gebhart/patrepeval huggingface dataset:
An In Vitro and In Vivo Evidence That Downregulation of Leukemia Inhibitory Factor (LIF) Receptor (LIF-R) Decreases the Metastatic Potential of Human Rhabdomyosarcoma (RMS) Cells. (2006)

Abstract Rhabdomyosarcoma (RMS) and skeletal muscle-derived tumors frequently infiltrate bone marrow (BM). We have demonstrated that the stromal-derived factor (SDF)-1-CXCR4 receptor (Blood2002;100:2597) and hepatocyte growth factor (HGF)-c-Met receptor (Cancer Res. 2003;63:7926) play an important role in RMS metastasis to BM. Leukemia inhibitory factor (LIF) is a well known factor that plays an important role in skeletal muscle development/regeneration and similarly as SDF-1 and HGF is secreted by BM stroma. This prompted us to examine whether the LIF-LIF receptor (LIF-R) axis affects the biology/metastasis of RMS cells. We employed in our studies, human established RMS cell lines, as well as RMS samples isolated from patients and noticed that LIF-R was expressed not only on established human RMS cell lines (7/7) but more importantly, it was also detectable in patient samples (23/23). We also found that in RMS cells LIF stimulatesphosphorylation of MAPKp42/44, AKT and STAT3,chemotaxis and adhesion andincreases resistance to cytostatics (e.g., etoposide). These LIF-mediated effects were inhibited after downregulating the LIF-R by siRNA. To learn more on the biological significance of the LIF-LIF-R axis in vivo we employed two models. First, human RMS cells (RH-30) were exposed or not exposed to LIF-R siRNA and subsequently injected into SCID™-Beige immunodeficient mice. To estimate the number of RMS cells that seed to BM and liver in these animals, we isolated DNA and using real- time RT-PCR, amplified human a-satellite sequences and murine b-actin. The number of human cells present in murine organs was subsequently calculated from a standard curve derived from mixing varying numbers of human cells with a constant number of murine cells. We noticed that downregulation of LIF-R by siRNA significantly decreased the number of human RMS cells in murine BM and liver (x4 and x2 respectively). In a second model, the RH30 cell line was selected by repetitive chemotaxis for cells that are highly responsive to LIF (RH-30 L) and subsequently the cells from parental RH-30 cell line and RH-30 L cells were injected intramuscularly. Six weeks after tumour inoculation, we detected more metastasis in bone marrow and lungs in mice injected with RH-30L cells as compared to parental RH-30 clone (x6 and x3 respectively). In conclusion, we present evidence for the first time that the inhibition of LIF-LIF-R axis may decrease the invasive potential of human RMS both in vitro and in vivo. Hence, molecular targeting of LIF-LIF-R axis could possibly become a more effective new strategy to control the progression and metastasis of RMS.
EPIDEMIOLOGICAL STUDIES ON RESPIRATORY INFECTIONS OF THE RABBIT (1927)

These observations have brought out three facts which may be stated briefly as follows. 1. An acute respiratory epidemic was incited by mucoid strains of Bact. lepisepticum of moderate and uniform virulence. 2. The epidemic was brought about not by an alteration in the virulence of the prevailing strains of Bact. lepisepticum but by a sudden distribution of virulent organisms among a susceptible population hitherto unexposed. 3. Individuals in this population showed different degrees of resistance to the infecting bacillus; some died from pneumonia and septicemia, while others localized the infection to the nasal passages. The significance of these facts has been discussed at length elsewhere (4).
Novel characteristic for distinguishing Lactococcus lactis subsp. lactis from subsp. cremoris (1999)

Lactococcus lactis strains were examined for their ability to produce gamma-aminobutyric acid (GABA). Results showed that strains of L. lactis subsp. lactis were able to produce this acid, whereas L. lactis subsp. cremoris were not. GABA production thus represents another effective characteristic for distinguishing L. lactis subsp. lactis from L. lactis subsp. cremoris.
A vibration sensor, using telecommunication grade monomode fiber, immune to temperature variations (1993)

A polarimetric fiber-optic vibration sensor immune to temperature variations is realized by forming coils using a standard single-mode fiber. The phase drift due to the linear birefringence changes induced by a modification of the environmental temperature is balanced by a feedback compression of a non vibrating coil. Experimental results show that without the feedback system the sensitivity to temperature is equal to 2%/°C. The compensated device has a maximum 10% relative variation of the output signal over a 30-55 °C range. This method is easy to implement on polarimetric sensors over any range of temperature.
Edge preserving pre-post filtering for low bitrate video coding (2002)

