gebhart/patrepeval huggingface dataset:
Abstract 2721: Comparative responses of HPV-positive vs HPV-negative head and neck cancer cells to radiation and/or chemotherapeutic drugs (2011)

Abstract Purpose: HPV is associated with a growing proportion of head and neck squamous cell carcinomas (HNSCCs), which show improved clinical outcome compared with non-HPV associated HNSCC. Whether this improved outcome reflects enhanced responsiveness to radiation and/or chemotherapy remains unclear. There is little data available regarding the radio- and chemo-sensitivity of HPV-associated HNSCC. We provide detailed analysis of radiation response profiles in verified HPV-positive HNSCC lines. Methods: Degenerate PCR and Southern blot were used to confirm HPV status in HNSCC human tumor cell lines. Clonogenic survival assays were used to assess radiation sensitivity. Proliferation assays were used to assess sensitivity to chemotherapy. Western blot was used to assess EGFR expression, activity, and the effect of EGFR inhibitor treatment. Results: Clonal expansion of existing HPV-positive HNSCC cell lines was performed to confirm the presence of a homogeneous population of cells and HPV-integration status confirmed by Southern Blot. HPV-positive cells were more sensitive to radiation-induced cell death compared to HPV-negative cells using single dose and fractionated radiation exposure regimens. Of the HPV+ cells tested to date, we have seen further radiosensitization with exposure to EGFR inhibitors (e.g., enhancement ratio 1.27 for UM-SCC47 with erlotinib) despite similar response to the EGFR inhibitor alone. HPV+ tumor xenografts have been raised in immunocompromised mice for in vivo radiation and chemotherapy response assessment. Conclusions: Consistent with clinical reports, HPV-associated HNSCC cells exhibit increased sensitivity to radiation. The in vitro sensitivity of HPV-positive HNSCC to chemotherapy is in progress, as is the response evaluation of HPV+ xenografts to radiation and chemotherapy. Underlying molecular mechanisms for altered response profiles in HPV+ HNSCC are considered as they pertain to future clinical trial designs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2721. doi:10.1158/1538-7445.AM2011-2721
Chain organization and thermodynamics in micelles and bilayers. II. Model calculations (1985)

Based on the theory presented in part I (preceding paper) we calculate molecular and thermodynamic properties of model chains packed in micellar aggregates of three typical geometries: spheres, cylinders, and planar bilayers. Each possible conformation of a model chain is equivalent to a sequence of walks on a regular cubic lattice. The internal energy of a given conformation is proportional to the number of ‘‘kinks’’ (π/2 bond angles). The kink (gauche) energy measures the inherent flexibility of the chain. We calculate bond order parameter profiles for chains packed in aggregates of various curvature and radius, and find that in all cases the degree of conformational freedom increases from the chain head towards its end. The same qualitative behavior is observed for entirely flexible (zero kink energy) chains. This implies that the internal energy of the chain plays only a secondary role, compared to that of the packing constraints in determining chain conformational statistics in micellar aggregates. In accordance with this conclusion we also find that the geometry dependence of the conformational free energy is dominated by the entropic contribution. The differences between the minimal free energies of chains in different geometries are generally small. Yet, they may be comparable in magnitude to the changes associated with the surface (‘‘opposing forces’’) contributions to the geometry dependence of the micelle’s free energy.
Introduction to the Special Collection—Beating Cancer with Early Detection: A Seasoned Idea with New Insights (2018)

This issue of JALM includes a collection of articles dealing with early cancer detection. Cancer is among the top 3 leading causes of death in North America. It is a fearsome disease mainly because of difficulties in treating it. Regarding funding, more money has been spent on cancer than on any other disease. Despite optimistic views over many decades that cancer will soon be beaten, these predictions have not as yet come true, and cancer remains a major health issue.

The best way to combat cancer is by preventing it. However, besides quitting smoking (a very effective measure), there are no specific recommendations on how to prevent cancer, except some general guidelines such as increased exercise and dietary modifications to reduce obesity. These are measures that apply to many other diseases, and such recommendations date back to Hippocrates! Subsequently, at present, we are left with the option of diagnosing and treating cancer effectively rather than preventing it.

