gebhart/patrepeval huggingface dataset:
Increased expression of glycosyl‐phosphatidylinositol anchor attachment protein 1 (GPAA1) is associated with gene amplification in hepatocellular carcinoma (2006)

Glycosyl-phosphatidylinositol (GPI) anchor attachment protein 1 (GPAA1) transcript level was frequently up-regulated in our earlier study on gene expression profile. We therefore analyzed the potential involvement of GPAA1 in hepatocellular carcinoma (HCC) as GPAA1 gene locates at chromosome 8q24.3 which chromosome region is frequently amplified in HCCs. In this study, we observed that GPAA1 transcript in the HCCs (n = 93) showed a significantly higher expression level compared with their paralleled adjacent nontumor liver tissues, cirrhosis (n = 15) and normal (n = 16) liver tissues using real-time quantitative RT-PCR (p < 0.005). We also demonstrated that GPAA1 protein up-regulation was common in HCCs (90%, 9/10), and GPAA1 gene was frequently amplified (73%, 11/15) using quantitative microsatellite analysis. Increased GPAA1 expression was significantly associated with HCCs poor cellular differentiation (p = 0.011) and poor prognosis (p = 0.010). We then modulated the GPAA1 expression level in HCC cells (Hep3B) by transfection experiments, which was shown to positively regulate cell adhesion ability (p = 0.004) and proliferation rate (p = 0.037). Our data revealed GPAA1 gene amplification with overexpression of RNA and protein in HCC. GPAA1 is a potential amplification target of chromosome 8q and responsible to regulate tumor cells behavior.
Irradiation-Induced Deinococcus radiodurans Genome Fragmentation Triggers Transposition of a Single Resident Insertion Sequence (2010)

Stress-induced transposition is an attractive notion since it is potentially important in creating diversity to facilitate adaptation of the host to severe environmental conditions. One common major stress is radiation-induced DNA damage. Deinococcus radiodurans has an exceptional ability to withstand the lethal effects of DNA-damaging agents (ionizing radiation, UV light, and desiccation). High radiation levels result in genome fragmentation and reassembly in a process which generates significant amounts of single-stranded DNA. This capacity of D. radiodurans to withstand irradiation raises important questions concerning its response to radiation-induced mutagenic lesions. A recent study analyzed the mutational profile in the thyA gene following irradiation. The majority of thyA mutants resulted from transposition of one particular Insertion Sequence (IS), ISDra2, of the many different ISs in the D. radiodurans genome. ISDra2 is a member of a newly recognised class of ISs, the IS200/IS605 family of insertion sequences.
A Model-Based Image Reconstruction Algorithm With Simultaneous Beam Hardening Correction for X-Ray CT (2015)

Beam hardening is a well-known effect in X-ray CT scanning that is caused by the interaction of a broad polychromatic source spectrum with energy-dependent material attenuation. If the scanned object only consists of a single material, the beam hardening effect can be corrected by sinogram precorrection techniques. However, when multiple materials are present, it becomes much more difficult to fully compensate for this distortion; in general, the beam hardening can contribute to reconstruction artifacts such as cupping and streaking. In this paper, we present a novel model-based iterative reconstruction algorithm that incorporates beam hardening correction (MBIR-BHC). Unlike most correction algorithms, which require knowledge of the X-ray spectrum or mass attenuation functions, the MBIR-BHC algorithm works by simultaneously reconstructing the image and estimating the beam-hardening function. The method is based on the assumption that the object is formed by a combination of two distinct materials that can be separated based on their densities. We formulate a poly-energetic X-ray forward model using a polynomial function of two material projections: one for the low-density material and one for the high. We then develop an alternating minimization algorithm for jointly estimating the reconstructed image, the material segmentation, and the coefficients of the two component polynomial that models the beam-hardening function. With this approach, the spectrum and mass attenuation functions are not needed in advance, and the correction is adapted to the dataset being reconstructed. We examine the performance of the proposed algorithm using both simulated and real datasets. Results indicate that the MBIR-BHC algorithm significantly reduces several reconstruction artifacts without advanced knowledge of the X-ray spectrum and material properties.
Online learning methods for discriminative training of phrase based statistical machine translation (2007)

