gebhart/patrepeval huggingface dataset:
Identification of rare cancer driver mutations by network reconstruction (2009)

Recent large-scale tumor resequencing studies have identified a number of mutations that might be involved in tumorigenesis. Analysis of the frequency of specific mutations across different tumors has been able to identify some, but not all of the mutated genes that contribute to tumor initiation and progression. One reason for this is that other functionally important genes are likely to be mutated more rarely and only in specific contexts. Thus, for example, mutation in one member of a collection of functionally related genes may result in the same net effect, and/or mutations in certain genes may be observed less frequently if they play functional roles in later stages of tumor development, such as metastasis. We modified and applied a network reconstruction and coexpression module identification-based approach to identify functionally related gene modules targeted by somatic mutations in cancer. This method was applied to available breast cancer, colorectal cancer, and glioblastoma sequence data, and identified Wnt/TGF-beta cross-talk, Wnt/VEGF signaling, and MAPK/focal adhesion kinase pathways as targets of rare driver mutations in breast, colorectal cancer, and glioblastoma, respectively. These mutations do not appear to alter genes that play a central role in these pathways, but rather contribute to a more refined shaping or "tuning" of the functioning of these pathways in such a way as to result in the inhibition of their tumor-suppressive signaling arms, and thereby conserve or enhance tumor-promoting processes.
Method for determining the position of seismic streamers in a reflection seismic measuring system (1991)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Jan‐Age Langeland; Method for determining the position of seismic streamers in a reflection seismic measuring system. J. Acoust. Soc. Am. 1 December 1991; 90 (6): 3384. https://doi.org/10.1121/1.401413 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search
Energy-Efficient Chain Topology in Ubiquitous Sensor Network (2008)

Many routing topologies have been proposed to extend lifetime of ubiquitous sensor network (USN) consisting of sensor nodes with limited energy. If measurement data is collected periodically for every nodes and perfect fusion during data aggregation, minimum spanning tree (MST) and chains have been two major topologies. MST minimizes total transmission energy and chain consumes energy very evenly throughout the nodes. Various publications such as LEACH, PEGASIS and PEDAP announced many good USN topologies, there still is little study about the topology itself especially in terms of energy consumption excluding USN system-related factors. This paper includes the following study. We proposed a new chain topology and solved minimum spanning chain (MSC) by linear programming (LP). Then we calculated and analysed topology length and standard deviation/coefficient of variation of link lengths through simulation. As results of simulation analysis we confirmed that the proposed chain solution is very useful routing topology in USNs.
Corporate Transparency and Human Rights (2000)

This article uses information theory and game theory to look at ways to make corporate codes of conduct more effective in promoting human rights. It explores the benefits of transparency, and imports the concept of separating equilibrium from game theory. Using these concepts, one can create a system that will raise overall information costs selectively for those multinational corporations (MNC's) that ignore or abuse generally-accepted international human rights standards. Among the elements of such a system would be lowered information acquisition and verification costs for parties concerned with human rights issues, and elimination of certification systems that impose lower costs upon human rights violators than upon human rights respecters. Through these approaches, the costs of participation would be significantly lower for those MNC's that comply with human rights norms than those that do not, and MNC's would be put to the open choice of whether to participate in transparent reporting and code systems.
A Correlating Equation for Forced Convection From Gases and Liquids to a Circular Cylinder in Crossflow (1977)

A single comprehensive equation is developed for the rate of heat and mass transfer from a circular cylinder in crossflow, covering a complete range of Pr (or Sc) and the entire range of Re for which data are available. This expression is a lower bound (except possibly for RePr < 0.2); free-stream turbulence, end effects, channel blockage, free convection, etc., may increase the rate. In the complete absence of free convection, the theoretical expression of Nakai and Okazaki may be more accurate for RePr < 0.2. The correlating equation is based on theoretical results for the effect of Pr in the laminar boundary layer, and on both theoretical and experimental results for the effect of Re. The process of correlation reveals the need for theoretical results for the effect of Pr in the region of the wake. Additional experimental data for the effect of Pr at small Pe and for the effect of Re during the transition in the point of separation are also needed.
Segmentation of remotely sensed images with fuzzy thresholding, and quantitative evaluation (2000)