Post filtering is an effective tool for reducing coding artifacts in video coding. Most post-filtering tools are based on lowpass filtering, and an edge preserving filtering is useful because edges have an important effect on visual quality. An edge preserving filtering has an edge detection step, region detection step, and filtering step. The effectiveness of such filtering is much affected by the edge detection feature. Therefore the edge detection threshold should be carefully determined. We created a new method of determining the edge detection threshold of a post filter, that is based on the prefiltering features and encoding conditions. Computer simulations show that this method achieves the best visual quality for given prefiltering and encoding conditions.
Growth Failure and Inflammatory Bowel Disease: Approach to Treatment of a Complicated Adolescent Problem (1983)

Severe retardation of linear growth occurs in a minority of children with Crohn's disease. It appears to be associated with increased disease activity and decreased caloric intake. Why some children are affected and others are not is unknown, but some degree of growth retardation is probably more prevalent than is generally appreciated. The use of somatomedin-C levels may be of some future value in predicting which children will be affected. Growth failure is often difficult to treat and requires vigorous medical and nutritional support. No current treatment is without attendant problems. Proper and frequent assessment of growth and development will help ensure intervention while growth potential still exists in these children. Large cooperative studies are needed to compare the effects of various treatment plans on the growth velocity and ultimate stature of children with Crohn's disease-related growth retardation.
Marker based camera pose estimation for underwater robots (2012)

Today, simple and accurate pose estimation is needed for small underwater robots to support and to replace submergence operation divers. Position and orientation estimation using luminous markers and the computer tracking library ARToolKit is one of the solutions for estimation, since it is fast enough for real time processing and is open sourced. Although, since it was made for augmented reality, its use for underwater is limited. In this paper, finding the limit and drawbacks of ARToolKit for underwater usage will be studied. The assessment was done under different levels of turbidities of water and different angles of the marker. The results can be applied to the usage of using ARToolKit underwater with luminous markers.
Use of Mud Gas Chromatograph for Reservoir Quality Prediction While Drilling - A Case Study (2015)

Abstract While drilling through a reservoir, a lot of valuable information can be obtained from mud logging to support formation evaluation. Field data will help wellsite geologists, petrophysicist and reservoir engineers to predict reservoir quality, fluid contacts and reservoir permeability based on formation gases detected while drilling. This study discusses some examples from exploratory wells that have recently been drilled in Kuwait. Gas readings were recorded while drilling through Cretaceous and deep Jurassic formations to evaluate hydrocarbon content using Advanced Gas Chromatography. The primary components of the system utilized are: a constant volume gas extractor, a gas sample flow control system, and a high resolution chromatographic system. To interpret the findings Gas readings are monitored by a complex system which provides real-time continuous measurements of the concentration of formation gases from very light components such as methane, to heavy components such as C6, C7 and C8 hydrocarbon species, comprising n-hexane, n-heptane, n-octane, benzene and toluene. Formation gas is considered as the first indication of a reservoir's fluid characterization and reflects the extent of the productivity of the well. Geochemical ratios and equations can enhance the interpretation of field data and give the first indication of zones of interest that need further evaluation. The integration of the gas data along with the drilling parameters (ROP, ΔFlow) can be of valuable inputs to quantify the Rock properties such as porosity and permeability, this new approach can extend the utilization of gas data not only for formation evaluation and fluid characterization but also for formation petro-physical structure. To take advantage of the field data, the gas readings are plotted on a depth log, which can be easily integrated with other data. Geochemical equations are plotted against depth and lithology to determine fluid type, contacts and evolution.
A Partitioned Translation Lookaside Buffer Approach to Reducing Address Bandwidth (2005)

Simulations indicate a simple modification of existing virtual memory hardware can significantly reduce the number of pins required to transmit address information from processor to off-chip memory. This modification consists of partitioning a TLB so that virtual page numbers are stored in a cache on the processor and corresponding real page numbers are stored in registers at the memory, making it possible to transmit a small register index instead of the entire real page number.
Compensation of input current distortion in three-phase buck rectifiers (2013)

An overlap time for two commutating switches is necessary to prevent current interruption in a three-phase buck rectifier, but it may cause input current distortion. In this paper, a modified pulse-based compensation method is proposed to compensate for the overlap time. In addition to the traditional method which places the overlap time based on the voltage polarity, this new method first minimizes the overlap time to reduce its effect and then compensates the pulse width according to the sampled voltage and current. It is verified by experiments that the proposed method has better performance than the traditional method, especially when the line-to-line voltage crosses zero. Another distortion comes from the irregular pulse distribution when two sectors change in a 12-sector space vector PWM. This paper proposes two compensation methods for that scenario as well, compensating the duty cycle and increasing switching frequency near the boundaries of two sectors. It is shown through experiments that both methods can reduce the input current distortion in the buck rectifier.
Visible resonant modes in GaN-based photonic crystal membrane cavities (2006)

