gebhart/patrepeval huggingface dataset:
Joint Quantization and Confidence-Based Generalized Combining Scheme for Cooperative Spectrum Sensing (2016)

Cooperative spectrum sensing can effectively protect licensed users from harmful interference and satisfy the quality-of-service requirements of secondary users (SUs) in cognitive radio networks. In this paper, a novel joint quantization and confidence-based generalized (JQCG) combining scheme is proposed. A centralized approach is considered for cooperative spectrum sensing with SUs using the energy detector as a local spectrum sensing scheme. The confidence level is calculated using a fuzzy logic membership function for each cooperative SU. In the proposed JQCG combining scheme, each cooperative SU transmits multiple bits instead of transmitting one bit (hard combining) or the complete test statistic (soft combining) to report local sensing results to the fusion center (FC). We also derive optimal weights (in Neyman–Pearson sense) for each quantized level at the FC to maximize the probability of detection for a given false alarm probability. The proposed JQCG combining scheme is validated by extensive simulation results showing that it has a comparable performance to the soft combining scheme with less overhead. Extensive computer simulations show that the JQCG combining scheme significantly outperforms the hard combining and existing quantized schemes for cooperative spectrum sensing.
A Vaccinia Virus Recombinant Transcribing an Alphavirus Replicon and Expressing Alphavirus Structural Proteins Leads to Packaging of Alphavirus Infectious Single Cycle Particles (2013)

Poxviruses and Alphaviruses constitute two promising viral vectors that have been used extensively as expression systems, or as vehicles for vaccine purposes. Poxviruses, like vaccinia virus (VV) are well-established vaccine vectors having large insertion capacity, excellent stability, and ease of administration. In turn, replicons derived from Alphaviruses like Semliki Forest virus (SFV) are potent protein expression and immunization vectors but stocks are difficult to produce and maintain. In an attempt to demonstrate the use of a Poxvirus as a means for the delivery of small vaccine vectors, we have constructed and characterized VV/SFV hybrid vectors. A SFV replicon cDNA was inserted in the VV genome and placed under the control of a VV early promoter. The replicon, transcribed from the VV genome as an early transcript, was functional, and thus capable of initiating its own replication and transcription. Further, we constructed a VV recombinant additionally expressing the SFV structural proteins under the control of a vaccinia synthetic early/late promoter. Infection with this recombinant produced concurrent transcription of the replicon and expression of SFV structural proteins, and led to the generation of replicon-containing SFV particles that were released to the medium and were able to infect additional cells. This combined VV/SFV system in a single virus allows the use of VV as a SFV delivery vehicle in vivo. The combination of two vectors, and the possibility of generating in vivo single-cycle, replicon containing alphavirus particles, may open new strategies in vaccine development or in the design of oncolytic viruses.
Spectral approximation of the IMSE criterion for optimal designs in kernel-based interpolation models (2013)

Abstract. We address the problem of computing IMSE-optimal designs for random fields inter-polation models. A spectral representation of the IMSE criterion is obtained from the eigendecom-position of the integral operator defined by the random field covariance kernel and the integration measure considered. The criterion can hence be evaluated without explicitly integrating the MSE and spectral truncation naturally defines an approximated criterion. The approach is of particular interest when a quadrature rule is used to approximate the integral of the MSE. In this situation and for quadrature designs (i.e., designs composed of quadrature points), the truncated criterion yields a significant reduction of the computational cost for multiple IMSE criterion evaluations. We present numerical experiments which illustrate that retaining a small number of eigenpairs is often sufficient to obtain an IMSE-optimal quadrature design while optimizing the truncated criterion. Key words. Random field model, interpolation, design of experiments, IMSE, integral operator,
A Nudix Enzyme Removes Pyrophosphate from Dihydroneopterin Triphosphate in the Folate Synthesis Pathway of Bacteria and Plants (2004)

