gebhart/patrepeval huggingface dataset:
Pan-cancer analysis of bi-allelic alterations in homologous recombination DNA repair genes (2017)

BRCA1 and BRCA2 are involved in homologous recombination (HR) DNA repair and are germ-line cancer pre-disposition genes that result in a syndrome of hereditary breast and ovarian cancer (HBOC). Whether germ-line or somatic alterations in these genes or other members of the HR pathway and if mono- or bi-allelic alterations of HR-related genes have a phenotypic impact on other cancers remains to be fully elucidated. Here, we perform a pan-cancer analysis of The Cancer Genome Atlas (TCGA) data set and observe that bi-allelic pathogenic alterations in homologous recombination (HR) DNA repair-related genes are prevalent across many malignancies. These bi-allelic alterations often associate with genomic features of HR deficiency. Further, in ovarian, breast and prostate cancers, bi-allelic alterations are mutually exclusive of each other. The combination of these two properties facilitates reclassification of variants of unknown significance affecting DNA repair genes, and may help personalize HR directed therapies in the clinic.Germline mutations in homologous recombination (HR) DNA repair genes are linked to breast and ovarian cancer. Here, the authors show that mutually exclusive bi-allelic inactivation of HR genes are present in other cancer types and associated with genomic features of HR deficiency, expanding the potential use of HR-directed therapies.
An Improved FEC Scheme for Mobile Wireless Communication at Vehicular Speeds (2008)

WiMAX has emerged as a promising wireless communication technology with potential to deliver high throughput and guaranteed quality of service to the end applications. Recent studies suggest that while WiMAX (802.16e) is capable of delivering a data rate of up to 75 Mbps for fixed wireless communications, data rate decreases drastically for mobile wireless communications, often providing a data rate less than 1 Mb/s when the mobile nodes travel at vehicular speeds. High bit error rate caused at high vehicular speeds is the key reason for low throughput. In noisy mobile communication environments, standard error control mechanisms like the transmission control protocol (TCP) has limited and often detrimental impacts on the overall throughput because of the excessive retransmission overheads. To address this issue, WiMAX standard incorporates forward error correction (FEC) mechanism that eliminates the need for retransmissions. In FEC, extra parity bits are added to the original message to recover the corrupted information. Adaptive FEC that adjusts the size of extra parity bits in response to packet retransmission requests is an enhancement over standard FEC that uses fixed block of party bits. Existing adaptive FEC schemes, however, have limited efficiency when the end terminal moves at vehicular speeds. In this paper, we propose a new FEC scheme that estimates and adjusts the size of extra parity bits to suit the channel conditions. We apply the concept of interval based data sampling to address the dynamic nature of communication environments at high vehicular speeds.
Liposome-mediated delivery of antiviral agents to human immunodeficiency virus-infected cells (1999)

Intracellular delivery of novel macromolecular drugs against human immunodeficiency virus type-1 (HIV-1), including antisense oligodeoxynucleotides, ribozymes and therapeutic genes, may be achieved by encapsulation in or association with certain types of liposomes. Liposomes may also protect these drugs against nucleases. Low-molecular-weight, charged antiviral drugs may also be delivered more efficiently via liposomes. Liposomes were targeted to HIV-1-infected cells via covalently coupled soluble CD4. An HIV-1 protease inhibitor encapsulated in conventional negatively charged multilamellar liposomes was about 10-fold more effective and had a lower EC90 than the free drug in inhibiting HIV-1 production in human monocyte-derived macrophages. The drug encapsulated in sterically stabilized liposomes was as effective as the free drug. The EC50 of the reverse transcriptase inhibitor 9-(2-phosphonylmethoxyethyl)adenine (PMEA) was reduced by an order of magnitude when delivered to HIV-1-infected macrophages in pH-sensitive liposomes. A 15-mer antisense oligodeoxynucleotide against the Rev response element was ineffective in free form against HIV-1 replication in macrophages, while delivery of the oligonucleotide in pH-sensitive liposomes inhibited virus replication. The oligodeoxynucleotide encapsulated in sterically stabilized pH-sensitive liposomes with prolonged circulation in vivo, which were recently developed in the laboratories of the authors, was also highly effective. A ribozyme complementary to HIV-1 5'-LTR delivered in pH-sensitive liposomes inhibited virus production by 90%, while the free ribozyme caused only a slight inhibition. Cationic liposome-mediated co-transfection of the HIV-regulated diphtheria toxin A fragment gene and a proviral HIV clone into HeLa cells completely inhibited virus production, while the frame-shifted mutant gene was ineffective. Co-transfection of the proviral genome and a gene encoding a Rev-binding aptamer into HeLa cells via transferrin-associated cationic liposomes inhibited virus production. These studies indicate that liposomes can be used to facilitate the intracellular delivery of certain anti-HIV agents and to enhance their therapeutic effects. These properties may be particularly advantageous in the development of novel macromolecular drugs, which may be necessary because of the emergence of virus strains resistant to the currently available drugs.
Adaptive fuzzy segmentation of magnetic resonance images (1999)

