gebhart/patrepeval huggingface dataset:
Epithelial-mesenchymal transition expression profiles as a prognostic factor for disease-free survival in hepatocellular carcinoma: Clinical significance of transforming growth factor-β signaling (2012)

Epithelial-mesenchymal transition (EMT) plays a pivotal role in cancer invasion and metastasis, and transforming growth factor (TGF)-β signaling is a potent inducer of EMT. However, the clinical significance of the correlation between EMT marker expression and TGF-β signaling in hepatocellular carcinoma (HCC) patients remains unknown. In this study, immunohistochemistry was used to analyze the expression of EMT markers and phospho-Smad2 nuclear positivity, and their association with clinicopathological features in 150 HCC patients. E-cadherin(high)/vimentin(low) and E-cadherin(low)/vimentin(high) expression profiles were determined in 55 (36.7%) and 21 (14.0%) patients, respectively. The E-cadherin(low)/vimentin(high) expression profile was significantly correlated with poor tumor differentiation (P<0.001), vascular invasion (P=0.007) and extrahepatic recurrence following curative surgery (P=0.026). Furthermore, the E-cadherin(low)/vimentin(high) expression profile was significantly correlated with shorter disease-free survival compared to E-cadherin(high)/vimentin(low) (P=0.002). Forty-one patients (27.3%) were demonstrated to have high phospho-Smad2 nuclear positivity, which was significantly correlated with the E-cadherin(low)/vimentin(high) expression profile (P<0.001). In conclusion, this study suggests that EMT expression profiles are useful prognostic markers for disease-free survival in HCC patients, and that the E-cadherin(low)/vimentin(high) expression profile is closely associated with high-grade malignant behavior such as tumoral vascular invasion and metastasis in HCC. Additionally, TGF-β-mediated EMT may play an important role in the aggressiveness of HCC.
Synthesis and Characterization of Organic/Inorganic Hybrid Nanoparticles:  Kinetics of Surface-Initiated Atom Transfer Radical Polymerization and Morphology of Hybrid Nanoparticle Ultrathin Films (2003)

The synthesis of hybrid nanoparticles was conducted by the atom transfer radical polymerization (ATRP) of styrene and (meth)acrylates from colloidal surfaces. Colloidal initiators were prepared by the functionalization of silica colloids with 2-bromoisobutyrate groups. ATRP from colloidal surfaces was then performed to attach well-defined homopolymers and block copolymers to an inorganic core. Kinetics of the ATRP of styrene (Sty), n-butyl acrylate (BA), and methyl methacrylate (MMA) under identical reaction conditions were investigated. Hybrid nanoparticles containing block copolymers of pSty-b-pBA (Mn = 22 300; Mw/Mn = 1.20), pMMA-b-pBA (Mn = 29 400; Mw/Mn = 1.28), and pBA-b-pMMA (Mn = 17 300; Mw/Mn = 1.28) were prepared, and hydrolysis of silica cores by hydrofluoric acid treatment enabled characterization of cleaved copolymers using size exclusion chromatography and 1H NMR. Ultrathin films of hybrid nanoparticles were examined using transmission electron microscopy and atomic force microscopy.
Effects of an Amino Acid/Creatine Energy Supplement on the Acute Hormonal Response to Resistance Exercise (2007)

The authors aimed to examine the acute hormonal and performance responses to resistance exercise with and without prior consumption of an amino acid/creatine/energy supplement. Eight men performed a resistance-exercise protocol at baseline (BL), 20 min after consuming a supplement (S) consisting of essential amino acids, creatine, taurine, caffeine, and glucuronolactone or a maltodextrin placebo (P). Venous blood samples were obtained before and immediately after (IP), 15 min (15P), and 30 min (30P) after each protocol. Area under the curve of resistance-exercise volume revealed that BL was significantly less than S (10%) and P (8.6%). For fatigue rate, only S (18.4% +/- 12.0%) was significantly lower than BL (32.9% +/- 8.4%). Total testosterone (TT) and growth hormone (GH) were significantly elevated at IP and 15P in all conditions. The GH response was significantly lower, however, in S and P than in BL. The TT and GH responses did not differ between S and P. These results indicated that a supplement consisting of amino acids, creatine, taurine, caffeine, and glucuronolactone can modestly improve high-intensity endurance; however, the anabolic-hormonal response was not augmented.
Development and characterization of a whole-cell bioluminescent sensor for bioavailable middle-chain alkanes in contaminated groundwater samples (1997)