This paper investigates the task of training discriminatively a phrase based SMT system with millions of features using the structured perceptron and the Margin Infused Relax Algorithm (MIRA), two popular online learning algorithms. We also compare two different update strategies, one where we update towards an oracle translation candidate extracted from an N-best list vs a more aggressive approach in which we update towards an oracle extracted prior to training using a minloss decoder. We evaluate our different training algorithms on the Czech-English translation task. Our results show that while both learning algorithms achieve similar results, with the perceptron converging more rapidly, the aggressive update strategy performs significantly worse than the more conservative strategy corroborating Liang et al. (2006)’s findings. 1.
Degenerative Spondylolisthesis Versus Spinal Stenosis (2010)

Overall, DS and SPS patients had similar baseline characteristics. However, DS patients improved more with surgery than SPS patients. Future studies should probably not combine these heterogeneous patient populations.
Diffraction theory of Fresnel lenses encoded in low-resolution devices (1994)

A mathematical model that describes the behavior of low-resolution Fresnel lenses encoded in any low-resolution device (e.g., a spatial light modulator) is developed. The effects of low-resolution codification, such the appearance of new secondary lenses, are studied for a general case. General expressions for the phase of these lenses are developed, showing that each lens behaves as if it were encoded through all pixels of the low-resolution device. Simple expressions for the light distribution in the focal plane and its dependence on the encoded focal length are developed and commented on in detail. For a given codification device an optimum focal length is found for best lens performance. An optimization method for codification of a single lens with a short focal length is proposed.
Regulation of deoxynucleotide metabolism in cancer: novel mechanisms and therapeutic implications (2015)

Regulation of intracellular deoxynucleoside triphosphate (dNTP) pool is critical to genomic stability and cancer development. Imbalanced dNTP pools can lead to enhanced mutagenesis and cell proliferation resulting in cancer development. Therapeutic agents that target dNTP synthesis and metabolism are commonly used in treatment of several types of cancer. Despite several studies, the molecular mechanisms that regulate the intracellular dNTP levels and maintain their homeostasis are not completely understood. The discovery of SAMHD1 as the first mammalian dNTP triphosphohydrolase provided new insight into the mechanisms of dNTP regulation. SAMHD1 maintains the homeostatic dNTP levels that regulate DNA replication and damage repair. Recent progress indicates that gene mutations and epigenetic mechanisms lead to downregulation of SAMHD1 activity or expression in multiple cancers. Impaired SAMHD1 function can cause increased dNTP pool resulting in genomic instability and cell-cycle progression, thereby facilitating cancer cell proliferation. This review summarizes the latest advances in understanding the importance of dNTP metabolism in cancer development and the novel function of SAMHD1 in regulating this process.
Wire sizing as a convex optimization problem: exploring the area-delay tradeoff (1996)

An efficient solution to the wire sizing problem using the Elmore delay model is proposed. Two formulations of the problem are put forth. In the first, the minimum interconnect delay is sought, while in the latter, we minimize the net delay under delay constraints at the leaf nodes; previous approaches solve only the former problem. Theoretical results on these problems are proved, and two algorithms are presented. One is a sensitivity-based heuristic, while the other is a rigorous convex optimization problem. It is shown experimentally that the sensitivity-based heuristic gives near-optimal results with reasonable runtimes. A smooth area-delay tradeoff is shown, and results are presented to illustrate the fact that sizing for minimum delay is not a good engineering goal. Instead, a delay goal of even 15% over the minimum provides significantly better engineering solutions.
Securing Ad Hoc Wireless Networks Against Data Injection Attacks Using Firewalls (2007)

