gebhart/patrepeval huggingface dataset:
A scalable algorithm for clustering sequential data (2002)

In recent years, we have seen an enormous growth in the amount of available commercial and scientific data. Data from domains such as protein sequences, retail transactions, intrusion detection, and Web-logs have an inherent sequential nature. Clustering of such data sets is useful for various purposes. For example, clustering of sequences from commercial data sets may help marketer identify different customer groups based upon their purchasing patterns. Grouping protein sequences that share similar structure helps in identifying sequences with similar functionality. Over the years, many methods have been developed for clustering objects according to their similarity. However these methods tend to have a computational complexity that is at least quadratic on the number of sequences. In this paper we present an entirely different approach to sequence clustering that does not require an all-against-all analysis and uses a near-linear complexity K-means based clustering algorithm. Our experiments using data sets derived from sequences of purchasing transactions and protein sequences show that this approach is scalable and leads to reasonably good clusters.
Btk dosage determines sensitivity to B cell antigen receptor cross-linking (1997)

Mutations in Btk result in the B cell immunodeficiencies X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency (xid) in mice. Btk is a critical component of signaling pathways regulating B cell development and function. We used a genetic approach to determine whether Btk is also limiting for these processes. One allele of a murine Btk transgene expressed a dosage of Btk (25% of endogenous levels in splenic B cells) sufficient to restore normal numbers of phenotypically mature conventional B cells in xid mice. 2,4,6-trinitrophenyl-Ficoll response, anti-IgM-induced proliferation, B1 cell development, and serum IgM and IgG3 levels remained significantly impaired in these animals. B cells from Btk -/- transgenic mice also responded poorly to anti-IgM, indicating that the xid mutation does not create a dominant negative form of Btk. Response to 2,4,6-trinitrophenyl-Ficoll and B cell receptor cross-linking were increased 3- to 4-fold in xid mice homozygous for the transgene. These results demonstrate that Btk is a limiting component of B cell antigen receptor signaling pathways and suggest that B cell development and response to antigen may require different levels of Btk activity.
ANACONDA: robust synthesis of analog circuits via stochastic pattern search (2003)

Analog synthesis tools have traditionally traded quality for speed, substituting simplified circuit evaluation methods for full simulation in order to accelerate the numerical search for solution candidates. In this paper we develop a new numerical search algorithm efficient enough to allow full circuit simulation of each circuit candidate, and robust enough to find good solutions for difficult circuits. Comparison of synthesized circuits against manual industrial designs demonstrates the utility of the approach.
Analysis and Correction of the Joensuu Munsell Glossy Spectral Database (2012)

The spectral reflectances for the Munsell glossy data found in the Joensuu spectral database were analyzed and differences with the Munsell Renotation data were visualized showing discrepancies. Two methods of correcting these differences were explored. The first method attempted to correct for differences in specular exclusion of the measurement devices. The second method of correcting the spectral reflectances resulted in correctly matching the colorimetry defined by the Munsell renotation data set. Additionally, color inconstancy index results were visualized depicting possible aspects of chromatic adaptation as well as the areas where spectral reflectances might be found that better maintain relationships with neighboring colors under different lighting conditions.
Preliminary Analysis of a Long Stroke Natural Gas Engine Based on LSRM (1999)

&lt;div class="htmlview paragraph"&gt;A natural gas engine based on the principle of a long stroke reciprocating mechanism (LSRM) is proposed. The crankshaft arrangement in a conventional internal combustion (IC) engine will be replaced by a LSRM featuring long stroke and low speed. A major advantage of this LSRM system is that it considerably reduces the side force, which is inherent in conventional crankshaft arrangements. Another advantage is that the LSRM engine will be more compact than an equivalent crank engine operating under the same conditions of speed, power output and so on. The reduced size and complexity of the engine lead to a favorable reduction in manufacturing and, more importantly, maintenance costs. Using gas fuel will allow an increased compression ratio, which is usually limited by the operating nature of the Otto cycle in gasoline engines. With a longer stroke length and lower engine speed, the engine fuel injection system can achieve better engine combustion and performance than current IC engines. This paper reports the preliminary analysis of the LSRM engine. The advantages and anticipated problems are discussed based on a comparison of the LSRM engine and the conventional IC engine. The potential problem of heat loss, which may be caused by the low engine operational speed, was examined through thermodynamic cycle analysis. The results of this analysis show that the heat loss from the LSRM engine will be in the normal range experienced by conventional IC engines if the ambient air is used as the cooling medium.&lt;/div&gt;
(216) Pain and Addiction: Screening Patients at Risk (2008)

