gebhart/patrepeval huggingface dataset:
Determining true HER2 status in breast cancers with polysomy using alternative chromosome 17 reference genes: Implications for trastuzumab therapy. (2010)

10549 Background: Detection of HER2 gene amplification by FISH is a key test to predict response of breast cancer to trastuzumab. The ratio of HER2 to CEP17 signals is often used to determine HER2 status, based on the assumption that centromeric probe to CEP17 indicates the chromosome 17 copy number. This study tests the hypothesis that increased copy numbers of CEP17 may not reflect the presence of polysomy and that the use of other genes on chromosome 17 might more accurately serve as reference genes to determine HER2 gene status. Methods: 122/5683 (2%) of HER2 FISH cases performed between October 2007 and December 2009 with CEP17 copy numbers 2.6 and above were selected for additional gene mapping studies using probes for other chromosome 17 genes, including SMS, RARA, and TP53. Revised HER2/chromosome-17-reference ratios utilizing these alternative loci were calculated. Results: 95/122 cases (78%) demonstrated at least one chromosome 17 gene locus with eusomic copy number. Using these new reference genes, 63 of 95 cases (66%) would have HER2 amplification status changed (negative to positive, equivocal to positive or negative to equivocal), with 46 cases (48%) now considered eligible for trastuzumab therapy. The cases were further divided into three groups based on level of HER2 signals (high [>6], intermediate [4-6], borderline/low [<4]) for analysis. The number of cases having HER2 status upgraded in these groups (high, intermediate and border/low) were 14/45 (31.1%), 43/50 (86%) and 4/27 (14.8%) respectively. Conclusions: Our results support recent findings of CGH studies suggesting that true polysomy 17 is rare in breast cancer, and that the CEP17 region is subject to chromosomal gains similar to other regions. Performing additional FISH using probes to the SMS, RARA and TP53 genes in order to obtain a HER2/chromosome-17-reference ratio is an effective way to determine the true HER2 amplification status in these
On Line Diagnosis of Gas Turbines using Probabilistic and Qualitative Reasoning (2006)

Artificial intelligence (AI) techniques are becoming an active area of research for real applications. Power industry is one of the best examples of this. Different problems have been solved with these techniques, for example monitoring, alarm management, diagnosis, and network planning. This paper presents an on-line diagnosis system for gas turbines in power plants. Since this application deals with unexpected behavior, probabilistic reasoning and specifically Bayesian networks, offer a natural mechanism for diagnosis. However, the use of Bayesian networks in real applications presents two challenges. First, the acquisition of representative models of the process with and without faults. Second, dealing with continuous variables makes very expensive the computation for inferences. This project utilizes automatic learning algorithms, together with expert advice to determine the models of the most common faults in gas turbines. Also, a quantification of the behavior is used to minimize the cost of the probability propagation in Bayesian networks. These produces an original probabilistic and qualitative diagnosis of gas turbines. Experiments were carried out utilizing real data in a simulator. The results are presented and discussed
Classical and Emerging Roles of Vitamin D in Hepatitis C Virus Infection (2011)

