gebhart/patrepeval huggingface dataset:
Pattern Discovery and Classification in Biosequences (1999)

With the significant growth of the amount of biosequence data, it becomes increasingly important to develop new techniques for finding “knowledge” from the data. Pattern discovery is a fundamental operation in such applications. It attempts to find patterns in biosequences that can help scientists to analyze the property of a sequence or predict the function of a new entity. The discovered patterns may also help to classify an unknown sequence, that is, assign the sequence to an existing family. In this chapter, we show how to discover active patterns in a set of protein sequences and classify an unlabeled DNA sequence. We use protein sequences as an example to illustrate our discovery algorithm, though the algorithm applies to sequences of any sort, including both protein and DNA. The patterns we wish to discover within a set of sequences are regular expressions of the form *X1 * X2 * ... . The X1,X2,... are segments of a sequence, that is, subsequences made up of consecutive letters, and * represents a variable length don’t care (VLDC). In matching the expression *X1 * X2 * ... with a sequence S, the VLDCs may substitute for zero or more letters in S at zero cost. The dissimilarity measure used in comparing two sequences is the edit distance, that is, the minimum cost of edit operations used to transform one subsequence to the other after an optimal and zero-cost substitution for the VLDCs, where the edit operations include insertion, deletion, and change of one letter to another (Wagner and Fischer, 1974; K. Zhang et al., 1994). That is, we find a one-to-one mapping from each VLDC to a subsequence of the data sequence and from each pattern subsequence to a subsequence of the data sequence such that the following two conditions are satisfied, (i) The mapping preserves the left-to-right ordering (if a VLDC at position i in the pattern maps to a subsequence starting at position i1 and ending at position i2 in the data sequence, and a VLDC at position j in the pattern maps to a subsequence starting at position j1 and ending at position j2 in the data sequence, and i &lt; j, then i2 &lt; j2).
Colored-Gaussian Multiple Descriptions: Spectral and Time-Domain Forms (2015)

It is well known that Shannon's rate-distortion function (RDF) in the colored quadratic Gaussian (QG) case can be parametrized via a single Lagrangian variable (the water level in the reverse water filling solution). In this paper, we show that the symmetric colored QG multiple description (MD) RDF in the case of two descriptions can be parametrized in the spectral domain via two Lagrangian variables, which control the tradeoff between the side distortion, the central distortion, and the coding rate. This spectral-domain analysis is complemented by a time-domain scheme-design approach: we show that the symmetric colored QG MD RDF can be achieved by combining ideas of delta-sigma modulation and differential pulse-code modulation. In particular, two source prediction loops, one for each description, are embedded within a common noise-shaping loop, whose parameters are explicitly found from the spectral-domain characterization.
Better Shading for Better Shape Recovery (2014)

The basic idea of shape from shading is to infer the shape of a surface from its shading information in a single image. Since this problem is ill-posed, a number of simplifying assumptions have been often used. However they rarely hold in practice. This paper presents a simple shading-correction algorithm that transforms the image to a new image that better satisfies the assumptions typically needed by existing algorithms, thus improving the accuracy of shape recovery. The algorithm takes advantage of some local shading measures that have been driven under these assumptions. The method is successfully evaluated on real data of human teeth with ground-truth 3D shapes.
MicroRNA–mediated downregulation of potassium-chloride-cotransporter and vesicular γ-aminobutyric acid transporter expression in spinal cord contributes to neonatal cystitis–induced visceral pain in rats (2017)

