gebhart/patrepeval huggingface dataset:
Rapid HLA‐DRB1 genotyping by nested PCR amplification (1992)

State of the art genotyping of HLA class II alleles with group-specific DNA amplification by the polymerase chain reaction (PCR) (1) and subsequent probing with sequence-specific oligonucleotides (2-4) is not suitable for typing cadaveric organ donors since the typing procedure takes far more than one working day. We designed specific oligonucleotide primer sets for nested PCR amplification which allowed typing for all serological HLA-DR specificities (DR1-DRw18) solely by the detection of amplified DNA in the reaction mixtures after agarose gel electrophoresis. Exon 2 of the DRB genes and a DRw52-group-specific part of DRB1 exon 2 was amplified directly from cell lysates without prior DNA extraction. The amplified DNA was subjected to a second round of amplification, which employed a set of 18 nested allele- or group-specific primer pairs. All alleles which have at least a single mismatched base at the terminal 3'-nucleotide of one primer were completely refractory to amplification. This assay is easy to perform and takes less than one working day to complete. Thus, this method may prove to be suitable for DNA typing of organ donors for prospective HLA-DR matching in renal transplantation.
The case for ethernet in automotive communications (2011)

Several factors seem to favor the introduction of Ethernet technology in automotive communications. The spreading of Ethernet as an in-vehicle network for today's cars or for those in the near future is being broadly announced by spokespersons for major carmakers and automotive electronics companies. Even in the scientific community there is a growing interest in the topic, shown by the increasing number of studies on the performance of Ethernet-based technologies such as Switched Ethernet or Time-Triggered Ethernet in automotive embedded systems. This position paper provides an overview on facts and trends towards the introduction of Ethernet in automotive communications and discusses how and to what extent Ethernet technology is likely to step in and provide benefits to the different automotive functional domains. The paper will also discuss which Ethernet technologies would be the possible candidates for the automotive industry.
Failure of highly purified lysyl hydroxylase to hydroxylate lysyl residues in the non-helical regions of collagen (1985)

The activity of highly purified lysyl hydroxylase towards lysyl residues within both the helical and the N-terminal non-helical telopeptide regions of chick type I collagen has been examined. The peptides alpha 1(I)-CB1 and alpha 2(I)-CB1, isolated from protocollagen following CNBr digestion and containing the N-terminal telopeptidyl lysyl residues, failed themselves to act as substrates. With protocollagen as substrate, analysis of products obtained following bacterial collagenase digestion of the reaction mixture showed that overall 37% hydroxylation of lysyl residues within the helical region of collagen had been obtained, which may be maximal. No hydroxylation, however, of the single lysyl residue in either alpha 1(I)-CB1 or alpha 2(I)-CB1, isolated following CNBr digestion of the reaction mixture, was observed, despite the known susceptibility of these residues to hydroxylation. These findings provide strong circumstantial evidence for the suggestion that a lysyl hydroxylase specific for the telopeptidyl residues and distinct from that active towards lysyl residues in the helical portion of the molecule may exist [Barnes, Constable, Morton & Royce (1974) Biochem. J. 139, 461-468].
Melanin content of hamster tissues, human tissues, and various melanomas. (1981)

Melanin content (percentage by weight) was determined in both pigmented and nonpigmented tissues of Syrian golden hamsters bearing Greene melanoma. Melanin content was also measured in various other melanoma models (B-16 in C57 mice, Harding-Passey in BALB/c mice, and KHDD in C3H mice) and in nine human melanomas, as well as in selected normal tissues. The purpose was to evaluate the possible efficacy of chlorpromazine, which is known to bind to melanin, as a vehicle for boron transport in neutron capture therapy. Successful therapy would depend upon selective uptake and absolute concentration of borated compounds in tumors; these parameters will in turn depend upon melanin concentration in melanomas and nonpigmented "background" tissues. Hamster whole eyes, hamster melanomas, and other well-pigmented animal melanomas were found to contain 0.3 to 0.8% melanin by weight, whereas human melanomas varied from 0.1 to 0.9% (average, 0.35%). Other tissues, with the exception of skin, were lower in content by a factor of greater than or equal to 30. Melanin pigment was extracted from tissues, and the melanin content was determined spectrophotometrically. Measurements were found to be sensitive to the presence of other proteins. Previous procedures for isolating and quantifying melanin often neglected the importance of removing proteins and other interfering nonmelanic substances.
The Electro-Acoustic Sensitivity of Cylindrical Ceramic Tubes (1954)

Increasing use is being made of cylindrical barium titanate tubes as underwater acoustic transducers. An exact derivation is given for the low-frequency acoustic sensitivity of such tubes for a variety of boundary and polarization conditions.
Programmable floating-gate MOS logic for low-power operation (2002)

