gebhart/patrepeval huggingface dataset:
Jockeying for position (2012)

With looming regulatory changes, retail superannuation funds have been shrewd with the launch and strong marketing of 'simple' and 'low-cost' products, such as BT's Super for Life and AMPs Flexible Super. These products are arguably positioning retail funds well for the new MySuper environment and to snare market share if they gain greater access to industrial award agreements.
Automated Image Analysis for Quantitative Fluorescence In Situ Hybridization with Environmental Samples (2007)

When fluorescence in situ hybridization (FISH) analyses are performed with complex environmental samples, difficulties related to the presence of microbial cell aggregates and nonuniform background fluorescence are often encountered. The objective of this study was to develop a robust and automated quantitative FISH method for complex environmental samples, such as manure and soil. The method and duration of sample dispersion were optimized to reduce the interference of cell aggregates. An automated image analysis program that detects cells from 4',6'-diamidino-2-phenylindole (DAPI) micrographs and extracts the maximum and mean fluorescence intensities for each cell from corresponding FISH images was developed with the software Visilog. Intensity thresholds were not consistent even for duplicate analyses, so alternative ways of classifying signals were investigated. In the resulting method, the intensity data were divided into clusters using fuzzy c-means clustering, and the resulting clusters were classified as target (positive) or nontarget (negative). A manual quality control confirmed this classification. With this method, 50.4, 72.1, and 64.9% of the cells in two swine manure samples and one soil sample, respectively, were positive as determined with a 16S rRNA-targeted bacterial probe (S-D-Bact-0338-a-A-18). Manual counting resulted in corresponding values of 52.3, 70.6, and 61.5%, respectively. In two swine manure samples and one soil sample 21.6, 12.3, and 2.5% of the cells were positive with an archaeal probe (S-D-Arch-0915-a-A-20), respectively. Manual counting resulted in corresponding values of 22.4, 14.0, and 2.9%, respectively. This automated method should facilitate quantitative analysis of FISH images for a variety of complex environmental samples.
In utero Exposure of Mice to Dibenzo[a,l]Pyrene Produces Lymphoma in the Offspring: Role of the Aryl Hydrocarbon Receptor (2006)

Lymphoma and leukemia are the most common cancers in children and young adults; in utero carcinogen exposure may contribute to the etiology of these cancers. A polycyclic aromatic hydrocarbon (PAH), dibenzo[a,l]pyrene (DBP), was given to pregnant mice (15 mg/kg body weight, gavage) on gestation day 17. Significant mortalities in offspring, beginning at 12 weeks of age, were observed due to an aggressive T-cell lymphoblastic lymphoma. Lymphocytes invaded numerous tissues. All mice surviving 10 months, exposed in utero to DBP, exhibited lung tumors; some mice also had liver tumors. To assess the role of the aryl hydrocarbon receptor (AHR) in DBP transplacental cancer, B6129SF1/J (AHR(b-1/d), responsive) mice were crossed with strain 129S1/SvIm (AHR(d/d), nonresponsive) to determine the effect of maternal and fetal AHR status on carcinogenesis. Offspring born to nonresponsive mothers had greater susceptibility to lymphoma, irrespective of offspring phenotype. However, when the mother was responsive, an AHR-responsive phenotype in offspring increased mortality by 2-fold. In DBP-induced lymphomas, no evidence was found for TP53, beta-catenin, or Ki-ras mutations but lung adenomas of mice surviving to 10 months of age had mutations in Ki-ras codons 12 and 13. Lung adenomas exhibited a 50% decrease and a 35-fold increase in expression of Rb and p19/ARF mRNA, respectively. This is the first demonstration that transplacental exposure to an environmental PAH can induce a highly aggressive lymphoma in mice and raises the possibility that PAH exposures to pregnant women could contribute to similar cancers in children and young adults.
siRNA relieves chronic neuropathic pain (2004)

