gebhart/patrepeval huggingface dataset:
Estimation of minimal size of translocated chromosome segments detectable by fluorescence in situ hybridization (1997)

Apparent non-reciprocal translocations are commonly observed using fluorescence in situ hybridization. We hypothesize that these are 'hidden' reciprocals due to one translocated segment being too small to detect. Assuming that the translocation breakpoints distribute randomly, the proportion of reciprocal to non-reciprocal exchanges can be used to estimate the minimal detectable size of translocated segments. To estimate segment size in this study, cytogenetic data for 120 A-bomb survivors were used. Among 2295 aberrant metaphases, 1629 exhibited reciprocal translocations and 666 non-reciprocal. Of the non-reciprocal translocations, 501 showed only a painted chromosome segment, translocated to an unpainted chromosome with centromere, and 165 showed only an unpainted chromosome segment, translocated to a painted chromosome with centromere. On the basis of the above two assumptions, we obtained the most likely estimates for minimal detectable sizes: 11.1 +/- 0.8 Mb for the painted and 14.6 +/- 0.6 Mb for the unpainted chromosomes. The implications of these findings are discussed.
Requirement of Cdk2-Cyclin E Activity for Repeated Centrosome Reproduction in <i>Xenopus</i> Egg Extracts (1999)

The abnormally high number of centrosomes found in many human tumor cells can lead directly to aneuploidy and genomic instability through the formation of multipolar mitotic spindles. To facilitate investigation of the mechanisms that control centrosome reproduction, a frog egg extract arrested in S phase of the cell cycle that supported repeated assembly of daughter centrosomes was developed. Multiple rounds of centrosome reproduction were blocked by selective inactivation of cyclin-dependent kinase 2-cyclin E (Cdk2-E) and were restored by addition of purified Cdk2-E. Confocal immunomicroscopy revealed that cyclin E was localized at the centrosome. These results demonstrate that Cdk2-E activity is required for centrosome duplication during S phase and suggest a mechanism that could coordinate centrosome reproduction with cycles of DNA synthesis and mitosis.
Beam propagation modeling of arbitrarily bent waveguides (2002)

A numerical method for computing the wave fields in arbitrarily bent waveguides is developed based on a curvilinear coordinate system and the beam propagation method. Unlike earlier approaches based on the conformal mapping or the polar coordinate system, waveguides with arbitrary bends can be conveniently modeled. The new method is accurate for bends with any curvature, since it avoids the small curvature approximation.
Prediction of the structure of symmetrical protein assemblies (2007)

Biological supramolecular systems are commonly built up by the self-assembly of identical protein subunits to produce symmetrical oligomers with cyclical, icosahedral, or helical symmetry that play roles in processes ranging from allosteric control and molecular transport to motor action. The large size of these systems often makes them difficult to structurally characterize using experimental techniques. We have developed a computational protocol to predict the structure of symmetrical protein assemblies based on the structure of a single subunit. The method carries out simultaneous optimization of backbone, side chain, and rigid-body degrees of freedom, while restricting the search space to symmetrical conformations. Using this protocol, we can reconstruct, starting from the structure of a single subunit, the structure of cyclic oligomers and the icosahedral virus capsid of satellite panicum virus using a rigid backbone approximation. We predict the oligomeric state of EscJ from the type III secretion system both in its proposed cyclical and crystallized helical form. Finally, we show that the method can recapitulate the structure of an amyloid-like fibril formed by the peptide NNQQNY from the yeast prion protein Sup35 starting from the amino acid sequence alone and searching the complete space of backbone, side chain, and rigid-body degrees of freedom.
Selective Extraction of Neutral Nitrogen-Containing Compounds from Straight-Run Diesel Feed Using Polymer-Supported Ionic Liquid Moieties (2009)

