gebhart/patrepeval huggingface dataset:
Consistent global structures of complex RNA states through multidimensional chemical mapping (2015)

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.
Robust 3D head tracking under partial occlusion (2002)

This paper describes a novel system for 3D head tracking under partial occlusion from 2D monocular image sequences. In this system, the extended superquadric (ESQ) is used to generate a geometric 3D face model in order to reduce the shape ambiguity. Optical flow is then employed with this model to estimate the 3D rigid motion. To deal with occlusion, a new motion segmentation algorithm using motion residual error analysis is developed. The occluded areas are successfully detected and discarded as noise by the system. Also, accumulation error is heavily reduced by a new post-regularization process based on edge flow. This makes the system more stable over long occlusion image sequences. To show the accuracy, the system is applied on a synthetic occlusion sequence and comparisons with the ground truth are reported. To show the robustness, experiments on long occlusion image sequences, including synthetic and real ones, are reported.
Alkaline-Earth-Metal Atoms as Few-Qubit Quantum Registers (2009)

We propose and analyze a novel approach to quantum information processing, in which multiple qubits can be encoded and manipulated using electronic and nuclear degrees of freedom associated with individual alkaline-earth-metal atoms trapped in an optical lattice. Specifically, we describe how the qubits within each register can be individually manipulated and measured with subwavelength optical resolution. We also show how such few-qubit registers can be coupled to each other in optical superlattices via conditional tunneling to form a scalable quantum network. Finally, potential applications to quantum computation and precision measurements are discussed.
VEGF expression in an osteoblast-like cell line is regulated by a hypoxia response mechanism (2000)

Angiogenesis is essential for the increased delivery of oxygen and nutrients required for the reparative processes of bone healing. Vascular endothelial growth factor (VEGF), a potent angiogenic growth factor, has been implicated in this process. We have previously shown that hypoxia specifically and potently regulates the expression of VEGF by osteoblasts. However, the molecular mechanisms governing this interaction remain unknown. In this study, we hypothesized that the hypoxic regulation of VEGF expression by osteoblasts occurs via an oxygen-sensing mechanism similar to the regulation of the erythropoietin gene (EPO). To test this hypothesis, we examined the kinetics of oxygen concentration on osteoblast VEGF expression. In addition, we analyzed the effects of nickel and cobalt on the expression of VEGF in osteoblastic cells because these metallic ions mimic hypoxia by binding to the heme portion of oxygen-sensing molecules. Our results indicated that hypoxia potently stimulates VEGF mRNA expression. In addition, we found that nickel and cobalt both stimulate VEGF gene expression in a similar time- and dose-dependent manner, suggesting the presence of a hemelike oxygen-sensing mechanism similar to that of the EPO gene. Moreover, actinomycin D, cycloheximide, dexamethasone, and mRNA stabilization studies collectively established that this regulation is predominantly transcriptional, does not require de novo protein synthesis, and is not likely mediated by the transcriptional activator AP-1. These studies demonstrate that hypoxia, nickel, and cobalt regulate VEGF expression in osteoblasts via a similar mechanism, implicating the involvement of a heme-containing oxygen-sensing molecule. This may represent an important mechanism of VEGF regulation leading to increased angiogenesis in the hypoxic microenvironment of healing bone.
Differences in the Expression Pattern of P-Glycoprotein and MRP1 in Low-Grade and High-Grade Gliomas (2008)

Multidrug resistance in gliomas is the major challenges in the clinical setting. We investigated the expression of P-glycoprotein (Pgp) and multidrug resistance-related protein 1 (MRP1) in 50 gliomas using immunohistochemistry. Compared to Pgp, MRP1 positivity was observed in highest percentage of gliomas grade IV samples (p = 0.008). Unlike MRP1 expression observed in high-grade, gliomas grade II exhibited a greater number of Pgp positive samples as compared to grades III and IV (p = 0.026). Our results suggest that the difference between the histological grade gliomas regarding MRP1 and Pgp expression must have implications in the choice of chemotherapeutic protocols.
Camera space volumetric shadows (2012)