Double stranded, short interfering RNAs (siRNA) of 21-22 nt length initiate a sequence-specific, post-trancriptional gene silencing in animals and plants known as RNA interference (RNAi). Here we show that RNAi can block a pathophysiological pain response and provide relief from neuropathic pain in a rat disease model by down regulating an endogenous, neuronally expressed gene. Rats, intrathecally infused with a 21 nt siRNA perfectly complementary to the pain-related cation-channel P2X3, showed diminished pain responses compared to missense (MS) siRNA-treated and untreated controls in models of both agonist-evoked pain and chronic neuropathic pain. This form of delivery caused no adverse effects in any of the animals receiving P2X3 siRNA, MS siRNA or vehicle. Molecular analysis of tissues revealed that P2X3 mRNA expressed in dorsal root ganglia, and P2X3 protein translocated into the dorsal horn of the spinal cord, were significantly diminished. These observations open a path toward use of siRNA as a genetic tool for drug target validation in the mammalian central nervous system, as well as for proof of concept studies and as therapeutic agents in man.
Uni-traveling-carrier variable confinement waveguide photodiodes (2011)

Uni-traveling-carrier waveguide photodiodes (PDs) with a variable optical confinement mode size transformer are demonstrated. The optical mode is large at the input for minimal front-end saturation and the mode transforms as the light propagates so that the absorption profile is optimized for both high-power and high-speed performance. Two differently designed PDs are presented. PD A demonstrates a 3-dB bandwidth of 12.6 GHz, and saturation currents of 40 mA at 1 GHz and 34 mA at 10 GHz. PD B demonstrates a 3-dB bandwidth of 2.5 GHz, a saturation current greater than 100 mA at 1 GHz, a peak RF output power of + 19 dBm, and a third-order output intercept point of 29.1 dBm at a photocurrent of 60 mA.
Pathogenesis and treatment of chronic rhinosinusitis (2010)

Chronic rhinosinusitis (CRS) is one of the most common diseases in western societies, causing significant morbidity and resulting in great financial cost. Some patients suffer persistent or recurrent symptoms despite receiving optimal medical and surgical treatment. The recent publication of revised diagnostic criteria and management guidelines will assist both clinical research and practice. Multiple theories have been advanced regarding the underlying pathogenesis including allergy, bacterial or fungal infection, genetic predisposition and structural anomalies, but at present the majority of cases are still considered idiopathic. Recent studies have shown that traditional laboratory culture techniques may fail to detect microorganisms growing within biofilms or within host mucosal cells. Both bacteria and fungi possess a number of mechanisms for both the evasion and modulation of host immune responses, including the formation of biofilms and the production of superantigens. Historically, treatments such as antibiotics that had been directed at putative causative agents have often been disappointing. There are, however, a broad range of medical and surgical therapies with proven efficacy available to the treating physician. Endoscopic surgical management is evolving rapidly, and there have been pronounced improvements in outcome and reduction in the risk of complications. Recent advances in the understanding of the pathogenesis of this condition have led to some promising therapeutic developments, particularly in respect to topical treatments. Despite improvements in therapy, CRS remains a challenging condition to manage.
Heat shock induces resistance in rat pancreatic islet cells against nitric oxide, oxygen radicals and streptozotocin toxicity in vitro. (1995)

When cultures of pancreatic islet cells are exposed to the nitric oxide donor sodium nitroprusside, to enzymatically generated reactive oxygen intermediates or to streptozotocin cell lysis occurs after 4-12 h. We report here that a heat shock at 43 degrees C for 90 min reduces cell lysis from nitric oxide (0.45 mM sodium nitroprusside) by 70%, from reactive oxygen intermediates (12 mU xanthine oxidase and 0.05 mM hypoxanthine) by 80% and from streptozotocin (1.5 mM) by 90%. Heat shock induced resistance was observed immediately after termination of the 90 min culture at 43 degrees C and correlated with enhanced expression of hsp70. The occurrence of DNA strand breaks, a major early consequence of nitric oxide, reactive oxygen intermediates, or streptozotocin action, was not suppressed by heat shock treatment. However, the depletion of NAD+, the major cause of radical induced islet cell death, was suppressed after heat shock (P < 0.01). We conclude that pancreatic islet cells can rapidly activate defence mechanisms against nitric oxide, reactive oxygen intermediates and streptozotocin by culture at 43 degrees C. Islet cell survival is due to the prevention of lethal NAD+ depletion during DNA repair, probably by slowing down poly(ADP-ribose)polymerase activation.
The N-Terminal Flanking Region Modulates the Actin Binding Affinity of the Utrophin Tandem Calponin-Homology Domain (2017)