An algorithm is presented for the fuzzy segmentation of two-dimensional (2-D) and three-dimensional (3-D) multispectral magnetic resonance (MR) images that have been corrupted by intensity inhomogeneities, also known as shading artifacts. The algorithm is an extension of the 2-D adaptive fuzzy C-means algorithm (2-D AFCM) presented in previous work by the authors. This algorithm models the intensity inhomogeneities as a gain field that causes image intensities to smoothly and slowly vary through the image space. It iteratively adapts to the intensity inhomogeneities and is completely automated. In this paper, we fully generalize 2-D AFCM to three-dimensional (3-D) multispectral images. Because of the potential size of 3-D image data, we also describe a new faster multigrid-based algorithm for its implementation. We show, using simulated MR data, that 3-D AFCM yields lower error rates than both the standard fuzzy C-means (FCM) algorithm and two other competing methods, when segmenting corrupted images. Its efficacy is further demonstrated using real 3-D scalar and multispectral MR brain images.
A Framework for Building Collaborative Applications (2004)

The advent of the Internet has been driven by the relentless effort of decades of research to develop a digital environment that would facilitate collaborative work on a global scale. The popularity of the Internet soared when the world saw the potential of the World Wide Web (WWW) as an Internet-based tool for sharing digital media and communicating. The success of the WWW has been so tremendous that most of the effort invested in the development of Internet-based tools are focused on improving the WWW rather than investigating other forms of collaboration. Another explanation behind why there are so few collaborative applications is because it can be quite complicated to design and develop them. To this end, we propose in this thesis a framework written in Java that would facilitate the development of collaborative tools. It does so by providing ready-made mechanisms such as, concurrency control which is common in every such applications. This study undertakes a constructive approach by identifying those features of
A cost-effective method to enhance adenoviral transduction of primary murine osteoblasts and bone marrow stromal cells (2016)

We report here a method for the use of poly-l-lysine (PLL) to markedly improve the adenoviral transduction efficiency of primary murine osteoblasts and bone marrow stromal cells (BMSCs) in culture and in situ, which are typically difficult to transduce. We show by fluorescence microscopy and flow cytometry that the addition of PLL to the viral-containing medium significantly increases the number of green fluorescence protein (GFP)-positive osteoblasts and BMSCs transduced with an enhanced GFP-expressing adenovirus. We also demonstrate that PLL can greatly enhance the adenoviral transduction of osteoblasts and osteocytes in situ in ex vivo tibia and calvaria, as well as in long bone fragments. In addition, we validate that PLL can improve routine adenoviral transduction studies by permitting the use of low multiplicities of infection to obtain the desired biologic effect. Ultimately, the use of PLL to facilitate adenoviral gene transfer in osteogenic cells can provide a cost-effective means of performing efficient gene transfer studies in the context of bone research.
Restoration of TNF-α-induced ceramide generation and apoptosis in resistant human leukemia KG1a cells by the P-glycoprotein blocker PSC833 (1998)