Loss of GABAergic inhibition in pain pathways has been considered to be a key component in the development of chronic pain. In the present study, we intended to examine whether miR-92b-mediated posttranscriptional dysregulation of spinal potassium chloride cotransporter (KCC2) and vesicular γ-aminobutyric acid transporter (VGAT) plays a major role in the development and maintenance of long-term visceral hyperalgesia in neonatal zymosan-treated rats. Neonatal cystitis was induced by transurethral zymosan administration from postnatal (P) days 14 to 16 (protocol 1). Two other zymosan protocols were also used: adult rechallenge on P57 to 59 following neonatal P14 to 16 exposures (protocol 2), and adult zymosan exposures on P57 to 59 (protocol 3). Both neonatal and adult bladder inflammation protocols demonstrated an increase in spinal miR-92b-3p expression and subsequent decrease in KCC2 and VGAT expression in spinal dorsal horn neurons. In situ hybridization demonstrated a significant upregulation of miR-92b-3p in the spinal dorsal horn neurons of neonatal cystitis rats compared with saline-treated controls. In dual in situ hybridization and immunohistochemistry studies, we further demonstrated coexpression of miR-92b-3p with targets KCC2 and VGAT in spinal dorsal horn neurons, emphasizing a possible regulatory role both at pre- and post-synaptic levels. Intrathecal administration of lentiviral pLSyn-miR-92b-3p sponge (miR-92b-3p inhibitor) upregulated KCC2 and VGAT expression in spinal dorsal horn neurons. In behavioral studies, intrathecal administration of lentiviral miR-92b-3p sponge attenuated an increase in visceromotor responses and referred viscerosomatic hypersensitivity following the induction of cystitis. These findings indicate that miR-92b-3p-mediated posttranscriptional regulation of spinal GABAergic system plays an important role in sensory pathophysiology of zymosan-induced cystitis.
In-Situ Orientation Rotation Behavior Study during Tensile Deformation of Aluminum Single Crystal and Polycrystal (2004)

Orientation rotation behaviors taking place in aluminum single crystal and polycrystal were studied during uniaxial tensile deformation at room temperature. Specimens were elongated in an in-situ deformation stage equipped on a high resolution electron backscattered diffraction (HREBSD)system. A series of crystallographic evolution and deformation behavior of concerned areas in the specimens during deformation was directly analyzed using HR-EBSD.
Caracterização da organização do processo ofensivo em pólo aquático feminino de elite (2009)

The purpose of the present study was to analyze the attacking tasks and tactical organization of elite Women’s Water Polo. The sample consisted of 442 attack sequences of 8 games played by the top teams in a European Championship. Seventeen variables were analyzed according to the position and player’s participation, tactical organization and playing styles, as well as the efficacy of actions performed. The results from this study indicate that positional attack was the predominant performance factor in the attacking process. To this occurrence, the mixed floating defense was identified as the most frequent opposition. The counter-attack proved to be the most efficient strategy. The attacking process frequently started by ball recovering, in anticipation, and by the defense of the goal-keeper in the 2m zone. In central path, a first long-range pass to the right wing predominated. Teams preferred spontaneous shot on goal supported by assisted displacements, and extra player man offence situations. In general, the attacking sequences, do not take longer than 35s to be developed.) Teams efficiency emerged related to the tactical means adopted, namely the spontaneous shot at goal on the front line and numerical superiority of players in attacking game situations.
Hoopl (2010)

Dataflow analysis and transformation of control-flow graphs is pervasive in optimizing compilers, but it is typically entangled with the details of a particular compiler. We describe Hoopl, a reusable library that makes it unusually easy to define new analyses and transformations for any compiler written in Haskell. Hoopl's interface is modular and polymorphic, and it offers unusually strong static guarantees. The implementation encapsulates state-of-the-art algorithms (interleaved analysis and rewriting, dynamic error isolation), and it cleanly separates their tricky elements so that they can be understood independently.
Role of the Diphosphine Chelate in Emissive, Charge‐Neutral Iridium(III) Complexes (2017)

