gebhart/patrepeval huggingface dataset:
Model building of DNA/RNA triple helix containing <scp>L</scp>‐deoxyadenosine (1992)

A three-dimensional model of DNA/RNA triple helix that contains a poly(L-deoxyadenosine) (L-dA) chain is proposed based on computer-assisted model building and energy calculations. The model building was performed by a new method that systematically searches possible conformations of nucleotide units in the helical chains. Two possible orientations of sugar-phosphate chains, in which two homopyrimidine strands are parallel or antiparallel with each other, were considered in the systematic search. Several possible base-pairing models, in which there are one Watson-Crick base pair and one other base pair, were also considered. Many possible models selected by the systematic search were further refined through molecular mechanics calculation incorporating a helical boundary condition. The preferred model, which was selected on the basis of potential energy, was the one with Watson-Crick and Hoogsteen base pairs and with its two polypyrimidine chains in the antiparallel orientation. The model can explain the experimental observation that poly(L-dA) forms a stable triple helix with poly(uridylic acid) (U) but not with poly(deoxythymidylic acid) (dT).
Contributions to the Resolution of the Data Workshop Test Cases (1998)

The following sections contain the different contributions from the ECARP consortium to the resolution of the workshop test cases defined in section II. Each contribution contains a theoretical description of the optimization technique used by each partner and the results obtained by using this techniques for the resolution of some test cases.
Effects of respiratory muscle unloading on exercise-induced diaphragm fatigue (2002)

We previously compared the effects of increased respiratory muscle work during whole body exercise and at rest on diaphragmatic fatigue and showed that the amount of diaphragmatic force output required to cause fatigue was reduced significantly during exercise (Babcock et al., J Appl Physiol 78: 1710, 1995). In this study, we use positive-pressure proportional assist ventilation (PAV) to unload the respiratory muscles during exercise to determine the effects of respiratory muscle work, per se, on exercise-induced diaphragmatic fatigue. After 8-13 min of exercise to exhaustion under control conditions at 80-85% maximal oxygen consumption, bilateral phrenic nerve stimulation using single-twitch stimuli (1 Hz) and paired stimuli (10-100 Hz) showed that diaphragmatic pressure was reduced by 20-30% for up to 60 min after exercise. Usage of PAV during heavy exercise reduced the work of breathing by 40-50% and oxygen consumption by 10-15% below control. PAV prevented exercise-induced diaphragmatic fatigue as determined by bilateral phrenic nerve stimulation at all frequencies and times postexercise. Our study has confirmed that high- and low-frequency diaphragmatic fatigue result from heavy-intensity whole body exercise to exhaustion; furthermore, the data show that the workload endured by the respiratory muscles is a critical determinant of this exercise-induced diaphragmatic fatigue.
Goniothalamin Inhibits Growth of Human Lung Cancer Cells through DNA Damage, Apoptosis, and Reduced Migration Ability (2011)

We evaluated the possible anticancer performance of a natural compound, goniothalamin (GTN), against human lung cancer using as a non-small cell lung cancer (NSCLC) cell line, H1299, as the model system. Cellular proliferation was significantly inhibited by GTN. Using an improved alkaline comet-nuclear extract (comet-NE) assay, GTN was found to induce a significant increase in the tail DNA. Wound healing and zymography assays showed that GTN attenuated cell migration and caused a reduction in the activity level of two major migration-associated matrix metalloproteinases, MMP-2 and MMP-9. It can be concluded that the DNA-damaging effect of GTN against lung cancer cells leads to growth inhibition as well as a depression in migration ability. Therefore, GTN has potential as a chemotherapeutic agent against lung cancer.
Observability analysis of the INS/GPS navigation system on the measurements in land vehicle applications (2007)

In this paper, the observability of the INS/GPS navigation system for a land vehicle is analyzed on measurements and different dimension filters with respect to the measurements are designed. In the stationary case, it is shown that the horizontal accelerometer biases and vertical attitude errors and gyro biases are unobservable. An 8th filter is designed based on the observability analysis. When GPS signal is available, a 15th filter is used with position and velocity measurements. To estimate the INS errors even in the case that GPS signal is blocked a filter is designed in consideration of the non-holonomic constraints of a land vehicle. In this case, the horizontal position and velocity errors and vertical attitude error are unobservable. However, a 12th filter including the velocity states is designed to estimate the accelerometer biases. Based on the results of the observability analysis and the different dimension filters, an efficient INS/GPS filter including the filters as sub-filters can be designed.
Volatile signature for the early diagnosis of lung cancer (2016)