Despite sharing a high degree of sequence similarity, the tandem calponin-homology (CH) domain of utrophin binds to actin 30 times stronger than that of dystrophin. We have previously shown that this difference in actin binding affinity could not be ascribed to the differences in inter-CH-domain linkers [Bandi, S., et al. (2015) Biochemistry 54, 5480-5488]. Here, we examined the role of the N-terminal flanking region. The utrophin tandem CH domain contains a 27-residue flanking region before its CH1 domain. We examined its effect by comparing the structure and function of full-length utrophin tandem CH domain Utr(1-261) and its truncated Utr(28-261) construct. Both full-length and truncated constructs are monomers in solution, with no significant differences in their secondary or tertiary structures. Truncated construct Utr(28-261) binds to actin 30 times weaker than that of the full-length Utr(1-261), similar to that of the dystrophin tandem CH domain with a much shorter flanking region. Deletion of the N-terminal flanking region stabilizes the CH1 domain. The magnitude of the change in binding free energy upon truncation is similar to that of the change in thermodynamic stability. The isolated N-terminal peptide by itself is significantly random coil and does not bind to F-actin in the affinity range of Utr(1-261) and Utr(28-261). These results indicate that the N-terminal flanking region significantly affects the actin binding affinity of tandem CH domains. This observation further stresses that protein regions other than the three actin-binding surfaces identified earlier, irrespective of whether they directly bind to actin, also contribute to the actin binding affinity of tandem CH domains.
Lamin B1 loss is a senescence-associated biomarker (2012)

Cellular senescence is a potent tumor-suppressive mechanism that arrests cell proliferation and has been linked to aging. However, studies of senescence have been impeded by the lack of simple, exclusive biomarkers of the senescent state. Senescent cells develop characteristic morphological changes, which include enlarged and often irregular nuclei and chromatin reorganization. Because alterations to the nuclear lamina can affect both nuclear morphology and gene expression, we examined the nuclear lamina of senescent cells. We show here than lamin B1 is lost from primary human and murine cell strains when they are induced to senesce by DNA damage, replicative exhaustion, or oncogene expression. Lamin B1 loss did not depend on the p38 mitogen-activated protein kinase, nuclear factor-κB, ataxia telangiectasia-mutated kinase, or reactive oxygen species signaling pathways, which are positive regulators of senescent phenotypes. However, activation of either the p53 or pRB tumor suppressor pathway was sufficient to induce lamin B1 loss. Lamin B1 declined at the mRNA level via a decrease in mRNA stability rather than by the caspase-mediated degradation seen during apoptosis. Last, lamin B1 protein and mRNA declined in mouse tissue after senescence was induced by irradiation. Our findings suggest that lamin B1 loss can serve as biomarker of senescence both in culture and in vivo.
General plasmids for producing RNA in vitro transcripts with homogeneous ends (2003)

In vitro transcripts of bacteriophage RNA polymerases (RNAPs), such as T7 RNAP, often suffer from a considerable degree of 3'-end heterogeneity and, with certain promoter sequences, 5'-end heterogeneity. For some applications, this transcript heterogeneity poses a significant problem. A potential solution is to incorporate ribozymes into the transcripts at the 5'- and/or 3'-end of the target RNA sequence. This approach has been used quite widely but has required the generation of new transcription vectors or PCR-derived templates for each new RNA to be studied. To overcome this limitation, we have created two general plasmids for producing homogeneous RNA transcripts: one encodes a 3'- hepatitis delta virus (HDV) ribozyme and the other, used in combination with a two-step PCR, allows the production of double [5'-hammerhead (HH) and 3'-HDV] ribozyme constructs. A choice of cloning and run-off transcription linearisation restriction enzyme sites ensures that virtually any RNA sequence can be cloned and transcribed from these plasmids. For all the RNA sequences tested, good yields of transcript were obtained. These plasmids provide the tools for the simple, rapid creation of new RNA-coding plasmids to produce milligram quantities of homogeneous in vitro transcripts for all applications.
Intracerebral Hemorrhage After Intravenous t-PA Therapy for Ischemic Stroke (1997)

