gebhart/patrepeval huggingface dataset:
DNA Repair in Cancer Therapy (2004)

Because of drug resistance, currently available anticancer therapies-drugs, radiotherapy, and other biological agents-have limited efficacy in treating cancer. In DNA Repair in Cancer Therapy, leading cancer researchers and oncologists comprehensively review the many recent developments in DNA repair that have potential for translational and clinical applications. The authors explain in detail the various mechanisms by which cancer cells can circumvent anticancer therapy and limit its usefulness in patients. They also review the clinical impact of such novel inhibitors of DNA repair mechanisms as methylguanine-DNA-methyltransferase. Inhibitors of such other DNA repair enzymes as PARP and DNA-PK, now under development and close to clinical trials, are also examined. Comprehensive and cutting-edge, DNA Repair in Cancer Therapy surveys-for both cancer researchers and practicing oncologists dealing with hallmark "relapse" or "drug resistance" phenomena on a daily basis-the many exciting new uses of DNA repair inhibitors, either alone or in combination with anticancer therapies
Detecting changes in XML documents (2003)

We present a diff algorithm for XML data. This work is motivated by the support for change control in the context of the Xyleme project that is investigating dynamic warehouses capable of storing massive volumes of XML data. Because of the context, our algorithm has to be very efficient in terms of speed and memory space even at the cost of some loss of quality. Also, it considers, besides insertions, deletions and updates (standard in diffs), a move operation on subtrees that is essential in the context of XML. Intuitively, our diff algorithm uses signatures to match (large) subtrees that were left unchanged between the old and new versions. Such exact matchings are then possibly propagated to ancestors and descendants to obtain more matchings. It also uses XML specific information such as ID attributes. We provide a performance analysis of the algorithm. We show that it runs in average in linear time vs. quadratic time for previous algorithms. We present experiments on synthetic data that confirm the analysis. Since this problem is NP-hard, the linear time is obtained by trading some quality. We present experiments (again on synthetic data) that show that the output of our algorithm is reasonably close to the optimal in terms of quality. Finally we present experiments on a small sample of XML pages found on the Web.
Phytochromes confer the photoperiodic control of flowering in rice (a short‐day plant) (2000)

The photoperiodic sensitivity 5 (se5) mutant of rice, a short-day plant, has a very early flowering phenotype and is completely deficient in photoperiodic response. We have cloned the SE5 gene by candidate cloning and demonstrated that it encodes a putative heme oxygenase. Lack of responses of coleoptile elongation by light pulses and photoreversible phytochromes in crude extracts of se5 indicate that SE5 may function in phytochrome chromophore biosynthesis. Ectopic expression of SE5 cDNA by the CaMV 35S promoter restored the photoperiodic response in the se5 mutant. Our results indicate that phytochromes confer the photoperiodic control of flowering in rice. Comparison of se5 with hy1, a counterpart mutant of Arabidopsis, suggests distinct roles of phytochromes in the photoperiodic control of flowering in these two species.
Effect of glycosaminoglycans on fibronectin‐mediated cell attachment (1982)

In this study, the role of glycosaminoglycans in fibronectin-mediated cell attachment to collagen has been investigated. While it has been established that fibronectin possesses binding sites for several glycosaminoglycans, it was found that only dextran sulfate and macromolecular heparin could decrease the initial rate of cell attachment to collagen. Low molecular weight heparin was inactive. This study suggests that the glycosaminoglycan binding site of fibronectin plays a role in the mechanism of cell attachment.
Subclavian Vein Thrombosis During Prolonged Catheterization for Parenteral Nutrition (1983)

The purpose of this study was to determine the immediate and long-term complications of subclavian vein thrombosis occurring during prolonged catheterization for parenteral nutrition. Ten cases of subclavian vein thrombosis documented by venography were initially treated by catheter removal, systemic heparin, and upper extremity elevation. Although fever was common (N = 9), only three patients had positive blood or catheter cultures and only one patient required antibiotic therapy. Nonfatal pulmonary embolism was suspected by lung scan in only one patient. After a follow-up period of six months to five years (mean two years), no long-term disability, such as arm swelling or pain, was identified. We conclude that immediate and late sequelae of catheter-associated subclavian vein thrombosis are minimized by prompt removal of the catheter, systemic administration of heparin to prevent clot propagation and embolism, and arm elevation to reduce early upper extremity edema.
Antibiotic resistance of bacterial biofilms (2010)