Exhaled breath contains hundreds of volatile organic compounds (VOCs). Several independent researchers point out that the breath of lung cancer patients shows a characteristic VOC-profile which can be considered as lung cancer signature and, thus, used for diagnosis. In this regard, the analysis of exhaled breath with gas sensor arrays is a potential non-invasive, relatively low-cost and easy technique for the early detection of lung cancer. This clinical study evaluated the gas sensor array response for the identification of the exhaled breath of lung cancer patients. This study involved 146 individuals: 70 with lung cancer confirmed by computerized tomography (CT) or positron emission tomography-(PET) imaging techniques and histology (biopsy) or with clinical suspect of lung cancer and 76 healthy controls. Their exhaled breath was measured with a gas sensor array composed of a matrix of eight quartz microbalances (QMBs), each functionalized with a different metalloporphyrin. The instrument produces, for each analyzed sample, a vector of signals encoding the breath (breathprint). Breathprints were analyzed with multivariate analysis in order to correlate the sensor signals to the disease. Breathprints of the lung cancer patients were differentiated from those of the healthy controls with a sensitivity of 81% and specificity of 91%. Similar values were obtained in patients with and without metabolic comorbidities, such as diabetes, obesity and dyslipidemia (sensitivity 85%, specificity 88% and sensitivity 76%, specificity 94%, respectively). The device showed a large sensitivity to lung cancer at stage I with respect to stage II/III/IV (92% and 58% respectively). The sensitivity for stage I did not change for patients with or without metabolic comorbidities (90%, 94%, respectively). Results show that this electronic nose can discriminate the exhaled breath of the lung cancer patients from those of the healthy controls. Moreover, the largest sensitivity is observed for the subgroup of patients with a lung cancer at stage I.
Estimation Vehicular Waiting Time at Traffic Build-Up Queues (2013)

Due to the high growth of social economic activities and the increased need for mobility in recent days, transportation problems like congestion, accidents, and pollution have been increased. However, improving the reliability of delay estimates and real-time dissemination of information remains a challenge. An advanced border-crossing system corresponding to the changes of cross-border circumstances becomes an urgent matter. An automated system for queue end monitoring has been proposed using image processing based transformed domain and empirical mode decomposition (EMD) feature extraction systems. The performance of feedforward backpropagation algorithm artificial neural networks (ANNs) was evaluated and tested, based on a selected set of features. The experimental results showed that the use of discrete wavelet transform (DWT) based Daubechies with decomposition of level 2 has accomplished the target with a processing time 2 sec and 3 epochs of training network only with best validation performance of (2.1053e-007) for vehicle recognition. Also the use of EMD as a feature extractor has accomplished the target of vehicle recognition with a best validation performance of (about 3.42e-09) and a processing time of 1 sec at epoch 3 of training network only with a minimal percentage of error for the recognition of each vehicle in the appropriate queue with the aid of the new concept of road side unit (RSU).
Electron Microscopy of <i>Neurospora crassa</i> Mycelia (1959)

The fine structure of vegetative mycelia of the filamentous Ascomycete, Neurospora crassa, has been investigated by the standard techniques of electron microscopy. Addition of uranyl nitrate to the methacrylate-embedding medium minimized disruption of the specimens-an accident often observed in the preparation of microbial material. This report describes the presence of a chitinous polysaccharide wall containing fine fibrils embedded in a homogeneous matrix. A sinuate plasma membrane lies adjacent to the inner wall surface. This membrane is often closely associated with the endoplasmic reticulum of the cytoplasm. Numerous mitochondria of the classical type, and dense particles of 10 mmicro diameter occur throughout the cytoplasm. The nuclear region is surrounded by a double membrane with pore openings. Associated with the nuclear envelope is a dense area, the nucleolus. The significance of these observations and their relationship to other forms is discussed.
Towards more effective techniques for catheter ablation of atrial fibrillation: to aim for electrical disconnection of pulmonary veins or not? (2005)

