gebhart/patrepeval huggingface dataset:
MetaFinder: A meta-search engine with an open architecture (2005)

A profile of exon-intron lengths in genes shows a normal distribution. This observation suggests that different genes may have portions of their total exon and/or intron lengths in common. In order to explore the common exon-intron structural patterns that may arise due to common lengths across genes, we compared the exon-intron length patterns of annotated human genes. We discovered 1762278 conserved arrangements of exon-intron length across the otherwise unrelated and diverse genomic landscape. The existence of common exon-intron length patterns across unrelated genes suggests for their role of in gene assemblage and human genome design and architecture.
A Case-Based Reasoning Application for Engineering Sales Support Using Introspective Reasoning (2000)

This paper describes the implementation of a case-based reasoning application that supports engineering sales staff. The application is distributed and operates on the world wide web using the XML standard as a communications protocol between client and server side Java applets. The paper describes the distributed architecture of the operational prototype, the two case retrieval techniques used, its implementation, trial, and subsequent improvements to its architecture and retrieval techniques using introspective reasoning to improve retrieval efficiency. Introduction Western Air is a distributor of HVAC (heating, ventilation and air conditioning systems in Australia with a turnover in 1997 of $25 million (US dollars). Based in Fremantle the company operates mainly in Western Australia, a geographic area of nearly two million square miles. The systems supported range from simple residential HVAC systems to complex installations in new build and existing factories and office...
Solution Structure of a DNA Complex with the Fluorescent Bis-Intercalator TOTO Determined by NMR Spectroscopy (1995)

We have used two-dimensional 1H NMR spectroscopy to determine the solution structure of the DNA oligonucleotide d(5'-CGCTAGCG-3')2 complexed with the bis-intercalating dye 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-(3-methyl -2,3- dihydrobenzo-1,3-thiazolyl-2-methylidene)qui nolinium] tetraiodide (TOTO). The determination of the structure was based on total relaxation matrix analysis of the NOESY cross-peak intensities using the program MARDIGRAS. Improved procedures to consider the experimental "noise" in NOESY spectra during these calculations have been employed. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the TOTO complex from both A-form and B-form dsDNA starting structures. The root-mean-square (rms) deviation of the coordinates for the 40 structures of the complex was 1.45 A. The local DNA structure is distorted in the complex. The helix is unwound by 60 degrees and has an overall helical repeat of 12 base pairs, caused by bis-intercalation of TOTO. The poly(propylenamine) linker chain is located in the minor groove of dsDNA. Calculations indicate that the benzothiazole ring system is twisted relative to the quinoline in the uncomplexed TOTO molecule. The site selectivity of TOTO for the CTAG-CTAG site is explained by its ability to adapt to the base pair propeller twist of dsDNA to optimize stacking and the hydrophobic interaction between the thymidine methyl group and the benzothiazole ring. There is a 3000-fold fluorescence enhancement upon binding of TOTO to dsDNA. Rotation about the cyanine methine bonds is possible in free TOTO, allowing relaxation nonradiatively. When bound to dsDNA, the benzothiazole ring and the quinolinium ring are clamped by the nucleobases preventing this rotation, and the chromophore loses excitation energy by fluorescence instead.
Uncalibrated motion capture exploiting articulated structure constraints (2002)

We present an algorithm for 3D reconstruction of dynamic articulated structures, such as humans, from uncalibrated multiple views. The reconstruction exploits constraints associated with a dynamic articulated structure, specifically the conservation over time of length between rotational joints. These constraints admit metric reconstruction from at least two different images in each of two uncalibrated parallel projection cameras. The algorithm is based on a stratified approach, starting with affine reconstruction from factorization, followed by rectification to metric structure using the articulated structure constraints. The exploitation of these specific constraints allows reconstruction and self-calibration with fewer feature paints and views compared to standard self-calibration. The method is extended to pairs of cameras that are zooming, Where calibration of the cameras allows compensation for the changing scale factor in a scaled orthographic camera. Results are presented in the form of stick figures and animated 3D reconstructions using pairs of sequences from broadcast television. The technique shows promise as a means of creating 3D animations of dynamic activities such as sports events.
Highly Stable and Reusable Multimodal Zeolite TS‐1 Based Catalysts with Hierarchically Interconnected Three‐Level Micro–Meso–Macroporous Structure (2011)