Photonic crystal membrane cavities play a key role as building blocks in the realization of several applications, including quantum information and photonic circuits. Thus far, there has been no work on defect cavities with active layers emitting in the UV to green range of the spectrum based on the (Al,In,Ga)N material system. While this material system has great potential for a new generation of optoelectronic devices, there are several obstacles for the fabrication of GaN-based membrane cavities, including the absence of a conventional selective chemical wet etch. Here, we demonstrate the first fabrication of fully undercut GaN photonic crystal membranes containing an InGaN multiquantum well layer, fabricated using band-gap-selective photoelectrochemical etching. A postfabrication coating of Ta2O5 is used to tune the cavity modes into resonance with the quantum well emission, and the fabricated membranes exhibit resonant modes with Q=300.
Recent advances in the genome-wide study of DNA replication origins in yeast (2015)

DNA replication, one of the central events in the cell cycle, is the basis of biological inheritance. In order to be duplicated, a DNA double helix must be opened at defined sites, which are called DNA replication origins (ORIs). Unlike in bacteria, where replication initiates from a single replication origin, multiple origins are utilized in the eukaryotic genomes. Among them, the ORIs in budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe have been best characterized. In recent years, advances in DNA microarray and next-generation sequencing technologies have increased the number of yeast species involved in ORIs research dramatically. The ORIs in some non-conventional yeast species such as Kluyveromyces lactis and Pichia pastoris have also been genome-widely identified. Relevant databases of replication origins in yeast were constructed, then the comparative genomic analysis can be carried out. Here, we review several experimental approaches that have been used to map replication origins in yeast and some of the available web resources related to yeast ORIs. We also discuss the sequence characteristics and chromosome structures of ORIs in the four yeast species, which can be utilized to improve yeast replication origins prediction.
Direct Measurement of Surface Residence Times:  Nitryl Chloride and Chlorine Nitrate on Alkali Halides at Room Temperature (1998)

To gain quantitative understanding of the “stickiness” of a molecule on a given surface, we have developed a new diffusion tube method that allows us to measure changes in the surface residence times of unreactive as well as reactive adsorbants on solid substrates in real time. The experiment involves sending a pulse of molecules through a tube coated internally with a material of interest. The arrival time of the pulse is recorded using a mass spectrometer, which is mounted at the tube exit in a high vacuum chamber. Since the number of wall collisions under molecular flow conditions is determined only by the tube geometry, the surface residence time can be calculated on a per collision basis. A Monte Carlo simulation, based on the assumption that the molecules are reflected upon collision with a cosine directional distribution, is used to model experimental results. In this study we have measured the surface residence times of two reactive, atmospherically relevant molecules, ClNO2 and ClONO2, on sea-salt aerosol mimics (NaCl, KBr). We found an upper limit of 0.02 ms for the interaction of ClNO2 with KBr and a surface residence time of 0.7 ± 0.2 ms for ClONO2 on NaCl at uptake coefficients of γ = 0.0002 and 0.1, respectively.
Artificial Neural Network Approach for Mapping Contrasting Tillage Practices (2010)

Tillage information is crucial for environmental modeling as it directly affects evapotranspiration, infiltration, runoff, carbon sequestration, and soil losses due to wind and water erosion from agricultural fields. However, collecting this information can be time consuming and costly. Remote sensing approaches are promising for rapid collection of tillage information on individual fields over large areas. Numerous regression-based models are available to derive tillage information from remote sensing data. However, these models require information about the complex nature of underlying watershed characteristics and processes. Unlike regression-based models, Artificial Neural Network (ANN) provides an efficient alternative to map complex nonlinear relationships between an input and output datasets without requiring a detailed knowledge of underlying physical relationships. Limited or no information currently exist quantifying ability of ANN models to identify contrasting tillage practices from remote sensing data. In this study, a set of Landsat TM-based ANN models was developed to identify contrasting tillage practices in the Texas High Plains. Observed tillage data from Moore and Ochiltree Counties were used to develop and evaluate the models, respectively. The overall classification accuracy for the 15 models developed with the Moore County dataset varied from 74% to 91%. Statistical evaluation of these models against the Ochiltree County dataset produced results with an overall classification accuracy varied from 66% to 80%. The ANN models based on TM band 5 or indices of TM Band 5 may provide consistent and accurate tillage information when applied to the Texas High Plains.
Enteritis in sheep and goats due to <i>Yersinia enterocolitica</i> infection (1990)

