gebhart/patrepeval huggingface dataset:
The Active Principle of Garlic at Atomic Resolution (2002)

Despite the fact that many cultures around the world value and utilize garlic as a fundamental component of their cuisine as well as of their medicine cabinets, relatively little is known about the plant's protein configuration that is responsible for the specific properties of garlic. Here, we report the three-dimensional structure of the garlic enzyme alliinase at 1.5 A resolution. Alliinase constitutes the major protein component in garlic bulbs, and it is able to cleave carbon-sulfur bonds. The active enzyme is a pyridoxal-5'-phosphate-dependent homodimeric glycoprotein and belongs to the class I family of pyridoxal-5'-phosphate-dependent enzymes. In addition, it contains a novel epidermal growth factor-like domain that makes it unique among all pyridoxal-5'-phosphate-dependent enzymes.
An image transport protocol for the Internet (2002)

Images account for a significant and growing fraction of Web downloads. The traditional approach to transporting images uses TCP, which provides a generic reliable, in-order byte-stream abstraction, but which is overly, restrictive for image data. We analyze the progression of image quality at the receiver with time and show that the in-order delivery abstraction provided by a TCP-based approach prevents the receiver application from processing and rendering portions of an image when they, actually, arrive. The end result is that an image is rendered in bursts interspersed with long idle times rather than smoothly. This paper describes the design, implementation, and evaluation of the Image Transport Protocol (ITP) for image transmission over loss-prone congested or wireless networks. ITP improves user-perceived latency using application level framing (ALF) and out-of-order pplication data unit (ADU) delivery achieving significantly better interactive performance as measured by the evolution of peak signal-to-noise ratio (PSNR) with time at the receiver ITP runs over UDP, incorporates receiver-driven selective reliability uses the congestion manager (CM) to adapt to network congestion, and is customizable for specific image formats (e.g., JPEG and JPEG2000). ITP enables a variety of new receiver post-processing algorithms such as error concealment that further improve the interactivity and responsiveness of reconstructed images. Performance experiments using our implementation across a variety of loss conditions demonstrate the benefits of ITP in improving the interactivity of image downloads at the receiver.
Parallel processing of spatial joins using R-trees (2002)

We show that spatial joins are very suitable to be processed on a parallel hardware platform. The parallel system is equipped with a so called shared virtual memory which is well suited for the design and implementation of parallel spatial join algorithms. We start with an algorithm that consists of three phases: task creation, task assignment and parallel task execution. In order to reduce CPU and I/O cost, the three phases are processed in a fashion that preserves spatial locality. Dynamic load balancing is achieved by splitting tasks into smaller ones and reassigning some of the smaller tasks to idle processors. In an experimental performance comparison, we identify the advantages and disadvantages of several variants of our algorithm. The most efficient one shows an almost optimal speed up under the assumption that the number of disks is sufficiently large.
Pressureless Sintering of Boron Carbide (2003)

B 4 C powder compacts were sintered using a graphite dilatometer in flowing He under constant heating rates. Densification started at 1800°C. The rate of densification increased rapidly in the range 1870°–2010°C, which was attributed to direct B 4 C–B 4 C contact between particles permitted via volatilization of B 2 O 3 particle coatings. Limited particle coarsening, attributed to the presence or evolution of the oxide coatings, occurred in the range 1870°–1950°C. In the temperature range 2010°–2140°C, densification continued at a slower rate while particles simultaneously coarsened by evaporation–condensation of B 4 C. Above 2140°C, rapid densification ensued, which was interpreted to be the result of the formation of a eutectic grain boundary liquid, or activated sintering facilitated by nonstoichiometric volatilization of B 4 C, leaving carbon behind. Rapid heating through temperature ranges in which coarsening occurred fostered increased densities. Carbon doping (3 wt%) in the form of phenolic resin resulted in more dense sintered compacts. Carbon reacted with B 2 O 3 to form B 4 C and CO gas, thereby extracting the B 2 O 3 coatings, permitting sintering to start at ∼1350°C.
Gene expression patterns that predict sensitivity to epidermal growth factor receptor tyrosine kinase inhibitors in lung cancer cell lines and human lung tumors (2006)