The authors propose to secure ad hoc networks against data injection attacks by placing firewall functionality at strategic locations in the ad hoc network. The authors first show that, given the locations of attackers and victims, the problem of placement of firewall functionality at a fixed number of ad hoc nodes while minimizing the impact of the data injection attack is identical to the k-coverage problem, this problem is known to be NP-hard. Then, the authors develop a near-optimal approximate algorithm for placing firewall functions. The authors also incorporate the loss behavior of wireless links in our algorithm. Next, the authors develop an architecture to determine the location of the attackers. Our architecture uses a separate control network (a cellular network in this paper) in conjunction with ad hoc networks to provide a provable attack detection mechanism. The authors evaluate our firewall placement algorithm for various topologies obtained from ns-2 simulations. Our results show that our algorithm can find near-optimal solutions. Based on a simple analysis and measurement results, the authors also find that the overhead of our provable attack detection mechanism is low.
Isospecific polymerization of racemic epoxides: a catalyst system for the synthesis of highly isotactic polyethers (2010)

A highly active bimetallic cobalt catalyst system is reported for the polymerization of racemic terminal epoxides to yield isotactic polyethers.
Multiparametric magnetic resonance imaging for the detection and localization of prostate cancer: combination of T2‐weighted, dynamic contrast‐enhanced and diffusion‐weighted imaging (2010)

• Adding DWI and DCE to T2W imaging increased MRI performance in cancer detection in the PZ significantly. • However, this multiparametric model failed to improve performance in the TZ. • Gleason score significantly influenced cancer detection in the PZ but not in the TZ.
A Deep-Learning Based Posture Detection System for Preventing Telework-Related Musculoskeletal Disorders (2021)

The change from face-to-face work to teleworking caused by the pandemic has induced multiple workers to spend more time than usual in front of a computer; in addition, the sudden installation of workstations in homes means that not all of them meet the necessary characteristics for the worker to be able to position himself/herself comfortably with the correct posture in front of their computer. Furthermore, from the point of view of the medical personnel in charge of occupational risk prevention, an automated tool able to quantify the degree of incorrectness of a postural habit in a worker is needed. For this purpose, in this work, a system based on the postural detection of the worker is designed, implemented and tested, using a specialized hardware system that processes video in real time through convolutional neural networks. This system is capable of detecting the posture of the neck, shoulders and arms, providing recommendations to the worker in order to prevent possible health problems, due to poor posture. The results of the proposed system show that this video processing can be carried out in real time (up to 25 processed frames/sec) with a low power consumption (less than 10 watts) using specialized hardware, obtaining an accuracy of over 80% in terms of the pattern detected.
Secrets in secretions: genes that control nematode parasitism of plants (2002)

The most evolutionary advanced adaptations for plant parasitism by nematodes are the products of parasitism genes expressed in their esophageal gland cells and secreted through their stylet into host tissue to control the complex process of parasitism. Molecular analyses of nematode parasitism genes are revealing the complexity of the tools a nematode possesses that enable it to attack plants and paints a more elaborate picture of host cellular events under specific control by the parasite than previously hypothesized. Interestingly, the majority of the nematode parasitism genes discovered encodes proteins unique to plant parasites. Identifying the complete profile of parasitism genes expressed throughout the parasitic cycle of a nematode is the key to understanding the molecular basis of nematode parasitism of plants and identifying vulnerable points in the parasitic process that can be interfered with to achieve nematode control to limit nematode-induced yield losses in crops.
<i>In situ</i> Particle Generation and Splat Formation During Solution Precursor Plasma Spraying of Yttria‐Stabilized Zirconia Coatings (2011)