The extraction of trace polar compounds, among them neutral nitrogen-containing compounds (N-compounds), has received much attention from refiners because of their inhibiting effect on the hydrodesulfurization (HDS) process. Recently, we have shown that chloride-based ionic liquids (ILs) can selectively extract N-compounds from straight-run diesel feeds. However, the measurable solubility of ILs in hydrocarbon fuel is not a desired outcome of the process. Thus, the covalent binding of ILs moieties on polymers was studied. Starting from Merrifield resin, three resins were prepared with imidazolium, pyridinium, and triethylammonium chloride functionality. The resins were evaluated using a synthetic solution with dibenzothiophene and carbazole as model compounds, and a high selectivity for N-compounds was found. Imidazolium and pyridinium resins were then further evaluated using straight-run diesel feed containing 13400 ppm S and 105 ppm N. The selectivity toward N-compounds was comparable to the selectivity observed with ILs. Moreover, the resins could be easily regenerated using a protic solvent like methanol.
Induction of tissue factor on monocytes by adhesion to endothelial cells. (1995)

Activated monocytes express tissue factor (TF), a protein that is important in the pathogenesis of thrombotic disorders. We sought to characterize an adhesion-dependent pathway for monocyte activation. In this study, we showed that adhesion of monocytes to cytokine-activated endothelial cells (EC) increased (approximately 5- to 10-fold) monocyte procoagulant activity (PCA). The PCA was attributed to TF because it was dependent on the coagulation factors VII and X, but not VIII, and was completely blocked by an anti-TF mAb. Direct cell-cell contact between monocytes and EC was required. The induction of TF was rapid, peaked at 30 min, and persisted for 4 h. Northern analysis revealed a rapid (approximately 30 min) increase in TF mRNA following adhesion, distinct from that induced by LPS (approximately 2-4 h). Four-hour TNF-treated EC supported TF expression, but 0.5- and 24-h TNF-treated EC had no effect. An anti-E-selectin mAb (H18/7) exerted partial inhibition, whereas anti-VCAM-1, ICAM-1, and CD11/CD18 mAbs had no inhibition. Synthetic Lewis X (Le(x)) oligosaccharide partially blocked TF induction, whereas sialyl-Le(x) (sLex) oligosaccharide had no effect. Cross-linking Le(x) on monocytes, but not sLex, significantly increased (approximately 10-fold) the TF expression. Le(x) cross-linking induced TF in 30 min and lasted for 4 h. All seventeen anti-Le(x) mAbs induced significant amount of TF generation, and epitope mapping revealed a single binding epitope on Le(x). These findings indicate that adhesion of monocytes to activated EC induces TF generation, and also suggest that Le(x) may represent an important signaling molecule on monocytes.
Quantification of Human Plasma-Busulfan Concentration by Liquid Chromatography-Tandem Mass Spectrometry (2014)

Our method using LC-MS/MS enables highly accurate, reproducible, and rapid busulfan monitoring with minimal sample preparation. The method may also enable safe and proper dosage.
MECHANISM OF DISPLACEMENT OF THE VENTRICULAR SYSTEM IN CHILDREN WITH ATROPHIC LESIONS (1941)

The fact that the midline structures and the contralateral ventricle sometimes move toward the atrophic side in patients with asymmetric lesions of the brain is universally recognized. It is also recognized that such movement does not always take place. In the rather confusing literature on the subject there are references to meningeal adhesions, to shrinkage of cerebral tissue and to asymmetric growth as factors of importance. In 1938 Casamajor and Laidlaw<sup>1</sup>stressed the role of unequal growth. In the same year one of us (B. C.)<sup>2</sup>suggested that, in children, asymmetric growth is of outstanding importance. In 1939 Robertson and Childe<sup>3</sup>showed that adhesions could not explain the dislocation in many cases. In this paper the results of a study of encephalograms of children are reported. All cases in the hospital files in which asymmetry was present were reviewed with particular reference to the mechanism which produces
Non invasive characterization of skin using micro thermal diffusion sensor (2002)

A non invasive microsensor was designed for the study of the time course of both water content and microcirculation of the skin related to physiological, pharmacological, and cosmetics experiments. This microsensor uses the principle of thermal diffusion in skin layers.
The Chemistry of Fresh Tomato Flavor (2001)