Removal of pyrophosphate from dihydroneopterin triphosphate (DHNTP) is the second step in the pterin branch of the folate synthesis pathway. There has been controversy over whether this reaction requires a specific pyrophosphohydrolase or is a metal ion-dependent chemical process. The genome of Lactococcus lactis has a multicistronic folate synthesis operon that includes an open reading frame (ylgG) specifying a putative Nudix hydrolase. Because many Nudix enzymes are pyrophosphohydrolases, YlgG was expressed in Escherichia coli and characterized. The recombinant protein showed high DHNTP pyrophosphohydrolase activity with a K(m) value of 2 microM, had no detectable activity against deoxynucleoside triphosphates or other typical Nudix hydrolase substrates, required a physiological level (approximately 1 mM) of Mg(2+), and was active as a monomer. Essentially no reaction occurred without enzyme at 1 mM Mg(2+). Inactivation of ylgG in L. lactis resulted in DHNTP accumulation and folate depletion, confirming that YlgG functions in folate biosynthesis. We therefore propose that ylgG be redesignated as folQ. The closest Arabidopsis homolog of YlgG (encoded by Nudix gene At1g68760) was expressed in E. coli and shown to have Mg(2+)-dependent DHNTP pyrophosphohydrolase activity. This protein (AtNUDT1) was reported previously to have NADH pyrophosphatase activity in the presence of 5 mM Mn(2+) (Dobrzanska, M., Szurmak, B., Wyslouch-Cieszynska, A., and Kraszewska, E. (2002) J. Biol. Chem. 277, 50482-50486). However, we found that this activity is negligible at physiological levels of Mn(2+) and that, with 1 mM Mg(2+), AtNUDT1 prefers DHNTP and (deoxy) nucleoside triphosphates.
Expression of human O6-methylguanine-DNA methyltransferase in a DNA excision repair-deficient Chinese hamster ovary cell line and its response to certain alkylating agents. (1992)

A plasmid has been constructed in which the expression of human O6-methylguanine-DNA methyltransferase (MGMT) complementary DNA is driven by the Rous sarcoma virus promoter sequence. We had previously shown that transfection of this plasmid into Chinese hamster ovary (CHO) cells results in the expression of MGMT and in increased cellular resistance to N-methyl-N'-nitro-N-nitrosoguanidine and 1-(2-chloroethyl)-1-nitrosourea (CNU) but not N-nitroso-N-ethylurea (ENU). In the present study, the Rous sarcoma virus promoter-MGMT was transfected into DNA excision repair-deficient CHO UV41 cells to investigate the phenotype associated with MGMT expression in the absence of DNA excision repair. Both the UV41/MGMT and CHO/MGMT cells expressed similar levels of MGMT and exhibited a similar increased resistance to N-methyl-N'-nitro-N-nitrosoguanidine. The UV41 cells were 20-fold more sensitive to CNU than the wild-type CHO cells. Expression of MGMT increased the resistance to CNU about 6-fold in both cell lines, but the difference between the two cell lines attributable to the excision repair defect still persisted. The UV41 cells were 2- to 3-fold more sensitive than the wild-type CHO cells to the monofunctional alkylating agents 1-(2-hydroxyethyl)-1-nitrosourea and ENU, but the MGMT phenotype did not alter sensitivity. This suggests that alkylation at the O6 position of guanine has no role in cytotoxicity of ethylating agents and that monofunctional DNA damage has little role in the cytotoxicity of CNU. Since MGMT can prevent the formation of G-C interstrand cross-links formed by CNU, other excision repair-sensitive DNA adducts must play a major role in the sensitivity of UV41 cells to this bifunctional alkylating agent. These results suggest that DNA intrastrand cross-links may be major contributors to the cytotoxicity of CNU.
In lieu of swap: Analyzing compressed RAM in Mac OS X and Linux (2014)

The forensics community is increasingly embracing the use of memory analysis to enhance traditional storage-based forensics techniques, because memory analysis yields a wealth of information not available on non-volatile storage. Memory analysis involves capture of a system's physical memory so that the live state of a system can be investigated, including executing and terminated processes, application data, network connections, and more. One aspect of memory analysis that remains elusive is investigation of the system's swap file, which is a backing store for the operating system's virtual memory system. Swap files are a potentially interesting source of forensic evidence, but traditionally, most swap file analysis has consisted of string searches and scans for small binary structures, which may in some cases be revelatory, but are also fraught with provenance issues. Unfortunately, more sophisticated swap file analysis is complicated by the difficulty of capturing mutually consistent memory dumps and swap files, the increasing use of swap file encryption, and other issues. Fortunately, compressed RAM facilities, such as those in Mac OS X Mavericks and recent versions of the Linux kernel, attempt to reduce or eliminate swapping to disk through compression. The storage of compressed pages in RAM both increases performance and offers an opportunity to gather digital evidence which in the past would have been swapped out. This paper discusses the difficulty of analyzing swap files in more detail, the compressed RAM facilities in Mac OS X and Linux, and our new tools for analysis of compressed RAM. These tools are integrated into the open-source Volatility framework.
Spin trapping in photochemistry of coordination compounds (1982)