According to the Institute of Medicine, the risk of clinically significant vitamin D deficiency increases at 25-hydroxyvitamin D levels below 20 ng/mL. By this standard, most cirrhotic hepatitis C virus- (HCV-) positive patients and many noncirrhotic patients are vitamin D-deficient. The high prevalence of vitamin D deficiency among HCV patients is a cause for concern for several specific reasons. Classic studies established the importance of vitamin D and calcium in maintaining bone. Vitamin D's beneficial effects on bone are likely to be vital for HCV-infected patients because these individuals have a high prevalence of low bone mineral density. Many pharmaceutical agents reduce bone density and exposure to these drugs may increase bone disease in HCV-positive patients. Bone loss occurs following liver transplantation and bone density is often low in patients with HIV/HCV co-infection who are on combination antiretroviral therapy. Some evidence suggests that ribavirin reduces bone density, underscoring the special need to monitor vitamin D in patients receiving HCV treatment and to prescribe supplements, as appropriate. In addition to its role in calcium metabolism, vitamin D is also an immune modulator that reduces inflammation while enhancing protective immune responses. Higher vitamin D levels are associated with less liver fibrosis and less inflammation in HCV patients. Recent studies show that low vitamin D levels are associated with treatment failure among HCV-infected patients receiving pegylated-interferon and ribavirin. If confirmed, these findings will provide an additional reason to ensure adequate levels of vitamin D. Information about how to monitor vitamin D status and how to use vitamin D supplements most effectively in HCV-infected patients is provided.
ChemInform Abstract: Guanosine Analogues. Synthesis of Nucleosides of Certain 3‐Substituted 6‐Aminopyrazolo(3,4‐d)pyrimidin‐4(5H)‐ones as Potential Immunotherapeutic Agents. (1991)

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.
The Parkes radio telescope modified for rapid receiver changes (1997)

This paper describes improvements to the Parkes 64 m radio telescope. It is being upgraded to allow rapid switching between receivers, and to track the best-fitting focus as the elevation angle changes. Carried out under contract on behalf of NASA, the upgrade included installing a low-noise 2.3 GHz receiver for tracking the spacecraft Galileo in 1997. We explain the mechanical and structural aspects of the upgrade, including the need to replace the existing focus cabin with a larger unit, and the effect of the increased weight at the prime focus on the focusing characteristics and reflector accuracy. Finally, we summarize the designs of the feed and receiver to optimize the antenna-efficiency/temperature ratio at 2.3 GHz for the Galileo mission.
A Virtual Reality Teleoperator Interface for Assembly of Hybrid MEMS Prototypes (1998)

Abstract In this paper we describe a teleoperated microassembly workcell that integrates a VRML-based virtual microworld with visual servoing micromanipulation strategies. Java is used to program the VRML-based supervisory interface and to communicate with the microassembly workcell. This provides platform independence and allows remote teleoperation over the Internet. A key aspect of our approach entails the integration of teleoperation and visual servoing strategies. This allows a supervisor to guide the task remotely, while visual servoing strategies compensate for the imprecisely calibrated microworld. Results are presented that demonstrate system performance when a supervisor manipulates a microobject remotely. Though Internet delays impact the dynamic performance of the system, teleoperated relative parts placements with submicron precision is successfully demonstrated.
Dimerization of human pS2 (TFF1) plays a key role in its protective/healing effects (1998)

Human pS2 (trefoil factor family 1, TFF1), a 60-amino acid member of the trefoil peptide family, forms dimers via Cys58 and may stimulate gut repair. The effects of dimeric pS2-TFF1 and monomeric pS2-TFF1 (Cys58 replaced by Ser58) were compared in models of wound healing. Rats given dimeric pS2-TFF1 at 25 and 50 μg/kg per h had 50 per cent and 70 per cent reduction in gastric damage induced respectively by indomethacin (20 mg/kg subcutaneously) and restraint (P<0·01). Monomeric pS2-TFF1, at the same doses, was significantly less effective at reducing injury (about half the amount of protection, P<0·01 vs. same doses of dimeric). The rate of migration of cells at the leading edge of wounded monolayers of the human colonic cell line HT29 was increased by addition of dimeric or monomeric forms of pS2-TFF1 (0·65–325 μg/ml). Dimeric pS2-TFF1 had a greater effect than the monomeric form at all doses tested (P<0·05). Cell migration induced by pS2-TFF1 was blocked by a pS2-TFF1 antibody, but not by a transforming growth factor β neutralizing antibody. pS2-TFF1 did not influence cell proliferation as assessed by thymidine incorporation. The increased biological effects of dimeric pS2-TFF1 might be due to direct interaction of Cys58 with a putative trefoil receptor or, more likely, dimerization of pS2-TFF1 might stabilize the interaction with its receptor. This may involve a bivalent interaction of residues on the surfaces of the two trefoil domains. © 1998 John Wiley & Sons, Ltd.
Iron‐Catalyzed Cross‐Coupling of Imidoyl Chlorides with Grignard Reagents. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Healthy volunteer studies in Great Britain: the results of a survey into 12 months activity in this field. (1989)

