gebhart/patrepeval huggingface dataset:
Detection and determination of oligonucleotide triplex formation-mediated transcription-coupled DNA repair in HeLa nuclear extracts (2001)

Transcription-coupled repair (TCR) plays an important role in removing DNA damage from actively transcribed genes. It has been speculated that TCR is the most important mechanism for repairing DNA damage in non-dividing cells such as neurons. Therefore, abnormal TCR may contribute to the development of many age-related and neurodegenerative diseases. However, the molecular mechanism of TCR is not well understood. Oligonucleotide DNA triplex formation provides an ideal system to dissect the molecular mechanism of TCR since triplexes can be formed in a sequence-specific manner to inhibit transcription of target genes. We have recently studied the molecular mechanism of triplex-forming oligonucleotide (TFO)-mediated TCR in HeLa nuclear extracts. Using plasmid constructs we demonstrate that the level of TFO-mediated DNA repair activity is directly correlated with the level of transcription of the plasmid in HeLa nuclear extracts. TFO-mediated DNA repair activity was further linked with transcription since the presence of rNTPs in the reaction was essential for AG30-mediated DNA repair activity in HeLa nuclear extracts. The involvement of individual components, including TFIID, TFIIH, RNA polymerase II and xeroderma pigmentosum group A (XPA), in the triplex-mediated TCR process was demonstrated in HeLa nuclear extracts using immunodepletion assays. Importantly, our studies also demonstrated that XPC, a component involved in global genome DNA repair, is involved in the AG30-mediated DNA repair process. The results obtained in this study provide an important new understanding of the molecular mechanisms involved in the TCR process in mammalian cells.
Transparent and opaque Schottky contacts on undoped In0.52Al0.48As grown by molecular beam epitaxy (1995)

The Schottky barrier height was measured for five different materials on undoped In0.52Al0.48As grown by molecular beam epitaxy (MBE). Of the materials tested, two were transparent conductors, indium-tin-oxide (ITO), and cadmium tin oxide (CTO) and for comparison, three were opaque metals (Au, Ti, and Pt). The barrier heights were measured using I–V measurements. Due to the high series resistance created by the undoped In0.52Al0.48As, the Norde method [J. Appl. Phys. 50, 5052 (1979)] was used to plot the I–V characteristics and extract the Schottky barrier height. The Schottky barrier heights were determined to be 0.639, 0.637, 0.688, 0.640, and 0.623 eV for ITO, CTO, Au, Ti, and Pt, respectively. Previously published results for Schottky barriers on In0.52Al0.48As are compared with our measurements.
Effects of nasal positive-pressure hyperventilation on the glottis in normal sleeping subjects (1995)

We have previously observed that, in normal awake subjects passively hyperventilated with intermittent positive-pressure ventilation delivered through nasal access (nIPPV), the glottis could interfere with the ventilation. We report on data obtained in the same subjects during stable sleep. In all cases, the glottis was continuously observed through a fiber-optic bronchoscope, and other indexes were also continuously recorded. Mechanical ventilation was progressively increased up to 30 l/min. We have observed during passive nIPPV in stable sleep that increases in delivered minute ventilation (VEd) resulted in progressive narrowing of the glottic aperture, with increases in inspiratory resistance and progressive reductions in the percentage of the delivered tidal volume effectively reaching the lungs. For a given level of VEd, comparisons showed that the glottis was significantly narrower during sleep than during wakefulness and that the glottis was significantly narrower during stage 2 than during stages 3/4 non-rapid-eye-movement sleep. Moreover, when CO2 is added to the inspired air, glottic aperture increased in five of nine trials without changes in sleep stage. We also observed a significant negative correlation between glottic width and the VED, independent of the CO2 level. We conclude that during nIPPV glottis narrowing results in a decrease in the proportion of the delivered tidal volume reaching the lungs.
Queueing strategies for multicast packet switching (2002)

