gebhart/patrepeval huggingface dataset:
Multilinear operators for higher-order decompositions. (2006)

We propose two new multilinear operators for expressing the matrix compositions that are needed in the Tucker and PARAFAC (CANDECOMP) decompositions. The first operator, which we call the Tucker operator, is shorthand for performing an n-mode matrix multiplication for every mode of a given tensor and can be employed to concisely express the Tucker decomposition. The second operator, which we call the Kruskal operator, is shorthand for the sum of the outer-products of the columns of N matrices and allows a divorce from a matricized representation and a very concise expression of the PARAFAC decomposition. We explore the properties of the Tucker and Kruskal operators independently of the related decompositions. Additionally, we provide a review of the matrix and tensor operations that are frequently used in the context of tensor decompositions.
Where is Color (2005)

Perceived color has been an object of wonder and fascination for laymen, artists, philosophers, and scientists for centuries. Obviously the illuminant and surface reflectances of objects affect perceived color. In the primate, cone pigments have different sensitivities to different regions of the visible spectrum. Recordings from many locations in the primate brain also show specificity to the wavelength properties of objects. Modern brain imaging studies in awake humans are just beginning to understand the brain processes that underlie color perception, as distinguished from simple wavelength processing. Principal components analysis of the wavelength response curves in many different color domains indicates that to a first approximation, three components can span most spectral spaces -- whether natural light illuminants, the reflectance spectra of natural objects or scenes, primate cone pigments, primate LGN cells, or the perceived colors of patches on a neutral background. Interestingly, the three components in the different domains are related by simple rotational transformations. A common model for representing simple color-related phenomena across these domains might therefore be possible. However, there are numerous perceived color phenomena which cannot be explained by a linear model. Some of these phenomena have immediate practical consequences, such as the effect of sunlight glare on radio displays in vehicles, which is not well modeled by current colorimetric theory. Many color “illusions” also cannot be explained by a linear model – Benham’s disk (multiple colors from 1 color channel), Land-like phenomena (multiple colors from 2 color channels), or brightness illusions such as the attached (which can easily be extended to the color domain). The patches marked “A” and “B” are identical.
Discussion (1940)

JOHN N. ADKINS—Six major quarry‐blasts obtained in L. B. Slichter's program of blast‐observation in New England have been studied. Three occurred south of Albany, New York, and three near New Haven, Connecticut. The blasts are recorded on 12 specially designed portable seismographs which are set up throughout New England before each blast. Each instrument records three components of motion on photographic film. Time is marked simultaneously on all records every second by radio. Accuracy of the observations is increased by using an extended time‐scale. In the study of the records, valid impulses are verified and spurious ones eliminated by comparison of the records of two distinct blasts from the same quarry recorded at the same observation‐station. The data from the blast records have been used to compute the crustal structure of New England.
A connection between fuzzy quantifiers and the classical modalities (2002)

The classical modalities, "necessity" and "possibility," are intuitively connected to probability theory by: proposition P is necessarily true if the probability of P's being true is I, and P possibly true if the probability of P's being true is greater than O. A prior work by the author introduced the logic QUAL, for reasoning symbolically with terms expressing fuzzy quantification, usuality, and likelihood. Within QUAL one can formalize syllogisms of the form "Most birds can fly; Tweety is a bird; therefore, it is likely that Tweety can By" and of the form "Usually, if something is a bird, it can fly; Tweety is a bird; therefore, it is likely that Tweety can fly," as well as other formulas and inference rules expressing the interrelationships between these three concepts. The present work shows how QUAL can be extended to include the above versions of possibility and necessity. The extent to which aspects of the well-known modal logics K, S.4, and S.5 can be encoded in this system are also explored.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Measurement, Modeling, and Diagnostics of Flowing Gas Composition Changes in Shale Gas Wells (2012)

