gebhart/patrepeval huggingface dataset:
Cost analysis of acute myocardial infarction management in DRG and PRG (2000)

The cost of diagnostic and therapeutic procedures in patients with acute myocardial infarction (AMI) during hospitalization was determined using both the Diagnosis Related Group (DRG) and Process Related Group (PRG) systems. This cost-analysis system was planned and performed to estimate the cost of medical and non-medical staff involved in patient care and the cost of commisurables. In a 3 month period, 45 patients discharged with diagnosis of AMI, equivalent to 410 code ICD-9-CM, were enrolled in the study. Data collected were then elaborated and costs for each DRG were derived. The mean cost sustained for patient with AMI was 3062,32 ECU with a maximum of 8949,50 ECU for DRG 112 and a minimum of 1740,11 ECU for DRG 123. Our data suggest that, in patients with AMI a deep discrepancy between the DRG reimbursements and the ?real? cost, for example for DRG 112 (a discrepancy equivalent to 166 %), exists. The cost difference is essentially related to different procedures involved in medical care; it follows that global cost of patients with AMI is primarily related to PRG cost and is largely independent from other components. These results prove that therapeutic strategies are very important to determine cost for each DRG and that the cost for each DRG can change in relation to PRG performed and to progress of the disease. The utilization of DRG and PRG systems appear to be an essential tool to build up a system in which not only efficiency but also quality of care are evaluated. J Clin Basic Cardiol 2000; 3: 23-8.
Anti-Cadherin-17 Antibody Modulates Beta-Catenin Signaling and Tumorigenicity of Hepatocellular Carcinoma (2013)

Cadherin-17 (CDH17) is an oncofetal molecule associated with poor prognostic outcomes of hepatocellular carcinoma (HCC), for which the treatment options are very limited. The present study investigates the therapeutic potential of a monoclonal antibody (Lic5) that targets the CDH17 antigen in HCC. In vitro experiments showed Lic5 could markedly reduce CDH17 expression in a dose-dependent manner, suppress β-catenin signaling, and induce cleavages of apoptotic enzymes caspase-8 and -9 in HCC cells. Treatment of animals in subcutaneous HCC xenograft model similarly demonstrated significant tumor growth inhibition (TGI) using Lic5 antibody alone (5 mg/kg, i.p., t.i.w.; ca.60-65% TGI vs. vehicle at day 28), or in combination with conventional chemotherapy regimen (cisplatin 1 mg/kg; ca. 85-90% TGI). Strikingly, lung metastasis was markedly suppressed by Lic5 treatments. Immunohistochemical and western blot analyses of xenograft explants revealed inactivation of the Wnt pathway and suppression of Wnt signaling components in HCC tissues. Collectively, anti-CDH17 antibody promises as an effective biologic agent for treating malignant HCC.
The Effect of the Reactor Type on the Selectivity of Thermal Reactions of <i>p</i>-Xylene in Temperature Gradient Systems (1991)

Abstract Thermal reactions of p-xylene were investigated in two kinds of reactors, batch type and flow type, with a large temperature gradient. Excellent differences of the resulting products were observed between these two types of reactors. As for a batch type reactor, 4,4′-dimethylbibenzyl was produced in a high yield with [2.2]paracyclophane and toluene as by-products, and as for a flow type reactor, toluene was obtained as a major product with a low selectivity of 4,4′-dimethylbibenzyl, respectively. These results were different from those of the conventional fast flow pyrolysis method in which [2.2]paracyclophane or poly(3,6-dimethylene-1,4-cyclohexadiene) was formed as a major product. These differences can be accounted for by the partial separation of a reaction mixture caused by the thermal diffusion effect, which arises when the mixture is subject to a temperature gradient.
The Senescence-Induced Staygreen Protein Regulates Chlorophyll Degradation (2007)