Effectiveness of various fuzzy thresholding techniques (based on entropy of fuzzy sets, fuzzy geometrical properties, and fuzzy correlation) is demonstrated on remotely sensed (IRS and SPOT) images. A new quantitative index for image segmentation using the concept of homogeneity within regions is defined. Results are compared with those of probabilistic thresholding, and fuzzy c-means and hard c-means clustering algorithms, both in terms of index value (quantitatively) and structural details (qualitatively). Fuzzy set theoretic algorithms are seen to be superior to their respective non-fuzzy counterparts. Among all the techniques, fuzzy correlation, followed by fuzzy entropy, performed better for extracting the structures. Fuzzy geometry based thresholding algorithms produced a single stable threshold for a wide range of membership variation.
Ion channels and epilepsy (2006)

In order for cells to retain their integrity to water and yet permeate charged ions, the phospholipid cell membrane contains transmembrane proteins that allow the passage of specific ions from the interior of the cell to outside, and vice versa. There is a huge diversity of these ion channels. Some are tissue-specific; others are widely distributed throughout the body. They contribute to the maintenance of the negative resting membrane potential inside cells. Unsurprisingly, these membrane channels are integral to the processes of electrical signalling and excitation that are central to the functioning of the nervous system. Figure 1a shows a generic ion channel. 



Figure 1. 
( A ) Diagrammatic representation of a voltage-gated ion channel α subunit. This could be a sodium or calcium channel. Note the four homologous repeats (I–IV), each with six transmembrane domains (1–6). The fourth transmembrane domain (4) has positively charged segments and acts as the voltage sensor. ( B ) Diagrammatic representation of an assembled calcium channel with auxiliary (β, α2δ and γ) subunits. The four homologous repeats (I–IV) are marked on the α1 subunit, and come together to make the channel pore. The assembly of sodium channels is similar, but only has auxiliary β subunits.



The past 15 years have seen rapid expansion in the discovery of disease-causing mutations in genes encoding ion channel proteins. These manifest as neurological, cardiac, renal and respiratory disorders, the most common being cystic fibrosis. This disparate collection of syndromes is now referred to as the channelopathies, a descriptive term referring to the common underlying pathophysiology of ion channel dysfunction. Ion channels themselves are divided into two broad categories, depending on their mode of activation. Voltage-gated channels are controlled by changes in membrane potential, ligand-gated channels by ligand binding (Table 1). 

View this table:

Table 1 
Ion channels implicated in epilepsy



Epilepsy affects up to … 

Address correspondence to Dr T.D. Graves, Department of Molecular Neurosciences, Institute of Neurology, University College London, Queen Square, London WC1N 3BG. email: t.graves{at}ion.ucl.ac.uk
<i>Rpi-vnt1.1</i>, a <i>Tm-2<sup>2</sup></i> Homolog from <i>Solanum venturii</i>, Confers Resistance to Potato Late Blight (2009)

Despite the efforts of breeders and the extensive use of fungicide control measures, late blight still remains a major threat to potato cultivation worldwide. The introduction of genetic resistance into cultivated potato is considered a valuable method to achieve durable resistance to late blight. Here, we report the identification and cloning of Rpi-vnt1.1, a previously uncharacterized late-blight resistance gene from Solanum venturii. The gene was identified by a classical genetic and physical mapping approach and encodes a coiled-coil nucleotide-binding leucine-rich repeat protein with high similarity to Tm-2(2) from S. lycopersicum which confers resistance against Tomato mosaic virus. Transgenic potato and tomato plants carrying Rpi-vnt1.1 were shown to be resistant to Phytophthora infestans. Of 11 P. infestans isolates tested, only isolate EC1 from Ecuador was able to overcome Rpi-vnt1.1 and cause disease on the inoculated plants. Alleles of Rpi-vnt1.1 (Rpi-vnt1.2 and Rpi-vnt1.3) that differed by only a few nucleotides were found in other late-blight-resistant accessions of S. venturii. The late blight resistance gene Rpi-phu1 from S. phureja is shown here to be identical to Rpi-vnt1.1, suggesting either that this strong resistance gene has been maintained since a common ancestor, due to selection pressure for blight resistance, or that genetic exchange between S. venturii and S. phureja has occurred at some time.
On the Predictive Properties of Binary Link Functions (2015)