We transform irregularly sampled shadow map data to deep image buffers in camera space, which are then used to create volumetric shadows in a deep compositing workflow. Our technique poses no restrictions on the sample locations of the shadow map and can thus be used with a variety of adaptive approaches to produce more precise shadows closer to the camera. To construct watertight shafts towards the light source forming crepuscular rays, we use a two-dimensional quad tree in light space. This structure is constructed from the shadow samples independent of the camera position, making stereo renders and camera animations for static light sources and geometry more efficient. The actual integration of volumetric light transport is then left to a fast image space deep compositing workflow, enabling short turnaround times for cinematic lighting design. We show a simple scalable ray tracing kernel to convert the quad tree representation to a deep image for each camera, where ray tracing takes only 25% of the processing time.
Translation of the human genome into clinical allergy, part 2 (2004)

After completion of sequencing of the human genome, you will no longer be able to discover a new gene and may not be able to find a new molecule in the human body. Instead, you may find many new molecule networks. It will be possible to select information obtained from animal models just where orthologous genes are functioning similarly. Mouse disease models will not be used any longer where key orthologous genes are working differently than in humans. Analysis of cell type-selective transcripts from database searches is now available to minimize the efforts required for drug discovery. As such, it will soon be possible to use computational modeling to analyze integrative biological function and to test hypotheses without performing any in vivo or in vitro experimentation. However, before establishing a system simulating the human body, which consists of a variety of organs, which further consist of various types of cells, which then consist of various types of proteins, which consist of 20 types of amino acids, there are many steps that need to be understood.
p27 Expression, a cyclin dependent kinase inhibitor in breast carcinoma. (1999)

p27 KIP1 is a cyclin dependent kinase inhibitor, which may act as a potential suppressor gene. Several lines of evidence support the hypothesis that reduced p27 KIP1 expression is related to uncontrolled cell proliferation and tumorigenesis. Low immunohistochemical expression of p27 KIP1 in human neoplasm seems related to tumor progression and poor prognosis. In breast cancer, low p27 is associated with high tumour grade and loss of oestrogen receptor, and it has been suggested that low p27 KIP1 is a powerful and independent prognostic marker of poor clinical outcome. There are however some discrepant results: a few studies, some of which conducted on large series of patients, do not support an independent role of p27 KIP1 as a prognostic marker. We are indeed faced with an intriguing hypothesis, but many more studies are needed to evaluate the real value of p27 KIP1 as a prognostic marker.
Known User Continuous Authentication System for Consumer Application Software (2010)

This paper presents KUCAS (Known User Continuous Authentication System), a work-in-progress security system, that has a continuous authentication mechanism of users/consumers. The KUCAS system makes use of environmental context information, users behavior analysis, the behavior theories of Skinner and the Mathematical Confidence of Dempster-Shafer Evidences Theory, that establishes trust levels to authenticate the user by his behavior analysis, during an application software, in a specific domain of the computer networks, in a period of time. The dynamics of enclosed management in this system compares the current behavior with the user's previous behaviors description and with the trust restrictions. In case of indications of changes in the user's behavior, the system provides the behavior analysis of the user using database restrictions information. If there are uncertainties and divergences, mechanisms of security and alert signals are triggered.
Using computerized games to teach face recognition skills to children with autism spectrum disorder: the <i>Let’s Face It!</i> program (2010)

These results indicate that a relatively short-term intervention program can produce measurable improvements in the face recognition skills of children with autism. As a treatment for face processing deficits, the Let's Face It! program has advantages of being cost-free, adaptable to the specific learning needs of the individual child and suitable for home and school applications.
FSGS permeability factor-associated nephrotic syndrome: remission after oral galactose therapy (2009)