Abstract Loss of green color in leaves results from chlorophyll (Chl) degradation in chloroplasts, but little is known about how Chl catabolism is regulated throughout leaf development. Using the staygreen (sgr) mutant in rice (Oryza sativa), which maintains greenness during leaf senescence, we identified Sgr, a senescence-associated gene encoding a novel chloroplast protein. Transgenic rice overexpressing Sgr produces yellowish-brown leaves, and Arabidopsis thaliana pheophorbide a oxygenase–impaired mutants exhibiting a stay-green phenotype during dark-induced senescence have reduced expression of Sgr homologs, indicating that Sgr regulates Chl degradation at the transcriptional level. We show that the leaf stay-greenness of the sgr mutant is associated with a failure in the destabilization of the light-harvesting chlorophyll binding protein (LHCP) complexes of the thylakoid membranes, which is a prerequisite event for the degradation of Chls and LHCPs during senescence. Transient overexpression of Sgr in Nicotiana benthamiana and an in vivo pull-down assay show that Sgr interacts with LHCPII, indicating that the Sgr-LHCPII complexes are formed in the thylakoid membranes. Thus, we propose that in senescing leaves, Sgr regulates Chl degradation by inducing LHCPII disassembly through direct interaction, leading to the degradation of Chls and Chl-free LHCPII by catabolic enzymes and proteases, respectively.
Evaluating effects of biobased 2,5‐furandicarboxylate esters as plasticizers on the thermal and mechanical properties of poly (vinyl chloride) (2014)

ABSTRACT We synthesized 2,5‐furandicarboxylate esters [i.e., dibutylfuran‐2,5‐dicarboxylate, diisoamylfuran‐2,5‐dicarboxylate, and di(2‐ethylhexyl)furan‐2,5‐dicarboxylate] and investigated their potential application as plasticizers of commercial poly(vinyl chloride) (PVC) products. Fourier transform infrared analysis, mechanical tests, scanning electron microscopy investigation, differential scanning calorimetry analysis, dynamic mechanical thermal analysis, thermogravimetric analysis (TGA), melt flow rate (MFR) measurement, and plasticizer migration measurements were used to the evaluate the comprehensive properties of the blended products. The results of the tensile tests demonstrate that the blends exhibited antiplasticization and flexible plastic characteristics at 10 and 50 phr in PVC, respectively. Moreover, flexural and impact test data indicate that the three types of blends exhibited a similar tendency: the hardness decreased continuously as the amount of plasticizer increased. Their morphology indicated that all of the plasticizers had good compatibility with PVC. The resulting glass‐transition temperature of the investigated plasticizers was lower than that of pure PVC, and reduction was largest for the plasticizer with the highest molecular weight. TGA revealed that the thermal degradation of blended polymers occurred in three stages and that all of the blends were stable up to 180°C. Finally, the MFRs of all of the specimens indicated that the addition of a higher concentration of lower molecular weight biobased esters resulted in improved fluidity, but these compounds migrated more easily from the blends. Hence, 2,5‐furandicarboxylic acid derived from biomass has potential as a plasticizer. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131 , 40938.
An Arabidopsis syntaxin homologue isolated by functional complementation of a yeast pep12 mutant. (1995)

The syntaxin family of integral membrane proteins are thought to function as receptors for transport vesicles, with different isoforms of this family localized to various membranes throughout the cell. The yeast Pep12 protein is a syntaxin homologue which may function in the trafficking of vesicles from the trans-Golgi network to the vacuole. We have isolated an Arabidopsis thaliana cDNA by functional complementation of a yeast pep12 mutant. The Arabidopsis cDNA (aPEP12) potentially encodes a 31-kDa protein which is homologous to yeast Pep12 and to other members of the syntaxin family, indicating that this protein may function in the docking or fusion of transport vesicles with the vacuolar membrane in plant cells. Northern blot analysis indicates that the mRNA is expressed in all tissues examined, although at a very low level in leaves. The mRNA is found in all cell types in roots and leaves, as shown by in situ hybridization experiments. The existence of plant homologues of proteins of the syntaxin family indicates that the basic vesicle docking and fusion machinery may be conserved in plants as it is in yeast and mammals.
Targeted DNA transposition in vitro using a dCas9-transposase fusion protein (2019)