Tumor necrosis factor (TNF-alpha) is a cytokine with antitumor activity against several cellular models. TNF-alpha-induced apoptosis seems to be mediated by a signaling pathway termed 'sphingomyelin-ceramide' pathway, which consists of the hydrolysis of sphingomyelin and the production of its breakdown product ceramide. Our study shows that KG1a cells, which are inherently resistant to TNF-alpha and do not produce ceramide upon cytokine stimulation, can be sensitized by the use of the P-glycoprotein inhibitor PSC833. Coincubation with 1 microM of this cyclosporin derivative restored the apoptotic potential of 10 ng/ml TNF-alpha. This effect was associated with the restoration of ceramide generation (315%) and activation of neutral, but not acid sphingomyelinase activity (143%). Furthermore, we demonstrate that treatment of KG1a cells with 1 microM PSC833 led to a threefold increase in inner plasma membrane sphingomyelin content and basal neutral sphingomyelinase activity. These results support the hypothesis whereby resistance to TNF-alpha-mediated apoptosis of certain leukemic cells is linked to the disposability of the sphingomyelin pool. These data also suggest a role for P-glycoprotein in sphingomyelin transverse plasma membrane asymmetry.
The Use of Graphene as Stripper Foils in the Siemens Eclipse Cyclotron (2017)

This paper presents the results of an experimental study for the use of graphene foils as an extractor (stripper) foil in the 11-MeV Siemens Eclipse Cyclotron. The main advantage of graphene foils compared with carbon and graphite foils is its very high thermal conductivity. The graphene also has significant mechanical strength for atomically thin carbon layers. The life time of these foils is more than 1,8 times more in compare with specification. The graphene foils showed a significant increase in the transmission factor (the ratio of the beam current on the stripper foil to the current on the target), which was approximately 90%. The technology in fabricating these graphene foils is shown. The pros and cons of using the graphene material as a stripper foil in cyclotrons are analyzed.
Automated up- and downlink capacity balancing in WCDMA networks (2007)

Dynamic optimization of UMTS systems has been gaining a growing interest by the research community. In this context, the current paper concentrates on dynamic automated tuning of RRM parameters to detect whether the uplink or the downlink is the limiting link and force a reconfiguration to balance both and maximize capacity. Modifications of the soft handover algorithm are revealed as a feasible solution to achieve this objective. A three blocks based functional architecture is described to adapt parameters to service mix dynamics and overcome capacity problems. Conducted tests show the feasibility of the approach. Effective adaptation to changes in traffic patterns and significant capacity gains are obtained.
Stimulation of L-ornithine uptake and L-citrulline and urea biosynthesis by D-arginine. (1991)

The action of D-arginine on isolated cells and mitochondria obtained from rat liver was studied. The D-amino acid at 200 microM stimulated by 40% the rate of urea biosynthesis by isolated hepatocytes. Citrulline formation was increased 60-70% in rat liver mitochondria incubated with 10 microM D-arginine. In these mitochondria, ornithine uptake was enhanced 204% with 1 microM D-arginine. Inhibition in urea and citrulline synthesis and in ornithine uptake was recorded with high concentrations of the D-amino acid. Respiratory control in liver mitochondria with glutamate-malate was inhibited 32% by 100 microM D-arginine. In isolated mitochondria loaded with Fluo-3-acetoxymethyl (AM) ester, 50 microM D-arginine diminished the matrix free calcium concentration.
Integrated genomic analysis of triple-negative breast cancers reveals novel microRNAs associated with clinical and molecular phenotypes and sheds light on the pathways they control (2013)