The application of spin-trapping technique to detect short-lived paramagnetic species formed during photochemical reactions of coordination compounds is reviewed. Interference of radical recombinations by scavenging action of spin traps has been pointed out to be important at high spin-trap concentrations only. Due to only a limited extent of side reactions, nitrosodurene and phenyl N-tert-butyl nitrone were found to be excellent spin traps for the study of photoreactions of metal complexes in nonpolar solutions, whereas 5,5-dimethyl pyrroline-1-oxide is recommended for aqueous solutions. Using these spin traps, both organic and inorganic radicals, e.g. H, Cl, N 3 , CN, OH, O 2 − , as well as solvated electrons and metal-centered free radicals have been detected during the photolysis of coordination compounds. The detection of singlet oxygen by reaction with 2,2,6,6-tetramethyl piperidine is briefly discussed.
<i>Bacillus thuringiensis</i> -toxin resistance management: Stable isotope assessment of alternate host use by <i>Helicoverpa</i> <i>zea</i> (2002)

Data have been lacking on the proportion of Helicovera zea larvae that develop on noncotton host plants that can serve as a refuge from selection pressure for adaptation to transgenic cotton varieties that produce a toxin from the bacterium Bacillus thuringiensis. We found that individual H. zea moths that develop as larvae on cotton and other plants with C3 physiology have a different ratio of 13C to 12C than moths that develop on plants with C4 physiology, such as corn. We used this finding in determining the minimum percentage of moths that developed on noncotton hosts in two cotton-growing areas. Our results indicate that local corn can serve as a refuge for H. zea in midsummer. Our results contrast dramatically with the prevailing hypothesis that the large majority of late-season moths are produced from larvae feeding on cotton, soybean, and other C3 plants. Typically, <50% of moths captured in August through October have isotope ratios indicative of larval feeding on C3 plants. In one October sample, 100% of the moths originated from C4 hosts even though C4 crops were harvested at least 1 mo earlier, and no common wild C4 hosts were available. These findings support other research indicating that many late-season H. zea moths captured in Louisiana and Texas are migrants whose larvae developed on corn in more northern locations. Our isotope data on moths collected in Texas early in the season indicate that the majority of overwintering H. zea do not originate from cotton-feeding larvae and may be migrants from Mexico. Non-Bt corn in Mexico and the U.S. corn belt appears to serve as an important refuge for H. zea.
Broadly Accessible Self-Consistent Field Theory for Block Polymer Materials Discovery (2016)

These are the examples in the publication cited below. They run with the OS-X executable that is also available in the UDC at https://hdl.handle.net/11299/223302 and the output can be analyzed using the polymer visual software at https://hdl.handle.net/11299/223303.
Quantification of Hepatitis C Virus (HCV) in Liver Specimens and Sera from Patients with Human Immunodeficiency Virus Coinfection by Using the Versant HCV RNA 3.0 (Branched DNA-Based) DNA Assay (2003)

The new generation assay Versant HCV RNA 3.0v (Bayer Diagnostics) was evaluated to quantify hepatitis C virus (HCV) RNA levels in liver biopsy specimens from patients with HCV and human immunodeficiency virus (HIV) coinfection. A total of 25 liver biopsies and sera collected at the time of liver biopsy were used. The efficiency of HCV RNA recovery from spiked samples was between 38.6 and 50.7%, and reproducible measurements of viral load were observed (the intra- and interrun coefficients of variation were 0.5 to 13% and 3.5 to 24.7%, respectively), with good specificity and sensitivity. Linearity was evaluated in the range of 96,154 to 769 IU/ micro g by using a serially diluted high-titer sample. Coinfected patients had high HCV RNA viral loads in serum and liver (498,471 IU/ml and 231,495 IU/ micro g, respectively), and both levels were correlated (r = 0.63; P < 0.01). The amount of hepatic HCV RNA was significantly higher among patients with genotype 1 than among patients with genotype 3 (P < 0.01). The virological end-of-treatment response in the serum was associated with a lower pretreatment intrahepatic HCV viral load (P = 0.03). The new version of b-DNA is a sensitive, specific, and reproducible method for quantitating HCV RNA in the liver. Given its positive analytical performance, the assay will be used to evaluate the HCV RNA levels in the serum and liver during follow-up of patients treated with an anti-HCV therapeutic regimen.
A Novel Subtype of Type 1 Diabetes Mellitus Characterized by a Rapid Onset and an Absence of Diabetes-Related Antibodies (2000)

