gebhart/patrepeval huggingface dataset:
Amplification of oncogenes in human cancer cells (1998)

Gene amplification refers to a genomic change that results in an increased dosage of the gene(s) affected. Amplification represents one of the major molecular pathways through which the oncogenic potential of proto-oncogenes is activated during tumorigenesis. The architecture of amplified genomic structures is simple in some tumor types, involving in the vast majority of cases only one gene, such as MYCN in neuroblastomas. On the other hand, it can be complex and discontinuous, involving several syntenic co-amplified genes, such as in the 11q13 amplification in breast cancer, although in many of these cases there may be a single target gene. The presence of different nonsyntenic amplified genes raises the possibility that cells of certain tumors are susceptible to independent amplification events. In general, the amplified genes do not undergo additional damage by mutations. The data indicate that it is the enhanced level of a wild-type protein that contributes to tumorigenesis.
Conformation of P22 tailspike folding and aggregation intermediates probed by monoclonal antibodies (1997)

The partitioning of partially folded polypeptide chains between correctly folded native states and off-pathway inclusion bodies is a critical reaction in biotechnology. Multimeric partially folded intermediates, representing early stages of the aggregation pathway for the P22 tailspike protein, have been trapped in the cold and isolated by nondenaturing polyacrylamide gel electrophoresis (PAGE) (speed MA, Wang DIC, King J. 1995. Protein Sci 4:900-908). Monoclonal antibodies against tailspike chains discriminate between folding intermediates and native states (Friguet B, Djavadi-Ohaniance L, King J, Goldberg ME. 1994. J Biol Chem 269:15945-15949). Here we describe a nondenaturing Western blot procedure to probe the conformation of productive folding intermediates and off-pathway aggregation intermediates. The aggregation intermediates displayed epitopes in common with productive folding intermediates but were not recognized by antibodies against native epitopes. The nonnative epitope on the folding and aggregation intermediates was located on the partially folded N-terminus, indicating that the N-terminus remained accessible and nonnative in the aggregated state. Antibodies against native epitopes blocked folding, but the monoclonal directed against the N-terminal epitope did not, indicating that the conformation of the N-terminus is not a key determinant of the productive folding and chain association pathway.
Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon (2005)

Single nucleotide polymorphisms (SNPs) are a class of genetic markers that are well suited to a broad range of research and management applications. Although advances in genotyping chemistries and analysis methods continue to increase the potential advantages of using SNPs to address molecular ecological questions, the scarcity of available DNA sequence data for most species has limited marker development. As the number and diversity of species being targeted for large-scale sequencing has increased, so has the potential for using sequence from sister taxa for marker development in species of interest. We evaluated the use of Oncorhynchus mykiss and Salmo salar sequence data to identify SNPs in three other species (Oncorhynchus tshawytscha, Oncorhynchus nerka and Oncorhynchus keta). Primers designed based on O. mykiss and S. salar alignments were more successful than primers designed based on Oncorhynchus-only alignments for sequencing target species, presumably due to the much larger number of potential targets available from the former alignments and possibly greater sequence conservation in those targets. In sequencing approximately 89 kb we observed a frequency of 4.30 x 10(-3) SNPs per base pair. Approximately half (53/101) of the subsequently designed validation assays resulted in high-throughput SNP genotyping markers. We speculate that this relatively low conversion rate may reflect the duplicated nature of the salmon genome. Our results suggest that a large number of SNPs could be developed for Pacific salmon using sequence data from other species. While the costs of DNA sequencing are still significant, these must be compared to the costs of using other marker classes for a given application.
Lithium fiber growth on the anode in a nanowire lithium ion battery during charging (2011)