A microbial whole-cell biosensor was developed, and its potential to measure water-dissolved concentrations of middle-chain-length alkanes and some related compounds by bioluminescence was characterized. The biosensor strain Escherichia coli DH5 alpha(pGEc74, pJAMA7) carried the regulatory gene alkS from Pseudomonas oleovorans and a transcriptional fusion of PalkB from the same strain with the promoterless luciferase luxAB genes from Vibrio harveyi on two separately introduced plasmids. In standardized assays, the biosensor cells were readily inducible with octane, a typical inducer of the alk system. Light emission after induction periods of more than 15 min correlated well with octane concentration. In well-defined aqueous samples, there was a linear relationship between light output and octane concentrations between 24 and 100 nM. The biosensor responded to middle-chain-length alkanes but not to alicyclic or aromatic compounds. In order to test its applicability for analyzing environmentally relevant samples, the biosensor was used to detect the bioavailable concentration of alkanes in heating oil-contaminated groundwater samples. By the extrapolation of calibrated light output data to low octane concentrations with a hyperbolic function, a total inducer concentration of about 3 nM in octane equivalents was estimated. The whole-cell biosensor tended to underestimate the alkane concentration in the groundwater samples by about 25%, possibly because of the presence of unknown inhibitors. This was corrected for by spiking the samples with a known amount of an octane standard. Biosensor measurements of alkane concentrations were further verified by comparing them with the results of chemical analyses.
CD109 expression in basal‐like breast carcinoma (2008)

Breast cancer can be classified into several subtypes based on gene expression profiling. Basal-like breast carcinoma (BLC) has a triple negative phenotype, that is, the subtype lacks the estrogen receptor (ER), progesterone receptor (PgR) and human epidermal growth factor receptor 2 (HER2). It has been recently reported that CD109, a glycosylphosphatidylinositol (GPI)-anchored cell surface protein, is a new breast myoepithelial marker. In the present study CD109 expression was investigated in invasive ductal carcinomas (IDC) of the breast on immunohistochemistry. Eighty-eight formalin-fixed, paraffin-embedded breast carcinoma sections were immunostained with anti-CD109, anti-cytokeratin 5/6 (CK5/6), anti-calponin, anti-vimentin and anti-p63 antibodies. CD109 expression was detected in 18 of 30 basal-like breast carcinomas (BLC) but not in other types of 53 IDC (non-BLC) that were positive for ER, PgR and/or HER2. The percentage of CD109-positive tissues (60%) in BLC was similar to that of CK5/6 (63%) and higher than that of other myoepithelial markers including p63 (23%), calponin (33%) and vimentin (33%). Statistical analysis indicated that the CD109-positive group in BLC, but not the CK5/6-positive group in BLC, was associated with reduced fat invasion (P < 0.05). These findings indicate that CD109 is a useful diagnostic marker for BLC and that CD109 expression may affect biological properties of cancer cells.
Precocious Puberty Secondary to Topical Testosterone Exposure (2003)

We report a case of pronounced virilization, including marked penile and pubic hair growth, accelerated height velocity and skeletal maturation, and increased muscle mass in a 2.67 year-old boy resulting from presumed inadvertent, long-term exposure to a topical testosterone cream being used by his father.
Quantitative determination of adenovirus-mediated gene delivery to rat cardiac myocytes in vitro and in vivo. (1993)

To optimize the use of modified adenoviruses as vectors for gene delivery to the myocardium, we have characterized infection of cultured fetal and adult rat cardiac myocytes in vitro and of adult cardiac myocytes in vivo by using a replication-defective adenovirus carrying the chloramphenicol acetyltransferase (CAT) reporter gene driven by the cytomegalovirus promoter (AdCMVCATgD). In vitro, virtually all fetal or adult cardiocytes express the CAT gene when infected with 1 plaque-forming unit of virus per cell. CAT enzymatic activity can be detected in these cells as early as 4 hr after infection, reaching near-maximal levels at 48 hr. In fetal cells, CAT expression was maintained without a loss in activity for at least 1 week. Using in vitro studies as a guide, we introduced the AdCMVCATgD virus directly into adult rat myocardium and compared the expression results obtained from virus injection with those obtained by direct injection of pAdCMVCATgD plasmid DNA. The amount of CAT activity resulting from adenovirus infection of the myocardium was orders of magnitude higher than that seen from DNA injection and was proportional to the amount of input virus. Immunostaining for CAT protein in cardiac tissue sections following adenovirus injection demonstrated large numbers of positive cells, reaching nearly 100% of the myocytes in many regions of the heart. Expression of genes introduced by adenovirus peaked at 5 days but was still detectable 55 days following infection. Adenoviruses are therefore a very useful tool for high-efficiency gene transfer into the cardiovascular system.
Stabilization of L-Asparaginase Modified with Comb-Shaped Poly(ethylene glycol) Derivatives, in vivo and in vitro (1994)