Some patients with idiopathic type 1 diabetes have a nonautoimmune, fulminant disorder characterized by the absence of insulitis and of diabetes-related antibodies, a remarkably abrupt onset, and high serum pancreatic enzyme concentrations.
Novel mutations in the long isoform of the <i>USH2A</i> gene in patients with Usher syndrome type II or non-syndromic retinitis pigmentosa (2010)

At least one mutation was identified in 57-63% of USH2 cases and 19-23% of cases of non-syndromic recessive RP (calculated without and including probable/possible deleterious changes) thus supporting that USH2A is the most common known cause of RP in the USA.
Loss of CACNA2D2 expression in non-small cell lung cancer (2006)

4195 Genetic events at chromosome 3p have been implicated in the development of non-small cell lung carcinoma (NSCLC). A number of known and putative tumour-suppressor genes reside within this region, including CACNA2D2 . This is a candidate tumour-suppressor gene which is located at 3p21. Although CACNA2D2 expression has previously been analysed in some lung cancer cell lines, its role in the development of primary NSCLC has yet to be elucidated. In this study, expression of the CACNA2D2 gene was investigated in 55 paired (normal/tumour), surgically excised lung tissue samples from patients with NSCLC. Promoter methylation status and loss of heterozygosity (LOH) at 3p were investigated in 48 of these samples. expression levels of CACNA2D2 were studied using comparative multiplex RT-PCR and subsequent analysis on an Agilent Bioanalyser. We have also developed a pyrosequencing assay on bisulphite treated DNA to examine the methylation status of part of the CACNA2D2 promoter. Analysis was carried out on a PSQ96MA System. LOH was carried out using fluorescent microsatellite markers at three loci (D3S1289, D3S1300, and D3S1263) and analysis on a 377 ABI automated sequencer. CACNA2D2 was underexpressed in 49 (89%) of 55 lung tumours compared to their adjacent normal tissue counterparts. The CACNA2D2 promoter was hypermethylated, in at least one CpG site out of four examined, in 2 (4%) of 48 samples investigated. LOH was detected in 26 (67%) of 39, 26 (60%) of 43 and 23 (70%) of 33 informative cases in markers D3S1289, D3S1263 and D3S1300 respectively. Loss of CACNA2D2 expression was more frequent in tumours with positive than tumours with negative nodes (Fisher’s exact, p=0.05). There was no association between CACNA2D2 expression and histology, T stage, M status and differentiation. These data demonstrate that loss of CACNA2D2 expression is a very frequent event in the development of NSCLC. Promoter hypermethylation of CACNA2D2 is rare and doesn’t appear as a major mechanism accounting for this loss of expression. Other intrinsic or extrinsic factors may contribute to the transcriptional silencing of CACNA2D2 in the molecular pathogenesis of NSCLC. This research was funded by the Roy Castle Foundation UK.
Protein Folding: A Perspective from Theory and Experiment (1998)

The mechanism of protein folding (represented schematically below) is one of the most fascinating problems in the field of chemical reactions. This review presents the progess made recently in understanding key elements of this reaction and describes a solution to the often quoted Levinthal Paradox.
Flexible suspended gate organic thin-film transistors for ultra-sensitive pressure detection (2015)