One of the reasons that cancer prevention is difficult is because we still do not understand very well the causes of cancer, despite spectacular advances in biomedicine over the past 50 years. The prevailing hypothesis about cancer initiation is the accumulation of mutations in cancer genes over the lifespan (1, 2). Our hopes of …
Study of low-temperature (4 degrees C) transport of mouse two-cell embryos enclosed in oviducts. (2003)

Low-temperature transport of two-cell embryos in oviducts is useful as a method of shipping mouse embryos between institutes.
Interferometric Coherent Raman Micro-Spectroscopy with a Low Coherence Supercontinuum Source (2010)

First Page
Specific Antioxidant Activity of Caffeoyl Derivatives and Other Natural Phenolic Compounds: LDL Protection against Oxidation and Decrease in the Proinflammatory Lysophosphatidylcholine Production (2001)

Specific antioxidant activity (SAA) (i.e., activity related to the molar or gallic acid equivalent amount of antioxidant) of natural polyphenolic mixtures or pure phenolic compounds was studied using their capacity to delay the conjugated diene production brought about by in vitro LDL copper-mediated or AAPH-mediated oxidation. The cinnamic acid series (caffeic, sinapic, ferulic acids) displayed a constant SAA over a large range of concentrations, whereas the benzoic acid series (gallic and protocatechuic acids) showed much higher SAA at low concentrations. The natural phenolic mixtures had a constant SAA. The highest SAA was obtained with caffeoyl esters (caffeoylquinic, rosmarinic, and caffeoyltartaric acids) and catechin for the copper-oxidation and the AAPH-oxidation system, respectively. Phenolic mixtures and acids delayed vitamin E depletion and decreased proinflammatory lysophosphatidylcholine production. As with polyphenols, probucol delayed lysophosphatidylcholine and conjugated dienes production, at higher concentrations, but was not effective at preventing vitamin E depletion. Polyphenols prevent the oxidation of LDL and its constituents (vitamin E, phosphatidylcholine), which is compatible with an antiinflammatory and antiatherosclerotic role in pathophysiological conditions.
CIGS growth on a GaP/Si(001) platform : towards CIGS/Si tandem solar cells (2021)

International audience
Selective measurements of NO, NO <sub>2</sub> and NO <sub>y</sub> in the free troposphere using quantum cascade laser spectroscopy (2012)

Abstract. A quantum cascade laser based absorption spectrometer for continuous and direct measurements of NO and NO2 was employed at the high-altitude monitoring site Jungfraujoch (3580 m a.s.l., Switzerland) during a three month campaign in Spring/Summer 2012. The total reactive nitrogen, NOy, was also measured in the form of NO after conversion on a gold catalyst. The aim was to assess the suitability of the instrument for long-term monitoring of the main reactive nitrogen species under predominantly free tropospheric air conditions. A precision (1σ) of 10 and 3 ppt for NO and NO2 was achieved with 180 s averaging time under field conditions. The linear dynamic range of the instrument has been verified for both species from the detection limit to &amp;approx;45 ppbv. The spectrometer shared a common sampling inlet with a chemiluminescence-based analyzer. The comparison of the time series shows excellent agreement between the two techniques and demonstrates the adequacy of the laser spectroscopic approach for this kind of demanding environmental applications.
Characterization of Peptostreptococcus asaccharolyticus Glutamate Dehydrogenase Purified by Dye-ligand Chromatography (1984)

Glutamate dehydrogenase (L-glutamate:NAD+ oxidoreductase (deaminating); EC 1.4.1.2) has been purified from Peptostreptococcus asaccharolyticus in a single step using dye-ligand chromatography. The enzyme (GDH) was present in high yields and was stabilized in crude extracts. A subunit molecular weight of 49000 +/- 500 was determined by SDS polyacrylamide gel electrophoresis and six bands were obtained after cross-linking the subunits with dimethyl suberimidate. This bacterial GDH was predominantly NAD+-linked, but was able to utilize both NADP+ and NADPH at 4% of the rates with NAD+ and NADH, respectively. An investigation of the amino acid specificity revealed some similarities with GDH from mammalian sources and some clear differences. The values of apparent Km for the substrates ammonia, 2-oxoglutarate, NADH, NAD+ and glutamate were 18.4, 0.82, 0.066, 0.031 and 6 mM, respectively. The P. asaccharolyticus GDH was not regulated by purine nucleotides, but was subject to strong inhibition with increasing ionic strength.
Microbial macroecology: highly structured prokaryotic soil assemblages in a tropical deciduous forest (2005)