Tomato flavor results from taste components, aromatic volatiles and a complex interaction between them. Lack of characteristic flavor in supermarket tomatoes is a common consumer complaint. Sugars, organic acids, free amino acids, and salts are the main taste components. With over 400 volatile compounds identified, only thirty are present in concentrations over one ppb and of these, only 16 contribute significantly to the perceptible flavor. Radiolabeled substrate and enzyme denaturation studies have indicated involvement of some pathway enzymes in the biosynthesis of tomato aroma compounds. Studies of fresh tomato flavor are important for the efforts at improving fruit quality through genetic modifications by molecular techniques.
Current trends in web data analysis (2006)

Considering potential reasons for the underutilization of clickstream data and suggesting ways to enhance its use.
Dynamic and Interactive Synthesis of Code Snippets (2014)

Many code fragments are difficult to write. For example, using new and unfamiliar APIs can be a complex task with a steep learning curve. In addition, implementing a complex data structure requires discovering and understanding all of the corner cases. And more and more end users with little to no formal training are trying to write code, whether they be scientists writing simulations or kids writing mobile apps. For all of these reasons and more, programming is a difficult task, which leads to bugs and delays in software.There are many tools that help programmers find code fragments involving complex APIs, but many are somewhat inexpressive and rely on static information. We present a new technique, which we call CodeHint, that generates and evaluates code at runtime and hence can synthesize real-world Java code that involves I/O, reflection, native calls, and other advanced language features. Our approach is dynamic (giving accurate results and allowing programmers to reason about concrete executions), easy-to-use (supporting a wide range of correctness specifications), and interactive (allowing users to refine the candidate code snippets). We evaluate CodeHint and show that its algorithms are efficient and that in two user studies it improves programmer productivity by more than a factor of two.As the second contribution, programmers and end users often find it easy to explain an algorithm on a whiteboard or with pictures in a textbook but struggle to write the code correctly. We propose a new methodology that allows users to program by demonstrating how an algorithm proceeds on concrete inputs. To reduce the burden of these demonstrations on the user, we have developed pruning algorithms to remove ambiguities in the demonstrations and control flow inference algorithms to infer missing conditionals in demonstrations. These two techniques take advantage of the knowledge encoded in the user's partial correctness condition. We show that this approach is effective in practice by analyzing its performance on several common algorithms.
Dissociation of NS5 from cell fractions containing West Nile virus-specific polymerase activity (1987)

West Nile virus replication complexes were partially purified from cytoplasmic extracts of virus-infected cells by centrifugation through a 20% glycerol cushion. Numerous cell proteins, as well as the largest nonstructural protein, NS5, were separated from the replication complexes without significant loss of in vitro West Nile virus polymerase activity.
“Rediscovery” of Liang A-Fa: From a Perspective of the 1911 Revolution and Reinterpreting the Taiping Rebellion (2014)

This paper analyzes how the Christian community (exclusively the Protestants in this case) in Guangzhou, Hong Kong, and Macau coped with social transformations after the collapse of the Qing Dynasty and the advent of the 1911 Revolution. There is an accumulation of English-, Chinese-, and Japanese- language research about the relationship between the 1911 Revolution and a history of Christianity in China. However, while previous researches focus on the direct impact of Christianity on the Revolution, the current paper analyses how missionaries and Chinese Christians attempted to adapt to social transformations during the Republic era. Given particular attention is the “rediscovery” of Liang A-Fa's (a Chinese Christian in the early 19th century) grave after the 1911 Revolution. These historical findings reveal that the historical reality of Christianity's influence on the Taiping Rebellion was constructed in Guangdong local society after the 1911 Revolution. Also, such construction provides additional insight for interpreting Taiping history.
Utilization of guided elastic waves for the characterization of circumferential cracks in hollow cylinders (1994)