Abstract Few attempts have been made to model shale gas reservoirs on a compositional basis. Multiple distinct micro-scale physical phenomena influence the transport and storage of reservoir fluids in shale, including differential desorption, preferential Knudsen diffusion, and capillary critical effects. Concerted, these phenomena cause a measureable compositional change in the produced gas over time. We developed a compositional numerical model capable of describing the coupled processes of diffusion and desorption in ultra-tight rocks as a function of pore size. The model captures the various fracture configurations believed to be induced by shale gas fracture stimulations. By combining the macro-scale (reservoir-scale fractures) and micro-scale (diffusion through nanopores) physics, we show how gas composition changes spatially and temporally during production. We compare our numerical model against measured gas composition data obtained at regular intervals from shale gas wells. We utilize the characteristic behavior illustrated in the model results to identify and to define features in the measured data. We present a workflow for the integration of measured gas composition data into production data analysis tools in order to develop a more complete well performance diagnostic process. The onset of fracture interference in horizontal wells with multiple transverse hydraulic fractures is shown to be uniquely identified by distinct fluctuations in the flowing gas composition. Using these measured composition data, the timescale and durations of the transitional flow regimes in shales are quantified, even for high levels of noise in the rate and pressure data. Reservoir properties are inferred from the integration of the compositional shift analysis of this work with modern production analysis. This work expands the current understanding of well performance for shale gas to include physical phenomena that lead to compositional change. This may be used to optimize fracture and completion design, improve well performance analysis and provide more accurate reserves estimation. This work demonstrates a numerical model which captures multicomponent desorption, diffusion, and phase behavior in ultra-tight rocks. We identify and validate diagnostic trends via high-resolution composition, saturation and pressure maps. We provide a workflow for incorporating measured gas composition data into modern production analysis.
Epstein-Barr virus: the impact of scientific advances on clinical practice (2005)

Epstein-Barr virus (EBV) is a tumorigenic herpes virus that infects and persists in B lymphocytes in the majority of humans, generally without causing disease. However, in a few individuals the virus is associated with significant pathology, particularly benign and malignant lymphoproliferations. Recently acquired knowledge on the mechanisms of EBV persistence, immune control of primary and persistent infection, and disease pathogenesis is now being translated into the clinic with novel methods of diagnosis, prevention and treatment contributing to improved patient care. This review concentrates on these recent advances in the field of hematology/oncology.
Purification of adenylosuccinate lyase from rat skeletal muscle by a novel affinity column. Stabilization of the enzyme, and effects of anions and fluoro analogues of the substrate (1987)

Adenylosuccinate lyase from rat skeletal muscle was purified to apparent homogeneity by a combination of ion-exchange chromatography and affinity chromatography on agarose containing covalently bound adenylophosphonopropionate. The purified enzyme is stable when stored in 20% glycerol at -70 degrees C, and can be thawed and re-frozen with minimal loss of activity. Adenylosuccinate lyase has a specific activity of 11 mumol/min per mg of protein at 25 degrees C. Its subunit Mr is 52,000, by SDS/polyacrylamide-gel electrophoresis, and its apparent native Mr is approx. 200,000, by gel filtration. The purified enzyme has Km values for adenylosuccinate and 4-(N-succino)-5-aminoimidazole-4-carboxamide ribonucleotide (SAICAR) of 1.5 microM and approximately 1 microM respectively, in Hepes/KOH buffer, pH 7.4. Several monoanions and dianions activate the enzyme at low concentration; several of these inhibit the enzyme at high concentrations. Fluoro analogues of adenylosuccinate and SAICAR were synthesized by using highly purified adenylosuccinate synthase and SAICAR synthase respectively, and erythro-beta-fluoroaspartate in place of aspartate. Both analogues are competitive inhibitors of adenylosuccinate lyase in both of the reactions catalysed by the enzyme, with Ki values well below the Km values for the two substrates.
Combined Therapy With a Calcium Channel Blocker and an Angiotensin II Type 1 Receptor Blocker (2008)