ABSTRACT Aim To assess the hypothesis that free‐living prokaryotes show a pattern of ‘no biogeography’ by examining the scaling of soil prokaryotic diversity and by comparing it with other groups’ biogeographical patterns. Location Two sites in the tropical deciduous forest of Chamela, Jalisco, on the western coast of Mexico. Methods We examined the diversity and distribution of soil prokaryotes in two 8 × 8 m quadrats divided in such manner that we could sample at four spatial scales. Restriction fragment length polymorphisms of 16S rRNA genes were used to define operational taxonomic units (OTUs) that we used in lieu of species to assess diversity. Results We found highly structured species assemblages that allowed us to reject multiple predictions of the hypothesis that soil bacteria show ‘no biogeography’. The frequency distribution of range size (measured as the occupancy of quadrats) of OTUs followed a hollow curve similar to that of vertebrates on continents. Assemblages showed high levels of beta diversity and a non‐random nested pattern of diversity. OTU diversity scaled with area followed a power function with slopes z = 0.42 and 0.47. Main conclusions We demonstrate a non‐ubiquitous dispersal for soil prokaryotes, which suggests a complex biogeography similar to that found for terrestrial vertebrates.
Unified performance analysis of blind feedforward timing estimation (2003)

By exploiting an unified cyclostationary (CS) statistics based framework, this study develops a rigorous and thorough performance analysis of blind feedforward timing estimators for linear modulations. Within the introduced CS-framework, it is shown that several estimators proposed in the literature can be asymptotically interpreted as maximum likelihood estimators, and the timing estimator proposed by Oerder and Meyr (1998) achieves the lowest asymptotic (large sample) variance in the class of estimators which exploit all the second order statistics of the received signal, and its performance is insensitive to the over sampling rate P as soon as P /spl ges/ 3. Further, based on the presented theoretical analysis, an asymptotically best consistent (ABC) estimator was derived, which exhibits asymptotically the best performance among all the existing blind feedforward timing estimators, especially when dealing with strongly bandlimited signaling.
Synthesis of Carbon Nanotubes on Fly Ashes by Chemical Vapor Deposition Processing (2009)

Abstract Fly ashes are the waste product following the combustion of coal. Disposal of fly ashes is a serious environmental problem; therefore, finding a new utilization of fly ashes is highly demanded. Carbon nano‐structures have been widely studied as key materials in a wide range of applications, including sensing, saturable absorber, and so on, because of its optical and electromagnetic absorption property. Adding the property of carbon nanotubes (CNTs) to fly ashes expands applications of fly ashes. In this paper, we present the fabrication of multi‐walled carbon nanotubes (MWCNTs) on fly ashes by thermal chemical vapor deposition (CVD) process, which result in simple, low‐cost, large‐amount production of MWCNTs. Copyright © 2009 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.
α-Synuclein Conformation Affects Its Tyrosine-Dependent Oxidative Aggregation (2008)

Oxidative stress and aggregation of the protein alpha-synuclein are thought to be key factors in Parkinson's disease. Previous work shows that cytochrome c with H(2)O(2) causes tyrosine-dependent in vitro peroxidative aggregation of proteins, including alpha-synuclein. Here, we examine the role of each of alpha-synuclein's four tyrosine residues and how the protein's conformation affects covalent oxidative aggregation. When alpha-synuclein adopts a collapsed conformation, tyrosine 39 is essential for wild-type-like covalent aggregation. This lone N-terminal tyrosine, however, is not required for wild-type-like covalent aggregation in the presence of a denaturant or when alpha-synuclein is present in noncovalent fibrils. We also show that preformed oxidative aggregates are not incorporated into noncovalent fibrils. These data provide insight into how dityrosine may be formed in Lewy bodies seen in Parkinson's disease.
Elektrolumineszierende konjugierte Polymere – Polymere erstrahlen in neuem Licht (1998)

Ein aufregendes interdisziplinäres Forschungsgebiet hat sich aus der Entdeckung entwickelt, daß konjugierte Polymere bei Anregung durch Strom Licht emittieren können – dies ermöglicht ihre Verwendung in Leuchtdioden. Eine Vielzahl lichtemittierender Polymere (Beispiele siehe unten), deren Farben das gesamte sichtbare Spektrum des Lichts abdecken, wurde durch chemische Intuition und rationales Design entwickelt.
Jaundice in Infancy (1989)