Homology-directed genome engineering is limited by transgene size. Although DNA transposons are more efficient with large transgenes, random integrations are potentially mutagenic. Here we present an in vitro mechanistic study that demonstrates efficient Cas9 targeting of the mariner transposon Hsmar1. Integrations were unidirectional and tightly constrained to one side of the sgRNA binding site. Further analysis of the nucleoprotein intermediates demonstrated that the transposase and Cas9 moieties can bind their respective substrates independently or in concert. Kinetic analysis of the reaction in the presence of the Cas9 target-DNA revealed a delay between first and second strand cleavage at the transposon end. This step involves a significant conformational change that may be hindered by the properties of the interdomainal linker. Otherwise, the transposase moiety behaved normally and was proficient for integration in vitro and in Escherichia coli. Specific integration into the lacZ gene in E. coli was obscured by a high background of random integrations. Nevertheless, Cas9 is an attractive candidate for transposon-targeting because it has a high affinity and long dwell-time at its target site. This will facilitate a future optogenetic strategy for the temporal control of integration, which will increase the ratio of targeted to untargeted events.
Core 2 beta1,6-N-acetylglucosaminyltransferases and alpha1,3-fucosyltransferases regulate the synthesis of O-glycans on selectin ligands on oral cavity carcinoma cells (2001)

Selectin-dependent cell binding has importance in the extravasation of blood-circulating tumor cells and in the generation of metastases. Cell surface glycoproteins decorated with sialylated, fucosylated epitopes, such as sialyl Lewis(x) (sLe(x)), are ligands for selectins. Not only terminal sLe(x) moieties but also proximal core structures contribute to the formation of binding epitopes for selectins. Core 2 beta1,6-N-acetylglucosaminyltransferases (C2GnT) and alpha1,3-fucosyltransferases (alpha1,3-FucT) have been suggested to be the rate-limiting enzymes in the synthesis of selectin ligands. We analyzed oral cavity epithelial carcinoma cell lines and showed their expression of RNA transcripts for C2GnT and alpha1,3-FucT, identified alpha1,3-FucT enzyme activities, and analyzed the cell surface sLe(x) expression levels. Neither the pattern of expressed enzymes nor the alpha1,3-FucT activity directly predicted the binding capacity of E-selectin. However, only the sLe(x)-expressing cell lines were capable of binding to E-selectin, but not to P-selectin, thus putatively promoting the selectin-mediated metastasis. These findings suggest that C2GnT in combination with alpha1,3-Fuc-T contribute to the selectin-mediated metastasis in oral cavity carcinomas.
Infectious RNA derived by transcription from cloned cDNA copies of the genomic RNA of an insect virus. (1986)

RNA transcripts of cloned cDNA of the genomic RNAs of BBV (black beetle virus) are infectious to cultured cells of Drosophila melanogaster. Individual transcripts had approximately 10% of the infectivity of the corresponding authentic virion RNA. Progeny virus resulting from transcript infection was phenotypically indistinguishable from the progenitor virus used to generate the original cDNA forms as judged by sucrose density gradient sedimentation, specific infectivity, plaque morphology, and serology. Although the transcript RNAs used to produce this virus had 20 nonviral bases headed by a capping group at their 5' termini, these 20 bases were absent in the progeny viral RNAs. The cDNA forms, and therefore the resulting transcript RNAs, should be readily modifiable by the techniques of recombinant DNA technology both for viral studies and for the insertion of foreign genes into the viral genome and thus into the host cytoplasm.
Is teaching with security in mind working? (2010)

Security topics have been taught for some time at universities. The most common approach has been to teach a required topic, and then introduce a security module later in the course. We have been promoting the notion of teaching security at the same time as main course's material. We found that this helps students to accept the idea of writing secure code at an early stage and encourages them to focus on the security issues before they start coding. We proposed teaching secure practices as the default model presented to the students, facilitating the adoption of those practices. Over a period of one year we promoted the concept among our colleagues both in our school and at teaching conferences. This paper is a report that shows where we are one year after of implementation of Teaching with Security in Mind.
Ion‐ and Atom‐Leaching Mechanisms from Palladium Nanoparticles in Cross‐Coupling Reactions (2007)