The authors consider multicast packet switching where an input may send the same packet to many outputs within an ATM (asynchronous transfer mode) time slot. A host of multicast queuing disciplines can be exercised. Assuming only independent HOL (head of line) service to an output from slot to slot, the delay performance and saturation throughput are derived. The accuracy of the assumption for different disciplines is examined via extensive simulation. It is shown that the FCFS (first come, first serve) HOL service discipline not only has almost completely identical results for simulation versus analysis, but also provides the best saturation throughput, fairness, and delay performance among all disciplines considered. The analysis shows that implementing packet priorities can significantly improve delay performance. It is concluded that offering priority according to age in the queue is a worthwhile feature for multicast (as well as unicast) packet switches.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Allocation of Scarce Resources After a Nuclear Detonation: Setting the Context (2011)

The purpose of this article is to set the context for this special issue of Disaster Medicine and Public Health Preparedness on the allocation of scarce resources in an improvised nuclear device incident. A nuclear detonation occurs when a sufficient amount of fissile material is brought suddenly together to reach critical mass and cause an explosion. Although the chance of a nuclear detonation is thought to be small, the consequences are potentially catastrophic, so planning for an effective medical response is necessary, albeit complex. A substantial nuclear detonation will result in physical effects and a great number of casualties that will require an organized medical response to save lives. With this type of incident, the demand for resources to treat casualties will far exceed what is available. To meet the goal of providing medical care (including symptomatic/palliative care) with fairness as the underlying ethical principle, planning for allocation of scarce resources among all involved sectors needs to be integrated and practiced. With thoughtful and realistic planning, the medical response in the chaotic environment may be made more effective and efficient for both victims and medical responders.
Extracting conceptual interoperability constraints from API documentation using machine learning (2016)

Successfully using a software web-service/platform API requires satisfying its conceptual interoperability constraints that are stated within its shared documentation. However, manual and unguided analysis of text in API documents is a tedious and time consuming task. In this work, we present our empirical-based methodology of using machine learning techniques for automatically identifying conceptual interoperability constraints from natural language text. We also show some initial promising results of our research.
Challenges of pin-point landing for planetary landing: the LION absolute vision-based navigation approach and experimental results (2013)

After ExoMars in 2016 and 2018, future ESA missions to Mars, the Moon, or asteroids will require safe and pinpoint precision landing capabilities, with for example a specified accuracy of typically 100 m at touchdown for a Moon landing. The safe landing requirement can be met thanks to state-of-the-art Terrain-Relative Navigation (TRN) sensors such as Wide-Field-of-View vision-based navigation cameras (VBNC), with appropriate hazard detection and avoidance algorithms. To reach the pinpoint precision requirement, on-board absolute navigation with respect to the landing site is mandatory, with a typical accuracy better than 100 m at touchdown for a Lunar mission, or below 10 km at entry interface for a Mars landing missions. In this paper, we present the validation approach and experimental results of an Absolute Visual Navigation system (AVN) known as Lion. The Lion functional architecture will be first presented, as well as the implemented incremental validation and verification approach ; experimental set-up and end-to-end tests results will be summarized. Finally, way forward and lessons learned will be discussed.
Dynamically applied <i>B</i><sub>1</sub><sup>+</sup> shimming solutions for non‐contrast enhanced renal angiography at 7.0 tesla (2012)