Jaundice in infancy may be physiologic or due to a pathologic cause. Fractionation of the serum bilirubin level is the first step in the evaluation. Unconjugated hyperbilirubinemia if left untreated may reach toxic levels. Primary hepatobiliary disorders, as well as infectious, toxic, genetic, and metabolic diseases, may manifest with conjugated hyperbilirubinemia. A carefully organized diagnostic evaluation in a timely fashion allows early identification of treatable disorders. Medical management of the complications of cholestatic liver disease remains a major challenge. Early surgical intervention for biliary atresia and significant advances in hepatic transplantation offer the opportunity for long-term survival for infants with previously fatal liver disorders.
Slow-growing Rhizobium japonicum comprises two highly divergent symbiotic types (1985)

We examined the interrelationships of the genomes of 10 slow-growing strains of Rhizobium japonicum to provide a foundation for molecular genetic studies of these agriculturally important endosymbiotic bacteria of commercial soybeans. The degree of base substitution in and around known symbiotic genes (nif and presumptive nod), constitutively expressed genes (glnA and recA), and two other cloned sequences was estimated from restriction site variation by using cloned DNAs as hybridization probes to genomic Southern blots. Two highly divergent patterns of conservation of nifDH genes and nod-homologous sequences were found. On this basis, we classified the strains as the symbiotic genotypes sTI or sTII. Existing maps of the nif genes of R. japonicum apply only to strains of the sTI genotype. This division was further characterized by four other probes which also distinguished two sublines within sTI. Phenograms were constructed depicting interrelationships according to DNA sequence divergence. sTI and sTII are two highly divergent evolutionary lines consistent with the status of individual species. Neither is related to fast-growing Rhizobium strains (PRC strains) nodulating soybeans.
Methylation profile in penile carcinoma reveals unique signature relative to surround tissue and HPV status (2013)

Background Penile carcinoma (PeCa) is an important public health problem in poor and developing countries. Despite the unpredictable behavior and aggressive treatment, there are few data on molecular and epigenetic mechanisms reported in PeCa. The aim of this study was to identify epigenetic profile in tumors and surrounding tissue as well as to identify molecular markers in PeCa, according to the Papillomavirus (HPV) infection.
Patients with Psoriasis Have High Serum Reactivity with EBNA-2B (1991)

Transgenic mice expressing the EBV latent membrane protein LMP demonstrate epithelial cell hyperplasia. LMP has also been shown to inhibit the terminal differentiation of human epithelial cells in vitro. Psoriasis is a human skin condition involving epithelial cell hyperplasia which histologically resembles LMP-transgenic skin. Psoriasis involves an increase in the thickness of the proliferative layer and a decrease in keratinisation and differentiation. Further the high levels of a number of growth factors produced in psoriatic skin could potentially provide an ideal environment for virus gene expression, virus transformation and virus productive replication. We are investigating the possibility that EBV may be involved in human psoriasis.
Individualized Whole-Body Vibration: Neuromuscular, Biochemical, Muscle Damage and Inflammatory Acute Responses (2020)

<b>Objective</b>. We aimed to investigate the acute residual hormonal, biochemical, and neuromuscular responses to a single session of individualized whole-body vibration (WBV) while maintaining a half-squat position. <b>Methods.</b> Twenty male sport science students voluntarily participated in the present study and were randomly assigned to an individualized WBV group (with the acceleration load determined for each participant) or an isometric group (ISOM). A double-blind, controlled parallel study design with repeated measures was employed. <b>Results.</b> Testosterone and growth hormone increased significantly over time in the WBV group (<i>P</i> < .05 and <i>P</i> < .01, respectively; effect size [ES] ranged from 1.00 to 1.23), whereas cortisol increased over time in both groups (<i>P</i> < .01; ES ranged from 1.04 and 1.36). Interleukin-6 and creatine kinase increased significantly over time only in the WBV group (<i>P</i> < .05; ES = 1.07). The maximal voluntary contraction decreased significantly over time in the ISOM group (<i>P</i> = .019; ES = 0.42), whereas in the WBV group, the decrease did not reach a significant level (<i>P</i> = .05). The ratio of electromyographic activity and power decreased significantly over time in the WBV group (<i>P</i> < .01; ES ranged from 0.57 to 0.72). <b>Conclusion.</b> Individualized WBV increased serum hormonal concentrations, muscle damage, and inflammation to levels similar to those induced by resistance training and hypertrophy exercises.
Human Acid ß-Glucosidase: Inhibition Studies Using GlucoseAnalogues and pH Variation to Characterize the Normal andGaucher Disease Glycon Binding Sites (1988)