A class of neutral tris-bidentate Ir<sup>III</sup> metal complexes incorporating a diphosphine as a chelate is prepared and characterized here for the first time. Treatment of [Ir(dppBz)(tht)Cl<sub>3</sub> ] (1, dppBz=1,2-bis(diphenylphosphino)benzene, tht=tetrahydrothiophene) with fppzH (3-trifluoromethyl-5-(2'-pyridyl)-1H-pyrazole) afforded the dichloride complexes, trans-(Cl,Cl)[Ir(dppBz)(fppz)Cl<sub>2</sub> ] (2) and cis-(Cl,Cl)[Ir(dppBz)(fppz)Cl<sub>2</sub> ] (3). The reaction of 3 with the dianionic chelate precursor, 5,5'-di(trifluoromethyl)-3,3'-bipyrazole (bipzH<sub>2</sub> ) or 5,5'-(1-methylethylidene)-bis(3-trifluoromethyl-1H-pyrazole) (mepzH<sub>2</sub> ), in DMF gave the tris-bidentate complex [Ir(dppBz)(fppz)(bipz)] (4) or [Ir(dppBz)(fppz)(mepz)] (5), respectively. In contrast, a hydride complex [Ir(dppBz)(fppz)(bipzH)H] (6) was isolated instead of 4 in protic solvent, namely: diethylene glycol monomethyl ether (DGME). All complexes 2-6 are luminescent in powder form and thin films where the dichlorides (2, 3) emit with maxima at 590-627 nm (orange) and quantum yields (QYs) up to 90 % whereas the tris-bidentate (4, 5) and hydride (6) complexes emit at 455-458 nm (blue) with QYs up to 70 %. Hybrid (time-dependent) DFT calculations showed considerable metal-to-ligand charge transfer contribution to the orange-emitting 2 and 3 but substantial ligand-centered <sup>3</sup> π-π* transition character in the blue-emitting 4-6. The dppBz does not participate in the radiative transitions in 4-6, but it provides the rigidity and steric bulk needed to promote the luminescence by suppressing the self-quenching in the solid state. Fabrication of an organic light-emitting diode (OLED) with dopant 5 gave a deep-blue CIE chromaticity of (0.16, 0.15). Superior blue emitters, which are vital in OLED applications, may be found in other neutral Ir<sup>III</sup> complexes containing phosphine chelates.
NEW CALCIUM ALUMINATE CEMENT FOR REFRACTORY PRE-CAST SHAPE PRODUCTION (2021)

A new high alumina calcium aluminate cement (CAC) has been developed. It is called CA-SYNC. This 75% Al<sub>2</sub>O<sub>3</sub> cement has a well-controlled hydration behaviour which provides advantages especially for pre-cast shape production of items such as well blocks or EAF delta sections, which incorporate inner moulds or cores. The setting shrinkage, strength development and setting behaviour were investigated in a self-flow and a vibration castable. These properties were compared to the well-known 70% Al<sub>2</sub>O<sub>3</sub> cement CA-14 M. A much slower shrinkage rate was achieved with CA-SYNC. The strength development is initially slower, but continues for days resulting in higher strength levels. At dried temperatures, CA-SYNC also showed higher strength levels. After firing at temperatures of 1000°C or higher, comparable strength levels were obtained.
CTRP1: A Molecular Link between Obesity and Hypertension (2016)

Background: CTRP1, a recently identified adipokine, was found to stimulate aldosterone production. Serum CTRP1 and plasma Aldosterone levels were significantly increased in patients with diabetes mellitus and metabolic syndrome. Therefore, it would be interesting to investigate whether the secretion of CTRP1 in human serum is associated with hypertension as well as with diabetes mellitus.
Abstract 4043: Design of a novel MGMT inhibitor targeted to EGFR overexpressing tumor cells: a new approach to selectively potentiate temozolomide in refractory tumors (2017)

Abstract Temozolomide (TMZ) is an oral alkylating agent commonly used as a first-line chemotherapeutic agent for the treatment of high-grade gliomas and melanoma. Alkylation of the O6-position of guanine in DNA is mainly responsible for the antitumor effect of TMZ. The primary mechanism of chemoresistance to TMZ has been shown to be the overexpression of the DNA repair enzyme O6-methylguanine methyltransferase (MGMT) that specifically removes the methyl lesions from the O6-position of guanine. While O6-benzylguanine (O6-BG), a potent inhibitor of MGMT, was shown to sensitize tumor cells to TMZ in vitro and in vivo, the O6-BG+TMZ combination failed in clinical trial due to acute hematologic toxicity. To circumvent this problem, we wish to target O6-BG to the epidermal growth factor receptor (EGFR), a receptor that is not generally expressed in the hematological cells but overexpressed in many solid tumors. We have now successfully designed and synthesized one such molecule termed MR30 and showed that: 1) MR30 is capable of blocking EGFR and depleting MGMT levels in whole cells; 2) MR30 is a unique molecule capable of inducing stronger growth inhibition than the 2-drug combination involving clinical EGFR and MGMT inhibitors in a panel of melanoma, lung, prostate and ovarian cancer cell lines; 3) MR30 in vitro potentiated the effect of TMZ on MGMT positive cell lines; 4) its kinase inhibitory profiling over 25 different kinases demonstrated selectivity for EGFR, HER2 and EGFR mutant forms; 5) an isogenic model showed more than 70-fold selectivity towards EGFR expressing cells in growth inhibitory assay; 6) MR30 showed good cell penetration with distribution in the perinuclear region. The results in toto suggest that MR30 has the potential to be developed as a tumor selective potentiator of TMZ. Citation Format: Martin Rupp, Bertrand J. Jean-Claude. Design of a novel MGMT inhibitor targeted to EGFR overexpressing tumor cells: a new approach to selectively potentiate temozolomide in refractory tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4043. doi:10.1158/1538-7445.AM2017-4043
A Persuasive Mobile Learning System for Informal Learning of Vegetable Farmers (2018)