Lithium (Li) dendrite formation has been recognized as one of the major safety concerns for Li metal batteries but not for conventional Li ion batteries (LIBs) where Li metal is not used. With the advanced in situ transmission electron microscopy enabling direct observation of battery operation, we found that Li fibers with length up to 35 μm grew on nanowire tip after charging. The Li fibers growth were highly directional, i.e., nucleating from the nanowire tip, and extending along the nanowire axis, which was attributed to the strong electric field enhancement effect induced by the sharp nanowire tip. This study reveals a potential safety concern of short-circuit failure for LIBs using nanowire anodes.
Intestinal absorption and metabolism of 9-cis-beta-carotene in vivo: biosynthesis of 9-cis-retinoic acid. (1995)

This study was done to examine the intestinal absorption and cleavage of 9-cis-beta-carotene in vivo. A micellar solution, containing either no addition or 10 mumol of 9-cis- or all-trans-beta-carotene, was perfused for 2 h through the upper portion of the small intestine of ferrets. The effluent of a mesenteric lymph duct cannulation was collected, as well as intestinal mucosa scrapings, a portal blood sample, and a liver biopsy, both before and after perfusion. Carotenoids and retinoids were measured by reverse-phase, high performance liquid chromatography. 9-Cis- and all-trans-beta-carotene were transported equally well into mesenteric lymph, although the intestinal concentration of the corresponding isomer was tenfold higher after perfusion of the 9-cis- isomer than after perfusion of all-trans-beta-carotene. Regardless of which isomer was used, perfusion of beta-carotene resulted in the biosynthesis of similar amounts of retinoic acid in portal blood, liver, and intestine. However, after the perfusion of all-trans-beta-carotene, all the retinoic acid formed was in the all-trans- form, whereas the perfusion of 9-cis-beta-carotene resulted in the biosynthesis of about 50% of the total retinoic acid as the 9-cis-isomer. We conclude that in the in vivo ferret model, 9-cis-beta-carotene has a good bioavailability and is a precursor of 9-cis-retinoic acid.
Reconfigurable LC-reflectarray setup and characterisation (2009)

This paper presents the realisation and characterisation of an electronically reconfigurable reflectarray based on liquid crystals at 35 GHz, which is able to electronically steer the main beam continuously in between ±35°. To extract the characteristics of each single tunable unit cell directly on the reflectarray, a specific near field measurement setup is used to enable spatial resolution of the reflected magnitudes and phases.
LABORATORY TESTS ON TOTAL JOINT REPLACEMENT PROSTHESES (1973)

1. Currently available total replacement hip and knee prostheses were tested in a machine enabling flexion-extension movements to be applied whilst the prostheses were surrounded with Ringer's solution or other liquid and loaded within the physiological range. 2. Prostheses of which both components were made in cobalt-chromium-molybdenum alloy produced visible quantities of alloy particles, whose sizes ranged down to about 0·1 microns, and cobalt and molybdenum ions in solution. 3. No metallic or plastic particles were detected during tests on a hip prosthesis made of stainless steel and high density polyethylene. 4. The frictional moments in cobalt-chromium-molybdenum hip prostheses were higher than in stainless steel-polyethylene hip prostheses, by a factor of at least 2 to 1. 5. It is accepted that the conditions of these tests were probably more severe than in life, but the difference is held to be one of degree and not one of kind. 6. The particulate alloy debris, when injected in massive doses into the muscles of rats, gave an incidence of malignant tumours which was comparable to that already established for pure cobalt powder, whereas particles of several other metals, tested in the same way, gave no tumours. 7. It is argued that the particles which are known to be produced in at least some patients using cobalt-chromium-molybdenum total replacement joint prostheses constitute a risk of tumour formation which is certainly small, possibly negligible, but not accurately calculable at present. 8. The results of these tests, particularly the differences in frictional moment and in the production of particulate debris, suggest a preference for high density polyethylene as one component of a total joint replacement prosthesis.
A new method of document structure extraction using generic layout knowledge (2003)

A method of document structure extraction using generic layout knowledge is described. With this method, it is possible to translate images of multimedia documents, i.e. documents that include pictures, graphics, and color information, to hypertext. Hypertext consists of decomposed elements linked with each other through some logical relationship. The principal components of the method are extraction of logical structure elements using a rectangular set operation and generation of hierarchical links of the logical structure between the extracted document elements. It is shown experimentally that the logical structure of a technical paper can be extracted.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
New views on the role of endothelin (minireview). (2002)