Introduction: Addictive disease is a common co-morbidity in chronic pain patients [1]. 26% of patients on methadone treatment believed that prescribed opioids led to their addiction [2]. We report initial validation of a Screening Tool for Addiction Risk (STAR). Methods: Questions based on prior studies of pain and addiction, addiction-screening tools [3,4], discussions with clinicians experienced in pain medicine and addiction, and our clinical experience were used to develop the STAR. After obtaining IRB approval, chronic pain patients completed the 14-item STAR questionnaire. 14 patients with chronic pain and history of drug addiction (DSM-IV Criteria) and 34 additional chronic pain patients completed the survey as part of their initial clinical evaluation. Patient responses were compared to determine which were questions accounted for statistically significant differences. Results: Questions related to respondent classification of addict based on chi-square analysis and Fisher's exact test were: prior treatment in a drug rehabilitation facility (p < 0.00001), nicotine use (p < 0.0032), feeling of excessive nicotine use (p < 0.0007), and treatment in another pain clinic (p < 0.018). A factor analysis linked addiction to first three questions mentioned above. Question: “Have you ever been treated in a drug or alcohol rehabilitation facility?” had a positive predictive value of 93% for addiction. Responses to recreational substance use, alcohol abuse, recent anxiety or depression, unemployment, emergency room visits, family history of drug or alcohol abuse, multiple physicians prescribing pain medication, or a prior history of physical or emotional abuse were not different between either patient group. Discussion: Screening for addiction is an important part of management of chronic pain patients. A history of treatment in drug or alcohol rehabilitation facility and questions related to cigarette smoking may be useful to screen for potential risk of addiction. Further investigations needed to validate results of this study.
Winter dispersal of rockhopper penguins Eudyptes chrysocome from the Falkland Islands and its implications for conservation (2002)

In 3 successive years (1998 to 2000), the winter migration of rockhopper penguins Eudyptes chrysocome from 3 separate breeding colonies on the Falkland Islands was monitored using satellite transmitters. After their moult, 34 penguins were followed for a mean transmission period of 81 ± 21 d. While there were substantial spatial and temporal variations in migration patterns, we identified several foraging areas where food availability is presumably higher than elsewhere. Coastal areas of the Falkland Islands and South America appeared to provide a sufficient food supply, and many penguins commuted between these 2 areas, which are about 600 km apart. Rockhopper penguins from northern breeding colonies also used areas along the slope of the Patagonian Shelf up to 39°S, about 1400 km northwards. By contrast, only a few birds from the southern breeding colony migrated to the Burdwood Bank, which is situated about 250 km to the south of the Falkland Islands, and adjacent oceanic waters. None of the penguins in this study left the maritime zone of the Falkland Islands in an easterly direction to forage in oceanic waters. The mean distances covered per day by individual birds varied greatly, depending on the phase of the foraging trip. The overall mean travelling speed was 26 km d-1 (range: 13 to 45 km d-1). Inter-annual variation was evident both in the use of different foraging areas, and also in the time at which the winter migration began. In 1998 and 2000, penguins from Seal Bay and Sea Lion Island left their breeding colony within 1 wk after being equipped with transmitters and did not return, whereas in 1999 most penguins made short foraging trips and returned repeatedly to their colonies for periods of up to 100 d. Potential threats to the rockhopper penguins during their winter migration, resulting from human activities such as fishing and oil pollution within the Falkland Islands maritime zone and the Argentine Exclusive Economic Zone, are discussed.
Accounting for limited sensing in real-time obstacle avoidance for mobile robots (2004)