1. A survey has been conducted amongst 459 members of the Clinical Section of the British Pharmacological Society to ascertain facts about the administration of drugs to healthy volunteers over the period October 1986 to September 1987. 2. A response rate of 87.1% was obtained with 114 individuals being involved in healthy volunteer studies. After exclusion of duplicate returns from the same unit 98 questionnaires were analysed. 3. Drugs were given in the year under review to 8163 healthy volunteers for research purposes. Minor adverse effects were reported in 565 (6.9%), moderately severe adverse effects in 45 (0.55%) and potentially life threatening adverse effects in 3 (0.04%). No lasting sequelae were reported. 4. Drugs were given to 7607 healthy student volunteers as part of class teaching practicals. Minor adverse effects were reported in 6.0% of student exposures but no moderately severe or life threatening adverse effects were reported. 5. The risk involved in healthy volunteer studies is very small indeed but some suggestions are made as a result of the questionnaire to improve further the safety of these studies.
Computing the impact of cyber attacks on complex missions (2011)

This paper describes how to evaluate the impact of a cyber attack on a mission. We accomplish this by computing impact as the changes to mission measures of effectiveness, based on the reported effects of a known or suspected attack on one or more parts of the information technology (IT) supporting the mission. Our previous papers have described our goals for computing mission impact and the choices of the techniques we use for modeling missions, IT, and cyber attacks. This paper focuses on how we compute the impact of cyber attacks on IT processes and information. These computations will improve decision-making when under cyber attack by providing accurate and detailed assessments of the impact of those attacks. Although the focus of our work has been on the calculation of cyber mission impacts during mission execution, we have also demonstrated how our representations and computations can be used for performing cyber risk analysis and crown jewels analysis.
Novel Galactose-binding Proteins in Annelida (1998)

Novel type lectins were found in the phylum Annelida, i.e. in the earthworm, tubifex, leech, and lugworm. The lectins (29-31 kDa) were extracted from the worms without the use of detergent and purified by affinity chromatography on asialofetuin-agarose. On the basis of the partial primary structures of the earthworm Lumbricus terrestris 29-kDa lectin (EW29), degenerate primers were synthesized for use in the reverse transcriptase-polymerase chain reaction. An amplified 155-base pair fragment was used to screen a cDNA library. Four types of full-length clones were obtained, all of which encoded 260 amino acids, but which were found to differ at 29 nucleotide positions. Since three of them resulted in non-silent substitutions, EW29 mRNA was considered to be a mixture of at least three distinct polynucleotides encoding the following proteins: Ala44-Gln197-Ile213 (clone 5), Gly44-Gln197-Val213 (clone 7), and Ala44-His197-Ile213 (clones 8 and 9; different at the nucleotide level, but encoding an identical polypeptide). Genomic polymerase chain reaction using DNA from a single worm revealed that the single worm already had four sets of cDNAs. The EW29 protein showed two features. First, the lectin was composed of two homologous domains (14,500 Da) showing 27% identity with each other. When each of the domains was separately expressed in Escherichia coli, the C-terminal domain was found to bind to asialofetuin-agarose as strongly as the whole protein, whereas the N-terminal domain did not bind and only retardation was observed. EW29 was found to exist as a monomer under non-denaturing conditions. It had significant hemagglutinating activity, which was inhibited by a wide range of galactose-containing saccharides. Second, EW29 contained multiple short conserved motifs, "Gly-X-X-X-Gln-X-Trp." Similar motifs have been found in many carbohydrate-recognizing proteins from an extensive variety of organisms, e.g. plant lectin ricin B-chain and Clostridium botulinum 33-kDa hemagglutinin. Therefore, these carbohydrate-recognition proteins appear to form a protein superfamily.
AlGaN deep ultraviolet LEDs on bulk AlN substrates (2007)