L-Asparaginase from Escherichia coli was coupled with two types of comb-shaped copolymer of poly-(ethylene glycol) derivative and maleic anhydride (activated PM), having molecular weights of 13,000 and 100,000 (activated PM13 and PM100, respectively) with multivalent reaction sites. After single intravenous injections of PM100-asparaginase and nonmodified asparaginase into rats, the enzymic activity of PM100-asparaginase in serum was well retained for at least 11 days, and the serum L-asparagine concentration remained undetectable for 27 days. The half-lives of PM100-asparaginase and nonmodified asparaginase were 50 and 1.5 h, respectively. Stabilization of L-asparaginase toward heat, urea, and acidity was caused by modifying the enzyme with activated PM13 and PM100. Especially, PM100-asparaginase retained high enzymic activity toward heat and urea, compared with PM13-asparaginase. It was suggested that these modifiers with a comb-shaped form and with multivalent reactive sites cover the whole surface of the asparaginase molecule and stabilize its conformation possibly through multiple covalent bindings and through various noncovalent interactions.
Risk for Newly Diagnosed Diabetes >30 Days After SARS-CoV-2 Infection Among Persons Aged <18 Years — United States, March 1, 2020–June 28, 2021 (2022)

The COVID-19 pandemic has disproportionately affected people with diabetes, who are at increased risk of severe COVID-19.* Increases in the number of type 1 diabetes diagnoses (1,2) and increased frequency and severity of diabetic ketoacidosis (DKA) at the time of diabetes diagnosis (3) have been reported in European pediatric populations during the COVID-19 pandemic. In adults, diabetes might be a long-term consequence of SARS-CoV-2 infection (4-7). To evaluate the risk for any new diabetes diagnosis (type 1, type 2, or other diabetes) >30 days<sup>†</sup> after acute infection with SARS-CoV-2 (the virus that causes COVID-19), CDC estimated diabetes incidence among patients aged <18 years (patients) with diagnosed COVID-19 from retrospective cohorts constructed using IQVIA health care claims data from March 1, 2020, through February 26, 2021, and compared it with incidence among patients matched by age and sex 1) who did not receive a COVID-19 diagnosis during the pandemic, or 2) who received a prepandemic non-COVID-19 acute respiratory infection (ARI) diagnosis. Analyses were replicated using a second data source (HealthVerity; March 1, 2020-June 28, 2021) that included patients who had any health care encounter possibly related to COVID-19. Among these patients, diabetes incidence was significantly higher among those with COVID-19 than among those 1) without COVID-19 in both databases (IQVIA: hazard ratio [HR] = 2.66, 95% CI = 1.98-3.56; HealthVerity: HR = 1.31, 95% CI = 1.20-1.44) and 2) with non-COVID-19 ARI in the prepandemic period (IQVIA, HR = 2.16, 95% CI = 1.64-2.86). The observed increased risk for diabetes among persons aged <18 years who had COVID-19 highlights the importance of COVID-19 prevention strategies, including vaccination, for all eligible persons in this age group,<sup>§</sup> in addition to chronic disease prevention and management. The mechanism of how SARS-CoV-2 might lead to incident diabetes is likely complex and could differ by type 1 and type 2 diabetes. Monitoring for long-term consequences, including signs of new diabetes, following SARS-CoV-2 infection is important in this age group.
Effective permittivity of mixtures: numerical validation by the FDTD method (2000)