Obstacle detection is a critical task in mobile robot navigation. To allow for rapid reactions to changes in the environment, it is required to complete its operation in short time intervals. That can be difficult if computing and/or sensing robot resources are limited. Therefore, it is important to design precisely what sensorial information would be needed to guarantee detection, and how it would be gathered to guarantee throughput. In this paper we present analysis and experiments related to the design of an obstacle detection system for a mobile robot with limited sensing capabilities. Objectives are to preserve safety while maintaining good motion performance. The design is made in two steps. Firstly, to find what is the minimum information needed to assure safety as a function of the sensors at hand, the robot capabilities and the intended motion control policy. Second, to manage the available sensors in order to provide the required information when needed. For the example studied, a justified solution has been defined which guarantees detection, robot safety, and good motion performance in real time. The solution has been tested with experiments that illustrate the effectivity achieved.
Structural Optimization of Indole Derivatives Acting at Colchicine Binding Site as Potential Anticancer Agents (2015)

A new series of indole analogues based on our earlier lead compound, 2-(1H-indol-5-yl)-4-(3,4,5-trimethoxyphenyl)-1H-imidazo[4,5-c]pyridine (42), was prepared as tubulin inhibitors in an effort to find a molecule with improved cytotoxic potency and metabolic stability. A series of indolyl-imidazopyridines (IIP) were synthesized and exhibited potent tubulin polymerization inhibitory activity with potent IC50 values ranging from 3 to 175 nM against a panel of human melanoma and prostate cancer cell lines. Among these compounds, the 6-indolyl compound 43 showed improved cytotoxic potency (average IC50 of 9.75 nM vs 55.75 nM) and metabolic stability in human liver microsomes (half-life time was 56.3 min vs. 45.4 min) as compared to previously reported 42. It was also shown to be effective against P-glycoprotein (P-gp) mediated multiple drug resistance (MDR) and taxol resistance.
DFM issues for 65nm and beyond (2007)

The 90nm technology node is a mature process and is currently in full production. It was the first node to challenge the limitations of 193 nm lithography in a significant way. Many creative solutions were devised to circumvent those limitations and a lot was learned in the process. Now 65nm, 45nm, and 32nm are pushing the envelope of every aspect of the design and manufacturing flow; not just lithography but also in device engineering, device modeling, and design methodology. Design for Manufacturability (DFM) and Design for Yield (DFY) dictate that we optimize every step in the design flow. Here we address a plurality of those challenges.
Long-Awaited Next-Generation Road Damage Detection and Localization System is Finally Here (2021)

With the ever-increasing emphasis on road maintenance to a high standard, the need for automated and robust road damage inspection (detection and localization) systems is becoming greater than ever. In this paper, we introduce a realtime road damage inspection system, which has been embedded in a drone to reconstruct 3D road geometry using stereo vision, as well as to detect and localize road damage using disparity map segmentation and visual simultaneous localization and mapping. In addition, the 3D road map is built and updated, which enables road damage inspectors to assess road conditions in a more convenient way.
Hydrothermally induced changes in the properties of MFC and characterization of the low molar mass degradation products (2019)

The aim of this study was to determine hydrothermally induced changes in the physico-chemical properties of a fine microfibrillated cellulose (MFC). The MFC was prepared from a monocomponent endoglucanase-treated never-dried birch kraft pulp which had been run several times through a microfluidizer in order to obtain a sample substantially free from fibers or fiber fragments. The fine MFC was subjected to hydrothermal treatment at $$150\,^{\circ }\hbox {C}$$ for 0.5, 2.5, 4.5, 8.5 and 20.5 h, after which the viscosity, water-retention capacity, surface charge, discoloration and formation of hydrolysis products were determined. The viscosity, surface charge and water-retention capacity of MFC decreased as a result of the treatment but in oscillatory measurements the storage and loss moduli increased. Hydrothermal treatment also caused discoloration of the sample which could not be fully washed away with water. Surface analysis with XPS revealed no significant changes in the surface structure of the dried MFC cakes but the filtrates after the hydrothermal treatment were complex mixtures of sugars, organic acids and furans. The main degradation products detected were xylose and xylobiose, but isomerization products of sugars (xylulose, fructose) were also found in the filtrates. In addition numerous organic acids, including formic, glycolic, lactic and xylonic acid, were identified in the filtrates, showing that both acid and alkaline catalyzed reactions occur due to dissociation of water into $$\hbox {H}^{+}$$ and $$\hbox {OH}^{-}$$ .
Blocked-based physical modeling for digital sound synthesis (2007)