Eine Quasi-Festkörperkristallisation ergab TS-1-Zeolithkatalysatoren mit mikro-meso-makroporöser (MMM) Struktur (siehe Bild) und erhöhter Stabilität. Sie haben eine definierte makroporöse Struktur und ein ineinandergreifendes mesoporöses Netzwerk aus einheitlichen TS-1-Nanokristallen. Die hierarchische Porenstruktur und hohe Stabilität führen zu einer überlegenen katalytischen Aktivität bei der Epoxidierung relativ großer Moleküle wie 2,4,6-Trimethylstyrol.
A new active cavitation mapping technique for pulsed HIFU applications-bubble doppler (2014)

In this work, a new active cavitation mapping technique for pulsed high-intensity focused ultrasound (pHIFU) applications termed bubble Doppler is proposed and its feasibility is tested in tissue-mimicking gel phantoms. pHIFU therapy uses short pulses, delivered at low pulse repetition frequency, to cause transient bubble activity that has been shown to enhance drug and gene delivery to tissues. The current gold standard for detecting and monitoring cavitation activity during pHIFU treatments is passive cavitation detection (PCD), which provides minimal information on the spatial distribution of the bubbles. B-mode imaging can detect hyperecho formation, but has very limited sensitivity, especially to small, transient microbubbles. The bubble Doppler method proposed here is based on a fusion of the adaptations of three Doppler techniques that had been previously developed for imaging of ultrasound contrast agents-color Doppler, pulse-inversion Doppler, and decorrelation Doppler. Doppler ensemble pulses were interleaved with therapeutic pHIFU pulses using three different pulse sequences and standard Doppler processing was applied to the received echoes. The information yielded by each of the techniques on the distribution and characteristics of pHIFU-induced cavitation bubbles was evaluated separately, and found to be complementary. The unified approach-bubble Doppler-was then proposed to both spatially map the presence of transient bubbles and to estimate their sizes and the degree of nonlinearity.
Cytoprotective Role of Ca <sup>2+</sup> - Activated K <sup>+</sup> Channels in the Cardiac Inner Mitochondrial Membrane (2002)

Ion channels on the mitochondrial inner membrane influence cell function in specific ways that can be detrimental or beneficial to cell survival. At least one type of potassium (K+) channel, the mitochondrial adenosine triphosphate-sensitive K+ channel (mitoKATP), is an important effector of protection against necrotic and apoptotic cell injury after ischemia. Here another channel with properties similar to the surface membrane calcium-activated K+ channel was found on the mitochondrial inner membrane (mitoKCa) of guinea pig ventricular cells. MitoKCa significantly contributed to mitochondrial K+ uptake of the myocyte, and an opener of mitoKCa protected hearts against infarction.
CELP speech coding based on an adaptive pulse position codebook (1999)

CELP coders using pulse codebooks for excitations such as ACELP have the advantages of low complexity and high speech quality. At low bit rates, however, the decrease of pulse position candidates and the number of pulses degrades reconstructed speech quality. This paper describes a method for adaptively allocating of pulse position candidates. In the proposed method, N efficient candidates of pulse positions are selected out of all possible positions in a subframe. The amplitude envelope of an adaptive code vector is used for selecting N efficient candidates. The larger the amplitude is, the more pulse positions are assigned. Using an adaptive code vector for the adaptation, the proposed method requires no additional bits for the adaptation. Experimental results show that the proposed method increases WSNRseg by 0.3 dB and MOS by 0.15.
Anti-Inflammatory, Antithrombotic, and Neuroprotective Effects of Activated Protein C in a Murine Model of Focal Ischemic Stroke (2001)

APC exerts anti-inflammatory, antithrombotic, and neuroprotective effects in stroke. Central effects of APC are likely to be related to improved maintenance of the blood-brain barrier to neutrophils and to reduced microvascular obstructions and fibrin deposition.
High performance multimode interference couplers for coherent communications in silicon (2011)