The scattering of guided elastic waves from a circumferential crack in an isotropic hollow cylinder is investigated analytically using the S-parameter formalism. A general formula, analogous to that of [B. A. Auld, Acoustic Fields and Waves in Solids (Krieger, Malabar, FL, 1990), 2nd ed., Vol. II, p. 200], is derived for the scattered amplitude of an arbitrary mode due to the incidence of an arbitrary mode. The amplitudes are expressed as an integral of the inner product of the crack opening displacement caused by the incident mode and the traction field of the scattered mode. Using a simple approximate form of known elastostatic solutions for the crack opening displacements due to pure tension, a formula is derived for the scattering of guided wave modes of arbitrary circumferential order due to the incidence of axisymmetric wave modes with large wavelength and uniform stress distribution. These results are analyzed and conclusions drawn on the possibility of crack sizing using relatively simple scattering amplitude information.
Dynamic Optimization of Water Flooding with Smart Wells Using Optimal Control Theory (2002)

Abstract We used optimal control theory to develop optimization algorithms for the valve settings in smart wells. We focussed on their use in injectors and producers for waterflooding of heterogeneous reservoirs. As a follow-up to an earlier, intuitive, optimization approach, we developed systematic algorithms and investigated the effect of well constraints on the scope for optimization. The objective was to maximize recovery or net present value over a given time period. We concluded that: 1) For wells operating on bottom hole pressure constraints the benefit of using smart wells is mainly reduced water production rather than increased oil production. 2) For wells operating on rate constraints, there is a very large scope for accellerating production and increasing recovery, in combination with a drastic reduction in water production.
Dihydropyrimidine dehydrogenase gene (DPYD) polymorphism among Caucasian and non-Caucasian patients with 5-FU- and capecitabine-related toxicity using full sequencing of DPYD. (2013)

Mutated DPYD is frequently observed in Caucasian patients who experience toxicities while receiving 5-FU/capecitabine. Screening of patients for DPYD mutations prior to administration of 5-FU/capecitabine using new pharmacogenetic testing methods, may help for identify those patients who are at greatest risk for adverse effects, allowing a more individualized approach to their chemotherapy management.
The effect of crosslinking on thermal and mechanical properties of perfluorocyclobutane aromatic ether polymers (1998)

As the minimum features in semiconductor devices decrease, it is a new trend to incorporate copper and polymers with dielectric constant less than 3.0 to enhance the performance of the devices. Two fluorinated polymers, poly(biphenyl perfluorocyclobutyl ether) (BPFCB) and poly(1,1,1-triphenyl ethane perfluorocyclobutyl ether) (PFCB), are newly developed polymers with dielectric constants below 3.0. These two polymers have a similar backbone structure, but PFCB has the capability of crosslinking. To know the implications of these two polymers in the semiconductor industry, properties that are important for the integral reliability of Integral Circuits (IC), such as thermal and mechanical properties, should be understood. This comparative study shows that the crosslinking in perfluorocyclobutane aromatic ether polymer can reduce vertical thermal expansion and increase glass transition temperature (Tg) while water absorption, crystalline-like phase, and dielectric constant are slightly increased. © 1998 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 36: 1383–1392, 1998
Hydrothermal chemistry of silicates. Part XV. Synthesis and nature of some salt-bearing aluminosilicates (1970)

It was earlier shown to be possible to synthesise novel salt-bearing aluminosilicates termed P, Q, N, and O, and to obtain molecular sieve sorbents from one of these. These aluminosilicates have now been characterised by extending the conditions of synthesis and by crystallographic and chemical investigations. Syntheses, especially of P and Q, can be effected not only from gels but also from a range of crystalline aluminosilicates. The species containing BaCl2 and BaBr2(respectively species P and Q) are based upon the same aluminosilicate framework as the synthetic zeolite ZK-5 while those containing KCl and KBr (respectively species N and O) are based upon the framework of the synthetic zeolite K–F reported in 1956. P and Q differ from ZK-5 notably in the salt content and exchange ions. In addition the variants P′ and Q′ were synthesised, which represent aluminous modifications of the ZK-5 framework, as well as an iodide-bearing form of zeolite K–F. Both K–F and ZK-5 frameworks were greatly heat-stabilised by the intracrystalline salts.The removal of barium halides, by extraction with distilled water and various electrolyte solutions, has been investigated for P, Q, P′, and Q′. Solutions of NaNO3 or LiNO3 are much more effective than distilled water. The influence of electrolyte type and concentration, of temperature, of the proportion of crystals to electrolyte solution of fixed concentration, and of time, upon the removal of barium halides have been particularly studied, to optimise the preparation of molecular sieve zeolites.
The biochemistry of aromatic amines. 2-Formamido-1-naphthyl hydrogen sulphate, a metabolite of 2-naphthylamine (1966)