Thermal barrier coatings ( TBC s) based on Yttria‐stabilized Zirconia ( YSZ ) deposited by the solution precursor plasma spray ( SPPS ) technique have been claimed to exhibit superior durability compared to conventional plasma spraying and even electron‐beam physical vapor deposition. This has been attributed to the interesting features, like vertical cracks, nanosized pores, and fine splats that are inherent to SPPS ‐deposited YSZ coatings. However, the mechanism of coating formation during SPPS processing is not yet well understood. This study is aimed at understanding the influence of some key SPPS process variables on in situ generated particles and subsequent splat formation to augment the current level of understanding. The plasma power employed was found to play a major role in governing the morphology and phase constitution of in situ generated particles. The shape and size of the YSZ splats were also significantly influenced by the plasma power, but the substrate pre‐heat was also noted to be a major determining factor. It was further observed that the SPPS typically involved in situ generation of very fine particulates (50–500 nm) and splats (typically 200–2000 nm), which lead to its nano‐porous and homogeneous microstructure. The YSZ coating characteristics were also found to correlate well with the above results.
Aspheric Lens Laser Diode Collimator Design for Optical Intersatellite Communications (1994)

A design for a laser diode collimator using aspheric lens technology was employed to achieve a 5-mm-diameter circular output beam with minimal wavefront aberration, and the minimum number of lenses of the smallest size. The presently designed collimator can achieve a wavefront aberration of better than λ/100 with a pair of aspheric anamorphic lenses, and a total length of 30 mm.
Staphylococcal complement evasion by various convertase-blocking molecules (2007)

To combat the human immune response, bacteria should be able to divert the effectiveness of the complement system. We identify four potent complement inhibitors in Staphylococcus aureus that are part of a new immune evasion cluster. Two are homologues of the C3 convertase modulator staphylococcal complement inhibitor (SCIN) and function in a similar way as SCIN. Extracellular fibrinogen-binding protein (Efb) and its homologue extracellular complement-binding protein (Ecb) are identified as potent complement evasion molecules, and their inhibitory mechanism was pinpointed to blocking C3b-containing convertases: the alternative pathway C3 convertase C3bBb and the C5 convertases C4b2aC3b and C3b2Bb. The potency of Efb and Ecb to block C5 convertase activity was demonstrated by their ability to block C5a generation and C5a-mediated neutrophil activation in vitro. Further, Ecb blocks C5a-dependent neutrophil recruitment into the peritoneal cavity in a mouse model of immune complex peritonitis. The strong antiinflammatory properties of these novel S. aureus-derived convertase inhibitors make these compounds interesting drug candidates for complement-mediated diseases.
Prevalence of the <i>BRCA2</i> 6174 del T mutation in Israeli uveal melanoma patients (2001)

Substantial differences exist in the incidence rates of uveal melanoma (UM) among Israeli Jewish subpopulations: high in immigrants from North America and Europe (Ashkenazic) and low in immigrants from Africa and Asia (Sepharadic). This trend persists in Israeli-born individuals when stratified by their ancestral place of birth. There have been several anecdotal reports of uveal melanoma occurring in breast cancer families with mutations in the BRCA2 gene as well as one systematic study reporting BRCA2 mutations in UM. A single BRCA2 mutation, 6174 del T, occurs in about 1% of the Ashkenazic population and rarely in non-Ashkenazic. To assess the contribution of this germline mutation to uveal melanoma in Jewish Israeli patients, we tested this relationship through analysis of blood samples from a series of UM patients. A total of 153 cases (84 female, 69 male) were available for study, which represents 30% of all cases of UM diagnosed in Israel during the period 1984-1999 (82% for the period 1992-1999). Of the 143 UM patients for which a result could be obtained (4 due to refusals, 6 due to damage to the blood sample), 4 (2.8%, 95% confidence interval [CI] 0-5.6) carried the 6174 del T mutation. Assuming a population frequency of the mutation of 1% as estimated among Ashkenazic Jews in the United States, the probability of observing 4 or more carriers with the 6174 del T mutation, assuming no relationship between uveal melanoma and BRCA2, is 0.057. Although our study confirms the relationship between uveal melanoma and BRCA2, it is clear that the 6174 del T mutation accounts for only a small fraction of all Israeli UM cases. Therefore, BRCA2 mutations are likely to account for an even smaller proportion in populations with low frequencies of BRCA2 alterations.
The interrelation between TNF, IL-6, and PAF secretion induced by LPS in an in vivo and in vitro murine model. (1991)