This paper provides a theoretical and computational justification of the long held claim that of the similarity of the probit and logit link functions often used in binary classification. Despite this widespread recognition of the strong similarities between these two link functions, very few (if any) researchers have dedicated time to carry out a formal study aimed at establishing and characterizing firmly all the aspects of the similarities and differences. This paper proposes a definition of both structural and predictive equivalence of link functions-based binary regression models, and explores the various ways in which they are either similar or dissimilar. From a predictive analytics perspective, it turns out that not only are probit and logit perfectly predictively concordant, but the other link functions like cauchit and complementary log log enjoy very high percentage of predictive equivalence. Throughout this paper, simulated and real life examples demonstrate all the equivalence results that we prove theoretically.
Direct Vinylation and Difluorovinylation of Arylboronic Acids Using Vinyl- and 2,2-Difluorovinyl Tosylates via the Suzuki−Miyaura Cross Coupling (2008)

General reaction conditions were developed for the Pd(0)-catalyzed Suzuki-Miyaura coupling reaction of aryl boronic acids with a simple electrophilic vinylation reagent, vinyl tosylate, providing access to styrene derivatives in good yields. The easily accessible vinyl tosylate represents a stable and less toxic alternative to the vinyl halides and the triflate/nonaflate derivatives. Furthermore, this methodology was expanded to provide a facile and straightforward approach for the introduction of a gem-difluorovinyl substituent onto an aromatic ring using the similar and also readily available 2,2-difluorovinyl tosylate as the electrophilic complement.
ACTH receptors in nervous tissue. High affinity binding–sequestration of [<sup>125</sup>I][Phe<sup>2</sup>,Nle<sup>4</sup>]ACTH 1–24 in homogenates and slices from rat brain (1989)

We have demonstrated specific, high affinity binding of a biologically active Tyr23-monoiodinated derivative of ACTH, [125I][Phe2,Nle4]ACTH 1-24, in rat brain homogenates. Similarly, in metabolically inhibited and noninhibited rat whole brain slices there is a specific "binding-sequestration" process that is dependent on time, protein concentration, and pH. In homogenates, binding curves were best described by a two-site model and provided the following parameters: Kd1 = 0.65 +/- 0.47 nM, Bmax1 = 21 +/- 41 fmol/mg protein; Kd2 = 97 +/- 48 nM, Bmax2 = 3.5 +/- 1.8 pmol/mg protein. In metabolically viable brain slices, concentration-competition curves of [125I][Phe2,Nle4]ACTH 1-24 binding-sequestration can be described by three components (Kd1 = 14 +/- 24 nM, Bmax1 = 50 +/- 95 fmol/mg protein; Kd2 = 2.4 +/- 1.9 microM, Bmax2 = 44 +/- 49 pmol/mg protein; Kd3 = 0.16 +/- 1.0 mM, Bmax3 = 5.3 +/- 54 nmol/mg protein). Metabolic inhibition, by removal of glucose and addition of 100 microM ouabain, abolishes the lowest affinity, highest capacity binding-sequestrian component only (Kd1 = 7.1 +/- 14 nM, Bmax1 = 8.7 +/- 16 fmol/mg protein; Kd2 = 7.4 +/- 4.49 microM, Bmax2 = 37 +/- 27 pmol/mg protein). The two binding-sequestration parameter estimates obtained from metabolically inhibited tissue slices are not significantly different from those of the two higher affinity components obtained with noninhibited tissue. Thus, metabolic inhibition permits demonstration of ACTH receptor binding only, unconfounded by sequestration or internalization of ligand:receptor complexes.(ABSTRACT TRUNCATED AT 250 WORDS)
Consequences of blocked sterol synthesis in cultured cells. DNA synthesis and membrane composition. (1977)