Leaching of palladium species from Pd nanoparticles under C--C coupling conditions was observed for both Heck and Suzuki reactions by using a special membrane reactor. The membrane allows the passage of palladium atoms and ions, but not of species larger than 5 nm. Three possible mechanistic scenarios for palladium leaching were investigated with the aim of identifying the true catalytic species. Firstly, we examined whether or not palladium(0) atoms could leach from clusters under non-oxidising conditions. By using our membrane reactor, we proved that this indeed happens. We then investigated whether or not small palladium(0) clusters could in fact be the active catalytic species by analysing the reaction composition and the palladium species that diffused through the membrane. Neither TEM nor ICP analysis supported this scenario. Finally, we tested whether or not palladium(II) ions could be leached in the presence of PhI by oxidative addition and the formation of [Pd(II)ArI] complexes. Using mass spectrometry, UV-visible spectroscopy and 13C NMR spectroscopy, we observed and monitored the formation and diffusion of these complexes, which showed that the first and the third mechanistic scenarios were both possible, and were likely to occur simultaneously. Based on these findings, we maintain that palladium nanoparticles are not the true catalysts in C--C coupling reactions. Instead, catalysis is carried out by either palladium(0) atoms or palladium(II) ions that leach into solution.
Rotterdam Criteria for Sentinel Node (SN) Tumor Burden and the Accuracy of Ultrasound (US) -Guided Fine-Needle Aspiration Cytology (FNAC): Can US-Guided FNAC Replace SN Staging in Patients With Melanoma? (2009)

US-guided FNAC of SNs is highly accurate. Up to 65% of the patients with SN-positive results in our institution could have been spared an SN procedure.
Synthesis and Properties of RNA Analogues Having Amides as Interuridine Linkages at Selected Positions (2003)

Oligoribonucleotide analogues having amide internucleoside linkages (AM1: 3'-CH(2)CONH-5' and AM2: 3'-CH(2)NHCO-5') at selected positions have been synthesized and the thermal stability of duplexes formed by these analogues with complementary RNA fragments has been evaluated by UV melting experiments. Two series of oligomers with either 2'-OH or 2'-OMe vicinal to the amide linkages were studied. Monomeric synthons (3' and 5'-C amines and carboxylic acids) were synthesized as follows: For synthesis of the AM1 analogue, the known sequence of radical allylation followed by the cleavage of the double bond was adopted. For synthesis of the AM2 analogue, novel routes via addition of nitromethane followed by conversion of the nitro function to either amino or carboxyl groups were developed. Coupling of monomeric amines and carboxylic acids followed by protecting group manipulation and phosphonylation gave dimeric 3'-hydrogenphosphonate building blocks for oligonucleotide synthesis. Monomeric model compounds having 3'-amide and 2'-OH or 2'-OMe groups were also prepared and their conformational equilibrium was determined by (1)H NMR. The AM1 and AM2 models showed equal preferences for the North conformers (at 40 degrees C, 88-89% with 2'-OH, and 92-93% with 2'-OMe). At physiological salt concentration (0.1 M NaCl) the duplexes between AM1 modified oligonucleotides and RNA had stability similar to unmodified RNA-RNA duplexes (Delta t(m)= -0.2 to +0.7 degrees C per modification). However, the AM2 modification resulted in substantial stabilization of duplexes: Delta t(m)= +1 to +2.4 degrees C per modification compared to all RNA. A 2'-O-methyl vicinal to the AM2 linkage further increased the duplex stability. Our results suggest that RNA analogues having amide internucleoside bonds are very promising candidates for medicinal applications.
First-principles calculations of the vibrational spectra of one-dimensional<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi mathvariant="normal">C</mml:mi><mml:mn>60</mml:mn></mml:msub></mml:math>polymers (2006)

The vibrational properties of several ${\mathrm{C}}_{60}$ dimers belonging to the Stone-Wales rearrangement sequence [described by E. Osawa and K. Honda, Full. Sci. Technol. 4, 939 (1996)], along with a trimer and a tetramer isomer are investigated by tight-binding and density functional calculations. The IR absorption bands found by Onoe, Nakayama, Aono and Hara [Appl. Phys. Lett. 82, 595 (2003)] in the spectra of electron-beam irradiated ${\mathrm{C}}_{60}$ films are explained and attributed mainly to surface vibrations located in the waist region of the considered polymers. The features of the Raman spectra are also discussed and related to experimental spectra of photopolymerized ${\mathrm{C}}_{60}$.
A Cardiovascular Drug Rescues Mice from Lethal Sepsis by Selectively Attenuating a Late-Acting Proinflammatory Mediator, High Mobility Group Box 1 (2007)