We review the need for coherent optical communication systems and briefly describe the receiver frontend they require.
The key element of the receiver is an optical 90° hybrid, which combines the received signal with the local oscillator
laser with the adequate amplitude and phase relations. Silicon technology offers several advantages for the realization of
such devices: compactness and CMOS compatibility, among others. However, the realization of high-performance
hybrids is hampered by the high index contrast of this technology. We show that using multimode interference couplers
with fully etched access waveguides and a shallowly etched multimode region, ultra-compact, high performance 90° hybrids can be realized. We experimentally demonstrate a device with a phase error below 5° and a common mode
rejection ratio better than -20dBe in a ~50nm bandwidth.
Membrane-associated inhibitor of DNA synthesis in senescent human diploid fibroblasts: characterization and comparison to quiescent cell inhibitor. (1986)

Cell membranes prepared from senescent human diploid fibroblasts (HDF) inhibited entry into S phase by 35% when added to the medium of replicating young HDF. This membrane-associated inhibitory activity was (i) sensitive to trypsin, heat, and periodate, which suggests that the inhibitor is a glycoprotein, and (ii) not able to inhibit DNA synthesis in simian virus 40-transformed HDF, which indicates that not all types of cells are sensitive to this inhibitor. Quiescent young HDF also have a surface membrane-associated inhibitor of DNA synthesis. A comparison of the senescent HDF and quiescent HDF inhibitor activities indicates that they may have the same chemical and physical nature and the same specific activity, but their regulation is different. The inhibitory activity of quiescent young HDF is abolished within 20 hr after refeeding with fresh serum-containing medium, whereas that of senescent HDF remains unchanged. Quiescent old HDF (two or three population doublings remaining) exhibit an intermediate response to serum with approximately two-thirds of the inhibitory activity abolished. The fraction of cells in S phase at 20-24 hr post-stimulation (37% in young HDF, 24% in old HDF, and 0% in senescent HDF) is inversely proportional to inhibitor levels. This suggests that inability to neutralize the inhibitory activity in response to serum stimulation could be involved in the inability of senescent HDF to enter S phase. Disappearance of the inhibitory activity from quiescent young HDF occurs late in G1 phase. Thus, the inhibitor may play a role in determining the length of the G0 to S phase transition in these cells.
The herpes simplex virus virion host shutoff function (1989)

The virion host shutoff (vhs) function of herpes simplex virus (HSV) limits the expression of genes in the infected cells by destabilizing both host and viral mRNAs. vhs function mutants have been isolated which are defective in their ability to degrade host mRNA. Furthermore, the half-life of viral mRNAs is significantly longer in cells infected with the vhs-1 mutant virus than in cells infected with the wild-type (wt) virus. Recent data have shown that the vhs-1 mutation resides within the open reading frame UL41. We have analyzed the shutoff of host protein synthesis in cells infected with a mixture of the wt HSV-1 (KOS) and the vhs-1 mutant virus. The results of these experiments revealed that (i) the wt virus shutoff activity requires a threshold level of input virions per cell and (ii) the mutant vhs-1 virus protein can irreversibly block the wt virus shutoff activity. These results are consistent with a stoichiometric model in which the wt vhs protein interacts with a cellular factor which controls the half-life of cell mRNA. This wt virus interaction results in the destabilization of both host and viral mRNAs. In contrast, the mutant vhs function interacts with the cellular factor irreversibly, resulting in the increased half-life of both host and viral mRNAs.
Comparative analysis of striatal FDOPA uptake in Parkinson's disease: ratio method versus graphical approach. (2002)

These results suggest that SOR determined from a single 10-min scan at 95 min is as accurate as K(i)(occ) in separating PD patients from healthy subjects and in predicting clinical measures of disease severity.
Cutting Edge: TFII-I Controls B Cell Proliferation via Regulating NF-κB (2007)