Fixed-dosed combination regimens consisting of a calcium channel blocker and an angiotensin II type 1 receptor blocker represent a new addition to the available antihypertensive treatment options. Clinical trials demonstrate that both the dihydropyridine calcium channel blocker amlodipine and angiotensin II receptor blockers are effective agents for the management of hypertension in individuals with or without cardiovascular disease. When combined, these 2 classes of agents have complementary effects on blood pressure, as each targets separate signaling pathways in the vasculature pivotal to the regulation of vascular function. In clinical trials this combination has demonstrated better efficacy, defined by time to reach blood pressure targets as well as levels of blood pressure achieved, compared with the individual agents. In a comparative trial, a combination of amlodipine plus valsartan (an angiotensin II receptor blocker) also produced greater reductions in blood pressure compared with a combination of lisinopril (an angiotensin-converting enzyme inhibitor) and hydrochlorothiazide. The combination of amlodipine and an angiotensin II receptor blocker is well tolerated, including in patients with stage 2 hypertension and the elderly.
Surface-Enhanced Raman Scattering Tags for Three-Dimensional Bioimaging and Biomarker Detection (2019)

We have recently witnessed a major improvement in the quality of nanoparticles encoded with Raman-active molecules (SERS tags). Such progress relied mainly on a major improvement of fabrication methods for building-blocks, resulting in widespread application of this powerful tool in various fields, with the potential to replace commonly used techniques, such as those based on fluorescence. We present hereby a brief Perspective on surface enhanced Raman scattering (SERS) tags, regarding their composition, morphology, and structure, and describe our own selection from the current state-of-the-art. We then focus on the main bioimaging applications of SERS tags, showing a gradual evolution from two-dimensional studies to three-dimensional analysis. Recent improvements in sensitivity and multiplexing ability have enabled great advancements toward in vivo applications, e.g., highlighting tumor boundaries to guide surgery. In addition, the high level of biomolecule sensitivity reached by SERS tags promises an expansion toward biomarker detection in cases for which traditional methods offer limited reliability, as a consequence of the frequently low analyte concentrations.
Applications of Calcium Phosphate-Based Cancellous Bone Void Fillers in Trauma Surgery (2002)

Abstract For more than a century, fracture repair has been augmented with autogenous cancellous bone grafting, which supplies 3 requisite properties: growth factors for osteoinduction, progenitor stem cells for osteogenesis, and scaffolding for osteoconduction. However, disadvantages to using autogenous bone include procurement morbidity, longer operative time, and limited availability. Allograft is more readily available but does not supply osteoinductive or osteogenic properties. Better alternatives for bone grafting currently include autologous bone marrow, ceramics, allograft demineralized bone matrix, and regulatory growth factors; however, none of these fulfills all 3 requisite properties. Replacement or augmentation of autograft with a calcium phosphate-based composite graft, which combines the best elements of each component into a single engineered graft, is discussed.
Copycat hand - robot hand generating imitative behavior (2007)

High speed, high accuracy and uniform processing time are essential in the hand posture estimation, to realize a robot hand capable of instantly imitating human actions. Therefore, in the present study, we have developed a method that enables the searching of similar images at high speeds and with high accuracy and the search involves uniform processing time, even in the case where a large-scale database is used. This is achieved by clustering databases having approximately uniform amounts of data using self-organization, including self- multiplication and self-extinction, and by collating the input images with the data in the database by means of the low-order image characteristics, while narrowing the search space in accordance with the past history. By estimating the sequential images of the finger shape by using this method, we successfully realized a process involving a joint angle estimation error within several degrees, a processing time of 150 - 160 fps, and an operating time without dispersion by using a PC having a CPU clock frequency of 2.8 GHz and a memory capacity of 512 MB.
The Motion Coherence Theory (2005)