Despite a higher rate of intracerebral hemorrhage, patients with severe strokes or edema or mass effect on the baseline-CT are reasonable candidates for t-PA, if it is administered within 3 hours of onset.
Lack of Effect of Captopril on the Sodium Retention of the Nephrotic Syndrome (1984)

The mechanism of sodium retention in the nephrotic syndrome remains controversial, though the classic pathophysiological explanation is stimulation of the renin-angiotensin-aldosterone system. Recent evidence has shown that many patients with the nephrotic syndrome have a normal or low plasma renin activity suggesting that there might be an intrarenal cause for their sodium retention. We gave captopril, an oral angiotensin-converting enzyme inhibitor, during 10 separate episodes of sodium retention in nephrotic syndrome. There was evidence of stimulation of the renin system in 7 of these episodes. Despite a marked fall in plasma aldosterone, all patients continued to retain sodium and water and gain weight. This demonstrates that the sodium retention of nephrotic syndrome is not due to stimulation of the renin-angiotensin-aldosterone system, but must be due to some other mechanism, which is probably intrarenal.
Sequential Binding of Cytosolic Phox Complex to Phagosomes through Regulated Adaptor Proteins: Evaluation Using the Novel Monomeric Kusabira-Green System and Live Imaging of Phagocytosis (2008)

We engineered a method for detecting intramolecular and intermolecular phox protein interactions in cells by fluorescence microscopy using fusion proteins of complementary fragments of a coral fluorescent reporter protein (monomeric Kusabira-Green). We confirmed the efficacy of the monomeric Kusabira-Green system by showing that the PX and PB1 domains of p40phox interact in intact cells, which we suggested maintains this protein in an inactive closed conformation. Using this system, we also explored intramolecular interactions within p47phox and showed that the PX domain interacts with the autoinhibited tandem Src homology 3 domains maintained in contact with the autoinhibitory region, along with residues 341-360. Furthermore, we demonstrated sequential interactions of p67phox with phagosomes involving adaptor proteins, p47phox and p40phox, during FcgammaR-mediated phagocytosis. Although p67phox is not targeted to phagosomes by itself, p47phox functions as an adaptor for the ternary complex (p47phox-p67phox-p40phox) in early stages of phagocytosis before phagosome closure, while p40phox functions in later stages after phagosomal closure. Interestingly, a mutated "open" form of p40phox linked p47phox to closed phagosomes and prolonged p47phox and p67phox retention on phagosomes. These results indicate that binding of the ternary complex to phagosomes can be temporally regulated by switching between adaptor proteins that have PX domains with distinct lipid-binding specificities.
Retinoic acid and granulocyte colony-stimulating factor synergistically induce leukocyte alkaline phosphatase in acute promyelocytic leukemia cells (1994)

Abstract In this report we show a strong synergistic interaction between granulocyte colony-stimulating factor (G-CSF) and all-trans retinoic acid (ATRA) on the expression of leukocyte alkaline phosphatase (LAP) in freshly isolated acute promyelocytic leukemia (APL) blasts as well as in NB40 and HL-60 cell lines. The strong synergism observed in these cell types was not evident in two acute leukemia cell lines (K562 and GF-D8), in normal granulocytes, and in monocytes. In freshly isolated leukocytes derived from chronic myelogenous leukemia (CML), in the stable phase of the disease, a weaker interaction between ATRA and G- CSF was documented. The cross-talk between the cytokine and the retinoid was studied in detail in NB4, an immortalized APL leukemia cell line, retaining the 15′17 chromosomal translocation involving the retinoic acid receptor type alpha. The treatment of NB4 cells with G- CSF alone or ATRA alone leads to no increase and to minor induction in LAP activity, respectively. If the cells are treated with the two compounds simultaneously, a dramatic elevation of LAP is observed after 4 days. The synergism between G-CSF and ATRA is evident at concentrations of the retinoid between 10(-7) and 10(-5) mol/L and at concentrations of the cytokine between 1 and 10 ng/mL. The simultaneous presence of the two compounds is necessary to obtain maximal increase of LAP activity and the effect is cell density-dependent. Synergism is specific for G-CSF, and it is not observed with other cytokines and functional inducers of the granulocyte. The augmentation of LAP activity is the consequence of an increased transcriptional rate of the liver/bone/kidney-type (L/B/K-type) alkaline phosphatase gene, as determined by Northern blotting and nuclear run-on analysis using specific cDNA probes. Only one of the two possible alternatively spliced forms of L/B/K-type alkaline phosphatase transcript is detected in NB4 cells after stimulation with G-CSF and ATRA. This mRNA form, which is the one observed in normal polymorphonuclear leukocytes, contains the most upstream leader exon. In NB4 cells, ATRA induces G- CSF, alpha, and beta retinoic acid receptor transcripts, whereas G-CSF has minor effects on the expression of these mRNAs.
Seeing with the Brain (2003)