Block-based physical modeling is a methodology for modeling physical systems with different subsystems. It is an important concept for the physical modeling of real or virtual musical instruments where different components may be modeled according to different paradigms. Connecting systems of diverse nature in the discrete-time domain requires a common interconnection strategy. This contribution presents suitable interconnection strategies that incorporate a wide range of modeling blocks and considers the automatic implementation of block-based structures. Software environments are presented, which allow to build complex sound synthesis systems without burdening the user with problems of block compatibility
Noninvasive intravital high-resolution imaging of pancreatic neuroendocrine tumours (2019)

Preclinical trials of cancer drugs in animal models are important for drug development. The Rip1Tag2 (RT2) transgenic mouse, a model of pancreatic neuroendocrine tumours (PNET), has provided immense knowledge about PNET biology, although tumour progression occurs in a location inaccessible for real-time monitoring. To overcome this hurdle we have developed a novel platform for intravital 3D imaging of RT2 tumours to facilitate real-time studies of cancer progression. Pre-oncogenic islets retrieved from RT2 mice were implanted into the anterior chamber of the eye (ACE) of host mice, where they engrafted on the iris, recruited blood vessels and showed continuous growth. Noninvasive confocal and two-photon laser-scanning microscopy through the transparent cornea facilitated high-resolution imaging of tumour growth and angiogenesis. RT2 tumours in the ACE expanded up to 8-fold in size and shared hallmarks with tumours developing in situ in the pancreas. Genetically encoded fluorescent reporters enabled high-resolution imaging of stromal cells and tumour cell migration. Sunitinib treatment impaired RT2 tumour angiogenesis and growth, while overexpression of the vascular endothelial growth factor (VEGF)-B increased tumour angiogenesis though tumour growth was impaired. In conclusion, we present a novel platform for intravital high-resolution and 3D imaging of PNET biology and cancer drug assessment.
Vehicles as Mobile Weather Observation Systems (2010)

National Center for Atmospheric ResearchUSDOT/Federal Highway AdministrationUSDOT/Research and Innovative Technology AdministrationNOAA/National Weather ServiceCORRESPONDING AUTHOR: Sheldon Drobot, National Center for Atmospheric Research, 3450 Mitchell Lane, Boulder, CO 80301, E-mail: drobot@ucar.edu
ChemInform Abstract: Design, Synthesis, and Evolution of a Novel, Selective, and Orally Bioavailable Class of Thrombin Inhibitors: P1‐Argininal Derivatives Incorporating P3‐P4 Lactam Sulfonamide Moieties. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Learning Convex QP Relaxations for Structured Prediction (2013)

We introduce a new large margin approach to discriminative training of intractable discrete graphical models. Our approach builds on a convex quadratic programming relaxation of the MAP inference problem. The model parameters are trained directly within this restricted class of energy functions so as to optimize the predictions on the training data. We address the issue of how to parameterize the resulting model and point out its relation to existing approaches. The primary motivation behind our use of the QP relaxation is its computational efficiency; yet, empirically, its predictive accuracy compares favorably to more expensive approaches. This makes it an appealing choice for many practical tasks. 1.
Metabolic profiles of canine cerebrovascular tree: a histochemical study. (1978)