Tliere are a number of important phenom- ena in motion perception involving colicrcnce. Examples include motion capture and motion cooperativity. We propose a theoretical model, called the motion coherence tlieory, that gives a possible explanation for these effects (Yuille and Grzywacz, 1988a,b). In this framework, the aperture problem can also be thought of as a problem of coherence and given a similar explanation. We propose the concept of a velocity field dcfined everywhere in the image, even where there is no explicit motion information available. Through a cost function, tlie model imposes smoothness on the velocity field in a more general way than previous theories. In this paper, we provide a de- tailed theoretical analysis of the motion coherence theory. We discuss its relations with previous theories and show that some of t1ic.m arc approximations to it. A sccorid pa- per (Grzywacz, Smith, and Yuillc, 1088) provides exten- sions and cletnilcd comparisons to psychophysical plienom- cna. Tlic theory applies to both short-range and long- range motion. It places them in the same computational framework aiid provides a way to define interactions be- twcr:11 the two 1)roccsses.
Maltose uptake and its regulation in Bacillus subtilis (1992)

Extracts prepared from cultures of Bacillus subtilis, grown on maltose as the sole carbon source, lacked maltose phosphotransferase system activity. There was, however, evidence for a maltose phosphorylase activity, and such extracts also possessed both glucokinase and glucose phosphotransferase system activities. Maltose was accumulated by whole cells of B. subtilis by an energy-dependent mechanism. This uptake was sensitive to the effects of uncouplers, suggesting a role for the proton-motive force in maltose transport. Accumulation of maltose was inhibited in the presence of glucose, and there was no accumulation of maltose by a strain carrying the ptsI6 null-mutation. A strain carrying the temperature-sensitive ptsI1 mutation accumulated maltose normally at 37 degrees C but, in contrast to the wild-type, was devoid of maltose transport activity at 47 degrees C. The results indicate a role for the phosphotransferase system in the regulation of maltose transport activity in this organism.
Coupling of Reformatsky Reagents with Aryl Chlorides Enabled by Ylide‐Functionalized Phosphine Ligands (2021)

Abstract The coupling of aryl chlorides with Reformatsky reagents is a desirable strategy for the construction of α‐aryl esters but has so far been substantially limited in the substrate scope due to many challenges posed by various possible side reactions. This limitation has now been overcome by the tailoring of ylide‐functionalized phosphines to fit the requirements of Negishi couplings. Record‐setting activities were achieved in palladium‐catalyzed arylations of organozinc reagents with aryl electrophiles using a cyclohexyl‐YPhos ligand bearing an ortho‐tolyl‐substituent in the backbone. This highly electron‐rich, bulky ligand enables the use of aryl chlorides in room temperature couplings of Reformatsky reagents. The reaction scope covers diversely functionalized arylacetic and arylpropionic acid derivatives. Aryl bromides and chlorides can be converted selectively over triflate electrophiles, which permits consecutive coupling strategies.
Genome diversity among regional populations of<i>Francisella tularensis</i>subspecies<i>tularensis</i>and<i>Francisella tularensis</i>subspecies<i>holarctica</i>isolated from the US (2004)

Francisella tularensis is a highly infectious facultative intracellular pathogen that is considered a potential agent of bioterrorism. Four different F. tularensis subspecies have been identified and they appear to display different ecological and virulence characteristics as well as differences in geographical distribution. One simple explanation for the variation in ecological and virulence characteristics is that they are conferred by differences in genome content. To characterize genome content among stains isolated from United States, we have used a DNA microarray designed from a shotgun library of a reference strain. Polymorphisms distributed among polyphyletic sets of strains was the most common pattern of genome alteration observed, indicating that strain-specific genome variability is significant. Nonetheless, 13 different contiguous segments of the genome were found to be missing exclusively in each of the subsp. holarctica strains tested. All 13 are associated with repeat sequences or transposases that could promote insertion/deletion events. Comparison of the live vaccine strain to other holarctica strains also identified three regions that are absent exclusively in the live vaccine strain derived from holarctica.
A new begomovirus species and betasatellite causing severe tomato leaf curl disease in Ranchi, India (2011)