Abstract We report the growth of sub‐300 nm ultraviolet light emitting diodes (UV LEDs) on bulk AlN substrates. Heteroepitaxial evolution study through interrupted growth experiments revealed that Al x Ga 1‐x N (x > 0.5) epilayers can be grown pseudomorphically with well‐defined step‐flow growth mode below a certain critical thickness. The build‐up of compressive strain energy eventually induces a morphological roughening followed by the admission of misfit dislocations. LEDs grown on bulk AlN substrates exhibit noticable improvement over those on sapphire in device impedance, efficiency and thermal characteristics under high‐level injection, pointing to a promising substrate platform for high performance III‐nitride ultraviolet optoelectronics. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Minimal order observers for estimating linear functions of a state vector (1975)

This paper studies the necessary and sufficient conditions for a pth-order observer to observe linear functions of the states of a linear dynamical system. The conditions are a set of multivariable polynomial equations which must be satisfied for some variable set in order for a pth-ncder observer to exist. It is possible to test for the existence of such a variable set in a finite number of steps via decision methods and thereby to construct an observer with the aid of polynomial factorization. To minimize the computational effort, the necessary and sufficient conditions are expressed in terms of the minimum number of variables.
Scale-Up of Agitation Fluidized Bed Granulation. II. Effects of Scale, Air Flow Velocity and Agitator Rotational Speed on Granule Size, Size Distribution, Density and Shape. (1995)

Scale-up characteristics of agitation fluidized bed granulation using a pharmaceutical standard formulation was described. The effects of scale, air flow velocity and agitator rotational speed on granule properties such as granule mass median size, size distribution, apparent density and shape factor were investigated experimentally. Based on the results obtained, the effects of these parameters on granule growth and the mechanism of granule formation in different sized equipment were discussed.
Vector quantization techniques for GMM based speaker verification (2003)

This paper explores the novel application of two vector quantization algorithms, namely Linde, Buzo, Gray (1980) and K-means algorithm for efficient speaker verification. Automatic speaker verification (ASV) is a memory and compute intensive process, giving rise to area and latency concerns in the way of its implementation for real-time efficient embedded systems. The training schemes for computing the speaker models, such as the expectation maximization are highly iterative and contribute significantly to the overall complexity in the implementation of the system. We demonstrate the use of the LBG and the K-means algorithm to realize compute efficient training method. Models trained with the LBG algorithm achieves as much as 99.88% of EM accuracy, whilst K-means achieves as much as 99.91% of EM accuracy. Moreover, the EM computational complexity is almost twice that of LBG or K-means. Thus, using LBG and K-means algorithms for training Gaussian mixture speaker models for text-independent speaker verification, we show that, that they deliver comparable performance as the EM algorithm at significantly reduced computational complexity. Thus making them an ideal choice for low-cost applications.
Motion estimation performance models with application to hardware error tolerance (2007)

The progress of VLSI technology towards deep sub-micron feature sizes, e.g., sub-100 nanometer technology, has created a growing impact of hardware defects and fabrication process variability, which lead to reductions in yield rate. To address these problems, a new approach, system-level error tolerance (ET), has been recently introduced. Considering that a significant percentage of the entire chip production is discarded due to minor imperfections, this approach is based on accepting imperfect chips that introduce imperceptible/acceptable system-level degradation; this leads to increases in overall effective yield. In this paper, we investigate the impact of hardware faults on the video compression performance, with a focus on the motion estimation (ME) process. More specifically, we provide an analytical formulation of the impact of single and multiple stuck-at-faults within ME computation. We further present a model for estimating the system-level performance degradation due to such faults, which can be used for the error tolerance based decision strategy of accepting a given faulty chip. We also show how different faults and ME search algorithms compare in terms of error tolerance and define the characteristics of search algorithm that lead to increased error tolerance. Finally, we show that different hardware architectures performing the same metric computation have different error tolerance characteristics and we present the optimal ME hardware architecture in terms of error tolerance. While we focus on ME hardware, our work could also applied to systems (e.g., classifiers, matching pursuits, vector quantization) where a selection is made among several alternatives (e.g., class label, basis function, quantization codeword) based on which choice minimizes an additive metric of interest.
Bias drift reduction in polarization-maintaining fiber gyroscope (1987)