The present paper reports the results of an extensive numerical analysis of electromagnetic fields in random dielectric materials. The effective permittivity of a two-dimensional (2-D) dielectric mixture is calculated by FDTD simulations of such a sample in a TEM waveguide. Various theoretical bounds are tested in light of the numerical simulations. The results show how the effective permittivity of a mixture with random inclusion positionings is distributed. All possible permittivity values lie between Wiener limits, and according to FDTD simulations the values are almost always between Hashin-Shtrikman limits. Calculated permittivity distribution is also compared with theoretical mixture models. No model seems to be able to predict the simulated behavior over the whole range of volume fraction.
Stereoelectroencephalography in the “difficult to localize” refractory focal epilepsy: Early experience from a North American epilepsy center (2012)

In patients who are not considered to be ideal candidates for subdural grids and strips implantation, the SEEG methodology is a safe, useful and reliable alternative option for invasive monitoring in patients with refractory focal epilepsy, providing an additional mean for seizure localization and control in a "difficult to localize" subgroup of patients.
Site-Specific DNA Transesterification by Vaccinia Topoisomerase:  Role of Specific Phosphates and Nucleosides (1999)

Vaccinia topoisomerase forms a covalent DNA-(3'-phosphotyrosyl)-enzyme intermediate at a pentapyrimidine target site 5'-CCCTTp downward arrow in duplex DNA. Here we present experiments that illuminate the contributions of specific nucleosides and phosphates to site affinity and transesterification. We find that the -1 phosphate and -2 nucleoside on the scissile strand (5'-CCCTTp / NpN) enhance the rate of transesterification by factors of 40 and 25, respectively, whereas the DNA segment downstream of the -2 nucleotide makes no significant kinetic contribution. Placement of a 5'-phosphate/3'-OH nick at position +2, +3, +4, or +5 within the CCCTT element results in a 5-10-fold reduction in the affinity of topoisomerase binding to DNA. A nick at the +2 phosphate also slows the rate of transesterification by approximately 500-fold. This finding, together with earlier studies of the effects of position-specific base and sugar modifications, points to the +2 Tp nucleotide as being the most critical element of the CCCTT target site other than the scissile phosphate itself. On the noncleaved strand, the segment downstream of the 3'-GGGAA element contributes minimally to the rate of transesterification provided that the substrate is otherwise fully base-paired within the 5'-CCCTT target site. By studying the effects of single nucleotide gaps and missing phosphate nicks within the 3'-GGGAA sequence, we find that the +1 and +2 adenosine nucleosides enhance the rate of transesterification by 20- and 1,000-fold respectively and that the +5 phosphate (3'-GpGGAA) is also important for cleavage. Cumulative functional analyses of the vaccinia topoisomerase-DNA interface are discussed in light of newly available structures for the vaccinia and human type IB enzymes.
Formation of Ammonia from an Iron Nitrido Complex (2009)

Radical ideas: Reaction of the iron(IV) nitrido complex [PhB(MesIm)(3)Fe[triple chemical bond]N] (see picture, Mes=2,4,6-Me(3)C(6)H(2)) with TEMPO-H (1-hydroxy-2,2,6,6-tetramethylpiperidine) results in high yields of ammonia and quantitative formation of [PhB(MesIm)(3)Fe(tempo)]. The mechanism likely involves hydrogen-atom transfer from TEMPO-H to the nitrido complex. Similar reaction with the triphenylmethyl radical yields [PhB(MesIm)(3)Fe[triple chemical bond]N--CPh(3)].
Representing the Other: 'Race', Text, and Gender in Spanish and Spanish American Narrative (1993)

Introduction: 'Race', Text, Gender I. Early Narrative and Poststructuralism: La Celestina, Castro, and the Conversos El Criticon, Allegory, and Nationality II. Women's Narrative and Alterity: Visions of Teresa: Lacan, Irigary, Kristeva Rosario Castellanos and Helen Cixous III. Postmodernism and Contemporary Male Narrative: Manuel Puig and Gianni Vattimo Juan Goytisolo and Jean Baudrillard Conclusion: Representing the Other Bibliography Index
Coding, analysis, interpretation, and recognition of facial expressions (1997)

We describe a computer vision system for observing facial motion by using an optimal estimation optical flow method coupled with geometric, physical and motion-based dynamic models describing the facial structure. Our method produces a reliable parametric representation of the face's independent muscle action groups, as well as an accurate estimate of facial motion. Previous efforts at analysis of facial expression have been based on the facial action coding system (FACS), a representation developed in order to allow human psychologists to code expression from static pictures. To avoid use of this heuristic coding scheme, we have used our computer vision system to probabilistically characterize facial motion and muscle activation in an experimental population, thus deriving a new, more accurate, representation of human facial expressions that we call FACS+. Finally, we show how this method can be used for coding, analysis, interpretation, and recognition of facial expressions.
Serum Creatinine Concentration and Risk of Cardiovascular Disease (1997)