(2003). Seeing with the Brain. International Journal of Human–Computer Interaction: Vol. 15, No. 2, pp. 285-295.
Active surveillance in prostate cancer (2012)

Active surveillance is a well tolerated treatment option in well selected groups of patients. There is no 'one size fits all' set of criteria for patient selection or triggers for intervention but decisions can be guided by information from histology, prostate-specific antigen kinetics and imaging.
Study on the morphology and thermomechanical properties of poly(urethane-siloxane) networks based on hyperbranched polyester (2013)

Two series of polyurethane films based on hyperbranched polyester of the second pseudogeneration (Boltorn?), 4,4'-methylenediphenyl diisocyanate and two different siloxane prepolymers, ?,?-dihydroxy-(ethylene oxide-poly(dimethylsiloxane)-ethylene oxide) (EO-PDMS-EO) and ?,?-dihydroxypropyl-poly(dimethylsiloxane) (HP-PDMS), were prepared by two-step polymerization in solution. The influence of the type and content of soft segment on the morphology, thermomechanical and surface properties of the synthesized polyurethanes was studied by atomic force microscopy (AFM), small-angle X-ray scattering (SAXS), scanning electron microscopy (SEM), dynamic mechanical thermal analysis (DMTA) and water absorption measurements. It was found that these techniques confirmed existence of microphase separated morphology. Synthesized polyurethanes exhibited two glass transition temperatures and one second relaxation process. The results showed that polyurethanes based on HP-PDMS had higher surface roughness, better microphase separation and waterproof performances. Samples synthesized with lower PDMS content had less hydrophobic surface, but higher crosslinking density and better thermomechanical properties. (Projekat Ministarstva nauke Republike Srbije, br. 172062]
Comprehensive Thermodynamic Approach to Modeling Refrigerant-Lubricating Oil Mixtures (1995)

A comprehensive thermodynamic approach for modeling mixtures of refrigerants and lubricating oils is presented. The new approach includes generalized methods for predicting the following thermodynamic properties of refrigerant-oil mixtures: bubble point temperatures, local oil concentrations, liquid specific heats and enthalpy changes during evaporation. Using this comprehensive method, heat release (enthalpy) curves are easily generated and also the effect of oil on the LMTD (log mean temperature difference) of evaporators can be modeled. Importantly, the definition of the boiling heat-transfer coefficient based on the bubble point temperature is included in the method. This new approach provides the basis for advances to be made in two-phase refrigeration heat-transfer research and design.
RNA Bacteriophage Capsid-Mediated Drug Delivery and Epitope Presentation (2002)

VLP technology has potential for therapeutic and prophylactic intervention in disease.
Synthesis of ZrB2 Ceramics by Novel Processes (1988)

Synthesis of zirconium boride ZrB{2} has been investigated by employing three methods. These methods were based upon solid state sintering by using three different combinations of starting powders: a) B{6}Si + Zr0{2}, b) B{6}Si + ZrSi0{4} and c) B + ZrSi0{4}. These are much simpler and more economical than conventional techniques. Comparable physical, mechanical and thermal properties were obtained for there ZrB{2} ceramics which also display excellent electrical conductivity. The crystallization behaviour, the phases formed and the evolution of microstructure-property relationships were studied by X-ray diffraction, differential thermal and thermogravimetric as well as scanning electrons microscopy.