Some cases of nephrotic syndrome in focal and segmental glomerulosclerosis (FSGS) are associated with a circulating factor, the FSGS permeability factor (FSPF). Galactose has a high affinity for FSPF, and experimental data suggest that it could reduce its activity. We describe the case of a 48-year-old male with a nephrotic syndrome found to be resistant to corticosteroids, immunosuppression and plasmaphaeresis. The patient was given oral galactose as a last resort treatment, which was followed by a remission of his nephrotic syndrome that correlated with a reduction of FSPF activity. This case is the first report of a long-standing remission of an FSPF-associated nephrotic syndrome on oral galactose therapy.
PET scanning with hydroxyephedrine: an approach to the localization of pheochromocytoma. (1992)

Pheochromocytomas are potentially curable causes of hypertension. These tumors are currently located by functional imaging with meta-iodobenzylguanidine (MIBG), usually labeled with 131I, or anatomic imaging (computed tomography, magnetic resonance). Hydroxyephedrine (HED) is a newly developed radiotracer that concentrates in adrenergic nerve terminals. When HED is labeled with 11C, its distribution can be mapped in vivo using PET. The purposes of this investigation were to characterize the uptake of 11C-HED in pheochromocytoma and to determine the feasibility and advantages of utilizing this compound as a tumor imaging agent. Ten patients with known or suspected pheochromocytoma were studied. Each patient underwent PET scanning with 11C-HED and conventional scintigraphy with MIBG. Pheochromocytomas were localized by PET scanning in 9 of the 10 patients. Image quality was excellent and superior to that obtained from planar and tomographic MIBG studies. The uptake of 11C-HED into pheochromocytomas was rapid; tumors were evident within 5 min following intravenous injection. All lesions within the field of view that were identified by MIBG scintigraphy were readily apparent. PET scanning with 11C-HED localizes pheochromocytoma using a specifically designed radiotracer and advanced imaging technology. The method has promise for locating the more elusive tumors.
Bacterial Degradation of Cyanide and Its Metal Complexes under Alkaline Conditions (2005)

A bacterial strain able to use cyanide as the sole nitrogen source under alkaline conditions has been isolated. The bacterium was classified as Pseudomonas pseudoalcaligenes by comparison of its 16S RNA gene sequence to those of existing strains and deposited in the Coleccion Espanola de Cultivos Tipo (Spanish Type Culture Collection) as strain CECT5344. Cyanide consumption is an assimilative process, since (i) bacterial growth was concomitant and proportional to cyanide degradation and (ii) the bacterium stoichiometrically converted cyanide into ammonium in the presence of l-methionine-d,l-sulfoximine, a glutamine synthetase inhibitor. The bacterium was able to grow in alkaline media, up to an initial pH of 11.5, and tolerated free cyanide in concentrations of up to 30 mM, which makes it a good candidate for the biological treatment of cyanide-contaminated residues. Both acetate and d,l-malate were suitable carbon sources for cyanotrophic growth, but no growth was detected in media with cyanide as the sole carbon source. In addition to cyanide, P. pseudoalcaligenes CECT5344 used other nitrogen sources, namely ammonium, nitrate, cyanate, cyanoacetamide, nitroferricyanide (nitroprusside), and a variety of cyanide-metal complexes. Cyanide and ammonium were assimilated simultaneously, whereas cyanide strongly inhibited nitrate and nitrite assimilation. Cyanase activity was induced during growth with cyanide or cyanate, but not with ammonium or nitrate as the nitrogen source. This result suggests that cyanate could be an intermediate in the cyanide degradation pathway, but alternative routes cannot be excluded.
The Identification of an 18,000-Molecular-Weight Antigen Specific to Big Liver and Spleen Disease (1995)