The purpose of this study was to detail a strategy for performing non-contrast enhanced renal magnetic resonance angiography studies at 7.0 T. It is demonstrated that with proper B1+ management, these studies can be successfully performed at ultrahigh field within local specific absorption rate constraints. An inversion prepared gradient echo acquisition, standard for non-contrast renal magnetic resonance angiography studies, required radiofrequency pulse specific B 1+ shimming solutions to be dynamically applied to address the field dependent increases in both B(0) and B1+ inhomogeneity as well as to accommodate limitation in available power. By using more efficient B1+ shimming solutions for the inversion preparation and more homogeneous solutions for the excitation, high quality images of the renal arteries were obtained without venous and background signal artifacts while working within hardware and safety constraints. Finite difference time domain simulations confirmed in vivo measurements with respect to B1+ distributions and homogeneity for the range of shimming strategies used and allowed the calculation of peak local specific absorption rate values normalized by input power and B1+. Increasing B1+ homogeneity was accompanied by decreasing local specific absorption rate per Watt and increasing maximum local specific absorption rate per [B1+](2), which must be considered, along with body size and respiratory rate, when finalizing acquisition parameters for a given individual.
Abnormal Skin Irritancy in Atopic Dermatitis and in Atopy Without Dermatitis (1994)

Our results showed significantly greater irritant responses in atopic subjects with no skin disease or in subjects with inactive AD and confirmed past findings that showed greatly increased irritancy in patients with active AD. We hypothesize that abnormal intrinsic hyperreactivity in inflammatory cells, rather than in skin cells, in atopic individuals predisposes to a lowered threshold of irritant responsiveness.
Universal Dermal Microbiome in Human Skin (2020)

Human skin microbiota has been described as a "microbial fingerprint" due to observed differences between individuals. Current understanding of the cutaneous microbiota is based on sampling the outermost layers of the epidermis, while the microbiota in the remaining skin layers has not yet been fully characterized. Environmental conditions can vary drastically between the cutaneous compartments and give rise to unique communities. We demonstrate that the dermal microbiota is surprisingly similar among individuals and contains a specific subset of the epidermal microbiota. Variability in bacterial community composition decreased significantly from the epidermal to the dermal compartment but was similar among anatomic locations (hip and knee). The composition of the epidermal microbiota was more strongly affected by environmental factors than that of the dermal community. These results indicate a well-conserved dermal community that is functionally distinct from the epidermal community, challenging the current dogma. Future studies in cutaneous disorders and chronic infections may benefit by focusing on the dermal microbiota as a persistent microbial community.<b>IMPORTANCE</b> Human skin microbiota is thought to be unique according to the individual's lifestyle and genetic predisposition. This is true for the epidermal microbiota, while our findings demonstrate that the dermal microbiota is universal between healthy individuals. The preserved dermal microbial community is compositionally unique and functionally distinct to the specific environment in the depth of human skin. It is expected to have direct contact with the immune response of the human host, and research in the communication between host and microbiota should be targeted to this cutaneous compartment. This novel insight into specific microbial adaptation can be used advantageously in the research of chronic disorders and infections of the skin. It can enlighten the alteration between health and disease to the benefit of patients suffering from long-lasting socioeconomic illnesses.
Trans-synaptic EphB2–ephrin–B3 interaction regulates excitatory synapse density by inhibition of postsynaptic MAPK signaling (2010)

Nervous system function requires tight control over the number of synapses individual neurons receive, but the underlying cellular and molecular mechanisms that regulate synapse number remain obscure. Here we present evidence that a trans-synaptic interaction between EphB2 in the presynaptic compartment and ephrin-B3 in the postsynaptic compartment regulates synapse density and the formation of dendritic spines. Observations in cultured cortical neurons demonstrate that synapse density scales with ephrin-B3 expression level and is controlled by ephrin-B3-dependent competitive cell-cell interactions. RNA interference and biochemical experiments support the model that ephrin-B3 regulates synapse density by directly binding to Erk1/2 to inhibit postsynaptic Ras/mitogen-activated protein kinase signaling. Together these findings define a mechanism that contributes to synapse maturation and controls the number of excitatory synaptic inputs received by individual neurons.
Extraction of Characters String Region from Color Scene Image (1996)