A high serum creatinine concentration within the normal range is a marker for increased risk of cerebrovascular disease in both normotensive and hypertensive subjects. These findings support the evidence indicating that subtle impairment of renal function is a factor for increased risk of stroke and suggest mechanisms in the pathogenesis of stroke that warrant further investigation.
Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network (2001)

We demonstrate an integrated approach to build, test, and refine a model of a cellular pathway, in which perturbations to critical pathway components are analyzed using DNA microarrays, quantitative proteomics, and databases of known physical interactions. Using this approach, we identify 997 messenger RNAs responding to 20 systematic perturbations of the yeast galactose-utilization pathway, provide evidence that approximately 15 of 289 detected proteins are regulated posttranscriptionally, and identify explicit physical interactions governing the cellular response to each perturbation. We refine the model through further iterations of perturbation and global measurements, suggesting hypotheses about the regulation of galactose utilization and physical interactions between this and a variety of other metabolic pathways.
Efficient microfluidic particle separation arrays (2009)

Microfluidic particle separation arrays are capable of passive sorting of microparticles or cells by size while avoiding blockage. Despite the usefulness of boundaries for concentration and parallel integration of arrays, separation efficiency is severely degraded in the areas adjacent to the boundaries due to the aberrant fluid flow found there. This letter shows how to eliminate this problem by modifying the boundary interface. At each row the boundary is moved by a specific amount to ensure a linear change in flux from row to row, which leads to uniform flow patterns and improved separation characteristics throughout the array.
Synthesis of three no‐carrier‐added O6‐4‐[125I] iodobenzylguanosine derivatives, new reagents for the assay of O6‐alkylguanine‐DNA alkyltransferase activity (1995)

Abstract O 6 ‐alkylguanine‐DNA alkyltransferase (AGT) is mainly responsible for tumour resistances observed in chemotherapeutic treatments by chloroethylnitrosoureas (CENUs). Measurement of AGT activity is thereby essential to predict the response of the patients to therapy with CENUs. In order to develop a sensitive and easy new assay for AGT, previously undescribed O 6 ‐4‐[ 125 I]iodobenzyl‐2′‐deoxyguanosine, O 6 ‐4‐ [ 125 I]iodobenzyl‐N‐acetylguanosine and O 6 ‐4‐[ 125 I] iodobenzylguanosine labelled with high specific activity were prepared. The most convenient synthetic route appeared to be a rapid and high yield iododestannylation of a tri‐n‐butylstannyl derivative with no‐carrieradded sodium [ 125 I] iodide. Final HPLC separation from the excess of precursor and unreacted [ 125 I] iodides afforded the radioiodinated guanosine derivatives in yields ranging from 70 to 77 %, chemical and radiochemical purities averaging 99%.
Stability without a centromere (1998)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
Direct evidence for binding of CD8 to HLA class I antigens. (1989)

Adhesion of T lymphocytes is an essential step for antigen recognition and lymphocyte activation. mAbs to T cell surface proteins have been used to define the receptor-ligand proteins that appear to be involved in adhesion. Since most assays measure the effects of mAbs on T lymphocyte function, it is not known whether mAb-mediated blocking is due to a disruption of receptor-ligand interactions or results in inhibition of some aspect of receptor-mediated triggering. It has been suggested that the CD8 molecule augments T cell avidity for the target cells by binding to determinants on target cell MHC class I molecules. In the present report, we demonstrated that purified CD8 molecules incorporated into large lipid vesicles (artificial target cells) mediate the adhesion of these vesicles to cells expressing HLA proteins, while vesicles expressing purified HLA class I antigens bind to CD8+ T cells. Furthermore, vesicles bearing CD8 will form conjugates with vesicles expressing HLA class I proteins. These conjugates were found to be specifically inhibited by mAbs to CD8 or HLA class I molecules. We also demonstrate that CD2-reconstituted vesicles can form conjugates with vesicles bearing LFA-3. These experiments provide direct evidence for an interaction of the CD8 molecule with class I MHC proteins as well as between CD2 proteins and LFA-3 proteins, thus supporting the hypothesis that these molecules can mediate cell-cell adhesion.