Big liver and spleen (BLS) disease is an infectious syndrome of broiler breeders that has been serologically diagnosed worldwide with the agar gel immunodiffusion test. Liver homogenate from an affected broiler breeder was used as the antigen source in this study. This paper reports the identification, from liver, of a soluble basic protein antigen (molecular weight 18,000) that is specific to BLS disease. The antigen was partially purified from soluble extract of liver using a two-step fractionation procedure comprising Sephacryl S200 gel filtration and carboxymethyl (CM) cellulose cation exchange. After cation exchange, the partially purified (CM) antigen contained approximately 12 proteins. Immunoblotting was used to identify the single BLS disease-specific antigen. In addition, a polyclonal rabbit antiserum raised to the CM antigen was found to be monospecific to the 18,000-molecular-weight antigen by immunoblotting on the CM antigen. This serum was also of use in specifically detecting intracellular BLS disease antigen in frozen cryostat sections by indirect immunofluorescence.
Beneficial Effects of Streptokinase on Left Ventricular Function After Myocardial Reoxygenation and Reperfusion Following Global Ischemia in the Isolated Rabbit Heart (1984)

To determine the effect of streptokinase on the ischemic myocardium independent of its effects on the occluding thrombus, the isolated rabbit heart, perfused with Krebs-Henseleit solution, was subjected to a 45-min period of ischemia--83% reduction in myocardial (perfusion) flow--plus anoxia (95% N2 and 5% CO2), followed by restoration of perfusion and reoxygenation. Streptokinase, 75 or 150 IU/min, was infused starting 15 min before reperfusion and continuing for 30 min after reperfusion. Compared with the control group, streptokinase was associated during reperfusion with a significant dose-dependent greater restoration or smaller depression of ventricular function, dP/dt, and developed pressure. To determine if streptokinase effects were mediated during the ischemic or reperfusion phase, the high streptokinase dose was administered in either the last 30 min of the ischemia or the first 30 min of reperfusion. The improvement in recovery of left ventricular function was primarily in the group having streptokinase administered only during the ischemic period. Thus, streptokinase affects the ischemic myocardium so that there is an acceleration in the recovery of ventricular function or a reduction of the impairment in ventricular function during myocardial reperfusion.
An Ultra Fast Fixed Frequency Buck Converter with Maximum Charging Current Control and Adaptive Delay Compensation for DVS Applications (2007)

A buck converter with maximum charging current control in achieving high tracking speed is presented. An adaptive delay compensation scheme is employed to keep the switching frequency at 850kHz within ±2.5% across the whole operation range. The integrated buck converter was fabricated using a 0.35μm CMOS process and all functions are verified by extensive measurements.
Contribution of a Novel Gene, <i>rpeA</i> , Encoding a Putative Autotransporter Adhesin to Intestinal Colonization by Rabbit-Specific Enteropathogenic <i>Escherichia coli</i> (2007)

Rabbit-specific enteropathogenic Escherichia coli (REPEC) is an attaching and effacing pathogen of young rabbits. Using signature-tagged mutagenesis, we identified several known colonization factors of REPEC as well as a gene predicted to encode a novel autotransporter protein. This novel gene was termed rpeA for REPEC plasmid-encoded autotransporter.
CRT And LCD Projection TV: A Comparison (1989)

Advances in performance of projection CRTs, electronic processing and lens and screen technology have brought CRT projection TV systems into a rapidly growing number of consumer homes. A reduction in cost of these systems will further stimulate their application. Also a demand exists for improved definition display systems; a number of new standards for improved definition TV have been proposed in recent years [1]. A large video screen ( > 37") enhances the emotional link with the viewer; more image details can be resolved by human vision. Projection TV technology can combine the attractiveness of a large TV screen with good picture quality and ease of installation. Two projection technologies, CRT projection and LCD projection, have been developed for the purpose of consumer TV display.
Sudden Sensorineural Hearing Loss (2011)

Sudden sensorineural hearing loss (SSNHL) is commonly encountered in audiologic and otolaryngologic practice. SSNHL is most commonly defined as sensorineural hearing loss of 30 dB or greater over at least three contiguous audiometric frequencies occurring within a 72-hr period. Although the differential for SSNHL is vast, for the majority of patients an etiologic factor is not identified. Treatment for SSNHL of known etiology is directed toward that agent, with poor hearing outcomes characteristic for discoverable etiologies that cause inner ear hair cell loss. Steroid therapy is the current mainstay of treatment of idiopathic SSNHL in the United States. The prognosis for hearing recovery for idiopathic SSNHL is dependent on a number of factors including the severity of hearing loss, age, presence of vertigo, and shape of the audiogram.
Upper-bound approximations for dynamic pruning (2011)