This paper proposes an extraction method of charcters string from scene image using HSL transform. In this method, an input color scene image is divied into 15 or 28 binary images by HSL transform. In case of 28 images, 13 images are obtained by dividing on H-S distribution map and 15 are obtained by dividing lightness histgram. Label allotment is carried out in each binary image and rectangle regions are extracted from label images by label allotment. These rectangles are merged by using 3 decision criteria. Candidate rectangles which surround characters are decided by the connectivity in each image and characters string area is extracted by integrating these candidates in all binary images. The experimental result shows that 92.4% of charcters included in 100 types of different color scene images are correctly extracted by this method.
Improvement in Integration Issues for Organic Low-k Hybrid-Organic-Siloxane-Polymer (2001)

The organic low-k hybrid-organic-siloxane-polymer (HOSP®) has been investigated as an intermetal dielectric. The presence of Si-H and bonds instead of partial Si-O bonds lowers the dielectric constant compared to conventional siloxane-based spin-on glass. However, dielectric degradation occurs due to the destruction of functional groups in HOSP during the photoresist ashing process. In this work, we have applied plasma nitridation to improve the quality of HOSP films. The plasma process converts the organic HOSP surface into an inorganic surface by formation of a thin inert passivation layer. The inert layer can enhance the resistance of the HOSP film to moisture uptake and plasma attack during photoresist stripping. In addition, it effectively prevents copper from penetrating the HOSP film. © 2001 The Electrochemical Society. All rights reserved.
Efficacy of immunization with outer membrane proteins for induction of pulmonary clearance of nontypeable Haemophilus influenzae in a rat respiratory model. (2006)

Three strains of nontypeable Haemophilus influenzae namely NTHi-I, NTHi-II and NTHi-III were isolated from the sputum of patients with bronchitis and identified by biochemical, serological and electron microscopy. The polypeptide patterns of isolates were compared and found to have similar sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) polypeptide patterns, although some of the bands were specific in some strains. A similar comparison was made on extracted outer membrane proteins (OMPs) on the above mentioned strains, using Triton X-100 and sodium dodecyle sulphate (SDS). It was found that the polypeptides with molecular weights of 70, 42, 33 and 27 KDa were identified as P1, P2, P4 and P5 respectively. The protein estimation of crude OMPs from the three strains were calculated, and OPM-I prepared from NTHi-I showed the highest amount of protein and was chosen for its immunogenicity in a rat respiratory model. The efficacy of immunization with OMP was determined by enhancement of pulmonary clearance of live bacteria in the rat lung. A significant protective immune response induced by OMP was observed by enhanced respiratory clearance of nontypeable H. influenzae following mucosal immunization.
<i>N</i>‐Acyl Derivatives of 4‐Phenoxyaniline as Neuroprotective Agents (2014)

Neuronal cell death is the main cause behind the progressive loss of brain function in age-related neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Despite the differing etiologies of these neurological diseases, the underlying neuronal damage is triggered by common mechanisms such as oxidative stress, impaired calcium homeostasis, and disrupted mitochondrial integrity and function. In particular, mitochondrial fragmentation, mitochondrial membrane permeability, and the release of death-promoting factors into the cytosol have been revealed as the "point of no return" in programmed cell death in neurons. Recent studies revealed a pivotal role for the pro-apoptotic Bcl-2-family protein Bid in models of neuronal cell death, which confirmed Bid as a potential drug target. Herein, we present N-acyl-substituted derivatives of 4-phenoxyaniline that were screened for their potential to attenuate Bid-mediated neurotoxicity. These compounds provided significant protection against glutamate- and Bid-induced toxicity in cultured neurons. Substitution of the amino group in the 4-phenoxyaniline scaffold with 4-piperidine carboxylic acid and N-hydroxyethyl-4-piperidine carboxylic acid yielded compounds that displayed significant neuroprotective activity at concentrations as low as 1 μM. Furthermore, findings of a tBid-overexpression assay and real-time measurements of cell impedance support the hypothesis that these compounds indeed address the Bid protein.
A novel algorithm for detection of soccer ball and player (2015)