This editorial refers to ‘Prevalence of pulmonary vein disconnection after anatomical ablation for atrial fibrillation: consequences of wide atrial encircling of the pulmonary veins’† by M. Hocini et al. , on page 696 

The recent discovery of a dominant role played by excitable tissues within the pulmonary veins (PVs) and at the left atrium–PV junction in the initiation and possibly also the maintenance of atrial fibrillation (AF) has led investigators to develop several catheter-based strategies aimed at limiting the electrophysiological interactions between these areas and the remaining atria. Among these, two have emerged as dominant strategies in current clinical practice: one aiming at ostial segmental disconnection (OSD) of all PVs from the adjacent atrial tissue and another aiming at anatomical circumferential ablation (ACA) away from the orifice of the PVs.

OSD is best accomplished with the help of a pre-shaped circumferential multi-electrode mapping catheter advanced to the orifice of the target PV while an ablation catheter is used for radiofrequency (RF) pulse delivery at the orifice of the same PV. Using this approach, RF pulses are delivered under the guidance of the circumferential electrical activation recorded from the multi-electrode mapping catheter until no propagation of atrial impulses to the PV is observed ( Figure 1A ). Ablation is repeated in each remaining PV until electrical disconnection of all PVs is achieved. OSD is commonly achieved through segmental rather than circumferential ablation at the orifice of the PVs.1



Figure 1. Schematics of the ablation designs aimed for using OSD ( A ) or ACA ( B ). The symbols (straight arrow and wavy arrow) indicate, respectively, conduction block and delayed conduction of the electrical impulses across ablation lines obtained at the end of the two ablation strategies. Note that after segmental disconnection at the ostium of each PV, electrical impulses are inhibited from entering into or … 



*Tel: +39 02 5277 4337; fax: +39 02 5560 3125. E-mail address : rcappato{at}libero.it
Specificity of Xenoreactive Natural Antibodies (2002)

The specificity of primate antibodies that bind to porcine tissues and organs is of great interest given the importance of antibodies in the rejection of porcine-to-human xenografts, as discussed in Chapter 3. Multiple epitopes on almost any porcine protein, as well as many porcine carbohydrates (1), might be recognized as foreign if surveyed by the human immune system. Indeed, this fact may have a large impact on the direction scientists take as they attempt to achieve the long-term survival of xenografts. However, naturally occurring xenoreactive antibodies, unlike the vast number of antibodies that might be elicited against a pig organ, are generally thought to be limited in specificity. In this chapter we will focus on the specificity of natural xenoreactive antibodies, those xenoreactive antibodies that already exist in the serum of individuals, despite their lack of history of exposure to xenogeneic antigens. It is these antibodies that pose the initial barrier to xenotransplantation. Furthermore, even if natural antibodies are insufficient to cause the rejection of a particular organ, they may initiate pathologic processes that result in a decrease in function of a transplanted organ. For example, binding of antibodies and/or subsequent activation of complement by those antibodies may dramatically increase the activity of antigen presenting cells, resulting in a devastating elicited immune response greater than the response seen in allografts.
Elastic Scattering and Reaction Mechanisms of the Halo Nucleus<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mmultiscripts><mml:mi>Be</mml:mi><mml:mprescripts/><mml:none/><mml:mn>11</mml:mn></mml:mmultiscripts></mml:math>around the Coulomb Barrier (2010)

Collisions induced by (9,10,11)Be on a 64Zn target at the same c.m. energy were studied. For the first time, strong effects of the 11Be halo structure on elastic-scattering and reaction mechanisms at energies near the Coulomb barrier are evidenced experimentally. The elastic-scattering cross section of the 11Be halo nucleus shows unusual behavior in the Coulomb-nuclear interference peak angular region. The extracted total-reaction cross section for the 11Be collision is more than double the ones measured in the collisions induced by (9,10)Be. It is shown that such a strong enhancement of the total-reaction cross section with 11Be is due to transfer and breakup processes.
Mitochondrial phospholipase A<sub>2</sub> activity and mitochondrial aging (1978)