Yersinia enterocolitica biotype 5, serotype 02,3 was isolated from the intestine of 38 sheep and 8 goats submitted to the laboratory for disease diagnosis. Infected animals were usually young, had diarrhoea and were in poor condition or emaciated. A number were moribund or dead when submitted. Characteristic microabscesses were demonstrated in the intestine of 5 of 38 sheep and 3 of 8 goats and no alternative cause of morbidity or mortality was established in these animals. Of the 33 sheep and 5 goats infected with Y. enterocolitica in which microabscesses were not demonstrated, a number of other diagnoses were made, including internal parasitism (18), selenium deficiency or white muscle disease (6) and cobalt deficiency (2), so that morbidity and mortality were possibly unrelated to Y. enterocolitica infection. Five of 6 sheep exposed experimentally by mouth to Y. enterocolitica biotype 5, serotype 02,3 developed an intestinal infection. Although infected sheep showed no clinical evidence of disease and haematological and biochemical indices remained normal, multiple intestinal microabscesses typical of yersiniosis were demonstrated in 3 of 5 infected sheep. It is concluded that Y. enterocolitica biotype 5, serotype 02,3 is an enteropathogen of sheep and goats. Since sheep and goats may be the specific hosts of this bacterium, its virulence for these species is apparently low. Morbidity and mortality may, therefore, be unusual manifestations of infection.
2,7-Poly(9-fluorenone): A Trap-Free Electron-Injection Material with a High Charge Carrier Mobility for Use in Light-Emitting Diodes (2000)

Electron-transporting materials are necessary for organic light-emitting diodes (OLEDs) if their efficiency is going to be increased sufficiently for commercial application. Evidence is presented that the novel, electron-deficient polymer 2,7-poly(9-fluorenone), see Figure, has the qualities required of an electron-injection material in multilayer LEDs.
Rapid assessment of early biophysical changes in K562 cells during apoptosis determined using dielectrophoresis. (2006)

Apoptosis, or programmed cell death, is a vital cellular process responsible for causing cells to self-terminate at the end of their useful life. Abrogation of this process is commonly linked to cancer, and rapid detection of apoptosis in vitro is vital to the discovery of new anti-cancer drugs. In this paper, we describe the application of the electrical phenomenon dielectrophoresis for detecting apoptosis at very early stages after drug induction, on the basis of changes in electrophysiological properties. Our studies have revealed that K562 (human myelogenous leukemia) cells show a persistent elevation in the cytoplasmic conductivity occurring as early as 30 minutes following exposure to staurosporine. This method therefore allows a far more rapid detection method than existing biochemical marker methods.
Effectiveness of 2D Fingerprints for Scaffold Hopping (2011)

2D fingerprints provide a simple and computationally efficient way of identifying novel chemotypes in lead-discovery programs.
A Hybrid Nano-Imprinting Lithography Based on Infrared Pulsed Laser Heating (2006)

In this paper we present a novel method of nano-imprinting which adopts important features of conventional nano-imprinting lithography (NIL) and the newly developed laser-assisted direct imprinting (LADI) method. It utilizes an Nd-YAG pulsed laser of wavelength 1064 nm which can easily penetrate and also heat up a silicon mold which is pressed against a resist layer deposited on a substrate. The fast rising temperature in the silicon mold can momentarily melt the resist layer so that the mold is imprinting into the resist layer. After the pattern is transformed, standard nano-imprinting lithography processes can be applied to the substrate for nano-fabrication. This new method has several advantages over existing nano-imprinting methods mostly due to the fast heating-up of silicon mold by high intensity IR laser pulse and therefore has no thermal drifting problem. Both the theoretical modeling and experimental results of this novel IR-laser assisted imprinting method will be presented
Metabolomics: Available Results, Current Research Projects in Breast Cancer, and Future Applications (2007)

Metabolomics is the newest "omics" science. It is a dynamic portrait of the metabolic status of living systems. Metabolomics has brought new insights on metabolic fluxes and a more comprehensive and holistic understanding of a cell's environment. This burgeoning field promises to be a potential tool to fill the gap between genotype and phenotype. As its preceding "omics" sciences (ie, genomics and proteomics), metabolomics' aim is to dredge information hidden in a sea of data. This technology permits simultaneous monitoring of many hundreds, or thousands, of macro- and small molecules, as well as functional monitoring of multiple pivotal cellular pathways. In addition, elucidation of cellular responses to molecular damage, including evolutionarily conserved inducible molecular defense systems, could be achieved with metabolomics and could lead to the discovery of new biomarkers of molecular responses to functional perturbations. If metabolomic information could be translated into diagnostic tests, it might have the potential to impact on clinical practice, and it might lead to the supplementation of traditional biomarkers of cellular integrity, cell and tissue homeostasis, and morphological alterations that result from cell damage or death. In this review the concept and characteristics of metabolomics are introduced. Main current applications of metabolomics in cancer research are reviewed, including its potential in the drug discovery field, and, last but not least, its potential impact in the field of monitoring response and toxicity to anticancer agents. In the last section, research projects ongoing at our institution and future challenges for metabolomics will be presented and briefly discussed.