Intriguing questions have recently been raised regarding the applicability of direct observations of the pial microcirculation to the behavior of the total cerebral microcirculation. Operating under the assumption that arteriolar tone and, thus, cerebrovascular resistance is, to some extent, directly related to the intrinsic energy metabolism of the arteriolar wall, a comparative histochemical analysis of cerebral microvessels, both pial and parenchymal, was undertaken. Reactions were chosen on the bases of representation of substrate and of enzymes of glycolysis, the hexose monophosphate shunt, beta-oxidation of fat, Krebs cycle, cytochrome system and ATP hydrolysis. Three metabolically distinct segments of the cerebral microvasculature were delineated with the pial vessels showing strong capacities for glycolysis, beta-oxidation of fats and utilization of glucose through the hexose monophosphate shunt. Microvessels of the gray matter have a qualitatively similar metabolic profile but the capacities of each pathway are lower when compared to pial arterioles. Arterioles of the white matter demonstrate the weakest energy-yielding capacities.
Graphene – CdSe/ZnS quantum dots conjugated systems: charge transfer phenomena and their applications (2012)

Zero-dimensional colloidal semiconductor nanocrystals, known as quantum dots (QDs), attract immense attention in the field of photonics due to their size-dependent tunable optoelectronic properties. Their interaction with conductive surfaces is often reported to provide energy transfer instead of the charge transfer mechanism under presence of optical excitation. In this work, we demonstrate the role of single layer graphene (SLG) as an efficient charge transfer agent when conjugated with CdSe/ZnS core/shell quantum dots.
Toxicities of 31 Volatile Low Molecular Weight Compounds AgainstAedes aegyptiandCulex quinquefasciatus (2009)

This research studied 31 volatile compounds for indoor control of the medically important mosquitoes Aedes aegypti L. and Culex quinquefasciatus Say. Only adult female mosquitoes were tested. The test compounds were from six families that included five heterobicyclics, eight formate esters, formic acid (a hydrolyzed metabolite of formate esters), eight acetate esters, four propionate esters, three butyrate esters, and two valerate esters. Also, the organophosphate compound dichlorvos (DDVP) was tested as a positive control. Cx. quinquefasciatus was generally more susceptible than Ae. aegypti. Cx. quinquefasciatus was most susceptible to a subset of heterobicyclics and formate esters (rank: n-butyl formate > hexyl formate = dihydrobenzofuran = menthofuran = heptyl formate = ethyl formate). Ae. aegypti was most susceptible to a subset of formate esters (rank: methyl > n-butyl > propyl = ethyl = hexyl). The most active materials against both species had LC50s of 0.4-1 mg active ingredient per 0.5 liter of air volume (0.8-2 mg/liter), which is 50- to 60-fold less toxic than dichlorvos (an organophosphate insecticide that is being phased out from indoor use). In relation to Drosophila melanogaster Meigen, both mosquito species were generally more susceptible to formate esters but more tolerant of heterobicyclics. Generally, the most toxic compound against all dipterans tested to date is n-butyl formate, whereas menthofuran is additionally toxic against Cx. quinquefasciatus and D. melanogaster. Finally, the toxicity differences between species point to the potential for differential toxicity among mosquito general/species, suggesting that further studies of a number of mosquito species might be warranted.
Characterization of Large Fullerenes in Single-Wall Carbon Nanotube Production by Ion Mobility Mass Spectrometry (2006)

Samples from nanotubes produced by various methods are analyzed by laser desorption-ionization ion mobility time-of-flight mass spectrometry (LDI-IM-TOF-MS). The measurements find mostly positive fullerene ions in the mass range from 240 to 10000 Da. These principal contaminants are produced along with single-wall carbon nanotubes, which are too large to be detected in the mass spectra. Large fullerenes in the spectra are identified by their regular pattern of two carbon atom intervals and agreement of their mobility with theory. The distribution of large fullerenes varies among the samples depending on the type of production technique. Large numbers of fullerenes are seen in samples produced by the arc process and by the laser ablation process, whereas relatively few fullerenes are seen in samples produced by CVD processes. Measured drift times are in good agreement with those calculated based on a rigid sphere model. From close examination of the drift time distributions, there appears to be isomers of lower mobility. Agreement of measured with calculated drift times suggest that these isomers may be elongated structures. To assess possible limiting shapes of isomers seen in the mobility spectra, it appears that the shapes of the large fullerenes of a given mass vary from spherical to possibly short cylinders.