Endothelin was isolated and identified in 1988 by Yanagisawa et al. The endothelin family consists of 21 amino acid isoforms endothelin-1, endothelin-2 and endothelin-3. Endothelin receptors are present in many internal organs, e.g. heart, adrenals, kidneys, lung tissue, central nervous system. ET-1 is the main isoform which is synthesized in endothelial cells, muscular coat of arterial wall as well as in heart, kidney and central nervous system. Endothelins affect multiple organ systems and are involved in the pathogenesis of many diseases. Moreover, ET-1 raises blood pressure, induces vascular and myocardial hypertrophy. This paper is also concerned with endothelin receptor blockers which mediate relaxation of resistance arteries and, since they show a hypotensive effect, can be useful in many cardiovascular diseases.
Kerr–Fourier imaging of hidden objects in thick turbid media (1993)

Test bar charts hidden in a 5.5-cm-thick 2.5% Intralipid solution were imaged as a function of phantom depth and size with steady-state Fourier and picosecond Kerr–Fourier imaging systems. With time and space gating, a series of 250-μm bars placed in a thick highly scattering medium were resolved at a signal level of ~10−10 of the illumination intensity.
Bird movements at rotor heights measured continuously with vertical radar at a<scp>D</scp>utch offshore wind farm (2015)

Assessing the impacts of avian collisions with wind turbines requires reliable estimates of avian flight intensities and altitudes, to enable accurate estimation of collision rates, avoidance rates and related effects on populations. At sea, obtaining such estimates visually is limited not only by weather conditions but, more importantly, because a high proportion of birds fly at night and at heights above the range of visual observation. We used vertical radar with automated bird‐tracking software to overcome these limitations and obtain data on the magnitude, timing and altitude of local bird movements and seasonal migration measured continuously at a Dutch offshore wind farm. An estimated 1.6 million radar echoes representing individual birds or flocks were recorded crossing the wind farm annually at altitudes between 25 and 115 m (the rotor‐swept zone). The majority of these fluxes consisted of gull species during the day and migrating passerines at night. We demonstrate daily, monthly and seasonal patterns in fluxes at rotor heights and the influence of wind direction on flight intensity. These data are among the first to show the magnitude and variation of low‐altitude flight activity across the North Sea, and are valuable for assessing the consequences of developments such as offshore wind farms for birds.
Laponite clay as a carrier for in situ delivery of tetracycline (2013)

Although smectite clays have gained much interest in recent years as potential sustained local drug delivery vehicles, they have not been yet utilized or assessed as a local drug delivery device for treatment of periodontal disease. In this paper we showed that unique nanostructure and gel-formation ability of clay holds great promise as an effective drug carrier. In particular, we demonstrated the feasibility of using laponite XLG, a smectite clay, as a carrier for in situ delivery of tetracycline that can potentially be used in the treatment and prevention of periodontal disease. The intercalation of tetracycline between the layers of laponite at different acidic pHs and different concentrations of tetracycline was examined. The laponite–tetracycline composite was characterized using X-ray diffraction (XRD), Fourier transformed infrared spectroscopy (FT-IR) and differential thermal analysis (DTA). The results showed that, in a pH and concentration dependent manner, tetracycline can be intercalated between the layers of laponite nanoparticles. The release study in a simulated saliva solution demonstrated a sustained release of tetracycline from laponite over a 72 hour period. The antimicrobial activity of the released tetracycline was maintained and was not affected by the intercalation of tetracycline into the carrier (laponite) and its release from the carrier.
Depletion of cellular calcium accelerates protein degradation in the endoplasmic reticulum (1991)