Leaf curl disease of tomato (ToLCD) has become a serious problem across the Ranchi district of Jharkhand, India. Infected plants exhibit symptoms consisting of severe leaf rolling, leaf curling and yellowing typical of begomoviruses. Viral replicative form (RF) DNA was isolated from affected tomato plants as described previously (Chakraborty et al., 2003) and the association of a begomovirus and betasatellite was confirmed by PCR using component-specific primers (Wyatt & Brown, 1996; Briddon et al., 2002). The viral genome (~2.7 kb) was cloned in pUC18 following digestion of RF DNA with Pst I. The PCR amplified betasatellite was cloned into pTZ57R/T. The complete sequences of the begomovirus (GenBankAccession No. GQ994095) and betasatellite (GQ994096) were shown to consist of 2,762nt and 1,349nt respectively. Sequence alignments using MegAlign (DNASTAR, Madison, WI, USA) showed the virus to have the highest levels of nucleotide sequence identity (88.3%) with Tobacco curly shoot virus (AJ457986) and the betasatellite (74.5%) with Tomato leaf curl Bangladesh betasatellite(AJ542489). To other begomoviruses infecting tomatoes in India the levels of sequence identity were between 71 and 85%. This indicates that both the virus and betasatellite are new species, for which the names Tomato leaf curl Ranchi virus (ToLCRnV) and Tomato leaf curl Ranchi betasatellite (ToLCRnB) are proposed. Agrobacterium-mediated inoculation of partial tandem repeat constructs of ToLCRnV and ToLCRnB induced typical ToLCD symptoms in tomato. However, in common with some betasatellite-associated begomoviruses, ToLCRnV alone was also capable of inducing leaf curl symptoms. Thus, ToLCRnV is a novel monopartite begomovirus which, in association with a new species of betasatellite, causes severe ToLCD in Ranchi, India. The presence of ToLCRnV needs to be considered, along with the already reported begomoviruses infecting tomatoes, in studies aiming to develop tomato cultivars with stable resistance to tomato-infecting begomoviruses in India.
Improving the Adoption and Use of Planning Support Systems in Practice (2008)

Planning Support Systems (PSS) are geo-information based tools intended to support planners in planning tasks such as information handling, communication and analysis in planning processes. They can be useful tools in helping planners to handle the ever-increasing complexity of planning. However, PSS technology is trapped in a vicious circle created by the large mismatch that exists between the supply of and the demand for PSS. Despite their many promising characteristics, PSS have not yet become widely used in planning practice; lessons must be learned on how to effectively develop and apply PSS. Without such experience, it becomes difficult to pursue the improvement of PSS technology, which in turn means fewer lessons can be learned. This paper aims to narrow the gap between supply and demand by providing lessons for planners, PSS developers and researchers of PSS development and use.
A 2680 year volcanic record from the DT‐401 East Antarctic ice core (2010)

Volcanic signals recorded in the Antarctic and Greenland ice cores can provide useful information on past explosive volcanism and its impact. In this study, we carried out a continuous sulfate analysis of a 102.65 m East Antarctic ice core (DT‐401, dated as 2682 years) and identified 36 extensive volcanic eruption signals using Cole‐Dai's method, which gives an average of 1.4 eruptions per century, consistent with the results from the Plateau Remote (PR‐B) ice core. When the record is divided into three parts, the latest millennium (1999–1000 A.D.), the middle millennium (999–1 A.D.), and the earliest 682 years (0 A.D. to 682 B.C.), it is found that there were more volcanic eruptions that occurred during the latest millennium (19 eruptions) than during the middle millennium (10 eruptions) of the record and that the intensities of the eruptions in the latest millennium are markedly larger than those in the middle one. There were only seven events recorded in the earliest 682 years, but their intensities were greater, and nearly half of the eruptions had a similar intensity to Tambora's (1815 A.D.), which differs from the PR‐B record. It is also found that volcanism and its average accumulation rate were lower during the “Little Ice Age” than during the “Medieval Warm Period.” Comparison of volcanic records between DT‐401 and other Antarctica ice cores (PR‐B, Dome C, DT‐263, and Byrd) show that in the East Antarctica area with its lower accumulation rates, postdepositional effects may play an important role in the deposition of the sulfate.