The multifunctional transcription factor TFII-I physically and functionally interacts with Bruton's tyrosine kinase in murine B cells. However, the downstream functions of TFII-I in B cells are unknown. Toward achieving this goal, we established stable posttranscriptional silencing of TFII-I in WEHI-231 immature murine B cells, which undergoes growth arrest and apoptosis either upon anti-IgM or TGF-beta signaling. In this study, we show that TFII-I promotes growth arrest of cells in a signal-dependent manner. Unlike control cells, B cells exhibiting loss of TFII-I function fail to undergo arrest upon signaling due to up-regulation of c-Myc expression and concomitant down-regulation of both p21 and p27. Loss of TFII-I is also associated with simultaneous increase in nuclear c-rel and decrease in p50 homodimer binding. Thus, besides controlling c-myc transcription, TFII-I controls B cell proliferation by regulating both nuclear translocation of c-rel and DNA-binding activity of p50 NF-kappaB.
Application of spacer filled silicone die adhesive in stacked chip technology (2003)

The increasing demand for feature content of portable electronic products drives requirements for smaller volume and lower cost device packaging. This has, in turn, led to the packaging industry’s interest in stacked chip technology, especially for memory applications. The growth of stacked chip package technology drove development of specific die adhesives that combine low cost with controlled thickness, critical for wirebonding multiple layers. Silicone, as a die adhesive material, shows many beneficial properties such as low moisture absorption and thermal stability especially for lead free needs. In stacked chip packages with conventional wire bonding, a spacer is needed to provide controlled bond line thickness, to meet wire bonding and molding tolerances for thin packages. While preform sheets can be used to maintain bond line uniformity, they are not always as easy to use in high volume manufacturing as liquid adhesives. This paper discusses testing of a two chip simulated memory stack package using a liquid die adhesive material based on a flexible silicone filled with spacer beads. Attributes of the spacer filled silicone adhesive are discussed, effects of process parameters on bond line thickness are demonstrated, and resistance to humidity and thermal reliability are evaluated. Wire bonding results show this low modulus material can be reliably assembled in stack applications.
Monoclonal antibodies that inhibit attachment of group B coxsackieviruses (1983)

Hybridoma cell lines that secrete monoclonal antibodies which react with HeLa cell surface antigens were produced. The monoclonal antibodies prevented cytopathic effects caused by coxsackievirus B1 and significantly reduced the amounts of coxsackieviruses B1, B5, and B6 that absorb to HeLa cells. These antibodies did not protect the cells from poliovirus cytopathic effects, and they had no effect on the attachment of other picornaviruses to HeLa cells.
Flying Fast and Low Among Obstacles (2007)

Safe autonomous flight is essential for widespread acceptance of aircraft that must fly close to the ground. We have developed a method of collision avoidance that can be used in three dimensions in much the same way as autonomous ground vehicles that navigate over unexplored terrain. Safe navigation is accomplished by a combination of online environmental sensing, path planning and collision avoidance. Here we report results with an autonomous helicopter that operates at low elevations in uncharted environments some of which are densely populated with obstacles such as buildings, trees and wires. We have recently completed over 1000 successful runs in which the helicopter traveled between coarsely specified waypoints separated by hundreds of meters, at speeds up to 10 meters/sec at elevations of 5-10 meters above ground level. The helicopter safely avoids large objects like buildings and trees but also wires as thin as 6 mm. We believe this represents the first time an air vehicle has traveled this fast so close to obstacles. Here we focus on the collision avoidance method that learns to avoid obstacles by observing the performance of a human operator.
Influence of Egg Size, Eggshell Quality, and Posthatch Holding Time on Broiler Performance (1985)

Effect of egg size, eggshell quality, and posthatch holding time in the hatcher on broiler performance was studied in two experiments. Eggs from commercial broiler breeders with similar genetic backgrounds (stock within an experiment was obtained from a single primary breeder) were divided into two groups by egg size (47 to 54 g and 58 to 66 g) in Experiment 1 and by specific gravity (≤1.070 and ≥1.080) in Experiment 2 and incubated. The hatching sequence was divided into four periods such that 25% of the chicks hatched in each period. After all dry chicks in each period were removed and weighed, half of each group was returned to the hatcher and the rest held in chick boxes for 6 hr prior to placement in floor pens. All chicks, including those previously returned to the hatcher, were removed at 21.5 days, weighed, held for 6 hr in chick boxes, and then placed in floor pens. Broilers from large eggs were significantly heavier (2080 vs 1889 g) and had greater livability through 49 days of age than broiler, from small eggs. Feed efficiency was significantly better for broilers from small eggs (.549) than from large eggs (.518) at 49 days of age. The two specific gravities used in the second experiment had no effect on body weight or feed efficiency. Chicks held in incubator trays from 14 to 32 hr posthatch weighed 5 to 12% less than chicks removed an average of 7 hr after hatch, and the reduction persisted to 49 days of age. Body weight at 49 days was reduced by 1 to 2% in Experiment 1 and by 3 to 4% in Experiment 2 for chicks held in the hatcher compared with those removed earlier. No difference in feed efficiency or in mortality was found between hatch periods or between removal schedules.
Image analysis of 36 cases of renal angiomyolipomas (2011)