Comparative kinetic studies with glycon inhibitors were used to investigate the properties of the active site of human acid ß-glucosidase (EC 3.2.1.45) from normal placenta and spleens of type 1 Ashkenazi Jewish Gaucher disease (AJGD) patients. With the pure normal enzyme, the specificity of glycon binding was assessed with 35 glucose derivatives and epimers. Most glycons were mixed type inhibitors with a predominantly competitive nature (i.e., K(is) < < K(ii)) and had low apparent affinity for the enzyme (K(is)app = 20-500 mmol/l). ß-Glucose- 1-phosphate was unusual, since it inhibited 4-methylumbelliferyl-ß-glucoside hydrolysis in an uncompetitive pattern (K(i)app = 0.55 mmol/l) but had no effect on glucosyl ceramide hydrolysis. C-1- (1-deoxy-1-amino-ß-D-glucose) and C-3- (3-deoxy-3-amino-D-glucose) amino and C-5- imino [1-deoxynojirimycin (dNM), nojirimycin and castanospermine] substituted sugars were highly potent inhibitors with K(is)app(ß-glucose)/K(is)app ≅ 10^3-10^5; an amine at C-2 did not alter K(is)app compared to ß-glucose. The variation of K(is)app with pH for the 5-imino- and 1- deoxy-1-aminoglycosides conformed to a model for the unprotonated inhibitors binding to the protonated forms (EH and EH(2)) of the diprotic (V(max)app and V(max)app/K(m)app) normal enzyme (pK(1) = 4.7; pK(2) = 6.7) with pH-independent K(is)app values of 2.9-9.0 µmol/l and 0.22 mmol/l, respectively. Several of the amine-containing inhibitors competitively protected the enzyme from inactivation by conduritol B epoxide, a covalent active site-directed inhibitor, indicating interaction with residues at that site. With the partially purified AJGD splenic enzymes, the results were the same except that K(is)app(AJGD)/K(is)app(normal) = 4-17 for dNM and 1- deoxy-1-amino-ß-glucose; this ratio was ≅ 1 with most other glycons, and particularly, nojirimycin and castanospermine. The results of these studies indicated that the glycon binding site of the normal acid ß-glucosidase contains important residues for interaction with the C-2, C-3 and C-4 hydroxyl groups of ß-glucose and a residue with pK(a) = 6.7 which was critical to the binding of amine-containing inhibitors and the hydrolysis of substrates. The findings were consistent with a specific alteration in or near the glycon binding site which results in the functional abnormalities of the mutant AJGD acid ß-glucosidase.
NONDEPLETING ANTI-CD4 ANTIBODY PROLONGS ADENOVIRUS-MEDIATED TRANSGENE EXPRESSION IN SYNGENEIC HEART TRANSPLANTS. (1998)

516 El-deleted adenoviral vectors are efficient vectors for somatic gene therapy but transgene expression is limited by cellular immune response against virally transduced cells. Recently, we have shown that treatment with a non-depleting anti-CD4 antibody (RIB 5/2) prolonged reporter gene expression in a model of lung-directed gene therapy. In this study we have investigated the expression of reporter gene E. coliβ-galactosidase (β-gal) in rat hearts after in vivo injection of the adenoviral vector (Adβ-gal). In addition, kinetics of expression and efficiency of anti-CD4 treatment (RIB 5/2, 20mg/kg body weight) in the prolongation of transgene expression was analysed using the model of syngeneic heart transplantation. Following gene transfer by injection of 109 pfu into A.subclavia dextra, heterotopic heart transplantation was carried out in abdominal localization. For analysis of kinetics of transgene expression, rats were killed 3,7,14,21,28 or 56 days after transplantation and gene expression was evaluated both by histochemistry and by production of recombinant protein (ONPG-assay). Both techniques for the analysis of transgene expression revealed successful transfer of β-gal into the grafted heart. Kinetics ofβ-gal expression showed maximal values at day 7 while at day 28β-gal expression was disappeared. In contrast treatment of transplanted animals with RIB 5/2 resulted both in prolonged and higher transgene expression (table 1).table 1: β-gal activity (μg/10 mg total protein) in transfected heart after syngeneic transplantationExperimental results of our study showed that the adenoviral vectorΔE1 Ad5 is applicable for further investigations in the cardiac transplantation model of the rat. The period of transgene expression can be prolonged by accompanied anti-CD4 therapy.