The changes in mitochondrial phospholipid metabolism and energy-linked functions have been followed as coupled mitochondria are allowed to age in isotonic sucrose at 18 degrees C. Analysis of the aging process has provided an approach for studying the structure--function relationships within the mitochondrion without adding external agents to perturb the membrane structure. The initial event observed in this process of deterioration is a loss of respiratory control which is paralleled by diminishing levels of ATP. As ATP levels decline, so do the rates of reacylation of monoacyglycerophosphorylethanolamine and fatty acid oxidation. In most cases the previously inactive phospholipase A2 (EC 3.1.1.4, phosphatide-2-acyl-hydrolase) begins rapid hydrolysis of membrane phosphatidylethanolamine as ATP levels approach zero. The final energy-linked phenomenon observed to decline is the anilinonaphthalenesulfonic acid fluorescence response. Evidence is presented which suggests strongly that the activity of the mitochondrial phospholipase A2 on endogenous phospholipids is suppressed in tightly coupled mitochondria. This suppression is temporally linked to ATP levels in the mitochondria. Furthermore, this study demonstrates that mitochondria which are only slightly damaged have the potential to effect membrane repair through reacylation of monoacyl phospholipids.
PRZEGLĄD METOD PLL DO SYNCHRONIZACJI Z SIECIĄ PRZEKSZTAŁTNIKÓW ENERGOELEKTRONICZNYCH (2013)

W artykule przedstawiono metody synchronizacji przekształtników energoelektronicznych z siecią elektroenergetyczna oparte na pętli sprzężenia fazowego PLL. Przedstawione modele matematyczne oparte są na transformacjach do wirującego układu odniesienia. Modele symulacyjne wykonano w kilku wersjach: w zamkniętej pętli fazowej z synchronicznie wirującym układem odniesienia PLL- SRF, w zmodyfikowanym układzie PLL-SRF z uogólnionym integratorem drugiego rzędu SOGI oraz w podwójnie odprzężonym systemem z dwoma wirującymi przeciwnie układami odniesienia DDSRF. Na podstawie wykonanych symulacji stwierdzono, że zamknięta pętla fazowa PPL z algorytmem SOGI pozwala uzyskać lepszą zbieżność, a algorytmy DDSRF poprawnie pracują nawet dla sieci niesymetrycznej z dużą zawartością harmonicznych czasowych.
Inhibition of human hepatocarcinoma cell proliferation by mammalian and fish gonadotropin-releasing hormones. (1995)

This study provides the first demonstration that human hepatocarcinoma-derived cell line HepG2 contains GnRH receptors and responds to various molecular forms of GnRH in terms of inhibition of proliferation in a time- and dose-related manner. In addition, GnRH peptides also significantly inhibited the uptake of [3H]thymidine by these cells. The effect of GnRH was specific because GnRH antagonists reversed the GnRH-mediated inhibition, and non-GnRH peptides had no effect on HepG2 cell proliferation. An important finding is that certain fish GnRH molecules such as lamprey GnRH, which has little gonadotropin (LH) release activity in mammals, suppress hepatocarcinoma cell proliferation with similar potency to a superactive mammalian GnRH analog, [D-Lys6]GnRH. These findings may have profound implications in the development of an effective chemotherapy for treatment of human liver cancer. An added advantage is that fish GnRH forms will likely exert little side effect in terms of human pituitary gonadotropin release, gonadal steroidogenesis, and reproductive functions in general.
Common Method Variance in IS Research: A Comparison of Alternative Approaches and a Reanalysis of Past Research (2006)