The interrelation between TNF, IL-6, and PAF secretion in an in vivo and in vitro murine model was studied. Mice were injected with LPS, giving rise to considerable TNF and IL-6 serum levels. To determine the influence of TNF production on the IL-6 secretion, one group of mice was treated with an anti-TNF mAb before LPS administration. The LPS-induced IL-6 secretion was reduced to 48% in the anti-TNF-pretreated group. Parallel to the in vivo experiments, cultures of murine peritoneal macrophages were stimulated with LPS. IL-6 secretion was diminished for 25% in presence of anti-TNF mAb. Further, the role of PAF released in response to a challenge with LPS in the regulation of TNF and IL-6 production was investigated. TNF secretion was strongly reduced when cultures of peritoneal macrophages were stimulated with LPS in the presence of a PAF antagonist, whereas IL-6 secretion was not altered by the PAF antagonist. However, pretreatment of mice with a PAF antagonist did not influence serum TNF, nor serum IL-6 levels induced by LPS injection. These data show that TNF was an intermediate in the induction of IL-6 production in vivo and in vitro. PAF played a central role in the TNF release in the in vitro experiments. This could, however, not be established in vivo. LPS-induced PAF secretion was not involved in the regulation of IL-6 secretion.
Learning modular and transferable forward models of the motions of push manipulated objects (2016)

The ability to predict how objects behave during manipulation is an important problem. Models informed by mechanics are powerful, but are hard to tune. An alternative is to learn a model of the object’s motion from data, to learn to predict. We study this for push manipulation. The paper starts by formulating a quasi-static prediction problem. We then pose the problem of learning to predict in two different frameworks: (i) regression and (ii) density estimation. Our architecture is modular: many simple, object specific, and context specific predictors are learned. We show empirically that such predictors outperform a rigid body dynamics engine tuned on the same data. We then extend the density estimation approach using a product of experts. This allows transfer of learned motion models to objects of novel shape, and to novel actions. With the right representation and learning method, these transferred models can match the prediction performance of a rigid body dynamics engine for novel objects or actions.
Artificial Intelligence Based Solarbot (2018)

A chatbot (Also known as Chatterbox) is a computer program which conducts communication between a human and machine, commonly through aural or textual methods. Chatbots are becoming popular since they have the potential to save any individual's hassle and time by automating mundane errands. Chatbots have been witnessing an era of highest demand powered by either a set of responses and rules that are already predefined or artificial intelligence method such as Natural Language Processor. Chatbots are often built-in into the chat systems, for example automated online assistants, which gives them the power for small talk or informal conversations secluded to the scopes of their prime expert systems. Solar power in India is rapid developing industry. As of December 2017 the country's solar power had 17.05 GW total capacities. It has been seen that using solar power is better than using electricity as it is an unlimited and renewable source. More and more people prefer using solar energy, they are being more curious about the uses of solar panels. They find it difficult to acquire information related to solar panels and their facilities. To ease their work a Solarbot can be designed that would provide them with all the necessary information they need quickly and without any hassle. The chatbot provides an interface as a platform for communication between the bot and the client. For pattern matching database is used for storing data and as per for functions and procedures. Pattern matching looks for definite patterns for words in the user's input, compares it with the database and responds to the consumer. A system that would provide facilities to the user very quickly and with least amount of work would be very beneficial.
Timing verification of dynamic circuits (2002)

A complete set of algorithmic rules is presented for timing verification of domino-style precharge logic circuits. These rules include identification of dynamic nodes in a circuit, generation of timing constraints based on the operating environment of a dynamic gate, and verification of the timing constraints as part of a complete timing verification process. An important part of this approach is propagation of gated-clock pulses which are used extensively in dynamic circuits. The algorithms have been implemented in a new static timing verifier called MTV (Mips Timing Verifier) which is targeted towards verification of custom microprocessor circuits. MTV has been demonstrated to be useful on a number of real-world custom circuits.