In this paper we propose a novel technique for programming floating gate MOS transistors (FGMOS) in low-power design. By threshold-shifting low-power operation is possible with the cost of an extra polysilicon layer. Combining the FGMOS transistor with a UV-activated (UV) conductance gives rise to the UV-light programmable floating-gate MOS (FGUVMOS) transistor. The FGUVMOS transistor is utilized to increase the efficiency at low supply voltages.
Robust TiN HM process to overcome under etch issue for SAV scheme on 14nm node (2015)

For advance node such as 14nm technology and beyond, back end of line interconnect has implemented self-aligned via (SAV) schemes for better via-metal short process window [1]. A TiN metal hard mask (MHM) is used for the trench pattern definition, after which via lithography and partial via (PV) etch is performed where the TiN was opened. The via etch condition has very good selectivity so that via is formed in a self-aligned fashion by TiN HM [2]. It is indeed to have significant benefit of via to metal short [3]. However, one of the trade off in SAV scheme is the via under etch that whether or not via can well land on an opened oxide area during PV etch. To define the contact area between via resist hole and opened HM oxide as an effective area for via to open successfully. “Fig. 1” shows the effective area change during process variation due to Via alignment, Via photo resist CD variation (Via ADICD) and post hard mask etch CD variation (AMICD). “Fig. 2” shows the mechanism of this under etch failure mode and typical TEM image from 64nm metal pitch test vehicle. In this work, we try to enlarge the process window by an aggressive AMICD targeting in combining with a higher density TiN material to maintain profile.
Compressibility of Helium-Nitrogen Mixtures. (1960)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCompressibility of Helium-Nitrogen Mixtures.J. E. Miller, Lowell Stroud, and L. W. BrandtCite this: J. Chem. Eng. Data 1960, 5, 1, 6–9Publication Date (Print):January 1, 1960Publication History Published online1 May 2002Published inissue 1 January 1960https://pubs.acs.org/doi/10.1021/je60005a002https://doi.org/10.1021/je60005a002research-articleACS PublicationsRequest reuse permissionsArticle Views178Altmetric-Citations8LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Prevalence of homologous recombination deficiency among all tumor types. (2017)

1502 Background: Triple negative breast and ovarian cancer are known to have a high frequency of homologous recombination deficiencies (HRDef). The prevalence of HRDef among all tumors is unknown. Methods: Molecular profiles of 48,733 tumors obtained from pts with bladder, breast, ovarian, pancreas, prostate, thyroid, cervical, hepatobiliary, colorectal (CRC), endometrial, gastric/esophageal (GE), head/neck, renal, non-small cell lung (NSCLC), small cell lung (SCLC), GIST, glioma, melanoma, sarcoma and unknown 1° cancers were reviewed to identify somatic pathogenic mutations (mut) in HR genes ATM, ATRX, BARD1, BLM, BRCA1/2, BRIP1, FANCA/C/D2/E/F/G/L, MRE11A, NBN, PALB2, PTEN, RAD50, RAD51, RAD51B, or WRN. Molecular profiles were generated from tumors submitted to Caris Life Sciences using multiple technologies including next generation sequencing (average read depth 500X). Results: Overall frequency of HR mut among all tumors is 11.61% (5658/48733). Cancer lineages with highest frequency of HR mut are endometrial (38.08%, 1956/5137), glioma (15.90%, 265/1667), ovarian (12.99%, 1151/8862), prostate (11.21%, 77/687), cervix (10.06%, 79/785) & breast (9.66%, 562/5818). Least commonly mutated lineages include GIST (1.50%, 3/200), sarcoma (3.12%, 55/1763), head/neck (3.70%, 24/648), hepatobiliary (4.72%, 39/827) & pancreas (5.05%, 102/2022). Frequencies of HR gene mutations are depicted in Table 1. Conclusions: HR mutations were seen in 11.61% of tumors. While the percentage of HRDef in pancreatic cancer pts is lower than what has been seen in other datasets, the percentage in breast and ovarian cancer, as well as the percentage of other tumors with HRDef, provide a path to employ HRDef-directed therapies such as platinums, but especially PARP inhibitors and newer agents such as ATRX inhibitors. [Table: see text]
A multilingual-supporting dialog system across multiple domains (2003)