A biofilm is a structured consortium of bacteria embedded in a self-produced polymer matrix consisting of polysaccharide, protein and DNA. Bacterial biofilms cause chronic infections because they show increased tolerance to antibiotics and disinfectant chemicals as well as resisting phagocytosis and other components of the body's defence system. The persistence of, for example, staphylococcal infections related to foreign bodies is due to biofilm formation. Likewise, chronic Pseudomonas aeruginosa lung infection in cystic fibrosis patients is caused by biofilm-growing mucoid strains. Characteristically, gradients of nutrients and oxygen exist from the top to the bottom of biofilms and these gradients are associated with decreased bacterial metabolic activity and increased doubling times of the bacterial cells; it is these more or less dormant cells that are responsible for some of the tolerance to antibiotics. Biofilm growth is associated with an increased level of mutations as well as with quorum-sensing-regulated mechanisms. Conventional resistance mechanisms such as chromosomal beta-lactamase, upregulated efflux pumps and mutations in antibiotic target molecules in bacteria also contribute to the survival of biofilms. Biofilms can be prevented by early aggressive antibiotic prophylaxis or therapy and they can be treated by chronic suppressive therapy. A promising strategy may be the use of enzymes that can dissolve the biofilm matrix (e.g. DNase and alginate lyase) as well as quorum-sensing inhibitors that increase biofilm susceptibility to antibiotics.
Detecting and Preventing Cyber Insider Threats: A Survey (2018)

Information communications technology systems are facing an increasing number of cyber security threats, the majority of which are originated by insiders. As insiders reside behind the enterprise-level security defence mechanisms and often have privileged access to the network, detecting and preventing insider threats is a complex and challenging problem. In fact, many schemes and systems have been proposed to address insider threats from different perspectives, such as intent, type of threat, or available audit data source. This survey attempts to line up these works together with only three most common types of insider namely traitor, masquerader, and unintentional perpetrator, while reviewing the countermeasures from a data analytics perspective. Uniquely, this survey takes into account the early stage threats which may lead to a malicious insider rising up. When direct and indirect threats are put on the same page, all the relevant works can be categorised as host, network, or contextual data-based according to audit data source and each work is reviewed for its capability against insider threats, how the information is extracted from the engaged data sources, and what the decision-making algorithm is. The works are also compared and contrasted. Finally, some issues are raised based on the observations from the reviewed works and new research gaps and challenges identified.
Adversarial learning (2005)

Many classification tasks, such as spam filtering, intrusion detection, and terrorism detection, are complicated by an adversary who wishes to avoid detection. Previous work on adversarial classification has made the unrealistic assumption that the attacker has perfect knowledge of the classifier [2]. In this paper, we introduce the adversarial classifier reverse engineering (ACRE) learning problem, the task of learning sufficient information about a classifier to construct adversarial attacks. We present efficient algorithms for reverse engineering linear classifiers with either continuous or Boolean features and demonstrate their effectiveness using real data from the domain of spam filtering.
Effect of subvolume excitation and spin-torque efficiency on magnetic switching (2011)

Recently developed magnetic tunnel junctions with full perpendicular magnetization that are spin-torque switchable allow for quantitative comparison of spin-torque switching statistics with a macrospin model. For typical devices above 50 nm in lateral size, the comparison suggests the presence of subvolume magnetic excitations which often dominate the switching process and which degrade the spin-torque switching efficiency. A simple model of subvolume spin-torque-driven magnetic switching is presented to account for the experimental observations. The origin of the subvolume thermal excitation is traced to a competition between the macrospin fluctuation within a simple uniaxial anisotropy potential and that of thermal magnon excitation. The subvolume excitation problem highlights the importance of improving the magnetic exchange stiffness of the junction free layer, and the reduction of junction lateral sizes below 50 nm where an improved spin-torque efficiency is seen as the switching dynamics cross over to a more macrospin-like process.
Tumor Necrosis Factor-α Induces mRNA for Collagenase and Timp in Human Skin Fibroblasts (1990)

We demonstrated previously that growth promoting factors in general could induce the secretion of interstitial collagenase into the medium of human fibroblast cells (HF). In this study, the effect of tumor necrosis factor-alpha (TNF-alpha) on the induction of collagenase and tissue inhibitor of metalloproteinases (TIMP) was examined. Stimulation of quiescent HF cells with 10 ng/ml TNF-alpha induced the secretion of Mr 57,000, 52,000 procollagenases into the medium. The collagenase activity was elevated 2.8-fold after TNF-alpha treatment. Northern blot analysis of the steady-state mRNA indicated a tenfold elevation of collagenase transcript after 24 h treatment with 10 ng/ml TNF-alpha. The increase in collagenase mRNA was due to transcriptional activation of collagenase gene activity. TIMP mRNA level increased three-fold after TNF-alpha treatment. The activity of TNF-alpha on collagenase and TIMP induction may play an important role in tissue inflammatory, repair and remodeling processes after wound and injury.
A Strategic Approach for Prioritizing Research and Action to Prevent Suicide (2013)