Abstract Background Increased focus surrounds identifying patients with advanced non-small cell lung cancer (NSCLC) who will benefit from treatment with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI). EGFR mutation, gene copy number, coexpression of ErbB proteins and ligands, and epithelial to mesenchymal transition markers all correlate with EGFR TKI sensitivity, and while prediction of sensitivity using any one of the markers does identify responders, individual markers do not encompass all potential responders due to high levels of inter-patient and inter-tumor variability. We hypothesized that a multivariate predictor of EGFR TKI sensitivity based on gene expression data would offer a clinically useful method of accounting for the increased variability inherent in predicting response to EGFR TKI and for elucidation of mechanisms of aberrant EGFR signalling. Furthermore, we anticipated that this methodology would result in improved predictions compared to single parameters alone both in vitro and in vivo . Results Gene expression data derived from cell lines that demonstrate differential sensitivity to EGFR TKI, such as erlotinib, were used to generate models for a priori prediction of response. The gene expression signature of EGFR TKI sensitivity displays significant biological relevance in lung cancer biology in that pertinent signalling molecules and downstream effector molecules are present in the signature. Diagonal linear discriminant analysis using this gene signature was highly effective in classifying out-of-sample cancer cell lines by sensitivity to EGFR inhibition, and was more accurate than classifying by mutational status alone. Using the same predictor, we classified human lung adenocarcinomas and captured the majority of tumors with high levels of EGFR activation as well as those harbouring activating mutations in the kinase domain. We have demonstrated that predictive models of EGFR TKI sensitivity can classify both out-of-sample cell lines and lung adenocarcinomas. Conclusion These data suggest that multivariate predictors of response to EGFR TKI have potential for clinical use and likely provide a robust and accurate predictor of EGFR TKI sensitivity that is not achieved with single biomarkers or clinical characteristics in non-small cell lung cancers.
Circuit design for a 2.2 GB/s memory interface (2002)

A 2.2 GB/s signaling interface for main memory uses a DLL that allows for in-system timing calibration with 1.4/spl deg/ resolution, and output drivers with limited positive feedback to increase voltage margin. In a 0.25 /spl mu/m CMOS process, the prototype chips operate to 2.6 GB/s.
Immunological Memory (2005)

Protein-polysaccharide conjugate vaccines that protect against Haemophilus influenzae type b (Hib), serogroup C Neisseria meningitidis, and multiple capsular serotypes of Streptococcus pneumoniae have had a major impact on invasive bacterial disease in childhood when incorporated into routine infant immunization schedules. However, effectiveness data from the United Kingdom suggest that primary infant immunization alone may not be associated with long-term protection. Both immunological priming and antibody persistence are important aspects of long-term protection induced by these vaccines. An improved understanding of the immunobiology of the B-cell response to these vaccines may direct development of immunization strategies that provide sustained protection.
Therapeutic approaches in the prevention of cardiovascular disease in metabolic syndrome and in patients with type 2 diabetes (2004)

An aggressive multifactorial approach to cardiovascular risk factor modification facilitates a delay in the onset of type 2 diabetes and cardiovascular events among individuals with the metabolic syndrome.
Fully-integrated CMOS single photon counter (2007)

Traditionally, Single Photon Avalanche Diodes (SPADs) are fabricated using dedicated processes that require additional technological steps when compared to standard CMOS. Instead, this paper presents the design of SPADs that attain good performances, by using a standard high-voltage CMOS process. The detector is monolithically integrated together with an Active Quenching Circuit (iAQC), a counter, and a serial communication interface. This opens the way to the design and fabrication of ultra compact multi-channel single-photon counters.
Three Prime Repair Exonuclease 1 (TREX1) expression correlates with cervical cancer cells growth in vitro and disease progression in vivo (2019)