This paper presents a multilingual-supporting dialog system that was implemented in Chinese and Japanese in tasks of sightseeing, accommodation-seeking and PC assembling guidance. Such a dialog system benefits from three main methods we proposed, including case frame conversion, template-based text generation and topic frame driven dialog control scheme. The former two methods are for improving the portability across languages, and the last one is for improving the portability across domains. The case frame conversion is used for translating a case frame described in a particular language into that described in a pivot language. The template-based text generation is used for generating text responses in a particular language from abstract responses described in the pivot language. The topic frame driven dialog control scheme makes it possible to manage mixed-initiative dialog based on a set of task-dependent topic frames. Both Chinese and Japanese experiments in several domains showed that the three methods proposed could be used to improve the portability of the dialog system across domains and languages.
Uncertainty Quantification in Metamodel-Based Reliability Prediction (2016)

Optimization under uncertainty has been studied in two directions — (1) Reliability-based Design Optimization (RBDO), and (2) Robust Design Optimization (RDO). One of the crucial elements in an RBDO problem is reliability analysis. Reliability analysis is affected by different types of epistemic uncertainty, due to inadequate data and modeling errors, along with aleatory uncertainty in input random variables. When the original physics-based model is computationally expensive, a metamodel has often been used in reliability analysis, introducing additional uncertainty due to the metamodel. This work presents a framework to include statistical uncertainty and model uncertainty in metamodel-based reliability analysis. Inadequate data causes uncertainty regarding the statistics (distribution types and distribution parameters) of the input variables, and regarding the system model parameters. Model errors include model form errors, solution approximation errors, and metamodel uncertainty. Two types of metamodels have been considered in literature for reliability analysis: (1) metamodels that compute the system model output over the desired ranges of the input random variables; and (2) metamodels that concentrate only on modeling the limit state. This work focuses on the latter type, using Gaussian process (GP) metamodels for performing both component reliability (single limit state) and system reliability (multiple limit states) analyses. A systematic procedure for the inclusion of model discrepancy terms in the limit-state metamodel construction is developed using an auxiliary variable approach. An efficient single-loop sampling approach using the probability integral transform is used for sampling the input variables with statistical uncertainty. The variability in the GP model prediction (metamodel uncertainty) is also included in reliability analysis through correlated sampling of the model predictions at different inputs. Two mechanical systems — a cantilever beam with point-load at the free end and a two-bar supported panel with point load at its center, are used to demonstrate the proposed techniques.
Mechanism of synergy between N-phosphonacetyl-L-aspartate and dipyridamole in a human ovarian carcinoma cell line. (1985)

Previous results from our laboratory have shown that the nucleoside transport inhibitor dipyridamole (DP) markedly augmented both the in vitro and in vivo activities of the pyrimidine antimetabolite N-phosphonacetyl-L-aspartate (PALA). In a human ovarian carcinoma cell line (2008), DP increased the activity of PALA by 1 to 2 logs in growth rate and clonogenic assays while exhibiting no cytotoxicity of its own. The concentration of DP used (1 microM) in these assays resulted in over 80% reduction in uridine uptake in the 2008 cells at the end of 1 h. The activity of PALA and PALA plus DP was completely antagonized by the addition of exogenous uridine in a dose-dependent manner. Addition of other nucleosides to concentrations as high as 1000 microM failed to rescue the ovarian cells from the drug combination, and combining two nucleosides together did not antagonize PALA and PALA plus DP activity to any greater extent. Cellular nucleotide pool analysis by anion-exchange high-performance liquid chromatography revealed that dipyridamole further reduced the already depressed uridine triphosphate and cytidine triphosphate pools of cells exposed to PALA, while the guanosine triphosphate pool was slightly elevated. Uridine supplementation resulted in partial replenishment of the uridine triphosphate and cytidine triphosphate pools, but the absolute levels remained below control values. The acute drug-induced changes in nucleotide pools in 2008 xenografts growing in athymic mice paralleled those observed in vitro. Evidence presented here supports the ability of DP to potentiate PALA activity against a human ovarian carcinoma cell line. The mechanism of synergy relates to the inhibition of pyrimidine salvage in the tumor cells via the blockade of uridine uptake.
Lattice Methods for Multiple Integration (1994)

Abstract This is the first book devoted to lattice methods, a recently developed way of calculating multiple integrals in many variables. Multiple integrals of this kind arise in fields such as quantum physics and chemistry, statistical mechanics, Bayesian statistics and many others. Lattice methods are an effective tool when the number of integrals are large. The book begins with a review of existing methods before presenting lattice theory in a thorough, self-contained manner, with numerous illustrations and examples. Group and number theory are included, but the treatment is such that no prior knowledge is needed. Not only the theory but the practical implementation of lattice methods is covered. An algorithm is presented alongside tables not available elsewhere, which together allow the practical evaluation of multiple integrals in many variables. Most importantly, the algorithm produces an error estimate in avery efficent manner. the book also provides a fast track for readers wanting to move rapidly to using methods in practical calculations. It concludes with extensive numerical test which compare lattice methods with other methods, such as the Monte Carlo.
Gaussian density guided deep neural network for single-channel speech enhancement (2017)