This study focuses on the analysis of miRNAs expression data in a cohort of 181 well characterised breast cancer samples composed primarily of triple-negative (ER/PR/HER2-negative) tumours with associated genome-wide DNA and mRNA data, extensive patient follow-up and pathological information. We identified 7 miRNAs associated with prognosis in the triple-negative tumours and an additional 7 when the analysis was extended to the set of all ER-negative cases. miRNAs linked to an unfavourable prognosis were associated with a broad spectrum of motility mechanisms involved in the invasion of stromal tissues, such as cell-adhesion, growth factor-mediated signalling pathways, interaction with the extracellular matrix and cytoskeleton remodelling. When we compared different intrinsic molecular subtypes we found 46 miRNAs that were specifically expressed in one or more intrinsic subtypes. Integrated genomic analyses indicated these miRNAs to be influenced by DNA genomic aberrations and to have an overall influence on the expression levels of their predicted targets. Among others, our analyses highlighted the role of miR-17-92 and miR-106b-25, two polycistronic miRNA clusters with known oncogenic functions. We showed that their basal-like subtype specific up-regulation is influenced by increased DNA copy number and contributes to the transcriptional phenotype as well as the activation of oncogenic pathways in basal-like tumours. This study analyses previously unreported miRNA, mRNA and DNA data and integrates these with pathological and clinical information, from a well-annotated cohort of breast cancers enriched for triple-negative subtypes. It provides a conceptual framework, as well as integrative methods and system-level results and contributes to elucidate the role of miRNAs as biomarkers and modulators of oncogenic processes in these types of tumours.
A Seamless Handoff Mechanism for DHCP-Based IEEE 802.11 WLANs (2007)

IEEE 802.11 wireless networks have gained great popularity. However, handoff is always a critical issue in this area. In this paper, we propose a novel seamless handoff mechanism for IEEE 802.11 wireless networks which support IEEE 802.11i security standard. Our approach consists of a dynamic tunnel establishing procedure and a seamless handoff mechanism. Both intra- and inter-subnet handoff cases are considered in our seamless handoff approach. Our work focuses on handoffs in DHCP-based IP networks rather than mobile IP-supported networks, but the proposed scheme can be easily tailored to mobile IP-supported networks.
Purification and partial characterization of two thioredoxins from Streptomyces aureofaciens (1996)

Thioredoxins are low molecular weight proteins, which participate in a wide spectrum of biochemical reactions. Two thioredoxins from Streptomyces aureofaciens 3239 have been purified to homogeneity by a sequence of chromatography steps including chromatography on Sephacryl S-300, Phenyl Sepharose CL 4B and MonoQ HR 5/5. Thioredoxin activity clearly separates into two protein fractions on MonoQ HR 5/5 chromatography. Molecular weights determined by chromatography on Superose 12 HR 10/30 and sodium dodecyl sulphate polyacrylamide gel electrophoresis revealed M(r) approximately 10,500 for thioredoxin 1 (TR1) and M(r) approximately 11,000 for thioredoxin 2 (TR2). The isoelectric points of the two thioredoxins are different pI = 4.7 for TR1 and 5.6 for TR2, respectively. Both were effectively reduced with NADPH in reaction catalyzed by Streptomyces aureofaciens thioredoxin reductase. The specific activity of viewly for discovered TR2 is about 1/4 of the specific activity of TR1. Both thioredoxins activate spinach NADPH-malate dehydrogenase. Activation of this enzyme by TR2 is only half effective than by TR1. The stability of TR1 is high and similar to thioredoxins from other organisms unlike the activity of TR2 which is decreased during purification. The proteins diversed in their contents in exponentially growing mycelium.
Effects of Artificial Defoliation of Pines on the Structure and Physiology of the Soil Fungal Community of a Mixed Pine-Spruce Forest (2005)

Loss of photosynthetic area can affect soil microbial communities by altering the availability of fixed carbon. We used denaturing gradient gel electrophoresis (DGGE) and Biolog filamentous-fungus plates to determine the effects of artificial defoliation of pines in a mixed pine-spruce forest on the composition of the fungal community in a forest soil. As measured by DGGE, two fungal species were affected significantly by the defoliation of pines (P < 0.001); the frequency of members of the ectomycorrhizal fungus genus Cenococcum decreased significantly, while the frequency of organisms of an unidentified soil fungus increased. The decrease in the amount of Cenococcum organisms may have occurred because of the formation of extensive hyphal networks by species of this genus, which require more of the carbon fixed by their host, or because this fungus is dependent upon quantitative differences in spruce root exudates. The defoliation of pines did not affect the overall composition of the soil fungal community or fungal-species richness (number of species per core). Biolog filamentous-fungus plate assays indicated a significant increase (P < 0.001) in the number of carbon substrates utilized by the soil fungi and the rate at which these substrates were used, which could indicate an increase in fungal-species richness. Thus, either small changes in the soil fungal community give rise to significant increases in physiological capabilities or PCR bias limits the reliability of the DGGE results. These data indicate that combined genetic and physiological assessments of the soil fungal community are needed to accurately assess the effect of disturbance on indigenous microbial systems.
Completion time multiple branch prediction for enhancing trace cache performance (2000)