The pathogenesis of sepsis is mediated in part by bacterial endotoxin, which stimulates macrophages/monocytes to sequentially release early (e.g., TNF, IL-1, and IFN-gamma) and late (e.g., high mobility group box 1 (HMGB1) protein) proinflammatory cytokines. The recent discovery of HMGB1 as a late mediator of lethal sepsis has prompted investigation for development of new experimental therapeutics. We found that many steroidal drugs (such as dexamethasone and cortisone) and nonsteroidal anti-inflammatory drugs (such as aspirin, ibuprofen, and indomethacin) failed to influence endotoxin-induced HMGB1 release even at superpharmacological concentrations (up to 10-25 microM). However, several steroid-like pigments (tanshinone I, tanshinone IIA, and cryptotanshinone) of a popular Chinese herb, Danshen (Salvia miltiorrhiza), dose dependently attenuated endotoxin-induced HMGB1 release in macrophage/monocyte cultures. A water-soluble tanshinone IIA sodium sulfonate derivative (TSNIIA-SS), which has been widely used as a Chinese medicine for patients with cardiovascular disorders, selectively abrogated endotoxin-induced HMGB1 cytoplasmic translocation and release in a glucocorticoid receptor-independent manner. Administration of TSNIIA-SS significantly protected mice against lethal endotoxemia and rescued mice from lethal sepsis even when the first dose was given 24 h after the onset of sepsis. The therapeutic effects were partly attributable to attenuation of systemic accumulation of HMGB1 (but not TNF and NO) and improvement of cardiovascular physiologic parameters (e.g., decrease in total peripheral vascular resistance and increase in cardiac stroke volume) in septic animals. Taken together, these data re-enforce the pathogenic role of HMGB1 in lethal sepsis, and support a therapeutic potential for TSNIIA-SS in the treatment of human sepsis.
Direct thermal dose control of constrained focused ultrasound treatments: phantom and<i>in vivo</i>evaluation (2005)

The first treatment control system that explicitly and automatically balances the efficacy and safety goals of noninvasive thermal therapies is described, and its performance is evaluated in phantoms and in vivo using ultrasound heating with a fixed, focused transducer. The treatment efficacy is quantified in terms of thermal dose delivered to the target. The developed feedback thermal dose controller has a cascade structure with the main nonlinear dose controller continuously generating the reference temperature trajectory for the secondary, constrained, model predictive temperature controller. The control system ensures thermal safety of the normal tissue by automatically complying with user-specified constraints on the maximum allowable normal tissue temperatures. To reflect hardware limitations and to prevent cavitation, constraints on the maximum transducer power can also be imposed. It is shown that the developed controller can be used to achieve the minimum-time delivery of the desired thermal dose to the target without violating safety constraints, which is a novel and clinically desirable feature. The developed controller is model based, and requires patient- and site-specific models for its operation. These models were obtained during pre-treatment identification experiments. In our implementation, predictive models, internally used by the automatic treatment controller, are dynamically updated each time new temperature measurements become available. The adaptability of internal models safeguards against adverse effects of modelling errors, and ensures robust performance of the control system in the presence of a priori unknown treatment disturbances. The successful validation with two experimental models of considerably different thermal and ultrasound properties suggests the applicability of the developed treatment control system to different anatomical sites.
Transcription of glycolytic genes and operons in <i>Bacillus subtilis</i>: evidence for the presence of multiple levels of control of the <i>gapA</i> operon (2001)

Glycolysis is one of the main pathways of carbon catabolism in Bacillus subtilis. Although the biochemical activity of glycolytic enzymes has been studied in detail, no information about the expression of glycolytic genes has so far been available in this organism. Therefore, transcriptional analysis of all glycolytic genes was performed. The genes cggR, gapA, pgk, tpi, pgm and eno, encoding the enzymes required for the interconversion of triose phosphates, are transcribed as a hexacistronic operon as demonstrated by Northern analysis. This gapA operon is repressed by the regulator CggR. The presence of sugars and amino acids synergistically results in the induction of the gapA operon. The transcriptional start site upstream of cggR was mapped by primer extension. Transcripts originating upstream of cggR are processed near the 3' end of cggR. This endonucleolytic cleavage leads to differential stability of the resulting processing products: the monocistronic cggR message is very rapidly degraded, whereas the mRNA species encoding glycolytic enzymes exhibit much higher stability. An additional internal constitutive promoter was identified upstream of pgk. Thus, gapA is the most strongly regulated gene of this operon. The pfk pyk operon encoding phosphofructokinase and pyruvate kinase is weakly induced by glucose. In contrast, the genes pgi and fbaA, coding for phosphoglucoisomerase and fructose-1,6-bisphosphate aldolase, are constitutively expressed.