Recently, the minimum mean squared error (MMSE) has been a benchmark of optimization criterion for deep neural network (DNN) based speech enhancement. In this study, a probabilistic learning framework to estimate the DNN parameters for single-channel speech enhancement is proposed. First, the statistical analysis shows that the prediction error vector at the DNN output well follows a unimodal density for each log-power spectral component. Accordingly, we present a maximum likelihood (ML) approach to DNN parameter learning by charactering the prediction error vector as a multivariate Gaussian density with a zero mean vector and an unknown covariance matrix. It is demonstrated that the proposed learning approach can achieve a better generalization capability than MMSE-based DNN learning for unseen noise types, which can significantly reduce the speech distortions in low SNR environments.
A Heuristic Algorithm Based on DBR and MAS for Solving Container Loading Problem (2006)

The container loading problem, a real hard problem, is usually difficult to obtain even a suboptimal solution because of not only multiple complicated restrictions but also of multiple objectives. In this paper, a heuristic algorithm is proposed for solving the container loading problem in real-world. The algorithm is based on Drum-Buffer-Rope presented in the theory of constraints and the multi-agent cooperation negotiation model. A particular attention is focused on improving the constrained agent by striving for the trade-off of restrictions and cooperated negotiations, so that the final solution can arrive its biggest profit
Proteogenomic characterization of human colon and rectal cancer (2014)

Extensive genomic characterization of human cancers presents the problem of inference from genomic abnormalities to cancer phenotypes. To address this problem, we analysed proteomes of colon and rectal tumours characterized previously by The Cancer Genome Atlas (TCGA) and perform integrated proteogenomic analyses. Somatic variants displayed reduced protein abundance compared to germline variants. Messenger RNA transcript abundance did not reliably predict protein abundance differences between tumours. Proteomics identified five proteomic subtypes in the TCGA cohort, two of which overlapped with the TCGA ‘microsatellite instability/CpG island methylation phenotype’ transcriptomic subtype, but had distinct mutation, methylation and protein expression patterns associated with different clinical outcomes. Although copy number alterations showed strong cis- and trans-effects on mRNA abundance, relatively few of these extend to the protein level. Thus, proteomics data enabled prioritization of candidate driver genes. The chromosome 20q amplicon was associated with the largest global changes at both mRNA and protein levels; proteomics data highlighted potential 20q candidates, including HNF4A (hepatocyte nuclear factor 4, alpha), TOMM34 (translocase of outer mitochondrial membrane 34) and SRC (SRC proto-oncogene, non-receptor tyrosine kinase). Integrated proteogenomic analysis provides functional context to interpret genomic abnormalities and affords a new paradigm for understanding cancer biology.
The function of improving phosphate level and the effect of increasing phosphate level or adding dry materials of plant by returning straw to soil directly (1997)

The inefficiency of applying phosphate fertilizer to soil is an improtant and economic effective problem in controling crops nutrition of agriculture production. The study is how to improve the efficiency of phosphate fertilizer considering the factors of soil surroundings Returning straw to soildirectly can be used as an effective method. This method can increase the fresh biological energy resources for soil microorganism growth and reproduction, improve the quantity and activity of soil microorganism. During the process of decomposing energy resources, microorganism can transform diffcult dissolving phosphate, protect effective phosphate and reduce the quantity of fixed phosphate by soil, so that the ability of soil supplying phosphate and the ability of cropsa bsorbing phosphate can be promoted.
Estimating the inter cell dependency matrix in a GSM network (2003)

Cellular network planning is often based on propagation prediction or manual measurements. Both these methods have disadvantages. An alternative approach is suggested here, where mobile station measurements are utilized to collect system data. This information can be used to tune or re-plan the frequency plan. The data acquisition part of this method is investigated by means of simulations in a realistic simulation environment, using a commercial urban network as a template. The results are compared to true values from the simulator, and high correlation was found.
Towards an advanced impact analysis of intangible resources in organisations (2005)

The paper refers to the discussion of measuring and assessing knowledge capital. In particular, the interconnectedness of the intangible resources in organizations is not well represented in the methodical approaches. Moreover, the identification of driver resources which is strongly connected with this question is far from being solved in a satisfactory manner. Therefore, this article reviews existing methods of the scenario analysis in view of the performance measurement discussion and contributes towards an advanced analysis of resources in organizations.