When cell cultures were incubated with certain oxygenated derivatives of cholesterol which specifically depress 3-hydroxy-3-methylglutaryl-coenzyme A reductase activity (i.e. 25-hydroxycholesterol, 7-ketocholesterol, or 20 alpha-hydroxycholesterol), a number of consequences followed the decline in enzyme activity. DNA synthesis, expressed in terms of (methyl-3H)thymidine incorporation/mg of cellular protein, declined progressively after the addition of an inhibitor to L-cell cultures and had essentially ceased by 80 h. A decline in the rate of cell growth, as determined by the measurement of cellular protein, became apparent about 24h after the addition of the inhibitor. These effects of the inhibitory sterols were reversed when mevalonate or cholesterol was added to the medium within 48 h after the addition of the inhibitor. Specific rates of uridine incorporation into RNA and of leucine into protein were not significantly altered during 80 h of incubation with the inhibitor. Sterol synthesis was suppressed; and the concentration of desmosterol in L-cells declined to about one-half of the control level within 36 h. Since phospholipid concentrations were not altered significantly by the treatment, the molar ratio of sterol to phospholipids declined to levels lower than any previously reported for mammalian cells. Changes in the molar ratio of sterol to phospholipids in plasma membranes isolated from L-cells that had been incubated with 25-hydroxycholesterol or cholesterol were in agreement with those found in cells under similar conditions. The inhibitory sterols caused a similar but slower decline in the concentrations of unesterified and total cholesterol in fetal mouse liver cell cultures and rat hepatoma cell cultures.
trans-dominant defective mutants of simian virus 40 T antigen (1987)

We constructed a collection of linker insertion mutants in the simian virus 40 (SV40) genome and studied several of these with changes limited to a part of the large T antigen gene corresponding to an amino acid sequence shared with other ATPases. Two of these mutants were found to have a novel phenotype in that they could not be complemented for plaque formation by a late-region deletion mutant. These two mutants, in contrast to other mutants in this region, were able to transform rat cells in culture at a frequency close to that of the wild-type gene. The noncomplementing mutants were found to be potent inhibitors of SV40 DNA replication despite the presence of wild-type T antigen in the transfected cells. This inhibition was shown to be the result of the introduced mutations in the large T antigen gene. We conclude that the large T antigens of the noncomplementing mutants can act as inhibitors of SV40 DNA replication.
Morphological processing of ultraviolet emissions of electrical corona discharge for analysis and diagnostic use (2016)

Electron cascades from electrical discharge produce secondary emissions from atmospheric plasma in the ultraviolet band. For a single point of discharge, these emissions exhibit a stereotypical discharge morphology, with latent information about the discharge location. Morphological processing can uncover the location and therefore have diagnostic utility.
The Potential for Hall Effect Breast Imaging (1998)

Hall effect imaging is a noninvasive imaging method that combines ultrasound with a strong magnetic field to investigate the electrical properties of tissue. Although technical development is at an early stage, its value for detecting or characterizing pathologies in the breast and other organs is promising. In vitro studies in the past showed that tissue electrical properties are closely related to its physiology and morphology. Hall effect imaging may become a new tool to study these electrical properties in the body and potentially provide unique diagnostic information.
Experimental analysis of a computationally efficient phase aberration correction technique (2003)