It is time to strategically apply science and accountability to the public health problem of preventable suicide. U.S. suicide rates have remained stable for decades. More than 36,000 individuals now die by suicide each year. A public health-based approach to quickly and substantially reduce suicides requires strategic deployment of existing evidence-based interventions, rapid development of new interventions, and measures to increase accountability for results. The purpose of this Open Forum is to galvanize researchers to further develop and consolidate knowledge needed to guide these actions. As researchers overcome data limitations and methodological challenges, they enable better prioritization of high-risk subgroups for targeted suicide prevention efforts, identification of effective interventions ready for deployment, estimation of the implementation impact of effective interventions in real-world settings, and assessment of time horizons for taking implementation to scale. This new knowledge will permit decision makers to take strategic action to reduce suicide and stakeholders to hold them accountable for results.
Interaction of .BETA.-cyclodextrin with bile salts in aqueous solutions. (1986)

β-Cyclodextrin (β-CD) forms inclusion complexes with bile salts (sodium cholate, sodium deoxycholate, sodium glycocholate and sodium taurocholate) in aqueous solutions. In the presence of bile salts, the guest molecules of β-CD complexes are excluded from the cavity of β-CD and the free molecules increase with the concentration of bile salt up to cmc. Above cmc they are partitioned between the aqueous and micellar phases. Below cmc the exchange reaction proceeds depending on the formation constants of the guest molecule with β-CD and the concentration of bile salt. Above cmc, the free molecules in aqueous phase decrease with increasing concentration of bile salt because of the partitioning to the micellar phase. These results may be related to the absorption of β-CD complexes administered orally and also the metabolism of cholesterol when the complexes are administered orally for a long period of time.
An Intelligent Tool for All-to-All Sales on the Internet - Platform for Compilation of Commercial Offers and Requests for Companies and Customers (2015)

This paper deals with the issues of building an intelligent sales portal. The portal features include a price comparator, entering of individual offerings and requests for concrete and specific products and services. Product offers can be entered by choosing from predefined product options and specifications, or as new specifications. The paper describes matching of sales for new products, services and used goods. The design philosophy combines the features of product aggregators, advertising and second-hand sale systems and auctions with so-called fair direct offers in both public and anonymous offer and request proceedings. The implementation is designed for both companies presenting their products, services and requests, and ordinary customers and their individual offers and requests. The core system component is the intelligent search and offer/request matching process. The identical product-to-product matching model and searching based on product similarity is described. A model ideal product and most similar offer can be defined. The paper includes a discussion of the issue of working with a large quantity of highly structured data, their pre-processing and effective visualisation. The conclusion outlines the project ambitions in the area of building a European offer and request platform among business and customer clients.
Structure-Function Analysis of Nel, a Thrombospondin-1-like Glycoprotein Involved in Neural Development and Functions (2011)

Nel (neural epidermal growth factor (EGF)-like molecule) is a multimeric, multimodular extracellular glycoprotein with heparin-binding activity and structural similarities to thrombospondin-1. Nel is predominantly expressed in the nervous system and has been implicated in neuronal proliferation and differentiation, retinal axon guidance, synaptic functions, and spatial learning. The Nel protein contains an N-terminal thrombospondin-1 (TSP-N) domain, five cysteine-rich domains, and six EGF-like domains. However, little is known about the functions of specific domains of the Nel protein. In this study, we have performed structure-function analysis of Nel, by using a series of expression constructs for different regions of the Nel protein. Our studies demonstrate that the TSP-N domain is responsible for homo-multimer formation of Nel and its heparin-binding activity. In vivo, Nel and related Nell1 are expressed in several regions of the mouse central nervous system with partly overlapping patterns. When they are expressed in the same cells in vitro, Nel and Nell1 can form hetero-multimers through the TSP-N domain, but they do not hetero-oligomerize with thrombospondin-1. Whereas both the TSP-N domain and cysteine-rich domains can bind to retinal axons in vivo, only the latter causes growth cone collapse in cultured retinal axons, suggesting that cysteine-rich domains interact with and activate an inhibitory axon guidance receptor. These results suggest that Nel interacts with a range of molecules through its different domains and exerts distinct functions.
Structures of human genes coding for cytokine LD78 and their expression. (1990)