Despite recurring concerns about common method variance (CMV) in survey research, the information systems (IS) community remains largely uncertain of the extent of such potential biases. To address this uncertainty, this paper attempts to systematically examine the impact of CMV on the inferences drawn from survey research in the IS area. First, we describe the available approaches for assessing CMV and conduct an empirical study to compare them. From an actual survey involving 227 respondents, we find that although CMV is present in the research areas examined, such biases are not substantial. The results also suggest that few differences exist between the relatively new marker-variable technique and other well-established conventional tools in terms of their ability to detect CMV. Accordingly, the marker-variable technique was employed to infer the effect of CMV on correlations from previously published studies. Our findings, based on the reanalysis of 216 correlations, suggest that the inflated correlation caused by CMV may be expected to be on the order of 0.10 or less, and most of the originally significant correlations remain significant even after controlling for CMV. Finally, by extending the marker-variable technique, we examined the effect of CMV on structural relationships in past literature. Our reanalysis reveals that contrary to the concerns of some skeptics, CMV-adjusted structural relationships not only remain largely significant but also are not statistically differentiable from uncorrected estimates. In summary, this comprehensive and systematic analysis offers initial evidence that (1) the marker-variable technique can serve as a convenient, yet effective, tool for accounting for CMV, and (2) common method biases in the IS domain are not as serious as those found in other disciplines.
Suppression of Ku70/80 or Lig4 leads to decreased stable transformation and enhanced homologous recombination in rice (2012)

Evidence for the involvement of the nonhomologous end joining (NHEJ) pathway in Agrobacterium-mediated transferred DNA (T-DNA) integration into the genome of the model plant Arabidopsis remains inconclusive. Having established a rapid and highly efficient Agrobacterium-mediated transformation system in rice (Oryza sativa) using scutellum-derived calli, we examined here the involvement of the NHEJ pathway in Agrobacterium-mediated stable transformation in rice. Rice calli from OsKu70, OsKu80 and OsLig4 knockdown (KD) plants were infected with Agrobacterium harboring a sensitive emerald luciferase (LUC) reporter construct to evaluate stable expression and a green fluorescent protein (GFP) construct to monitor transient expression of T-DNA. Transient expression was not suppressed, but stable expression was reduced significantly, in KD plants. Furthermore, KD-Ku70 and KD-Lig4 calli exhibited an increase in the frequency of homologous recombination (HR) compared with control calli. In addition, suppression of OsKu70, OsKu80 and OsLig4 induced the expression of HR-related genes on treatment with DNA-damaging agents. Our findings suggest strongly that NHEJ is involved in Agrobacterium-mediated stable transformation in rice, and that there is a competitive and complementary relationship between the NHEJ and HR pathways for DNA double-strand break repair in rice.
New microcavity substrates for enhancing Raman signals of microscopic samples (2009)

A novel method for improving the detection limit of normal Raman spectra of chemicals using a micro-Raman system and pico-liters volume is presented. A micro-cavity substrate uses various mechanisms that collectively improve the normal Raman signal from the sample without surface-enhanced Raman scattering (SERS) enhancement. The microcavity substrate enhances the entire Raman spectra of the molecules under investigation and maintains the relative intensity ratios of the various Raman bands. This feature of maintaining the overall integrity of the Raman features during signal enhancement makes the micro-cavity substrate ideal for forensic science applications requiring chemical detection of residual traces and other applications requiring low sample volumes and concentrations. It will be further shown that micro-cavities coated with nano films of gold and silver takes advantage of both SERS and micro-cavity method and significantly improve the detection limits of samples.
A 1,2‐<i>trans</i>‐Selective Glycosyl Donor Bearing Cyclic Protection at the C‐2 and C‐3 Hydroxy Groups (2017)

A new 1,2‐ trans ‐selective glycosylation reaction is described. Glucosyl donors protected cyclically at the C‐2 and C‐3 hydroxy groups as six‐ (butane diacetal), seven‐ (tetraisopropyldisiloxanylidene), or eight‐ (2,3‐ o ‐xylylene) membered fused rings were synthesized in a straightforward manner. The glycosylation reactions of the glucosyl donors with various acceptors mainly generated β‐glycosides under conventional reaction conditions. The results show that the o ‐xylylene group is a suitable 1,2‐ trans ‐directing group from the points of view of stereoselectivity and chemical stability. A conformational study of the oxocarbenium ion of an o ‐xylylene‐protected glucose derivative by NMR spectroscopy and computational simulation was carried out. The results imply that the oxocarbenium ion mainly adopts a 4 H 3 conformation owing to the rigid trans ‐fused ring at C‐2 and C‐3, while a noncyclically protected derivative might fluctuate between conformations. These results suggest that an eclipsing interaction between the pseudoequatorial xyloxy group at C‐2 and the incoming nucleophile hampers 1,2‐ cis attack.