Technological developments have increased rapidly in recent years in various fields. In the field of agriculture, in particular, the use of mobile learning is still fairly rare for the dissemination of knowledge. Lack of information, interest, material conformity, interactivity, and awareness in using mobile learning becomes an issue in the field. Therefore, this research focuses on developing mobile learning system to increase enthusiasm, interest, and awareness of farmers by using instructional design, ADDIE (Analyze, Design, Development, Implementation, Evaluation) and persuasive system design. Based on the experimental results with the Technology Acceptance Model that represent farmers reaction in cognitive, affective and psychomotor aspects, it has been confirmed that from the use of twenty-four hypothetical variables that have been made, the seventeen hypothesis variables are positive. Predictions show that, with 95% confidence level, seventeen hypothesis variables support behavioral intention variable. Descriptive statistics shows that 70.4% of farmers agree to continue using mobile learning.
Compact Layers of Hybrid Halide Perovskites Fabricated via the Aerosol Deposition Process—Uncoupling Material Synthesis and Layer Formation (2016)

We present the successful fabrication of CH₃NH₃PbI₃ perovskite layers by the aerosol deposition method (ADM). The layers show high structural purity and compactness, thus making them suitable for application in perovskite-based optoelectronic devices. By using the aerosol deposition method we are able to decouple material synthesis from layer processing. Our results therefore allow for enhanced and easy control over the fabrication of perovskite-based devices, further paving the way for their commercialization.
Caloric Restriction Prevents Visceral Adipose Tissue Accumulation and Maintains Erectile Function in Aging Rats (2012)

CR effectively prevented VAT accumulation in normotensive rats. Independently of changes in other metabolic markers, this intervention ameliorated the negative impact on erectile responses that occurs with age. Functional changes of the IPA may be a key mechanism by which erections are preserved with CR. AG was shown to be a strong index of VAT in rats.
Annual Incidence of Hospitalization for Nonfatal Firearm-Related Injuries in New York From 2005 to 2016 (2021)

The annual incidence of hospitalization for nonfatal firearm-related injuries in New York during the study period was 18.4 per 100 000 population. Reliable tracking of nonfatal firearm-related injury data may be useful for policy makers, hospital systems, community organizers, and public health officials as they consider resource allocation for trauma systems and injury prevention programs.
IMMUNOMAGNETIC CELL ENRICHMENT DETECTS MORE DISSEMINATED CANCER CELLS THAN IMMUNOCYTOCHEMISTRY IN VITRO (2000)

Compared to immunocytochemistry, immunomagnetic cell enrichment significantly improves the sensitivity of detection of epithelial cells added to mononuclear cells. Both methods of enrichment were equally effective and may be important for clinical practice in the future.
DNA methylation, nuclear structure, gene expression and cancer (2000)

DNA methylation, chromatin structure, transcription, and cancer have traditionally been studied as separate phenomena. Recent data provide now direct physical and functional links between these processes revealing a complex network of interactions and mutual dependences. Methylated DNA is bound by methyl-CpG binding protein (MeCP) complexes that include histone deacetylases (HDACs). This recruitment of HDACs is suggested to promote local chromatin condensation and thereby repress gene expression. Most recently, also complexes of DNA methyltransferase (Dnmt1) with transcriptional repressors, DMAP1 and pRB, have been described providing a direct link to transcriptional regulation and tumor suppression. Inactivation of the DNA methyltransferase genes (Dnmt1, 3a, and 3b) was found to be lethal in mice and several human diseases (ICF and Rett syndrome) turned out to be linked to DNA methylation. In particular, global hypomethylation has been found in tumor samples together with cancer-type-specific, local hypermethylation. Taken together, these lines of evidence clearly underscore the central role of DNA methylation in the regulation of gene expression and chromatin structure during normal development and diseases like cancer. J. Cell. Biochem. Suppl. 35:78-83, 2000.
Installing Multifunctionality on Titanium with RGD‐Decorated Polyurethane‐Polyurea Roxithromycin Loaded Nanoparticles: Toward New Osseointegrative Therapies (2015)