In this work, we propose an efficient, mere algorithm for detection of a soccer ball and players. In long shots, existing algorithms may not be able to detect the ball when it merged with the lines in the field. So, we introduce a method that can separate lines from the ball and segment the ball competently. Primarily, the ground and the edges of the original image are detected. Then, Hough transform line detection algorithm is applied to identify lines. After line detection, the lines are eliminated from the original image so that only detected players and the ball remain in the scene. The experimental results show how durable that our algorithm can detect ball when the ball attached to the line and also can detect players under occluded situations.
Comparative<i>in vitro</i>study of the immunomodulatory activity of humanized and chimeric anti-CD25 monoclonal antibodies (2003)

Humanized or chimeric monoclonal antibodies (MoAbs) directed against the interleukin-2 (IL-2) receptor alpha-chain, CD25, are promising immunosuppressive agents due to improved pharmacokinetic profiles and less toxicity. These MoAbs have been used effectively in preventing and/or treating rejection in solid organ transplantation and are currently under investigation for prevention/treatment of graft-versus-host disease (GvHD) in stem cell transplantation. We analysed the in vitro activities of the chimeric anti-CD25 MoAb basiliximab and the humanized anti-CD25 MoAb daclizumab in various test systems for alloimmune response and T cell activation in comparison to cyclosporin A (CsA) and prednisolone. Anti-CD3- and alloantigen-induced T cell proliferation were decreased significantly by the anti-CD25 MoAbs in a dose-dependent fashion. At a concentration of 10 ng/ml daclizumab and CsA synergistically decreased T cell proliferation of mixed lymphocyte cultures, whereas basiliximab showed only subadditive activity. Simultaneous addition of the anti-CD25 MoAbs and prednisolone did not result in combined activity. Addition of exogenous IL-2 completely overcame the inhibitory effect on T cell proliferation of both anti-CD25 MoAbs, but not that of CsA and prednisolone. Anti-CD25 MoAbs inhibited the generation of antigen-specific cytotoxic T lymphocytes in a limiting dilution assay, whereas they showed no effect on the cytolytic activity of established antigen-specific T cell clones. This in vitro study demonstrates strong immunosuppressive activity by both chimeric and humanized MoAbs against CD25. The combined activity with CsA justifies their early use for prevention rather than treatment of GvHD.
Least-dependent-component analysis based on mutual information (2004)

We propose to use precise estimators of mutual information (MI) to find the least dependent components in a linearly mixed signal. On the one hand, this seems to lead to better blind source separation than with any other presently available algorithm. On the other hand, it has the advantage, compared to other implementations of "independent" component analysis (ICA), some of which are based on crude approximations for MI, that the numerical values of the MI can be used for (i) estimating residual dependencies between the output components; (ii) estimating the reliability of the output by comparing the pairwise MIs with those of remixed components; and (iii) clustering the output according to the residual interdependencies. For the MI estimator, we use a recently proposed k -nearest-neighbor-based algorithm. For time sequences, we combine this with delay embedding, in order to take into account nontrivial time correlations. After several tests with artificial data, we apply the resulting MILCA (mutual-information-based least dependent component analysis) algorithm to a real-world dataset, the ECG of a pregnant woman.
Inhibition of Metastatic Tumor Growth in Mouse Lung by Repeated Administration of Polyethylene Glycol-Conjugated Catalase (2004)

These findings indicate that sustained catalase activity in the blood circulation can prevent the multiple processes of tumor metastasis in the lung, which could lead to a state of tumor dormancy.
Heart rate changes during partial seizures: A study amongst Singaporean patients (2001)

Significant heart rate changes during partial seizures were seen in half of Singaporean patients. Although sinus tachycardia was the most common heart rate change, the frequency was considerably lower compared to Caucasian patients. This might be due to methodological and ethnic differences. Rates of bradycardia are similar to those recorded in the literature.