1. 2-Formamido-1-naphthyl hydrogen sulphate is excreted by dogs and rats dosed with 2-naphthylamine or with 2-amino-1-naphthyl hydrogen sulphate and was isolated from dog urine. 2. 2-Formamido-1-naphthol, naphtho[2,1-d]oxazole and N-formyl-2-naphthylhydroxylamine are excreted as (2-formamido-1-naphthyl glucosid)uronic acid. 2-Formamidonaphthalene is converted into conjugates of 2-amino-6-naphthol and 2-amino-8-naphthol, but 2-methylaminonaphthalene is excreted as 2-amino-1-naphthyl hydrogen sulphate and its N-methyl and N-formyl derivatives and (2-amino-1-naphthyl glucosid)uronic acid. 3. 2-Methylamino-1-naphthyl hydrogen sulphate is converted into 2-formamido-1-naphthyl hydrogen sulphate and 2-amino-1-naphthyl hydrogen sulphate on charcoal. 2-Amino-1-naphthyl hydrogen sulphate and formaldehyde react on charcoal to yield 2-methylamino- and 2-formamido-1-naphthyl hydrogen sulphate. 4. 2-Formamido-1-naphthol, 2-formamido-1-naphthyl hydrogen sulphate, N-formyl-2-naphthylhydroxylamine and N-formyl-2-naphthylhydroxylamine-O-sulphonic acid were synthesized.
MediBoost: a Patient Stratification Tool for Interpretable Decision Making in the Era of Precision Medicine (2016)

Machine learning algorithms that are both interpretable and accurate are essential in applications such as medicine where errors can have a dire consequence. Unfortunately, there is currently a tradeoff between accuracy and interpretability among state-of-the-art methods. Decision trees are interpretable and are therefore used extensively throughout medicine for stratifying patients. Current decision tree algorithms, however, are consistently outperformed in accuracy by other, less-interpretable machine learning models, such as ensemble methods. We present MediBoost, a novel framework for constructing decision trees that retain interpretability while having accuracy similar to ensemble methods, and compare MediBoost's performance to that of conventional decision trees and ensemble methods on 13 medical classification problems. MediBoost significantly outperformed current decision tree algorithms in 11 out of 13 problems, giving accuracy comparable to ensemble methods. The resulting trees are of the same type as decision trees used throughout clinical practice but have the advantage of improved accuracy. Our algorithm thus gives the best of both worlds: it grows a single, highly interpretable tree that has the high accuracy of ensemble methods.
Developing a cohesive traffic management strategy for ATM networks (1991)

The background and some of the rationale for the development of an asynchronous transfer mode (ATM) traffic management framework to support the wide variety of services to be carried over the B-ISDN are discussed. The advantages of statistical, as opposed to deterministic, multiplexing are examined. Given the anticipated B-ISDN service characteristics, two classes of quality of service are defined based on cell delay and cell loss. The key ATM traffic management tools are reviewed. These tools are broadly classified as either preventive, limiting the total amount of traffic admitted to the network in order to virtually eliminate probability of cell-level congestion, or reactive, assisting the network and individual connections to avoid the onset of congestion and minimize its severity when it does occur. A strategy for the initial introduction and the long-term evolution of an ATM traffic management framework is described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
PQS: A New Platform for Micellar Catalysis. RCM Reactions in Water, with Catalyst Recycling (2008)

The first "designer" surfactant containing a covalently bound ruthenium catalyst is reported. This species dissolves freely in water, forming nanomicelles in which ring-closing metathesis reactions on water-insoluble dienic substrates can occur in pure water at room temperature. It can also be recycled continuously without reaction workup.