Alterations in specific DNA damage repair mechanisms in the presence of human papillomavirus (HPV) infection have been described in different experimental models. However, the global effect of HPV on the expression of genes involved in these pathways has not been analyzed in detail. In the present study, we compared the expression profile of 135 genes involved in DNA damage repair among primary human keratinocytes (PHK), HPV-positive (SiHa and HeLa) and HPV-negative (C33A) cervical cancer derived cell lines. We identified 9 genes which expression pattern distinguishes HPV-positive tumor cell lines from C33A. Moreover, we observed that Three Prime Repair Exonuclease 1 (TREX1) expression is upregulated exclusively in HPV-transformed cell lines and PHK expressing HPV16 E6 and E7 oncogenes. We demonstrated that TREX1 silencing greatly affects tumor cells clonogenic and anchorage independent growth potential. We showed that this effect is associated with p53 upregulation, accumulation of subG1 cells, and requires the expression of E7 from high-risk HPV types. Finally, we observed an increase in TREX1 levels in precancerous lesions, squamous carcinomas and adenocarcinomas clinical samples. Altogether, our results indicate that TREX1 upregulation is important for cervical tumor cells growth and may contribute with tumor establishment and progression.
Inhibition of autoimmune encephalomyelitis by a tetracycline (2001)

We have explored the use of minocycline, a tetracycline with antiinflammatory properties, to treat chronic relapsing-remitting experimental allergic encephalomyelitis, an animal model of multiple sclerosis. Therapeutic treatment with minocycline dramatically suppresses ongoing disease activity and limits disease progression. Disease suppression is associated with immune deviation in the periphery and with suppression of the inflammatory cascade in the central nervous system. This association is demonstrated by inhibition of microglial activation and metalloproteinase-2 expression, which results in a concomitant decrease in inflammation and demyelination. As an established antiinflammatory drug with neuroprotective properties, minocycline may provide a novel therapeutic agent for relapsing-remitting multiple sclerosis.
Kernel Count Reduction in Model Based Optical Proximity Correction Process Models (2009)

As the leading-edge photolithography is approaching rapidly closer to the theoretical optical resolution limit, model based optical proximity correction (MBOPC) has evolved from a nice-to-have feature to a must-have feature. The purpose of MBOPC is to adjust the designed pattern on the photomask to introduce mask perturbations such that the layout printed on the wafer is as close as possible to the drawn layout. Before MBOPC is performed across a full chip, a process model is calibrated based upon manufacturing process data measured from scanning electron microscope (SEM) pictures of test patterns. The process model is usually composed of two components, signal intensity and threshold, and the intersections of these two components determine the layout contours that will be printed on wafer. It is found that the accuracy of the process model is improved as more kernels are used to represent the model. However, pattern correction runtime is proportional to the number of kernels used for the model, thereby introducing a constraint to incorporate least number of kernels in the process model. In this study, a novel method of computing the signal change in the MBOPC process is proposed, which is used to maintain the correction accuracy and reduce the MBOPC runtime.
Macrophage-Secreted Factors Promote a Profibrotic Phenotype in Human Preadipocytes (2008)

White adipose tissue (WAT) in obese humans is characterized by macrophage accumulation the effects of which on WAT biology are not fully understood. We previously demonstrated that macrophage-secreted factors impair preadipocyte differentiation and induce inflammation, and we described the excessive fibrotic deposition in WAT from obese individuals. Microarray analysis revealed significant overexpression of extracellular matrix (ECM) genes in inflammatory preadipocytes. We show here an organized deposition of fibronectin, collagen I, and tenascin-C and clustering of the ECM receptor alpha5 integrin, characterizing inflammatory preadipocytes. Anti-alpha5 integrin-neutralizing antibody decreased proliferation of these cells, underlining the importance of the fibronectin/integrin partnership. Fibronectin-cultured preadipocytes exhibited increased proliferation and expression of both nuclear factor-kappaB and cyclin D1. Small interfering RNA deletion of nuclear factor-kappaB and cyclin D1 showed that these factors link preadipocyte proliferation with inflammation and ECM remodeling. Macrophage-secreted molecules increased preadipocyte migration through an increase in active/phosphorylated focal adhesion kinase. Gene expression and neutralizing antibody experiments suggest that inhibin beta A, a TGF-beta family member, is a major fibrotic factor. Interactions between preadipocytes and macrophages were favored in a three-dimensional collagen I matrix mimicking the fibrotic context of WAT. Cell-rich regions were immunostained for preadipocytes, proliferation, and macrophages in the vicinity of fibrotic WAT from obese individuals. In conclusion, an inflammatory environment leads to profound modifications of the human preadipocyte phenotype, producing fibrotic components with increased migration and proliferation. This phenomenon might play a role in facilitating the constitution of quiescent preadipocyte pools and eventually in the maintenance and aggravation of increased fat mass in obesity.
Update on nonsmall cell lung cancer (2010)