Objective Comprehensive analysis of renal angiomyolipomas imaging manifestations to improve the diagnostic accuracy.Methods Color Doppler ultrasound,CT,and MRI were used in 36 cases of renal angiomyolipoma to analyze the imaging manifestations.Results There were 51 tumors in all the 36 cases,out of which 25 cases were in the single side,12 in the left kidney and 13 in the right.There was no statistical difference(P 0.05).26 tumors in 11 cases were multiple.Of the 51 tumors,29 were highly echoed in the ultrasound test,15 presented mixed echo,and 7 equal low echo.CT scan showed low density in 31 persons,equal low density in 17 and high density in 3.Enhanced scanning saw nonhomogeneous enhancement and delayed enhancement in corticomedullary phase.7 cases(a total of 9 tumors) were examined by MRI.7 tumors presented high signal by T1WI,and 2 tumors medium signal.7 tumors showed high signal by T2WI,and 2 tumors equal or slightly lower signal,9 tumors in the T2WI fat suppression showed low signal or significantly lower signal.Conclusion Reasonable and combined use of ultrasound,CT and MRI can increase the diagnostic accuracy of renal angiomyolipoma and reduce the rate of missed diagnosis and misdiagnosis.
Learning random walk models for inducing word dependency distributions (2004)

Many NLP tasks rely on accurately estimating word dependency probabilities P(ω1|ω2), where the words w1 and w2 have a particular relationship (such as verb-object). Because of the sparseness of counts of such dependencies, smoothing and the ability to use multiple sources of knowledge are important challenges. For example, if the probability P(N|V) of noun N being the subject of verb V is high, and V takes similar objects to V', and V' is synonymous to V", then we want to conclude that P(N|V") should also be reasonably high---even when those words did not cooccur in the training data.To capture these higher order relationships, we propose a Markov chain model, whose stationary distribution is used to give word probability estimates. Unlike the manually defined random walks used in some link analysis algorithms, we show how to automatically learn a rich set of parameters for the Markov chain's transition probabilities. We apply this model to the task of prepositional phrase attachment, obtaining an accuracy of 87.54%.
Enhancement of Radiation Effects by Flavopiridol in Uterine Cervix Cancer Cells (2005)

Flavopiridol enhanced the effects of radiation on a uterine cervix cancer cell line in vitro, and this enhancement was both sequence- and time-dependent.
DNA and RNA Aptamers: From Tools for Basic Research Towards Therapeutic Applications (2006)

The systematic evolution of ligands by exponential enrichment (SELEX) is a combinatorial oligonucleotide library-based in vitro selection approach in which DNA or RNA molecules are selected by their ability to bind their targets with high affinity and specificity, comparable to those of antibodies. Nucleic acids with high affinity for their targets have been selected against a wide variety of compounds, from small molecules, such as ATP, to membrane proteins and even whole organisms. Recently, the use of the SELEX technique was extended to isolate oligonucleotide ligands, also known as aptamers, for a wide range of proteins of importance for therapy and diagnostics, such as growth factors and cell surface antigens. The number of aptamers generated as inhibitors of various target proteins has increased following automatization of the SELEX process. Their diagnostic and therapeutic efficacy can be enhanced by introducing chemical modifications into the oligonucleotides to provide resistance against enzymatic degradation in body fluids. Several aptamers are currently being tested in preclinical and clinical trials, and aptamers are in the process of becoming a new class of therapeutic agents. Recently, the anti-VEGF aptamer pegaptanib received FDA approval for treatment of human ocular vascular disease.