Dynamic pruning strategies for information retrieval systems can increase querying efficiency without decreasing effectiveness by using upper bounds to safely omit scoring documents that are unlikely to make the final retrieved set. Often, such upper bounds are pre-calculated at indexing time for a given weighting model. However, this precludes changing, adapting or training the weighting model without recalculating the upper bounds. Instead, upper bounds should be approximated at querying time from various statistics of each term to allow on-the-fly adaptation of the applied retrieval strategy. This article, by using uniform notation, formulates the problem of determining a term upper-bound given a weighting model and discusses the limitations of existing approximations. Moreover, we propose an upper-bound approximation using a constrained nonlinear maximization problem. We prove that our proposed upper-bound approximation does not impact the retrieval effectiveness of several modern weighting models from various different families. We also show the applicability of the approximation for the Markov Random Field proximity model. Finally, we empirically examine how the accuracy of the upper-bound approximation impacts the number of postings scored and the resulting efficiency in the context of several large Web test collections.
Toughening of crosslinked polystyrene with liquid rubber (2001)

Abstract The optimum conditions for preparing poly(styrene‐ co ‐divinylbenzene) were determined and the variation of the mechanical properties of the networks with the crosslinking density was evaluated. The molecular weight between crosslinks was in the 800–12,000 range. The flexural modulus and flexural strength were 5000 and 110 MPa, respectively, for the more crosslinked materials. When liquid rubber (hydroxyl‐terminated polybutadiene) was incorporated into the glassy matrix, these values dropped to 2500 and 70 MPa, respectively, but the impact resistance increased to 70 J/m. These values were comparable to some commercial grade high impact polystyrene resins. The particle size of the dispersed rubber phase was on the nanometer scale, and attempts to increase its dimensions should provide further improvement in the impact properties. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 82: 2098–2105, 2001
Phase I study of SU5416, a small molecule inhibitor of the vascular endothelial growth factor receptor (VEGFR) in refractory pediatric central nervous system tumors (2008)

SU5416 is a novel small molecule tyrosine kinase inhibitor of the VEGF receptors 1 and 2. A phase I dose escalation study stratified by concurrent use (stratum II) or absence (stratum I) of enzyme-inducing anticonvulsant drugs was undertaken to estimate the maximum-tolerated dose (MTD) and to describe the toxicity profile of SU5416 in pediatric patients with refractory brain tumors. Dose escalations were conducted independently for stratum I starting at 110 mg/m(2) while stratum II started at 48 mg/m(2). Thirty-three eligible patients were treated on stratum I (n = 23) and stratum II (n = 10). Tumor types included 23 glial tumors, 4 neural tumors, 4 ependymomas, and 2 choroid plexus carcinomas. The MTD in stratum I was initially estimated to be 110 mg/m(2). The protocol was amended to determine the MTD after excluding transient AST elevation. Re-estimation of the MTD began at the 145 mg/m(2) dose level but due to development of SU5416 being stopped by the sponsor, the trial was closed before completion. The most serious drug-related toxicities were grade 3 liver enzyme abnormalities, arthralgia, and hallucinations. The plasma pharmacokinetics of SU5416 was not significantly affected by the concurrent administration of enzyme-inducing anticonvulsant drugs. Mean values of the total body clearance, apparent volume of distribution, and terminal phase half-life of SU5416 for the 19 patients in stratum I were 26.1 +/- 12.5 l/hr/m(2), 41.9 +/- 21.4 l/m(2), and 1.11 +/- 0.41 hr, respectively. The plasma pharmacokinetics of SU5416 in children was similar to previously reported findings in adult cancer patients. Prolonged disease stabilization was observed in 4 of 16 stratum I patients.