LD78 is a member of a newly identified superfamily of small inducible proteins involved in inflammatory responses, wound healing, and tumorigenesis. Southern blot analysis of the EcoRI-digested human genomic DNAs, using previously isolated LD78 cDNA as a probe, showed that in each individual there are 4.2- and 4.8-kilobase-pair (kb) fragments and that some have an additional 6.5-kb fragment. The 4.2-kb fragment contained genomic DNA sequences corresponding to the LD78 cDNA and was named the LD78 alpha gene. The 4.8-kb fragment contained similar sequences, showing 94% homology to the LD78 alpha gene, and was named the LD78 beta gene. The LD78 alpha gene was present in a single or a few copies per haploid genome, whereas the copy number of the LD78 beta gene and of the 6.5-kb fragment hybridizable to LD78 cDNA varied among the samples tested. Treatment of human myeloid cell lines HL-60 and U937 with phorbol 12-myristate 13-acetate (PMA) increased within 2 h cellular levels of the RNA hybridizable to LD78 cDNA. The human glioma cell line U105MG and primary culture of human fibroblasts also expressed the hybridizable RNA in response to PMA. Addition of cycloheximide had no apparent effect on this response in U937 cells and inhibited the response in fibroblasts, whereas it stimulated the response in HL-60 and U105MG cells. mRNA phenotyping experiments revealed that the LD78 alpha and LD78 beta genes were both transcribed in PMA-stimulated U937 cells.
Size of Intracranial Aneurysms (1983)

Abstract Intracranial aneurysms are common lesions, occurring in as many as 2% of the age-corrected population of North America. Most aneurysms are small and innocuous, but some will enlarge and rupture. The clinical frequency of intact aneurysms has been increasing as a result of computed tomographic scanning and digital subtraction angiography, and this trend can be expected to accelerate in the future. Intact aneurysms are an important neurosurgical problem. Once an aneurysm ruptures, there is an associated 50 to 60% overall mortality and morbidity. In contrast, surgical correction of an unruptured aneurysm in skilled hands carries a mortality and morbidity of approximately 3%. Obviously, the optimal time for correction of aneurysm is before it ruptures. For effective management of patients with intact aneurysms, prognostic criteria for rupture are clearly needed. Aneurysm size is both theoretically and empirically a key prognostic factor for rupture. However, the critical size at which an aneurysm becomes hazardous is not known. The purpose of this investigation was to study the size of ruptured aneurysms in an attempt to infer the behavior of unruptured aneurysms. The angiographic size of aneurysms in the 1092 patients admitted to the Cooperative Aneurysm Study between 1970 and 1977 was measured. The average maximal diameter was 8.2 + 3.9 (SD) mm, and the median diameter was 7.0 mm. Seventy-one per cent of the sacs were smaller than 10 mm and 13% were less than 5 mm in diameter. Middle cerebral artery aneurysms were the largest and anterior communicating artery aneurysms were the smallest. These data suggest that aneurysms less than 1 cm in diameter are hazardous and that operation should be considered for lesions more than approximately 5 mm in diameter. Additional prognostic factors for rupture are clearly needed.
Poly(o-aminobenzylphosphonic acid): a novel water soluble, self-doped functionalized polyaniline (1995)

A novel self-doped polymer having aikylphosphonic acid moieties on polyaniline is synthesized from persulfate oxidative coupling of O-aminobenzylphosphonic acid 3; the resulting polymer, apart from being water soluble in its self-doped monosodium salt form, demonstrates excellent redox stability when subjected to potentiometric cycling between 0.0 and 1.0 V.
Silicon-compatible low resistance S/D technologies for high-performance top-gate self-aligned InGaZnO TFTs with UTBB (ultra-thin body and BOX) structures (2015)

We have fabricated high-performance self-aligned top-gate InGaZnO TFTs with novel silicon-like source and drain (S/D) parasitic resistance (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SD</sub> ) reduction processes. Ar ion implantation (Ar I/I) formed S/D extension layers and reduced R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SD</sub> by inducing high-density carriers. First demonstration of self-aligned S/D metallization processes on InGaZnO surface (In-Ti alloy formation), just like silicidation, realized further R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">SD</sub> reduction. In addition, threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ) controllability by back-gate bias was enhanced by adopting thin InGaZnO body and BOX. Successful applications of these booster technologies developed for Si LSIs enable us to fabricate high-performance top-gate scaled InGaZnO TFT in 3D LSI.
Enhanced casein kinase II activity during mouse embryogenesis (1986)

Mouse embryos at various stages of development were used to study the relationship of protein kinase activities with normal embryogenesis. Casein kinase II (CKII) activity in developing mouse embryos shows a 3-4-fold activity increase at day 12 of gestation. Together with the CKII activity, increased phosphorylation of a 110-kDa protein is observed. Treatment of the embryo extracts with heparin, a highly specific inhibitor of CKII activity, results in a drastic reduction of the 110-kDa protein phosphorylation indicating that the protein might be a CKII-specific substrate. Rapidly proliferating mouse tumour cells also show an enhanced CKII activity. Here too, a 110-kDa phosphoprotein was the major phosphoryl acceptor. Partial proteolytic digestion shows that both proteins are identical. Other protein kinases tested (cAMP- and cGMP-dependent protein kinases) only show a basal level of enzyme activity with minor alterations throughout the different stages of embryogenesis investigated.