In this study the effects of A23187 and thapsigargin on the degradation of T-cell antigen receptor-beta (TCR-beta) and CD3-delta in the endoplasmic reticulum have been studied. Preliminary experiments showed that these drugs had different effects on the secretory pathway. Depletion of cellular calcium pools by incubation of cells with A23187 in calcium-free medium blocked transport between the endoplasmic reticulum and the Golgi apparatus whereas thapsigargin caused a modest increase in transport. When added to cells transfected with TCR-beta or CD3-delta the drugs caused an immediate stimulation of proteolysis of presynthesized protein and at maximum effective concentrations caused a 3-fold increase in the rate of degradation. They did not affect the lag period of 1 h which precedes degradation of newly synthesized proteins. Chelation of cytosolic calcium also accelerated degradation, suggesting that depletion of calcium from the endoplasmic reticulum was the main stimulus of proteolysis and that increased degradation was not caused by a transient increase in cytosolic calcium levels. The selectivity of degradation in the endoplasmic reticulum was maintained. A23187 had no effect on the stability of CD3-gamma nor co-transfected epsilon-beta dimers. Calcium depletion increased the overall rate of degradation in the endoplasmic reticulum and increased the rate of proteolysis of an "anchor minus" beta chain. The results suggested that proteolysis within the endoplasmic reticulum may be regulated by the high concentrations of Ca2+ which are stored in the organelle. Ca2+ may be required for protein folding. Calcium depletion may have caused the beta and delta chains to adopt a conformation that was more susceptible to proteolysis. Alternatively, calcium depletion may have disrupted the lumenal content of the endoplasmic reticulum and increased the access of proteases to potential substrates.
Association of the Intestinal Microbiome with the Development of Neovascular Age-Related Macular Degeneration (2017)

Age-related macular degeneration (AMD) is the most frequent cause of blindness in the elderly. There is evidence that nutrition, inflammation and genetic risk factors play an important role in the development of AMD. Recent studies suggest that the composition of the intestinal microbiome is associated with metabolic diseases through modulation of inflammation and host metabolism. To investigate whether compositional and functional alterations of the intestinal microbiome are associated with AMD, we sequenced the gut metagenomes of patients with AMD and controls. The genera Anaerotruncus and Oscillibacter as well as Ruminococcus torques and Eubacterium ventriosum were relatively enriched in patients with AMD, whereas Bacteroides eggerthii was enriched in controls. Patient's intestinal microbiomes were enriched in genes of the L-alanine fermentation, glutamate degradation and arginine biosynthesis pathways and decreased in genes of the fatty acid elongation pathway. These findings suggest that modifications in the intestinal microbiome are associated with AMD, inferring that this common sight threatening disease may be targeted by microbiome-altering interventions.
Isolation of trilobatin, a sweet dihydrochalcone-glucoside from leaves of Vitis piasezkii MAXIM. and V. saccharifera MAKINO. (1983)

As part of our China-Japan co-operative studies on the biologically active principles of Chinese wild plants, the isolation and identification of the following sweet glycosides have been reported: rubusoside (steviol-bisglucoside) from Chinese Rubus chigii Hu, Chinese name "Tian-Liang-Cha" (Rosaceae)^; Baiyunoside (a new labdane
Care of the premature infant: Part I. Monitoring growth and development. (1998)

When monitoring growth and development in the premature infant, physicians should make adjustments for the estimated due date. With minor exceptions, administration of immunizations is based on the chronologic age. Administration of hepatitis B vaccine should be delayed until the infant weighs 2,000 g (4 lb, 5 oz). Administration of influenza vaccine should be considered in infants with chronic medical problems, and the pneumococcal vaccine may be beneficial at age two in children with chronic problems, especially pulmonary disease. Premature infants should also be monitored to assure appropriate nutrition. Breast-fed infants should probably receive vitamin supplements during the first year. Supplemental iron should be initiated at two weeks to two months after birth and continued for 12 to 15 months. Office care includes screening for problems that occur more frequently in premature infants, especially vision and hearing problems. Because many of these infants require care from multiple medical disciplines, coordination of care is another important role for the family physician. The goals of this care are to promote normal growth and development and minimize morbidity and mortality.
Active measurement and analysis of delay time in the Internet (2003)

