinese hamster ovary cells overexpressing the human insulin receptor, metabolic potencies were evaluated using primary mouse adipocytes, and mitogenic potencies were determined in human osteosarcoma cells. Metabolic potencies correlated well with insulin receptor affinities. Mitogenic potencies in general correlated better with IGF-I receptor affinities than with insulin receptor off-rates. The 2 rapid-acting insulin analogs aspart and lispro resembled human insulin on all parameters, except for a slightly elevated IGF-I receptor affinity of lispro. In contrast, the 2 long-acting insulin analogs, glargine and detemir, differed significantly from human insulin. The combination of the B31B32diArg and A21Gly substitutions provided insulin glargine with a 6- to 8-fold increased IGF-I receptor affinity and mitogenic potency compared with human insulin. The attachment of a fatty acid chain to LysB29 provided insulin detemir with reduced receptor affinities and metabolic and mitogenic potencies but did not change the balance between mitogenic and metabolic potencies. The safety implications of the increased growth-stimulating potential of insulin glargine are unclear. The reduced in vitro potency of insulin detemir might explain why this analog is not as effective on a molar basis as human insulin in humans.
Influence of Salt and Rinsing Protocol on the Structure of PAH/PSS Polyelectrolyte Multilayers (2010)

A quartz crystal microbalance (QCM) and dual polarization interferometry (DPI) have been utilized to study how the structure of poly(allylamine hydrochloride) (PAH)/poly(styrene sulfonate) (PSS) multilayers is affected by the rinsing method (i.e., the termination of polyelectrolyte adsorption). The effect of the type of counterions used in the deposition solution was also investigated, and the polyelectrolyte multilayers were formed in a 0.5 M electrolyte solution (NaCl and KBr). From the measurements, it was observed that thicker layers were obtained when using KBr in the deposition solution than when using NaCl. Three different rinsing protocols have been studied: (i) the same electrolyte solution as used during multilayer formation, (ii) pure water, and (iii) first a salt solution (0.5 M) and then pure water. When the multilayer with PAH as the outermost layer was exposed to pure water, an interesting phenomenon was discovered: a large change in the energy dissipation was measured with the QCM. This could be attributed to the swelling of the layer, and from both QCM and DPI it is obvious that only the outermost PAH layer swells (to a thickness of 25-30 nm) because of a decrease in ionic strength and hence an increase in intra- and interchain repulsion, whereas the underlying layers retain a very rigid and compact structure with a low water content. Interestingly, the outermost PAH layer seems to obtain very similar thicknesses in water independent of the electrolyte used for the multilayer buildup. Another interesting aspect was that the measured thickness with the DPI evaluated by a single-layer model did not correlate with the estimated thickness from the model calculations performed on the QCM-D data. Thus, we applied a two-layer model to evaluate the DPI data and the results were in excellent agreement with the QCM-D results. To our knowledge, this evaluation of DPI data has not been done previously.
Development of Dark Skin Discoloration on Peach and Nectarine Fruit in Response to Exogenous Contaminations (1994)

Dark skin discoloration development on peach and nectarine cultivars was investigated in response to exogenous pH and metallic ions. The influence of skin abrasion and washing in combination with exogenous contaminants was studied in a factorial design experiment by using skin discs. Only abraded skin discs with and without washing developed discoloration after being exposed to high pH and different metallic ion concentrations. Among the metallic ion contaminants studied (Fe, Al, Cu, Sn, Zn, and Na), iron was the most effective in causing dark skin discoloration at physiological pH (3.5). Iron concentrations ≥10 ppm induced dark discoloration on abraded fruit skin. Dark discoloration development produced by exposing the skin tissue to pH levels &gt;6 was reversible, whereas the dark discoloration induced by iron and aluminum remained stable.
A Sialylated Glycan Microarray Reveals Novel Interactions of Modified Sialic Acids with Proteins and Viruses (2011)

Many glycan-binding proteins in animals and pathogens recognize sialic acid or its modified forms, but their molecular recognition is poorly understood. Here we describe studies on sialic acid recognition using a novel sialylated glycan microarray containing modified sialic acids presented on different glycan backbones. Glycans terminating in β-linked galactose at the non-reducing end and with an alkylamine-containing fluorophore at the reducing end were sialylated by a one-pot three-enzyme system to generate α2-3- and α2-6-linked sialyl glycans with 16 modified sialic acids. The resulting 77 sialyl glycans were purified and quantified, characterized by mass spectrometry, covalently printed on activated slides, and interrogated with a number of key sialic acid-binding proteins and viruses. Sialic acid recognition by the sialic acid-binding lectins Sambucus nigra agglutinin and Maackia amurensis lectin-I, which are routinely used for detecting α2-6- and α2-3-linked sialic acids, are affected by sialic acid modifications, and both lectins bind glycans terminating with 2-keto-3-deoxy-D-glycero-D-galactonononic acid (Kdn) and Kdn derivatives stronger than the derivatives of more common N-acetylneuraminic acid (Neu5Ac) and N-glycolylneuraminic acid (Neu5Gc). Three human parainfluenza viruses bind to glycans terminating with Neu5Ac or Neu5Gc and some of their derivatives but not to Kdn and its derivatives. Influenza A virus also does not bind glycans terminating in Kdn or Kdn derivatives. An especially novel aspect of human influenza A virus binding is its ability to equivalently recognize glycans terminated with either α2-6-linked Neu5Ac9Lt or α2-6-linked Neu5Ac. Our results demonstrate the utility of this sialylated glycan microarray to investigate the biological importance of modified sialic acids in protein-glycan interactions.
Chronic Liver Allograft Rejection (1998)

A study was conducted to assess the inter and intrarater agreement for the histopathologic features and diagnosis of chronic rejection (CR) and several other important causes of late liver allograft dysfunction. On two occasions, five pathologists, experienced with liver transplantation, reviewed a set of 49 slides representing a range of diagnoses, without knowledge of the clinical history or liver injury test results. The readings were correlated with the original histopathologic diagnosis, liver injury tests, and clinicopathologic follow-up. Assessment of biopsy adequacy (kappa = 0.69) and portal tract counts (kappa = 0.79) showed good to excellent intrarater agreement, whereas interrater agreement for these variables was moderate to good, respectively (kappa = 0.44 and 0.65). Likewise, the intrarater agreement for the diagnosis of CR (kappa = 0.68), hepatitis (kappa = 0.77), and obstructive cholangiopathy (kappa = 0.55) showed good to excellent agreement, whereas the interrater agreement for these same diagnoses ranged from fair to good (kappa = 0.58, 0.46, and 0.25, respectively). In 18 specimens, there was a near unanimous diagnosis of CR across both readings. These biopsies were obtained at a median of 7.1 months (range, 42 days to 4.9 years) after transplantation, and the average number of portal tracts was 8.4 (range, 4-15). Interestingly, only 13 of these 18 specimens showed bile duct loss in >50% of the portal triads; the remaining cases showed atrophy/pyknosis of the biliary epithelium in a majority of small bile ducts. Clinicopathologic correlation showed that these 18 biopsies were obtained from 16 grafts from 15 patients, 14 of whom ultimately required retransplantation or died of or with CR, whereas two of the grafts/patients recovered. A high rate of sensitivity (92%) and a somewhat lower, but acceptable, rate of specificity (71% to 80%) was found for the diagnosis of CR. Chronic rejection and other causes of late liver allograft dysfunction can be diagnosed reliably by a group of pathologists experienced with liver transplantation, and the diagnosis of CR correlates with clinical course and liver function abnormalities. Expanded criteria for the diagnosis of CR are presented, and potential problem areas for practicing pathologists are discussed.