The utilization of organic devices as pressure-sensing elements in artificial intelligence and healthcare applications represents a fascinating opportunity for the next-generation electronic products. To satisfy the critical requirements of these promising applications, the low-cost construction of large-area ultra-sensitive organic pressure devices with outstanding flexibility is highly desired. Here we present flexible suspended gate organic thin-film transistors (SGOTFTs) as a model platform that enables ultra-sensitive pressure detection. More importantly, the unique device geometry of SGOTFTs allows the fine-tuning of their sensitivity by the suspended gate. An unprecedented sensitivity of 192 kPa(-1), a low limit-of-detection pressure of <0.5 Pa and a short response time of 10 ms were successfully realized, allowing the real-time detection of acoustic waves. These excellent sensing properties of SGOTFTs, together with their advantages of facile large-area fabrication and versatility in detecting various pressure signals, make SGOTFTs a powerful strategy for spatial pressure mapping in practical applications.
Wired Drill Pipe Telemetry Enables Real-Time Evaluation of Kick During Managed Pressure Drilling (2010)

Abstract Distributed pressure sensors along the drill string from wired drill pipe telemetry, combined with real-time analysis of the data at the rig, may give valuable information to the drilling control system and the decision makers when utilized properly. The step change in bandwidth, reliability and availability lead to better premises for developing new technology for more advanced drilling methodology. In this paper, improved methodology for evaluation of kick in Managed Pressure Drilling (MPD) is presented based on this step change in availability of downhole pressure measurements. The objective of the presented methodology is to improve well control for MPD by faster and better diagnostics of flow interaction between well and formation and thereby reducing formation damage and non-productive time. A representative North-Sea well is used as test case geometry and an advanced well flow model is used as a virtual well in computer simulations that provide the basis for the presented results. The proposed methodology is demonstrated to estimate the depth of influx zones as well as the size and distribution of the kick. This will improve the handling of the influx incident, prevent the risk of hole stability problems and thereby reduce cost associated with non-productive time.
Differential Activities of the Ubiquitin–Proteasome System in Neurons versus Glia May Account for the Preferential Accumulation of Misfolded Proteins in Neurons (2008)

A variety of neurological disorders and polyglutamine (polyQ) diseases are caused by misfolded proteins. The common feature of these diseases is late-onset cellular degeneration that selectively affects neurons in distinct brain regions. polyQ diseases, including Huntington's disease (HD), present a clear case of selective neurodegeneration caused by polyQ expansion-induced protein misfolding, which also leads to predominant inclusions in neuronal nuclei. It remains unclear how these ubiquitously expressed disease proteins selectively kill neurons. In HD, mutant huntingtin accumulates in both neurons and glia, but more neuronal cells display huntingtin aggregates. These aggregates colocalize with components of the ubiquitin-proteasome system (UPS), which plays a critical role in clearing misfolded proteins. Using fluorescent reporters that reflect cellular UPS activity, we found that UPS activity in cultured neurons and glia decreases in a time-dependent manner. Importantly, UPS activity is lower in neurons than in glia and also lower in the nucleus than the cytoplasm. By expressing the UPS reporters in glia and neurons in the mouse brain, we also observed an age-dependent decrease in UPS activity, which is more pronounced in neurons than glial cells. Although brain UPS activities were similar between wild-type and HD 150Q knock-in mice, inhibiting the UPS markedly increases the accumulation of mutant htt in cultured glial cells. These findings suggest that the lower neuronal UPS activity may account for the preferential accumulation of misfolded proteins in neurons, as well as their selective vulnerability.
Heterogeneously Integrated III-V/Si Mach-Zehnder Modulator (2018)

A heterogeneously integrated metal-oxide-semiconductor capacitor Mach-Zehnder modulator with an n-type InGaAsP layer shows V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">π</sub> L of 0.09 Vcm. It overcomes the V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">π</sub> L limit of conventional Si modulators without degrading the optical loss.
Malignant melanoma: prevention, early detection, and treatment in the 21st century (2000)

Malignant melanoma continues to present a significant public health problem as its incidence is rising faster than that of any other cancer in the US. At current rates, 1 in 74 Americans will develop melanoma during his or her lifetime. Management of melanoma is a complex issue requiring a multidisciplinary approach. The most effective method of protection against the development of melanoma is minimization of ultraviolet exposure from sunlight. Early detection and treatment are critical and result in improved patient survival rates. Surgical excision remains the mainstay of treatment but many new promising therapies are being investigated. It is hoped that increased public and professional awareness and education in all areas relating to the prevention, detection, and treatment of malignant melanoma will contribute to decreasing trends in the incidence and mortality from this cancer in the future.