Despite recent advances and declining its incidence in males in Western countries, lung cancer remains the main cause of cancer deaths worldwide, mainly because of tobacco smoking epidemics in developing countries and the still moderate efficacy of therapeutic strategies [1–3]. More than 80% of lung cancers are nonsmall cell lung cancer (NSCLC), which can be further sub-divided into squamous cell carcinoma (SCC), adenocarcinoma and large cell carcinoma (LCC). Metastatic stage IV NSCLC remains an incurable disease with a median survival that reached a plateau of 8–10 months at the beginning of the century with available cisplatinum-based regimens [4].

In stage I to III NSCLC, the occurrence of extrathoracic metastasis also leads to a poor 5-yr survival rate of 50% [5]. Indeed, NSCLC has a high metastasis potential, and is often drug resistant, so even after early diagnosis and resection with curative intent, patient prognosis remains poor [6]. Efforts have been made to improve overall survival (OS) of early NSCLC patients, by lowering the distant metastasis rate with adjuvant or neoadjuvant chemotherapy. The LACE (Lung Adjuvant Cisplatin Evaluation) meta-analysis of adjuvant cisplatinum-based chemotherapy only found a 5-yr absolute benefit of 5.4% (hazard ratio (HR) 0.89; p = 0.004) restricted to stage II and III patients, and 5-yr OS remained below 60% [7]. However, in the IALT (International Adjuvant Lung Cancer Trial) study, the benefit was lost at 7 yrs, because of an excess of non-cancer deaths in the chemotherapy arm [8]. Conversely, the long-term follow-up in the ANITA (Adjuvant Navelbine International Trialist Association) trial, using a more recent vinorelbine-cisplatinum doublet strategy, showed that the chemotherapy arm benefit was maintained at 7 yrs [9]. Two meta-analyses [10, 11] of neoadjuvant chemotherapy trials also …
Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions (2011)

Low-rank matrix approximations, such as the truncated singular value decomposition and the rank-revealing QR decomposition, play a central role in data analysis and scientific computing. This work surveys and extends recent research which demonstrates that randomization offers a powerful tool for performing low-rank matrix approximation. These techniques exploit modern computational architectures more fully than classical methods and open the possibility of dealing with truly massive data sets. This paper presents a modular framework for constructing randomized algorithms that compute partial matrix decompositions. These methods use random sampling to identify a subspace that captures most of the action of a matrix. The input matrix is then compressed—either explicitly or&#13;\nimplicitly—to this subspace, and the reduced matrix is manipulated deterministically to obtain the desired low-rank factorization. In many cases, this approach beats its classical competitors in terms of accuracy, robustness, and/or speed. These claims are supported by extensive numerical experiments and a detailed error analysis. The specific benefits of randomized techniques depend on the computational environment. Consider the model problem of finding the k dominant components of the singular value decomposition of an m × n matrix. (i) For a dense input matrix, randomized algorithms require O(mn log(k))&#13;\nfloating-point operations (flops) in contrast to O(mnk) for classical algorithms. (ii) For a sparse input matrix, the flop count matches classical Krylov subspace methods, but the randomized approach is more robust and can easily be reorganized to exploit multiprocessor architectures. (iii) For a matrix that is too large to fit in fast memory, the randomized techniques require only a constant number of passes over the data, as opposed to O(k) passes for classical algorithms. In fact, it is sometimes possible to perform matrix approximation with a single pass over the data.
Loss of malignancy during serial passage of human carcinoma in culture and discordance between malignancy and transformation parameters. (1980)

Human epidermoid carcinoma (HEp-3), a tumor which grows on chorioallantoic membrane and metastasizes with high efficiency into the organs of chick embryo, was adapted to growth in culture.