A novel class of polyurethane-polyurea nanoparticles (PUUa NPs) to install multifunctionality on biomaterials is presented. Biofunctionalization of titanium with roxithromycin loaded RGD-decorated PUUa NPs results in an outstanding improvement of osteoblast adhesion and strong suppression of bacterial attachment. This strategy represents a powerful approach to enhance the osseointegration of implant materials.
Pulsed Lidar for Measurement of C02 Concentrations for the ASCENDS Mission - Update (2011)

We have been developing a laser-based sounding technique for the remote measurement of the tropospheric CO2 concentrations from orbit for NASA is ASCENDS mission. The mission's goals are to provide measurements of tropospheric CO2 abundance with global-coverage, a few hundred km spatial and monthly temporal resolution. These are needed to better understand CO2 fluxes and the processes that regulate CO2 storage by the land and oceans. For the lIP, we are developing and demonstrating the lidar techniques and key lidar technology that will permit measurements of the CO2 column abundance in the lower troposphere from aircraft. Our final goal is to demonstrate the key capabilities needed for a space lidar and mission approach for the ASCENDS mission. We use a pulsed lidar technique, which is much less sensitive to errors from cloud and atmospheric scattering and to noise from solar background. It allows continuous measurements of CO2 mixing ratio in the lower troposphere during day and night. Our approach uses the 1570nm CO2 band and a two-wavelength laser absorption spectrometer, which continuously measures at nadir from a circular polar orbit. It directs the narrow co-aligned laser beams from the instrument's lasers toward nadir, and measures the energy of the laser echoes reflected from land and water surfaces. It uses a pair of tunable laser transmitters, which allowing measurement of the extinction from a single selected CO2 absorption line in the 1570 nm band and from a line pair in the Oxygen A-band near 765 nm. These regions have temperature insensitive absorption lines are free from interference from other gases. The lasers pulse at 10KHz, use tunable diode seed lasers followed by laser amplifiers, and have MHz spectral widths. During the measurement the lasers are stepped across the selected lines at a kHz rate. The receiver uses a 1-m class telescope and photon sensitive detectors and measures the background light and energies of the laser echoes from the surface. The extinction and column densities for the CO2 and O2 gases are estimated from the ratio of the on and off line echo pulse energies via the integrated path differential absorption (IPDA) technique. Our technique exploits the atmospheric pressure broadening of the lines to weight the measurement sensitivity to the atmospheric column below 5 km. Pulsed laser signals, time gated receiver are used to isolate the surface laser echo signals and to exclude photons scattered from clouds and aerosols. We have successfully demonstrated many key aspects of the approach and lidar technology in the laboratory. We have demonstrated CO2 column measurements in airborne flights during the summers of 2009 and 2010. These included measurements from 3-l3 km altitudes made over a variety of surfaces and through thin and broken clouds. We demonstrated initial airborne measurements of O2 column density to 10 km altitudes during the summer 2010 flights. More details approach, key technologies, and demonstration measurements will be given in the presentation.
Scheduling Explicitly-speculative Tasks (CMU-CS-03-204) (2018)

Large-scale computing often consists of many speculative tasks to test hypotheses, search for insights, and review potentially finished products. For example, speculative tasks are issued by bioinformaticists comparing DNA sequences and computer graphics artists adjusting scene properties. This paper promotes a new computing model for shared clusters and grids in which researchers and end-users exploring search spaces disclose sets of speculative tasks, request results as needed, and cancel unfinished tasks if early results suggest no need to continue. Doing so matches natural usage patterns, making users more effective, and also enables a new class of schedulers. In simulation, we demonstrate how batchactive schedulers significantly reduce user-observed response times relative to conventional models in which tasks are requested one at a time (interactively) or requested in batches without specifying which are speculative. Over a range of simulated user behavior, for 20% of our simulations, user-observed response time is at least two times better under a batchactive scheduler, and about 50¾tter on average. Batchactive schedulers achieve such improvements by segregating tasks into two queues based on whether a task is speculative and scheduling these queues separately. Moreover, we show how user costs can be reduced under an incentive cost model of charging only for tasks whose results are requested.