The need for multiple branch prediction is inherent to wide instruction fetching. This paper presents a completion time multiple branch predictor called the Tree-based Multiple Branch Predictor (TMP) that builds on previous single branch prediction techniques. It employs a tree structure of branch predictors, or tree-node predictors, and achieves accurate multiple branch prediction by leveraging the high accuracies of the individual branch predictors. A highly-efficient TMP design uses the 2-bit saturating counters for the tree-node predictors. To achieve higher prediction rate, the TMP employs two-level schemes for the tree-node predictors resulting in a three-level TMP design. Placing the TMP at completion time reduces the critical latency in the front-end of the pipeline; the resultant longer update latency does not significantly impact the overall performance. In this paper the TMP is applied to a trace cache design and shown to be very effective in increasing its performance.
Design and Implementation of a Data Mining Query Processor (2001)

A data mining system includes various data mining functions such as aggregation, association and classification, among others. To express these data mining function, a powerful data mining query language is needed. In addition, a graphic user interface(GUI) based on the data mining query language is needed for users. In addition, processing a data mining query targeted for a data warehouse, which is the appropriate data repository for decision making, is needed. In this paper, we first build a GUI to enable users to easily define data mining queries. We then propose a data mining query processing framework that can be used to process a data mining query targeted for a data warehouse. We also implement a schema generate a data warehouse schema that is needed to build a data warehouse. Lastly, we show the implementation details of a query processor that can process queries that discover association rules.
Strong Excitonic Emission from (001)-Oriented Diamond P–N Junction (2005)

We have succeeded in fabricating (001)-oriented diamond p – n junctions with good diode characteristics and realized UV light emission by current-injection at room temperature. As p – n junctions, a phosphorus-doped n -type layer was formed on (001)-oriented boron-doped p -type one by applying an optimized homoepitaxial growth technique based on micro-wave plasma-enhanced chemical vapor deposition. Current–voltage characteristics showed a rectification ratio of 10 6 at ±30 V at room temperature. The existence of the space-charge layer through the p – n junction was confirmed from capacitance–voltage characteristics. A strong UV light emission at 235 nm was observed at forward current over 20 mA and is attributed to free exciton recombination.
Characterization of the stilbenedisulphonate binding site on band 3 Memphis variant II (Pro-854→Leu) (1996)

Band 3 Memphis variant II is a mutant anion-exchange protein associated with the Diego a+ blood group antigen. There are two mutations in this transporter: Lys-56-->Glu within the cytoplasmic domain, and Pro-854-->Leu within the membrane-bound domain. The Pro-854 mutation, which is thought to give rise to the antigenicity, is located within the C-terminal subdomain of the membrane-bound domain. Yet, there is an apparent enhancement in the rate of covalent binding of H2DIDS (4,4'-di-isothiocyanatodihydro-2, 2'-stilbenedisulphonate) to 'lysine A' (Lys-539) in the N-terminal subdomain, suggesting widespread conformational changes. In this report, we have used various kinetic assays which differentiate between conformational changes in the two subdomains, to characterize the stilbenedisulphonate site on band 3 Memphis variant II. We have found a significantly higher H2DIDS (a C-terminal-sensitive inhibitor) affinity for band 3 Memphis variant II, due to a lower H2DIDS 'off' rate constant, but no difference was found between mutant and control when DBDS (4,4'-dibenzamido-2,2'-stilbenedisulphonate) (a C-terminal-insensitive inhibitor) 'off' rates were measured. Furthermore, there were no differences in the rates of covalent binding to lysine A, for either DIDS (4,4'-di-isothiocyanato-2,2'-stilbenedisulphonate) or H2DIDS. However, the rate of covalent intrasubunit cross-linking of Lys-539 and Lys-851 by H2DIDS was abnormally low for band 3 Memphis variant II. These results suggest that the Pro-854-->Leu mutation causes a localized conformational change in the C-terminal subdomain of band 3.