Upon serial passage in vitro , a progressive loss of metastatic potential and of tumorigenicity was noted. The metastatic potential was completely lost within the first 2 to 10 weeks in culture (4 to 14 passages), while tumorigenicity declined rapidly during a period of 50 passages, as reflected in the progressively larger inoculum required for development of detectable tumors. Beyond this time, macroscopically visible tumors were not observed during the standard 7-day growth period even when the inoculum was increased 100-fold to 107 cells. Identical results were obtained with six individual tumors adapted to grow in vitro . Metastatic potential could be recovered from cell populations that retained some degree of tumorigenicity. This required at least two sequential passages on the chorioallantoic membrane.

Loss of metastatic ability and tumorigenicity was accompanied by change in hormone responsiveness and by a distinct improvement in growth efficiency in culture as manifested by shortened doubling time and increased saturation density. Further, anchorage independence and serum independence, two properties that are generally correlated with the transformed phenotype, were inversely correlated with malignancy.

The malignant and the nontumorigenic cells were compared with respect to production of plasminogen activator, an enzyme associated with malignancy and transformation. Malignant cells produced larger amounts of plasminogen activator, and enzyme production was resistant to modulation by several hormonal and nonhormonal effectors; in contrast, plasminogen activator synthesis in nontumorigenic cells was stimulated by cholera toxin and inhibited by glucocorticoids.
Nanoscale reinforcement of polyhedral oligomeric silsesquioxane (POSS) in polyurethane elastomer (2000)

A unique class of polyurethane (PU) elastomer containing inorganic molecules (polyhedral oligomeric silsesquioxane, POSS) as molecular reinforcement in the hard segment was investigated by means of wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS) techniques. WAXD results indicate that POSS molecules form nanoscale crystals showing distinct reflection peaks. The formation of POSS crystals is probably prompted by the microphase separation between solid-like hard segments and rubbery soft segments in PU. The microphase separation of hard and soft segments was observed by SAXS, which shows a long period of 111 Å for 34 wt% POSS-PU and 162 Å for 21 wt% POSS-PU, and hard segment domains with sizes of about 34 Å for both of them. WAXD results from a series of POSS compounds with a corner substituted by a functional group of varying length were compared with POSS-PU, which also confirms the presence of nanoscale POSS crystals in the polymer matrix. © 2000 Society of Chemical Industry
A review of recent applications of cyclodextrins for drug discovery (1999)

This review summarises the pharmaceutical applications of cyclodextrins (CDs), particularly including the patent literature 1996 - 1999. To place these developments in context there is an introduction to the previously reported molecular and supramolecular (complex formation) properties of CDs and their biological properties, and clinical applications, which mainly involve drug (re)formulation. The growing utility of CDs as pharmaceutical excipients is discussed in three main categories. Firstly, complexes formed between CDs and previously known drugs wherein the new conjugate confers improved efficacy or reduced side effects. Secondly, conjugates conferring improved aqueous solubility and thirdly, a miscellaneous category including conjugates with new compounds. In addition, the emerging areas of covalently bound CD-drug complexes and potential applications of CDs acting directly as medicinal agents in their own right are reviewed. In some of these applications chemically modified CDs are found to augment the patentability and properties of the well known α-, β- and γ-CDs. The chemical structures of these novel CDs are discussed together with the challenge of their synthesis and purification. During the period covered by this review the number of patents and publications describing therapeutic applications of CDs has continued to grow whilst the industrial production of this fascinating class of supramolecular compounds has increased substantially leading to a corresponding fall in price.
Epitope Mapping by Antibody Competition: Methodology and Evaluation of the Validity of the Technique (2003)

Most epitope mapping techniques can be classified into two groups: those that use antigenic fragments (subunits, peptides, and so forth) and the specific antibody-binding regions are directly determined, and those that use intact antigen and the epitope determination is usually indirect.