The output signal of a birefringent fiber gyroscope is analyzed, and sources of error due to polarization cross coupling in the fiber and fiber components are identified. Techniques to suppress such errors by modulating the fiber birefringence and balancing the optical power in the two polarization modes are proposed and demonstrated.
Measurement of Transcobalamin by ELISA (2000)

The ELISA measures total transcobalamin in serum and thus can be used for measurement of transcobalamin in patients treated with cobalamin.
The Role of Weight Normalization in Competitive Learning (1994)

The effect of different kinds of weight normalization on the outcome of a simple competitive learning rule is analyzed. It is shown that there are important differences in the representation formed depending on whether the constraint is enforced by dividing each weight by the same amount (“divisive enforcement”) or subtracting a fixed amount from each weight (“subtractive enforcement”). For the divisive cases weight vectors spread out over the space so as to evenly represent “typical” inputs, whereas for the subtractive cases the weight vectors tend to the axes of the space, so as to represent “extreme” inputs. The consequences of these differences are examined.
Comparative cardiovascular, analgesic, and sedative effects of medetomidine, medetomidine-hydromorphone, and medetomidine-butorphanol in dogs (2004)

Medetomidine-hydromorphone or medetomidine-butorphanol is associated with improved analgesia and sedation but has cardiopulmonary effects comparable to those for medetomidine alone.
Business Process Intergration Methodology-A study of Rosetta net (2000)

This paper applies the Business Process Integration Methodology to the specifications\nput forth by the RosettaNet. Both Methodology and specifications deal with problems\nthat arise when integrating processes. New principles for managing companies is\nstressing a shift from functional orientation towards a process oriented organization,\nfocusing on activities that add value to the customer. The advent of Internet has put\nforth new suggestion on how to perform inter-organizational work between\ncompanies, like the RosettaNet. RosettaNet is a set of recommendation that an\norganization can use to enable their applications to participate in the electronic\ncommerce in the electronic component and information technology industry.\nRosettaNet defines every aspect of doing business electronically. To implement the\nprocess integrations put forth by the RosettaNet, the need for suitable methodological\nsupport is demanded. The purpose of this paper is to test if one such methodology,\nBusiness Process Integration Methodology, can align the recommendation given out\nby the RosettaNet. Business Process Integration Methodology is a methodology,\nwhich support the development lifecycle. Business Process Integration Methodology\ndefines modeling objects, modeling rules, actors/roles, different phases and analysis\nmethods. RosettaNet is a joint effort in the electronic component and information\ntechnology-industry that comprises the whole supply chain. RosettaNet define\napplication integration scenarios, which utilizes the Internet as a carrier of information\nbetween partners. RosettaNet provide methodology for creating eBusiness scenarios,\npartner interface processes, dictionaries and implementation framework. The\nintegration effort between ACME Inc. and Xenitec HB is described utilizing the\nBusiness Design and Modeling Phase of the Business Process Integration\nMethodology applied to the Product Review process from RosettaNet. Analyzing the\nwork performed of integrating the two companies processes lead to the conclusion\nthat the analyzed phase of Business Process Integration Methodology, i.e. Business\nDesign and Modeling is well suited for handling the Business Operation View in the\nPartner Interface Process specification put forth by the RosettaNet. Business Process\nIntegration Methodology lack a requirement phase that could give developers\nguidance identifying the most relevant issues. RosettaNet does not discuss the\nproblems when it comes to aligning the legacy systems towards the specified\nscenarios.