A phase aberration correction method, based on time delay estimation via minimization of the sum of absolute differences between radio frequency samples of adjacent array elements, is presented. Effects of averaging estimated aberration patterns over scan angles and of truncation to a single bit word length are examined. Phase distortions due to near field inhomogeneities are simulated using silicone rubber aberrators. Simulation studies addressing different factors affecting efficiency of the method, such as the number of iterations and the number of scan angles used for averaging, are presented. Images of a standard resolution phantom are reconstructed and used for qualitative testing.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Influence of Phenylalanine Intake on the Chemistry and Behaviour of a Phenylketonuria Child (1954)

Summary Phenylketonuria is a not uncommon cause of mental deficiency (there are probably 1600 cases in Great Britain alone). On the supposition that the high level of phenylalanine or its breakdown products in the blood and cerebrospinal fluid might be responsible for the mental retardation in this disorder we have treated a two year‐old child with a diet low in phenylalanine. The introduction of this diet was associated with an appreciable improvement in the patient's mental status and a fall in the level of phenylalanine in the blood and urine. When phenylalanine was again given in fairly large amounts there was an immediate and dramatic deterioration in the child's mental and biochemical condition. A similar phenylalanine intake produced no clinical reaction in a control child. The main source of aminoacids in the diet was an acid casein hydrolysate which was specially treated to remove phenylalanine. The aim of the phenylalanine‐poor diet was to keep the phenylalanine blood level as near the normal range as possible. The preparation of such a diet presents little difficulty if a phenylalanine‐free casein hydrolysate is available. Its value in the treatment of other children is at present being investigated; it seems reasonable to assume that patients in the first two years of life will benefit most.
Towards fingerprints as strings: Secure indexing for fingerprint matching (2013)

This work, for the first time, combines fingerprint matching, security, and indexing in one system. We use the fuzzy vault construct with minutia path information to achieve this. Since we only store translation and rotation invariant information from the paths, we achieve pre-alignment for “free,” which is a requirement of the fuzzy vault. We introduce a hash table that allows indexing to be used with our system, which effectively reduces the search space of the database. Our system is secure in the sense that if the database is compromised, it will be computationally infeasible for the intruder to recover the enrolled fingerprint templates.
The use of the SF-36 questionnaire in adult survivors of childhood cancer: evaluation of data quality, score reliability, and scaling assumptions (2006)

The findings presented in this paper provide support for the validity and reliability of the SF-36 when used in long-term survivors of childhood cancer. These findings should encourage other researchers and health care practitioners to use the SF-36 when assessing health status in this population, although it should be recognised that ceiling effects can occur.
Requirements specification for process-control systems (1994)

The paper describes an approach to writing requirements specifications for process-control systems, a specification language that supports this approach, and an example application of the approach and the language on an industrial aircraft collision avoidance system (TCAS II). The example specification demonstrates: the practicality of writing a formal requirements specification for a complex, process-control system; and the feasibility of building a formal model of a system using a specification language that is readable and reviewable by application experts who are not computer scientists or mathematicians. Some lessons learned in the process of this work, which are applicable both to forward and reverse engineering, are also presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Detection of Pseudomonas aeruginosa Metabolite Pyocyanin in Water and Saliva by Employing the SERS Technique (2017)

Pyocyanin (PYO) is a metabolite specific for <i>Pseudomonas aeruginosa</i>. In the case of immunocompromised patients, it is currently considered a biomarker for life-threating <i>Pseudomonas</i> infections. In the frame of this study it is shown, that PYO can be detected in aqueous solution by employing surface-enhanced Raman spectroscopy (SERS) combined with a microfluidic platform. The achieved limit of detection is 0.5 μM. This is ~2 orders of magnitude below the concentration of PYO found in clinical samples. Furthermore, as proof of principle, the SERS detection of PYO in the saliva of three volunteers was also investigated. This body fluid can be collected in a non-invasive manner and is highly chemically complex, making the detection of the target molecule challenging. Nevertheless, PYO was successfully detected in two saliva samples down to 10 μM and in one sample at a concentration of 25 μM. This indicates that the molecules present in saliva do not inhibit the efficient adsorption of PYO on the surface of the employed SERS active substrates.