This paper analyzes the delay time distribution in the Internet. We send sample packets with a time stamp to measure the delay time. It is well known that the delay time in communication links follows the exponential distribution. However, the earlier models cannot explain the distribution when a communication link is heavily overloaded. This paper proposes to use a new model for the Internet. We have applied our model to the measurement results successfully.
Low dark current InGaAs/InAlAs/InP avalanche photodiode (2009)

The performance of uncooled InGaAs/InAlAs/InP avalanche photodiodes operating near 1.5 μm has been studied theoretically. Device modelling based on advanced drift and diffusion model with commercial software, the Crosslight APSYS, has been performed. Separate absorption, grading, charge and multiplication avalanche photodiodes with a relatively thick undepleted p-type InGaAs absorption region and thin InAlAs multiplication layer have been considered. Basic physical quantities like band diagram, optical absorption and generation have been calculated. Performance characteristics such as dark- and photo-current, photo-responsivity, multiplication gain, breakdown voltage, excess noise, frequency response and bandwidth have been simulated. Device design optimisation issues have been discussed with respect to the applicable features of the Crosslight APSYS within the framework of drift-diffusion theory. The modelling results are selectively presented and analysed. Simulations of avalanche photodiode structures enable one to increase the device quantum efficiency, reduce the dark current and eliminate impact ionization processes within absorbing layer.
Prognostic value of <i>KRAS</i> mutation in advanced non-small-cell lung cancer treated with immune checkpoint inhibitors: A meta-analysis and review (2017)

Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment option in the fight against advanced non-small-cell lung cancer (NSCLC). KRAS is the most frequently mutated oncogene in NSCLC. We performed this meta-analysis to investigate if KRAS mutation status affects survival benefits of ICIs in patients with advanced NSCLC. Electronic databases were searched for eligible studies. We included randomized trials with the data of overall survival stratified by KRAS mutation status. From 3 eligible studies, 138 patients with KRAS mutant NSCLC and 371 with KRAS wild-type tumor were included in the meta-analysis. Compared to chemotherapy with docetaxel, ICIs improved overall survival in patients with previously treated KRAS mutant NSCLC (hazard ratio = 0.64 [95% confidence interval, 0.43-0.96], P = 0.03). For patients with KRAS wild-type NSCLC, however, ICIs did not prolong overall survival over that with chemotherapy (hazard ratio = 0.88 [95% confidence interval, 0.68-1.13], P = 0.30). In conclusion, ICIs as a salvage therapy improved overall survival over that with docetaxel in advanced NSCLC patients with KRAS mutation, but not in those with KRAS wild-type tumor. These results suggest that KRAS mutation status may be a potential biomarker for survival benefits to ICIs.
Charlie Rides the Elevator -- Integrating Vision, Navigation and Manipulation towards Multi-floor Robot Locomotion (2013)

This paper presents the design, implementation and experimental evaluation of a semi-humanoid robotic system for autonomous multi-floor navigation. This robot, a Personal Robot 2 named Charlie, is capable of operating an elevator to travel between rooms located on separate floors. Our goal is to create a robotic assistant capable of locating points of interest, manipulating objects, and navigating between rooms in a multi-storied environment equipped with an elevator. Taking the elevator requires the robot to (1) map and localize within its operating environment, (2) navigate to an elevator door, (3) press the up or down elevator call button, (4) enter the elevator, (5) press the control button associated with the target floor, and (6) exit the elevator at the correct floor. To that end, this work integrates the advanced sensorimotor capabilities of the robot - laser range finders, stereo and monocular vision systems, and robotic arms - into a complete, task-driven autonomous system. While the design and implementation of individual sensorimotor processing components is a challenge in and of itself, complete integration in intelligent systems design often presents an even greater challenge. This paper presents our approach towards designing the individual components, with focus on machine vision, manipulation, and systems integration. We present and discuss quantitative results of our live robotic system, discuss difficulties faced and expose potential pitfalls.